so.owl
type: Ontology
version IRI: so.owl
IAO_0000700: sequence_feature
IAO_0000700: sequence_attribute
IAO_0000700: sequence_variant
IAO_0000700: sequence_collection
date: 18:11:2024 23:05
default-namespace: sequence
has_obo_format_version: 1.2
saved-by: Evan Christensen

definition
type: AnnotationProperty

term replaced by
type: AnnotationProperty

amino acid modification
type: AnnotationProperty
sub property of: synonym_type_property

Alliance of Genome Resources
type: AnnotationProperty
sub property of: synonym_type_property

Alliance of Genome Resources
type: AnnotationProperty
comment: Alliance of Genome Resources Gene Biotype Slim
sub property of: subset_property

biosapiens
type: AnnotationProperty
sub property of: synonym_type_property

DBVAR
type: AnnotationProperty
comment: database of genomic structural variation
sub property of: subset_property

RNA modification
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

SOFA
type: AnnotationProperty
comment: SO feature annotation
sub property of: subset_property

variant annotation term
type: AnnotationProperty
sub property of: synonym_type_property

amino acid 1 letter code
type: AnnotationProperty
sub property of: synonym_type_property

amino acid 3 letter code
type: AnnotationProperty
sub property of: synonym_type_property

biosapiens
type: AnnotationProperty
comment: biosapiens protein feature ontology
sub property of: subset_property

dbsnp variant terms
type: AnnotationProperty
sub property of: synonym_type_property

DBVAR
type: AnnotationProperty
sub property of: synonym_type_property

ensembl variant terms
type: AnnotationProperty
sub property of: synonym_type_property

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

consider
type: AnnotationProperty

created by
type: AnnotationProperty

creation date
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_scope
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

id
type: AnnotationProperty

in_subset
type: AnnotationProperty

adjacent_to
type: ObjectProperty
definition: A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
has_obo_namespace: sequence
id: adjacent_to
in_subset: SOFA

Axiom
annotated source: adjacent_to
annotated property: definition
annotated target: A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
database_cross_reference: PMID:20226267
database_cross_reference: SO:ke

associated_with
type: ObjectProperty
has_obo_namespace: sequence
id: associated_with
comment: This relationship is vague and up for discussion.

complete_evidence_for_feature
type: ObjectProperty
sub property of: evidence_for_feature
type: TransitiveProperty
definition: B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
has_obo_namespace: sequence
id: complete_evidence_for_feature
comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.

Axiom
annotated source: complete_evidence_for_feature
annotated property: definition
annotated target: B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
database_cross_reference: SO:ke

connects_on
type: ObjectProperty
definition: X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
created by: kareneilbeck
creation date: 2010-10-14T01:38:51Z
has_obo_namespace: sequence
id: connects_on
comment: Example: A splice_junction connects_on exon, exon, mature_transcript.

Axiom
annotated source: connects_on
annotated property: definition
annotated target: X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
database_cross_reference: PMID:20226267

contained_by
type: ObjectProperty
type: TransitiveProperty
definition: X contained_by Y iff X starts after start of Y and X ends before end of Y.
created by: kareneilbeck
creation date: 2010-10-14T01:26:16Z
has_obo_namespace: sequence
id: contained_by
comment: The inverse is contains. Example: intein contained_by immature_peptide_region.

Axiom
annotated source: contained_by
annotated property: definition
annotated target: X contained_by Y iff X starts after start of Y and X ends before end of Y.
database_cross_reference: PMID:20226267

contains
type: ObjectProperty
type: TransitiveProperty
definition: The inverse of contained_by.
created by: kareneilbeck
creation date: 2010-10-14T01:32:15Z
has_obo_namespace: sequence
id: contains
comment: Example: pre_miRNA contains miRNA_loop.

Axiom
annotated source: contains
annotated property: definition
annotated target: The inverse of contained_by.
database_cross_reference: PMID:20226267

derives_from
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: sequence
id: derives_from
in_subset: SOFA

disconnected_from
type: ObjectProperty
definition: X is disconnected_from Y iff it is not the case that X overlaps Y.
created by: kareneilbeck
creation date: 2010-10-14T01:42:10Z
has_obo_namespace: sequence
id: disconnected_from

Axiom
annotated source: disconnected_from
annotated property: definition
annotated target: X is disconnected_from Y iff it is not the case that X overlaps Y.
database_cross_reference: PMID:20226267

edited_from
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:19:45Z
has_obo_namespace: sequence
id: edited_from

edited_to
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:19:11Z
has_obo_namespace: sequence
id: edited_to

evidence_for_feature
type: ObjectProperty
type: TransitiveProperty
definition: B is evidence_for_feature A, if an instance of B supports the existence of A.
has_obo_namespace: sequence
id: evidence_for_feature
comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.

Axiom
annotated source: evidence_for_feature
annotated property: definition
annotated target: B is evidence_for_feature A, if an instance of B supports the existence of A.
database_cross_reference: SO:ke

exemplar_of
type: ObjectProperty
definition: X is exemplar of Y if X is the best evidence for Y.
has_obo_namespace: sequence
id: exemplar_of
comment: Tracker id: 2594157.

Axiom
annotated source: exemplar_of
annotated property: definition
annotated target: X is exemplar of Y if X is the best evidence for Y.
database_cross_reference: SO:ke

finished_by
type: ObjectProperty
definition: Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
created by: kareneilbeck
creation date: 2010-10-14T01:45:45Z
has_obo_namespace: sequence
id: finished_by
comment: Example CDS finished_by stop_codon.

Axiom
annotated source: finished_by
annotated property: definition
annotated target: Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
database_cross_reference: PMID:20226267

finishes
type: ObjectProperty
definition: X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
created by: kareneilbeck
creation date: 2010-10-14T02:17:53Z
has_obo_namespace: sequence
id: finishes
comment: Example: stop_codon finishes CDS.

Axiom
annotated source: finishes
annotated property: definition
annotated target: X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
database_cross_reference: PMID:20226267

gained
type: ObjectProperty
definition: X gained Y if X is a variant_of X' and Y part of X but not X'.
created by: kareneilbeck
creation date: 2011-06-28T12:51:10Z
has_obo_namespace: sequence
id: gained
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may gain a stop codon not present in the reference sequence.

Axiom
annotated source: gained
annotated property: definition
annotated target: X gained Y if X is a variant_of X' and Y part of X but not X'.
database_cross_reference: SO:ke

genome_of
type: ObjectProperty
has_obo_namespace: sequence
id: genome_of

guided_by
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:27:04Z
has_obo_namespace: sequence
id: guided_by

guides
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:27:24Z
has_obo_namespace: sequence
id: guides

has_integral_part
type: ObjectProperty
sub property of: has_part
definition: X has_integral_part Y if and only if: X has_part Y and Y part_of X.
created by: kareneilbeck
creation date: 2009-08-19T12:01:46Z
has_obo_namespace: sequence
id: has_integral_part
comment: Example: mRNA has_integral_part CDS.

Axiom
annotated source: has_integral_part
annotated property: definition
annotated target: X has_integral_part Y if and only if: X has_part Y and Y part_of X.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

has_origin
type: ObjectProperty
has_obo_namespace: sequence
id: has_origin

has_part
type: ObjectProperty
definition: Inverse of part_of.
has_obo_namespace: sequence
id: has_part
comment: Example: operon has_part gene.

Axiom
annotated source: has_part
annotated property: definition
annotated target: Inverse of part_of.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

has_quality
type: ObjectProperty
has_obo_namespace: sequence
id: has_quality
comment: The relationship between a feature and an attribute.

homologous_to
type: ObjectProperty
sub property of: similar_to
type: SymmetricProperty
has_obo_namespace: sequence
id: homologous_to
in_subset: SOFA

integral_part_of
type: ObjectProperty
sub property of: part_of
definition: X integral_part_of Y if and only if: X part_of Y and Y has_part X.
created by: kareneilbeck
creation date: 2009-08-19T12:03:28Z
has_obo_namespace: sequence
id: integral_part_of
comment: Example: exon integral_part_of transcript.

Axiom
annotated source: integral_part_of
annotated property: definition
annotated target: X integral_part_of Y if and only if: X part_of Y and Y has_part X.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

is_consecutive_sequence_of
type: ObjectProperty
definition: R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
created by: kareneilbeck
creation date: 2010-10-14T02:19:48Z
has_obo_namespace: sequence
id: is_consecutive_sequence_of
comment: Example: region is consecutive_sequence of base.

Axiom
annotated source: is_consecutive_sequence_of
annotated property: definition
annotated target: R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
database_cross_reference: PMID:20226267

lost
type: ObjectProperty
definition: X lost Y if X is a variant_of X' and Y part of X' but not X.
created by: kareneilbeck
creation date: 2011-06-28T12:53:16Z
has_obo_namespace: sequence
id: lost
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may have lost a stop codon present in the reference sequence.

Axiom
annotated source: lost
annotated property: definition
annotated target: X lost Y if X is a variant_of X' and Y part of X' but not X.
database_cross_reference: SO:ke

maximally_overlaps
type: ObjectProperty
definition: A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
created by: kareneilbeck
creation date: 2010-10-14T01:34:48Z
has_obo_namespace: sequence
id: maximally_overlaps
comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.

Axiom
annotated source: maximally_overlaps
annotated property: definition
annotated target: A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
database_cross_reference: PMID:20226267

member_of
type: ObjectProperty
sub property of: part_of
type: TransitiveProperty
has_obo_namespace: sequence
id: member_of
in_subset: SOFA
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.

non_functional_homolog_of
type: ObjectProperty
sub property of: homologous_to
definition: A relationship between a pseudogenic feature and its functional ancestor.
has_obo_namespace: sequence
id: non_functional_homolog_of
in_subset: SOFA

Axiom
annotated source: non_functional_homolog_of
annotated property: definition
annotated target: A relationship between a pseudogenic feature and its functional ancestor.
database_cross_reference: SO:ke

orthologous_to
type: ObjectProperty
sub property of: homologous_to
type: SymmetricProperty
has_obo_namespace: sequence
id: orthologous_to
in_subset: SOFA

overlaps
type: ObjectProperty
definition: X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
created by: kareneilbeck
creation date: 2010-10-14T01:33:15Z
has_obo_namespace: sequence
id: overlaps
comment: Example: coding_exon overlaps CDS.

Axiom
annotated source: overlaps
annotated property: definition
annotated target: X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
database_cross_reference: PMID:20226267

paralogous_to
type: ObjectProperty
sub property of: homologous_to
type: SymmetricProperty
has_obo_namespace: sequence
id: paralogous_to
in_subset: SOFA

part_of
type: ObjectProperty
type: TransitiveProperty
definition: X part_of Y if X is a subregion of Y.
has_obo_namespace: sequence
id: part_of
in_subset: SOFA
comment: Example: amino_acid part_of polypeptide.

Axiom
annotated source: part_of
annotated property: definition
annotated target: X part_of Y if X is a subregion of Y.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

partial_evidence_for_feature
type: ObjectProperty
sub property of: evidence_for_feature
definition: B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
has_obo_namespace: sequence
id: partial_evidence_for_feature

Axiom
annotated source: partial_evidence_for_feature
annotated property: definition
annotated target: B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
database_cross_reference: SO:ke

position_of
type: ObjectProperty
has_obo_namespace: sequence
id: position_of

processed_from
type: ObjectProperty
definition: Inverse of processed_into.
created by: kareneilbeck
creation date: 2009-08-19T12:14:00Z
has_obo_namespace: sequence
id: processed_from
comment: Example: miRNA processed_from miRNA_primary_transcript.

Axiom
annotated source: processed_from
annotated property: definition
annotated target: Inverse of processed_into.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

processed_into
type: ObjectProperty
definition: X is processed_into Y if a region X is modified to create Y.
created by: kareneilbeck
creation date: 2009-08-19T12:15:02Z
has_obo_namespace: sequence
id: processed_into
comment: Example: miRNA_primary_transcript processed into miRNA.

Axiom
annotated source: processed_into
annotated property: definition
annotated target: X is processed_into Y if a region X is modified to create Y.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

recombined_from
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:21:03Z
has_obo_namespace: sequence
id: recombined_from

recombined_to
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:20:07Z
has_obo_namespace: sequence
id: recombined_to

sequence_of
type: ObjectProperty
has_obo_namespace: sequence
id: sequence_of

similar_to
type: ObjectProperty
type: SymmetricProperty
has_obo_namespace: sequence
id: similar_to
in_subset: SOFA

started_by
type: ObjectProperty
definition: X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
created by: kareneilbeck
creation date: 2010-10-14T01:43:55Z
has_obo_namespace: sequence
id: started_by
comment: Example: CDS started_by start_codon.

Axiom
annotated source: started_by
annotated property: definition
annotated target: X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
database_cross_reference: PMID:20226267

starts
type: ObjectProperty
definition: X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
created by: kareneilbeck
creation date: 2010-10-14T01:47:53Z
has_obo_namespace: sequence
id: starts
comment: Example: start_codon starts CDS.

Axiom
annotated source: starts
annotated property: definition
annotated target: X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
database_cross_reference: PMID:20226267

trans_spliced_from
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:22:14Z
has_obo_namespace: sequence
id: trans_spliced_from

trans_spliced_to
type: ObjectProperty
created by: kareneilbeck
creation date: 2009-08-19T02:22:00Z
has_obo_namespace: sequence
id: trans_spliced_to

transcribed_from
type: ObjectProperty
definition: X is transcribed_from Y if X is synthesized from template Y.
created by: kareneilbeck
creation date: 2009-08-19T12:05:39Z
has_obo_namespace: sequence
id: transcribed_from
comment: Example: primary_transcript transcribed_from gene.

Axiom
annotated source: transcribed_from
annotated property: definition
annotated target: X is transcribed_from Y if X is synthesized from template Y.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

transcribed_to
type: ObjectProperty
definition: Inverse of transcribed_from.
created by: kareneilbeck
creation date: 2009-08-19T12:08:24Z
has_obo_namespace: sequence
id: transcribed_to
comment: Example: gene transcribed_to primary_transcript.

Axiom
annotated source: transcribed_to
annotated property: definition
annotated target: Inverse of transcribed_from.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

translates_to
type: ObjectProperty
definition: Inverse of translation _of.
created by: kareneilbeck
creation date: 2009-08-19T12:11:53Z
has_obo_namespace: sequence
id: translates_to
comment: Example: codon translates_to amino_acid.

Axiom
annotated source: translates_to
annotated property: definition
annotated target: Inverse of translation _of.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

translation_of
type: ObjectProperty
definition: X is translation of Y if Y is translated by ribosome to create X.
created by: kareneilbeck
creation date: 2009-08-19T12:09:59Z
has_obo_namespace: sequence
id: translation_of
comment: Example: Polypeptide translation_of CDS.

Axiom
annotated source: translation_of
annotated property: definition
annotated target: X is translation of Y if Y is translated by ribosome to create X.
database_cross_reference: http://precedings.nature.com/documents/3495/version/1

variant_of
type: ObjectProperty
definition: A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
has_obo_namespace: sequence
id: variant_of
comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.

Axiom
annotated source: variant_of
annotated property: definition
annotated target: A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
database_cross_reference: SO:immuno_workshop

BS_00003
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_secondary_structure
deprecated: true

BS_0000338
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_structural_motif
deprecated: true

BS_0000339
type: Class
IAO_0000231: IAO_0000227
term replaced by: right_handed_peptide_helix
deprecated: true

BS_0000340
type: Class
IAO_0000231: IAO_0000227
term replaced by: three_ten_helix
deprecated: true

BS_0000341
type: Class
IAO_0000231: IAO_0000227
term replaced by: antiparallel_beta_strand
deprecated: true

BS_00012
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_domain
deprecated: true

BS_00026
type: Class
IAO_0000231: IAO_0000227
term replaced by: catalytic_residue
deprecated: true

BS_00027
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_metal_contact
deprecated: true

BS_00028
type: Class
IAO_0000231: IAO_0000227
term replaced by: disulfide_bond
deprecated: true

BS_00029
type: Class
IAO_0000231: IAO_0000227
term replaced by: non_covalent_binding_site
deprecated: true

BS_00032
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_motif
deprecated: true

BS_00033
type: Class
IAO_0000231: IAO_0000227
term replaced by: binding_site
deprecated: true

BS_00036
type: Class
IAO_0000231: IAO_0000227
term replaced by: mutated_variant_site
deprecated: true

BS_00040
type: Class
IAO_0000231: IAO_0000227
term replaced by: alpha_helix
deprecated: true

BS_00041
type: Class
IAO_0000231: IAO_0000227
term replaced by: coiled_coil
deprecated: true

BS_00042
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_strand
deprecated: true

BS_00052
type: Class
IAO_0000231: IAO_0000227
term replaced by: post_translationally_modified_region
deprecated: true

BS_00055
type: Class
IAO_0000231: IAO_0000227
term replaced by: transit_peptide
deprecated: true

BS_00063
type: Class
IAO_0000231: IAO_0000227
term replaced by: propeptide_cleavage_site
deprecated: true

BS_00067
type: Class
IAO_0000231: IAO_0000227
term replaced by: cleaved_initiator_methionine
deprecated: true

BS_00068
type: Class
IAO_0000231: IAO_0000227
term replaced by: compositionally_biased_region_of_peptide
deprecated: true

BS_00069
type: Class
IAO_0000231: IAO_0000227
term replaced by: sequence_conflict
deprecated: true

BS_00070
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_repeat
deprecated: true

BS_00071
type: Class
IAO_0000231: IAO_0000227
term replaced by: natural_variant_site
deprecated: true

BS_00072
type: Class
IAO_0000231: IAO_0000227
term replaced by: non_terminal_residue
deprecated: true

BS_00073
type: Class
IAO_0000231: IAO_0000227
term replaced by: alternate_sequence_site
deprecated: true

BS_00076
type: Class
IAO_0000231: IAO_0000227
term replaced by: active_peptide
deprecated: true

BS_00077
type: Class
IAO_0000231: IAO_0000227
term replaced by: propeptide
deprecated: true

BS_00124
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_region
deprecated: true

BS_00125
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_sequencing_information
deprecated: true

BS_00128
type: Class
IAO_0000231: IAO_0000227
term replaced by: membrane_structure
deprecated: true

BS_00129
type: Class
IAO_0000231: IAO_0000227
term replaced by: immature_peptide_region
deprecated: true

BS_00131
type: Class
IAO_0000231: IAO_0000227
term replaced by: protein_protein_contact
deprecated: true

BS_00134
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_domain
deprecated: true

BS_00136
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_cobalt_ion_contact_site
deprecated: true

BS_00137
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_iron_ion_contact_site
deprecated: true

BS_00140
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_manganese_ion_contact_site
deprecated: true

BS_00141
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_molybdenum_ion_contact_site
deprecated: true

BS_00142
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_nickel_ion_contact_site
deprecated: true

BS_00143
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_tungsten_ion_contact_site
deprecated: true

BS_00144
type: Class
IAO_0000231: IAO_0000227
term replaced by: non_cytoplasmic_polypeptide_region
deprecated: true

BS_00145
type: Class
IAO_0000231: IAO_0000227
term replaced by: cytoplasmic_polypeptide_region
deprecated: true

BS_00146
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_copper_ion_contact_site
deprecated: true

BS_00147
type: Class
IAO_0000231: IAO_0000227
term replaced by: helix_turn_helix
deprecated: true

BS_00148
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_turn_motif
deprecated: true

BS_00149
type: Class
IAO_0000231: IAO_0000227
term replaced by: mature_protein_region
deprecated: true

BS_00151
type: Class
IAO_0000231: IAO_0000227
term replaced by: parallel_beta_strand
deprecated: true

BS_00152
type: Class
IAO_0000231: IAO_0000227
term replaced by: peptide_helix
deprecated: true

BS_00153
type: Class
IAO_0000231: IAO_0000227
term replaced by: pi_helix
deprecated: true

BS_00154
type: Class
IAO_0000231: IAO_0000227
term replaced by: extramembrane_polypeptide_region
deprecated: true

BS_00155
type: Class
IAO_0000231: IAO_0000227
term replaced by: membrane_peptide_loop
deprecated: true

BS_00156
type: Class
IAO_0000231: IAO_0000227
term replaced by: intramembrane_polypeptide_region
deprecated: true

BS_00157
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_ligand_contact
deprecated: true

BS_00158
type: Class
IAO_0000231: IAO_0000227
term replaced by: transmembrane_polypeptide_region
deprecated: true

BS_00159
type: Class
IAO_0000231: IAO_0000227
term replaced by: signal_peptide
deprecated: true

BS_00178
type: Class
IAO_0000231: IAO_0000227
term replaced by: cross_link
deprecated: true

BS_00181
type: Class
IAO_0000231: IAO_0000227
term replaced by: sequence_uncertainty
deprecated: true

BS_00182
type: Class
IAO_0000231: IAO_0000227
term replaced by: non_adjacent_residues
deprecated: true

BS_00185
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_zinc_ion_contact_site
deprecated: true

BS_00186
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_calcium_ion_contact_site
deprecated: true

BS_00187
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_magnesium_ion_contact_site
deprecated: true

BS_00202
type: Class
IAO_0000231: IAO_0000227
term replaced by: asx_motif
deprecated: true

BS_00203
type: Class
IAO_0000231: IAO_0000227
term replaced by: asx_turn
deprecated: true

BS_00204
type: Class
IAO_0000231: IAO_0000227
term replaced by: asx_turn_left_handed_type_two
deprecated: true

BS_00205
type: Class
IAO_0000231: IAO_0000227
term replaced by: asx_turn_right_handed_type_two
deprecated: true

BS_00206
type: Class
IAO_0000231: IAO_0000227
term replaced by: asx_turn_left_handed_type_one
deprecated: true

BS_00207
type: Class
IAO_0000231: IAO_0000227
term replaced by: asx_turn_right_handed_type_one
deprecated: true

BS_00208
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_bulge
deprecated: true

BS_00209
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_bulge_loop
deprecated: true

BS_00210
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_bulge_loop_five
deprecated: true

BS_00211
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_bulge_loop_six
deprecated: true

BS_00212
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_turn
deprecated: true

BS_00213
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_turn_left_handed_type_two
deprecated: true

BS_00214
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_turn_right_handed_type_two
deprecated: true

BS_00215
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_turn_left_handed_type_one
deprecated: true

BS_00216
type: Class
IAO_0000231: IAO_0000227
term replaced by: beta_turn_right_handed_type_one
deprecated: true

BS_00219
type: Class
IAO_0000231: IAO_0000227
term replaced by: gamma_turn
deprecated: true

BS_00220
type: Class
IAO_0000231: IAO_0000227
term replaced by: gamma_turn_classic
deprecated: true

BS_00221
type: Class
IAO_0000231: IAO_0000227
term replaced by: gamma_turn_inverse
deprecated: true

BS_00222
type: Class
IAO_0000231: IAO_0000227
term replaced by: left_handed_peptide_helix
deprecated: true

BS_00223
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_nest_motif
deprecated: true

BS_00224
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_nest_left_right_motif
deprecated: true

BS_00225
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_nest_right_left_motif
deprecated: true

BS_00226
type: Class
IAO_0000231: IAO_0000227
term replaced by: schellmann_loop
deprecated: true

BS_00227
type: Class
IAO_0000231: IAO_0000227
term replaced by: schellmann_loop_six
deprecated: true

BS_00228
type: Class
IAO_0000231: IAO_0000227
term replaced by: schellmann_loop_seven
deprecated: true

BS_00229
type: Class
IAO_0000231: IAO_0000227
term replaced by: serine_threonine_motif
deprecated: true

BS_00230
type: Class
IAO_0000231: IAO_0000227
term replaced by: serine_threonine_staple_motif
deprecated: true

BS_00231
type: Class
IAO_0000231: IAO_0000227
term replaced by: serine_threonine_turn
deprecated: true

BS_00232
type: Class
IAO_0000231: IAO_0000227
term replaced by: st_turn_left_handed_type_two
deprecated: true

BS_00233
type: Class
IAO_0000231: IAO_0000227
term replaced by: st_turn_right_handed_type_two
deprecated: true

BS_00234
type: Class
IAO_0000231: IAO_0000227
term replaced by: st_turn_left_handed_type_one
deprecated: true

BS_00235
type: Class
IAO_0000231: IAO_0000227
term replaced by: st_turn_right_handed_type_one
deprecated: true

BS_00246
type: Class
IAO_0000231: IAO_0000227
term replaced by: covalent_binding_site
deprecated: true

BS_00331
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_region
deprecated: true

BS_00336
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_variation_site
deprecated: true

BS_00337
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_structural_region
deprecated: true

Sequence_Ontology
type: Class
has_obo_namespace: sequence
id: SO:0000000
in_subset: SOFA
deprecated: true

region
type: Class
subclass of: sequence_feature
definition: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
has_exact_synonym: sequence
has_obo_namespace: sequence
id: SO:0000001
in_subset: SOFA

Axiom
annotated source: region
annotated property: definition
annotated target: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
database_cross_reference: SO:ke

sequence_secondary_structure
type: Class
subclass of: biological_region
definition: A folded sequence.
has_exact_synonym: INSDC_feature:misc_structure
has_exact_synonym: sequence secondary structure
has_obo_namespace: sequence
id: SO:0000002

Axiom
annotated source: sequence_secondary_structure
annotated property: definition
annotated target: A folded sequence.
database_cross_reference: SO:ke

G_quartet
type: Class
subclass of: sequence_secondary_structure
definition: G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.
database_cross_reference: http://en.wikipedia.org/wiki/G-quadruplex
has_exact_synonym: G quartet
has_exact_synonym: G tetrad
has_exact_synonym: G-quadruplex
has_exact_synonym: G-quartet
has_exact_synonym: G-tetrad
has_exact_synonym: G_quadruplex
has_exact_synonym: guanine tetrad
has_obo_namespace: sequence
id: SO:0000003

Axiom
annotated source: G_quartet
annotated property: definition
annotated target: G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/7919797

wiki
type: Axiom
annotated source: G_quartet
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/G-quadruplex

interior_coding_exon
type: Class
subclass of: coding_exon
definition: A coding exon that is not the most 3-prime or the most 5-prime in a given transcript.
has_exact_synonym: interior coding exon
has_obo_namespace: sequence
id: SO:0000004
in_subset: SOFA

satellite_DNA
type: Class
subclass of: tandem_repeat
definition: The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Satellite_DNA
has_exact_synonym: INSDC_qualifier:satellite
has_exact_synonym: satellite DNA
has_obo_namespace: sequence
id: SO:0000005
in_subset: SOFA

Axiom
annotated source: satellite_DNA
annotated property: definition
annotated target: The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: satellite_DNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Satellite_DNA

PCR_product
type: Class
subclass of: reagent
definition: A region amplified by a PCR reaction.
database_cross_reference: http://en.wikipedia.org/wiki/RAPD
has_exact_synonym: PCR product
has_obo_namespace: sequence
has_related_synonym: amplicon
id: SO:0000006
in_subset: SOFA
comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.

Axiom
annotated source: PCR_product
annotated property: definition
annotated target: A region amplified by a PCR reaction.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: PCR_product
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/RAPD

read_pair
type: Class
subclass of: read
subclass of: Restriction
  on property: part_of
  some values from: contig
subclass of: Restriction
  on property: part_of
  some values from: SO_0001790
definition: One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
has_exact_synonym: mate pair
has_exact_synonym: read-pair
has_obo_namespace: sequence
id: SO:0000007
in_subset: SOFA

Axiom
annotated source: read_pair
annotated property: definition
annotated target: One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
database_cross_reference: SO:ls

gene_sensu_your_favorite_organism
type: Class
has_obo_namespace: sequence
id: SO:0000008
deprecated: true

gene_class
type: Class
has_obo_namespace: sequence
id: SO:0000009
deprecated: true

protein_coding
type: Class
subclass of: gene_attribute
definition: A gene which, when transcribed, can be translated into a protein.
has_exact_synonym: protein-coding
has_obo_namespace: sequence
id: SO:0000010

non_protein_coding
type: Class
subclass of: gene_attribute
definition: A gene which can be transcribed, but will not be translated into a protein.
has_exact_synonym: non protein-coding
has_obo_namespace: sequence
id: SO:0000011

scRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
definition: The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.
has_exact_synonym: scRNA primary transcript
has_exact_synonym: scRNA transcript
has_exact_synonym: small cytoplasmic RNA transcript
has_obo_namespace: sequence
has_related_synonym: small cytoplasmic RNA
has_related_synonym: small_cytoplasmic_RNA
id: SO:0000012

Axiom
annotated source: scRNA_primary_transcript
annotated property: definition
annotated target: The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.
database_cross_reference: http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html

scRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: scRNA_primary_transcript
definition: A small non coding RNA sequence, present in the cytoplasm.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:scRNA
has_exact_synonym: small cytoplasmic RNA
has_obo_namespace: sequence
id: SO:0000013
in_subset: SOFA

Axiom
annotated source: scRNA
annotated property: definition
annotated target: A small non coding RNA sequence, present in the cytoplasm.
database_cross_reference: SO:ke

INR_motif
type: Class
subclass of: core_eukaryotic_promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_core_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.
has_exact_synonym: INR motif
has_exact_synonym: initiator
has_exact_synonym: initiator motif
has_obo_namespace: sequence
has_related_synonym: DMp2
id: SO:0000014
comment: Binds TAF1, TAF2.

Axiom
annotated source: INR_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.
database_cross_reference: PMID:12651739
database_cross_reference: PMID:16858867

DPE_motif
type: Class
subclass of: core_eukaryotic_promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_core_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).
has_exact_synonym: DPE motif
has_exact_synonym: downstream core promoter element
has_narrow_synonym: CRWMGCGWKCGCTTS
has_obo_namespace: sequence
id: SO:0000015
comment: Binds TAF6, TAF9.

Axiom
annotated source: DPE_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).
database_cross_reference: PMID:12515390
database_cross_reference: PMID:12537576
database_cross_reference: PMID:12651739
database_cross_reference: PMID:16858867

BREu_motif
type: Class
subclass of: core_eukaryotic_promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_core_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.
has_exact_synonym: B-recognition element
has_exact_synonym: BRE motif
has_exact_synonym: BREu motif
has_exact_synonym: transcription factor B-recognition element
has_obo_namespace: sequence
has_related_synonym: BREu
has_related_synonym: TFIIB recognition element
id: SO:0000016
comment: Binds TFIIB.

Axiom
annotated source: BREu_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.
database_cross_reference: PMID:12651739
database_cross_reference: PMID:16858867

PSE_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: promoter
definition: A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). The basal transcription factor, snRNA-activating protein complex (SNAPc), binds the PSE_motif and is required for the transcription of both RNA polymerase II and III transcribed small-nuclear RNA genes.
has_exact_synonym: PSE motif
has_exact_synonym: proximal sequence element
has_obo_namespace: sequence
id: SO:0000017

Axiom
annotated source: PSE_motif
annotated property: definition
annotated target: A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). The basal transcription factor, snRNA-activating protein complex (SNAPc), binds the PSE_motif and is required for the transcription of both RNA polymerase II and III transcribed small-nuclear RNA genes.
database_cross_reference: PMID:11390411
database_cross_reference: PMID:12621023
database_cross_reference: PMID:12651739
database_cross_reference: PMID:23166507
database_cross_reference: PMID:8339931

linkage_group
type: Class
subclass of: biological_region
definition: A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
database_cross_reference: http://en.wikipedia.org/wiki/Linkage_group
has_exact_synonym: linkage group
has_obo_namespace: sequence
id: SO:0000018

Axiom
annotated source: linkage_group
annotated property: definition
annotated target: A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
database_cross_reference: ISBN:038752046

wiki
type: Axiom
annotated source: linkage_group
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Linkage_group

SO_0000019
type: Class
IAO_0000231: IAO_0000227
term replaced by: stem_loop
deprecated: true

RNA_internal_loop
type: Class
subclass of: RNA_motif
definition: A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.
has_exact_synonym: RNA internal loop
has_obo_namespace: sequence
id: SO:0000020

Axiom
annotated source: RNA_internal_loop
annotated property: definition
annotated target: A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.
database_cross_reference: SO:ke

asymmetric_RNA_internal_loop
type: Class
subclass of: RNA_internal_loop
definition: An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.
has_exact_synonym: asymmetric RNA internal loop
has_obo_namespace: sequence
id: SO:0000021

Axiom
annotated source: asymmetric_RNA_internal_loop
annotated property: definition
annotated target: An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.
database_cross_reference: SO:ke

A_minor_RNA_motif
type: Class
subclass of: RNA_motif
definition: A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.
has_exact_synonym: A minor RNA motif
has_obo_namespace: sequence
id: SO:0000022

Axiom
annotated source: A_minor_RNA_motif
annotated property: definition
annotated target: A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.
database_cross_reference: SO:ke

K_turn_RNA_motif
type: Class
subclass of: asymmetric_RNA_internal_loop
definition: The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.
database_cross_reference: http://en.wikipedia.org/wiki/K-turn
has_exact_synonym: K turn RNA motif
has_exact_synonym: K-turn
has_exact_synonym: kink turn
has_exact_synonym: kink-turn motif
has_obo_namespace: sequence
id: SO:0000023

Axiom
annotated source: K_turn_RNA_motif
annotated property: definition
annotated target: The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: K_turn_RNA_motif
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/K-turn

sarcin_like_RNA_motif
type: Class
subclass of: asymmetric_RNA_internal_loop
definition: A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.
has_exact_synonym: sarcin like RNA motif
has_exact_synonym: sarcin/ricin RNA domain
has_exact_synonym: sarcin/ricin domain
has_exact_synonym: sarcin/ricin loop
has_obo_namespace: sequence
id: SO:0000024

Axiom
annotated source: sarcin_like_RNA_motif
annotated property: definition
annotated target: A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/7897662

symmetric_RNA_internal_loop
type: Class
subclass of: RNA_internal_loop
definition: An internal RNA loop where the extent of the loop on both stands is the same size.
has_exact_synonym: A-minor RNA motif
has_obo_namespace: sequence
id: SO:0000025

Axiom
annotated source: symmetric_RNA_internal_loop
annotated property: definition
annotated target: An internal RNA loop where the extent of the loop on both stands is the same size.
database_cross_reference: SO:ke

RNA_junction_loop
type: Class
subclass of: RNA_motif
has_exact_synonym: RNA junction loop
has_obo_namespace: sequence
id: SO:0000026

RNA_hook_turn
type: Class
subclass of: RNA_junction_loop
has_exact_synonym: RNA hook turn
has_exact_synonym: hook-turn motif
has_obo_namespace: sequence
has_related_synonym: hook turn
id: SO:0000027

base_pair
type: Class
subclass of: sequence_secondary_structure
definition: Two bases paired opposite each other by hydrogen bonds creating a secondary structure.
database_cross_reference: http://en.wikipedia.org/wiki/Base_pair
has_exact_synonym: base pair
has_obo_namespace: sequence
id: SO:0000028

wiki
type: Axiom
annotated source: base_pair
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Base_pair

WC_base_pair
type: Class
subclass of: base_pair
definition: The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.
has_exact_synonym: WC base pair
has_exact_synonym: Watson Crick base pair
has_exact_synonym: Watson-Crick pair
has_exact_synonym: canonical base pair
has_obo_namespace: sequence
has_related_synonym: Watson-Crick base pair
id: SO:0000029

Axiom
annotated source: WC_base_pair
annotated property: definition
annotated target: The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.
database_cross_reference: PMID:12177293

sugar_edge_base_pair
type: Class
subclass of: base_pair
definition: A type of non-canonical base-pairing.
has_exact_synonym: sugar edge base pair
has_obo_namespace: sequence
id: SO:0000030

Axiom
annotated source: sugar_edge_base_pair
annotated property: definition
annotated target: A type of non-canonical base-pairing.
database_cross_reference: PMID:12177293

aptamer
type: Class
subclass of: oligo
definition: DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.
database_cross_reference: http://en.wikipedia.org/wiki/Aptamer
has_obo_namespace: sequence
id: SO:0000031

Axiom
annotated source: aptamer
annotated property: definition
annotated target: DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.
database_cross_reference: http://aptamer.icmb.utexas.edu

wiki
type: Axiom
annotated source: aptamer
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Aptamer

DNA_aptamer
type: Class
subclass of: aptamer
definition: DNA molecules that have been selected from random pools based on their ability to bind other molecules.
has_exact_synonym: DNA aptamer
has_obo_namespace: sequence
id: SO:0000032

Axiom
annotated source: DNA_aptamer
annotated property: definition
annotated target: DNA molecules that have been selected from random pools based on their ability to bind other molecules.
database_cross_reference: http:aptamer.icmb.utexas.edu

RNA_aptamer
type: Class
subclass of: aptamer
definition: RNA molecules that have been selected from random pools based on their ability to bind other molecules.
has_exact_synonym: RNA aptamer
has_obo_namespace: sequence
id: SO:0000033

Axiom
annotated source: RNA_aptamer
annotated property: definition
annotated target: RNA molecules that have been selected from random pools based on their ability to bind other molecules.
database_cross_reference: http://aptamer.icmb.utexas.edu

morpholino_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: morpholino_backbone
subclass of: synthetic_oligo
subclass of: Restriction
  on property: has_quality
  some values from: morpholino_backbone
definition: Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.
has_broad_synonym: morphant
has_exact_synonym: morpholino
has_exact_synonym: morpholino oligo
has_obo_namespace: sequence
id: SO:0000034

Axiom
annotated source: morpholino_oligo
annotated property: definition
annotated target: Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.
database_cross_reference: http://www.gene-tools.com/

riboswitch
type: Class
subclass of: mRNA_region
subclass of: Restriction
  on property: part_of
  some values from: mRNA
definition: A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Riboswitch
has_exact_synonym: INSDC_qualifier:riboswitch
has_exact_synonym: riboswitch RNA
has_obo_namespace: sequence
id: SO:0000035

Axiom
annotated source: riboswitch
annotated property: definition
annotated target: A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites.
database_cross_reference: PMID:2820954

wiki
type: Axiom
annotated source: riboswitch
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Riboswitch

matrix_attachment_site
type: Class
subclass of: chromosomal_regulatory_element
definition: A DNA region that is required for the binding of chromatin to the nuclear matrix.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Matrix_attachment_site
has_exact_synonym: INSDC_qualifier:matrix_attachment_region
has_exact_synonym: MAR
has_exact_synonym: S/MAR
has_exact_synonym: SMAR
has_exact_synonym: matrix association region
has_exact_synonym: matrix attachment region
has_exact_synonym: matrix attachment site
has_exact_synonym: nuclear matrix association region
has_exact_synonym: nuclear matrix attachment site
has_exact_synonym: scaffold attachment site
has_exact_synonym: scaffold matrix attachment region
has_obo_namespace: sequence
has_related_synonym: S/MAR element
id: SO:0000036

Axiom
annotated source: matrix_attachment_site
annotated property: definition
annotated target: A DNA region that is required for the binding of chromatin to the nuclear matrix.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: matrix_attachment_site
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Matrix_attachment_site

locus_control_region
type: Class
subclass of: cis_regulatory_module
definition: A DNA region that includes DNAse hypersensitive sites located near a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Locus_control_region
has_exact_synonym: INSDC_qualifier:locus_control_region
has_exact_synonym: LCR
has_exact_synonym: locus control region
has_obo_namespace: sequence
has_related_synonym: locus control element
id: SO:0000037
comment: Definition updated Nov 10 2020, Colin Logie from GREEKC helped us realize that LCRs can also be located 3' to a gene.

Axiom
annotated source: locus_control_region
annotated property: definition
annotated target: A DNA region that includes DNAse hypersensitive sites located near a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: locus_control_region
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Locus_control_region

match_set
type: Class
definition: A collection of match parts.
has_obo_namespace: sequence
id: SO:0000038
in_subset: SOFA
deprecated: true

Axiom
annotated source: match_set
annotated property: definition
annotated target: A collection of match parts.
database_cross_reference: SO:ke

match_part
type: Class
subclass of: experimental_feature
subclass of: Restriction
  on property: part_of
  some values from: match
definition: A part of a match, for example an hsp from blast is a match_part.
has_exact_synonym: match part
has_obo_namespace: sequence
id: SO:0000039
in_subset: SOFA

Axiom
annotated source: match_part
annotated property: definition
annotated target: A part of a match, for example an hsp from blast is a match_part.
database_cross_reference: SO:ke

genomic_clone
type: Class
equivalent class: Class
  intersection of: clone
  intersection of: Restriction
    on property: has_quality
    some values from: genomic_DNA
subclass of: clone
subclass of: Restriction
  on property: has_quality
  some values from: genomic_DNA
definition: A clone of a DNA region of a genome.
has_exact_synonym: genomic clone
has_obo_namespace: sequence
id: SO:0000040

Axiom
annotated source: genomic_clone
annotated property: definition
annotated target: A clone of a DNA region of a genome.
database_cross_reference: SO:ma

sequence_operation
type: Class
definition: An operation that can be applied to a sequence, that results in a change.
has_exact_synonym: sequence operation
has_obo_namespace: sequence
id: SO:0000041
deprecated: true

Axiom
annotated source: sequence_operation
annotated property: definition
annotated target: An operation that can be applied to a sequence, that results in a change.
database_cross_reference: SO:ke

pseudogene_attribute
type: Class
definition: An attribute of a pseudogene (SO:0000336).
has_exact_synonym: pseudogene attribute
has_obo_namespace: sequence
id: SO:0000042
deprecated: true

Axiom
annotated source: pseudogene_attribute
annotated property: definition
annotated target: An attribute of a pseudogene (SO:0000336).
database_cross_reference: SO:ma

processed_pseudogene
type: Class
subclass of: pseudogene
definition: A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail.
has_broad_synonym: INSDC_feature:gene
has_exact_synonym: INSDC_qualifier:processed
has_exact_synonym: processed pseudogene
has_exact_synonym: retropseudogene
has_obo_namespace: sequence
has_related_synonym: R psi G
has_related_synonym: pseudogene by reverse transcription
id: SO:0000043
comment: Please not the synonym R psi M uses the spelled out form of the greek letter.

Axiom
annotated source: processed_pseudogene
annotated property: definition
annotated target: A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail.
database_cross_reference: GENCODE:http://www.gencodegenes.org/gencode_biotypes.html

pseudogene_by_unequal_crossing_over
type: Class
subclass of: SO_0001760
definition: A pseudogene caused by unequal crossing over at recombination.
has_exact_synonym: pseudogene by unequal crossing over
has_obo_namespace: sequence
id: SO:0000044

Axiom
annotated source: pseudogene_by_unequal_crossing_over
annotated property: definition
annotated target: A pseudogene caused by unequal crossing over at recombination.
database_cross_reference: SO:ke

delete
type: Class
definition: To remove a subsection of sequence.
has_obo_namespace: sequence
id: SO:0000045
deprecated: true

Axiom
annotated source: delete
annotated property: definition
annotated target: To remove a subsection of sequence.
database_cross_reference: SO:ke

insert
type: Class
definition: To insert a subsection of sequence.
has_obo_namespace: sequence
id: SO:0000046
deprecated: true

Axiom
annotated source: insert
annotated property: definition
annotated target: To insert a subsection of sequence.
database_cross_reference: SO:ke

invert
type: Class
definition: To invert a subsection of sequence.
has_obo_namespace: sequence
id: SO:0000047
deprecated: true

Axiom
annotated source: invert
annotated property: definition
annotated target: To invert a subsection of sequence.
database_cross_reference: SO:ke

substitute
type: Class
definition: To substitute a subsection of sequence for another.
has_obo_namespace: sequence
id: SO:0000048
deprecated: true

Axiom
annotated source: substitute
annotated property: definition
annotated target: To substitute a subsection of sequence for another.
database_cross_reference: SO:ke

translocate
type: Class
definition: To translocate a subsection of sequence.
has_obo_namespace: sequence
id: SO:0000049
deprecated: true

Axiom
annotated source: translocate
annotated property: definition
annotated target: To translocate a subsection of sequence.
database_cross_reference: SO:ke

gene_part
type: Class
definition: A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
has_obo_namespace: sequence
id: SO:0000050
in_subset: SOFA
deprecated: true

Axiom
annotated source: gene_part
annotated property: definition
annotated target: A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
database_cross_reference: SO:ke

probe
type: Class
subclass of: oligo
definition: A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
database_cross_reference: http://en.wikipedia.org/wiki/Hybridization_probe
has_obo_namespace: sequence
id: SO:0000051

Axiom
annotated source: probe
annotated property: definition
annotated target: A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: probe
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Hybridization_probe

assortment_derived_deficiency
type: Class
has_obo_namespace: sequence
has_related_synonym: assortment-derived_deficiency
id: SO:0000052
deprecated: true

sequence_variant_affecting_regulatory_region
type: Class
definition: A sequence_variant_effect which changes the regulatory region of a gene.
term replaced by: increased_translational_product_level
has_exact_synonym: sequence variant affecting regulatory region
has_obo_namespace: sequence
has_related_synonym: mutation affecting regulatory region
id: SO:0000053
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
deprecated: true

Axiom
annotated source: sequence_variant_affecting_regulatory_region
annotated property: definition
annotated target: A sequence_variant_effect which changes the regulatory region of a gene.
database_cross_reference: SO:ke

aneuploid
type: Class
subclass of: SO_1000182
definition: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
database_cross_reference: http://en.wikipedia.org/wiki/Aneuploid
has_obo_namespace: sequence
id: SO:0000054

Axiom
annotated source: aneuploid
annotated property: definition
annotated target: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: aneuploid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Aneuploid

hyperploid
type: Class
subclass of: aneuploid
definition: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.
database_cross_reference: http://en.wikipedia.org/wiki/Hyperploid
has_obo_namespace: sequence
id: SO:0000055

Axiom
annotated source: hyperploid
annotated property: definition
annotated target: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: hyperploid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Hyperploid

hypoploid
type: Class
subclass of: aneuploid
definition: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.
database_cross_reference: http://en.wikipedia.org/wiki/Hypoploid
has_obo_namespace: sequence
id: SO:0000056

Axiom
annotated source: hypoploid
annotated property: definition
annotated target: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: hypoploid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Hypoploid

operator
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
database_cross_reference: http://en.wikipedia.org/wiki/Operator_(biology)#Operator
has_exact_synonym: operator segment
has_obo_namespace: sequence
id: SO:0000057
in_subset: SOFA
comment: Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.

Axiom
annotated source: operator
annotated property: definition
annotated target: A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: operator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Operator_(biology)#Operator

assortment_derived_aneuploid
type: Class
has_obo_namespace: sequence
has_related_synonym: assortment-derived_aneuploid
id: SO:0000058
deprecated: true

nuclease_binding_site
type: Class
subclass of: nucleotide_to_protein_binding_site
definition: A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
has_exact_synonym: nuclease binding site
has_obo_namespace: sequence
id: SO:0000059
in_subset: SOFA

Axiom
annotated source: nuclease_binding_site
annotated property: definition
annotated target: A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
database_cross_reference: SO:cb

compound_chromosome_arm
type: Class
subclass of: SO_1000042
definition: One arm of a compound chromosome.
has_exact_synonym: compound chromosome arm
has_obo_namespace: sequence
id: SO:0000060
comment: FLAG - this term is should probably be a part of rather than an is_a.

restriction_enzyme_binding_site
type: Class
subclass of: nuclease_binding_site
definition: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.
has_exact_synonym: restriction endonuclease binding site
has_exact_synonym: restriction enzyme binding site
has_obo_namespace: sequence
id: SO:0000061
comment: A region of a molecule that binds to a restriction enzyme.

Axiom
annotated source: restriction_enzyme_binding_site
annotated property: definition
annotated target: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.
database_cross_reference: SO:cb

deficient_intrachromosomal_transposition
type: Class
subclass of: SO_1000029
subclass of: SO_1000041
subclass of: Restriction
  on property: has_part
  some values from: deletion
definition: An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
has_exact_synonym: deficient intrachromosomal transposition
has_obo_namespace: sequence
id: SO:0000062

Axiom
annotated source: deficient_intrachromosomal_transposition
annotated property: definition
annotated target: An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
database_cross_reference: FB:reference_manual

deficient_interchromosomal_transposition
type: Class
subclass of: SO_1000155
definition: An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
has_exact_synonym: deficient interchromosomal transposition
has_obo_namespace: sequence
id: SO:0000063

Axiom
annotated source: deficient_interchromosomal_transposition
annotated property: definition
annotated target: An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
database_cross_reference: SO:ke

gene_by_transcript_attribute
type: Class
has_obo_namespace: sequence
id: SO:0000064
comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.
deprecated: true

free_chromosome_arm
type: Class
subclass of: SO_1000183
definition: A chromosome structure variation whereby an arm exists as an individual chromosome element.
has_exact_synonym: free chromosome arm
has_obo_namespace: sequence
id: SO:0000065

Axiom
annotated source: free_chromosome_arm
annotated property: definition
annotated target: A chromosome structure variation whereby an arm exists as an individual chromosome element.
database_cross_reference: SO:ke

gene_by_polyadenylation_attribute
type: Class
has_obo_namespace: sequence
id: SO:0000066
deprecated: true

gene_to_gene_feature
type: Class
subclass of: gene_attribute
has_exact_synonym: gene to gene feature
has_obo_namespace: sequence
id: SO:0000067

overlapping
type: Class
subclass of: gene_to_gene_feature
definition: An attribute describing a gene that has a sequence that overlaps the sequence of another gene.
has_obo_namespace: sequence
id: SO:0000068

Axiom
annotated source: overlapping
annotated property: definition
annotated target: An attribute describing a gene that has a sequence that overlaps the sequence of another gene.
database_cross_reference: SO:ke

inside_intron
type: Class
subclass of: overlapping
definition: An attribute to describe a gene when it is located within the intron of another gene.
has_exact_synonym: inside intron
has_obo_namespace: sequence
id: SO:0000069

Axiom
annotated source: inside_intron
annotated property: definition
annotated target: An attribute to describe a gene when it is located within the intron of another gene.
database_cross_reference: SO:ke

inside_intron_antiparallel
type: Class
subclass of: inside_intron
definition: An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.
has_exact_synonym: inside intron antiparallel
has_obo_namespace: sequence
id: SO:0000070

Axiom
annotated source: inside_intron_antiparallel
annotated property: definition
annotated target: An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.
database_cross_reference: SO:ke

inside_intron_parallel
type: Class
subclass of: inside_intron
definition: An attribute to describe a gene when it is located within the intron of another gene and on the same strand.
has_exact_synonym: inside intron parallel
has_obo_namespace: sequence
id: SO:0000071

Axiom
annotated source: inside_intron_parallel
annotated property: definition
annotated target: An attribute to describe a gene when it is located within the intron of another gene and on the same strand.
database_cross_reference: SO:ke

end_overlapping_gene
type: Class
has_obo_namespace: sequence
id: SO:0000072
deprecated: true

five_prime_three_prime_overlap
type: Class
subclass of: overlapping
definition: An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.
has_exact_synonym: five prime-three prime overlap
has_obo_namespace: sequence
id: SO:0000073

Axiom
annotated source: five_prime_three_prime_overlap
annotated property: definition
annotated target: An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.
database_cross_reference: SO:ke

five_prime_five_prime_overlap
type: Class
subclass of: overlapping
definition: An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.
has_exact_synonym: five prime-five prime overlap
has_obo_namespace: sequence
id: SO:0000074

Axiom
annotated source: five_prime_five_prime_overlap
annotated property: definition
annotated target: An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.
database_cross_reference: SO:ke

three_prime_three_prime_overlap
type: Class
subclass of: overlapping
definition: An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.
has_exact_synonym: three prime-three prime overlap
has_obo_namespace: sequence
id: SO:0000075

Axiom
annotated source: three_prime_three_prime_overlap
annotated property: definition
annotated target: An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.
database_cross_reference: SO:ke

three_prime_five_prime_overlap
type: Class
subclass of: overlapping
definition: An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.
has_exact_synonym: 5' 3' overlap
has_exact_synonym: three prime five prime overlap
has_obo_namespace: sequence
id: SO:0000076

Axiom
annotated source: three_prime_five_prime_overlap
annotated property: definition
annotated target: An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.
database_cross_reference: SO:ke

antisense
type: Class
subclass of: overlapping
definition: A region sequence that is complementary to a sequence of messenger RNA.
database_cross_reference: http://en.wikipedia.org/wiki/Antisense
has_obo_namespace: sequence
id: SO:0000077

Axiom
annotated source: antisense
annotated property: definition
annotated target: A region sequence that is complementary to a sequence of messenger RNA.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: antisense
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Antisense

polycistronic_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: polycistronic
subclass of: transcript
subclass of: Restriction
  on property: has_quality
  some values from: polycistronic
definition: A transcript that is polycistronic.
has_exact_synonym: polycistronic transcript
has_obo_namespace: sequence
id: SO:0000078

Axiom
annotated source: polycistronic_transcript
annotated property: definition
annotated target: A transcript that is polycistronic.
database_cross_reference: SO:xp

dicistronic_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: dicistronic
subclass of: polycistronic_transcript
subclass of: Restriction
  on property: has_quality
  some values from: dicistronic
definition: A transcript that is dicistronic.
has_exact_synonym: dicistronic transcript
has_obo_namespace: sequence
id: SO:0000079

Axiom
annotated source: dicistronic_transcript
annotated property: definition
annotated target: A transcript that is dicistronic.
database_cross_reference: SO:ke

operon_member
type: Class
subclass of: gene_array_member
definition: A gene that is a member of an operon, which is a set of genes transcribed together as a unit.
has_exact_synonym: operon member
has_obo_namespace: sequence
id: SO:0000080

gene_array_member
type: Class
subclass of: gene_attribute
has_exact_synonym: gene array member
has_obo_namespace: sequence
id: SO:0000081

processed_transcript_attribute
type: Class
has_obo_namespace: sequence
id: SO:0000082
deprecated: true

macronuclear_sequence
type: Class
subclass of: organelle_sequence
definition: DNA belonging to the macronuclei of ciliates.
has_exact_synonym: macronuclear sequence
has_obo_namespace: sequence
id: SO:0000083

micronuclear_sequence
type: Class
subclass of: organelle_sequence
definition: DNA belonging to the micronuclei of a cell.
has_exact_synonym: micronuclear sequence
has_obo_namespace: sequence
id: SO:0000084

gene_by_genome_location
type: Class
has_obo_namespace: sequence
id: SO:0000085
deprecated: true

gene_by_organelle_of_genome
type: Class
has_obo_namespace: sequence
id: SO:0000086
deprecated: true

nuclear_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: nuclear_sequence
subclass of: gene
subclass of: Restriction
  on property: has_origin
  some values from: nuclear_sequence
definition: A gene from nuclear sequence.
database_cross_reference: http://en.wikipedia.org/wiki/Nuclear_gene
has_exact_synonym: nuclear gene
has_obo_namespace: sequence
id: SO:0000087

Axiom
annotated source: nuclear_gene
annotated property: definition
annotated target: A gene from nuclear sequence.
database_cross_reference: SO:xp

wiki
type: Axiom
annotated source: nuclear_gene
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Nuclear_gene

mt_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: mitochondrial_sequence
subclass of: gene
subclass of: Restriction
  on property: has_origin
  some values from: mitochondrial_sequence
definition: A gene located in mitochondrial sequence.
database_cross_reference: http://en.wikipedia.org/wiki/Mitochondrial_gene
has_exact_synonym: mitochondrial gene
has_exact_synonym: mt gene
has_obo_namespace: sequence
id: SO:0000088

Axiom
annotated source: mt_gene
annotated property: definition
annotated target: A gene located in mitochondrial sequence.
database_cross_reference: SO:xp

wiki
type: Axiom
annotated source: mt_gene
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Mitochondrial_gene

kinetoplast_gene
type: Class
equivalent class: Class
  intersection of: mt_gene
  intersection of: Restriction
    on property: has_origin
    some values from: kinetoplast
subclass of: mt_gene
subclass of: Restriction
  on property: has_origin
  some values from: kinetoplast
definition: A gene located in kinetoplast sequence.
has_exact_synonym: kinetoplast gene
has_obo_namespace: sequence
id: SO:0000089

Axiom
annotated source: kinetoplast_gene
annotated property: definition
annotated target: A gene located in kinetoplast sequence.
database_cross_reference: SO:xp

plastid_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: plastid_sequence
subclass of: gene
subclass of: Restriction
  on property: has_origin
  some values from: plastid_sequence
definition: A gene from plastid sequence.
has_exact_synonym: plastid gene
has_obo_namespace: sequence
id: SO:0000090

Axiom
annotated source: plastid_gene
annotated property: definition
annotated target: A gene from plastid sequence.
database_cross_reference: SO:xp

apicoplast_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: apicoplast_sequence
subclass of: plastid_gene
subclass of: Restriction
  on property: has_origin
  some values from: apicoplast_sequence
definition: A gene from apicoplast sequence.
has_exact_synonym: apicoplast gene
has_obo_namespace: sequence
id: SO:0000091

Axiom
annotated source: apicoplast_gene
annotated property: definition
annotated target: A gene from apicoplast sequence.
database_cross_reference: SO:xp

ct_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: chloroplast_sequence
subclass of: plastid_gene
subclass of: Restriction
  on property: has_origin
  some values from: chloroplast_sequence
definition: A gene from chloroplast sequence.
has_exact_synonym: chloroplast gene
has_exact_synonym: ct gene
has_obo_namespace: sequence
id: SO:0000092

Axiom
annotated source: ct_gene
annotated property: definition
annotated target: A gene from chloroplast sequence.
database_cross_reference: SO:xp

chromoplast_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: chromoplast_sequence
subclass of: plastid_gene
subclass of: Restriction
  on property: has_origin
  some values from: chromoplast_sequence
definition: A gene from chromoplast_sequence.
has_exact_synonym: chromoplast gene
has_obo_namespace: sequence
id: SO:0000093

Axiom
annotated source: chromoplast_gene
annotated property: definition
annotated target: A gene from chromoplast_sequence.
database_cross_reference: SO:xp

cyanelle_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: cyanelle_sequence
subclass of: plastid_gene
subclass of: Restriction
  on property: has_origin
  some values from: cyanelle_sequence
definition: A gene from cyanelle sequence.
has_exact_synonym: cyanelle gene
has_obo_namespace: sequence
id: SO:0000094

Axiom
annotated source: cyanelle_gene
annotated property: definition
annotated target: A gene from cyanelle sequence.
database_cross_reference: SO:xp

leucoplast_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: leucoplast_sequence
subclass of: plastid_gene
subclass of: Restriction
  on property: has_origin
  some values from: leucoplast_sequence
definition: A plastid gene from leucoplast sequence.
has_exact_synonym: leucoplast gene
has_obo_namespace: sequence
id: SO:0000095

Axiom
annotated source: leucoplast_gene
annotated property: definition
annotated target: A plastid gene from leucoplast sequence.
database_cross_reference: SO:xp

proplastid_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: proplastid_sequence
subclass of: plastid_gene
subclass of: Restriction
  on property: has_origin
  some values from: proplastid_sequence
definition: A gene from proplastid sequence.
has_exact_synonym: proplastid gene
has_obo_namespace: sequence
id: SO:0000096

Axiom
annotated source: proplastid_gene
annotated property: definition
annotated target: A gene from proplastid sequence.
database_cross_reference: SO:ke

nucleomorph_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: nucleomorphic_sequence
subclass of: gene
subclass of: Restriction
  on property: has_origin
  some values from: nucleomorphic_sequence
definition: A gene from nucleomorph sequence.
has_exact_synonym: nucleomorph gene
has_obo_namespace: sequence
id: SO:0000097

Axiom
annotated source: nucleomorph_gene
annotated property: definition
annotated target: A gene from nucleomorph sequence.
database_cross_reference: SO:xp

plasmid_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: plasmid_location
subclass of: gene
subclass of: Restriction
  on property: has_origin
  some values from: plasmid_location
definition: A gene from plasmid sequence.
has_exact_synonym: plasmid gene
has_obo_namespace: sequence
id: SO:0000098

Axiom
annotated source: plasmid_gene
annotated property: definition
annotated target: A gene from plasmid sequence.
database_cross_reference: SO:xp

proviral_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: proviral_location
subclass of: gene
subclass of: Restriction
  on property: has_origin
  some values from: proviral_location
definition: A gene from proviral sequence.
has_exact_synonym: proviral gene
has_obo_namespace: sequence
id: SO:0000099

Axiom
annotated source: proviral_gene
annotated property: definition
annotated target: A gene from proviral sequence.
database_cross_reference: SO:xp

endogenous_retroviral_gene
type: Class
equivalent class: Class
  intersection of: proviral_gene
  intersection of: Restriction
    on property: has_origin
    some values from: endogenous_retroviral_sequence
subclass of: proviral_gene
subclass of: Restriction
  on property: has_origin
  some values from: endogenous_retroviral_sequence
definition: A proviral gene with origin endogenous retrovirus.
has_exact_synonym: endogenous retroviral gene
has_obo_namespace: sequence
id: SO:0000100

Axiom
annotated source: endogenous_retroviral_gene
annotated property: definition
annotated target: A proviral gene with origin endogenous retrovirus.
database_cross_reference: SO:xp

transposable_element
type: Class
subclass of: integrated_mobile_genetic_element
definition: A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
database_cross_reference: http://en.wikipedia.org/wiki/Transposable_element
has_exact_synonym: transposable element
has_exact_synonym: transposon
has_obo_namespace: sequence
id: SO:0000101
in_subset: SOFA

Axiom
annotated source: transposable_element
annotated property: definition
annotated target: A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
database_cross_reference: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html

wiki
type: Axiom
annotated source: transposable_element
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Transposable_element

expressed_sequence_match
type: Class
subclass of: nucleotide_match
definition: A match to an EST or cDNA sequence.
has_exact_synonym: expressed sequence match
has_obo_namespace: sequence
id: SO:0000102
in_subset: SOFA

Axiom
annotated source: expressed_sequence_match
annotated property: definition
annotated target: A match to an EST or cDNA sequence.
database_cross_reference: SO:ke

clone_insert_end
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: clone_insert
definition: The end of the clone insert.
has_exact_synonym: clone insert end
has_obo_namespace: sequence
id: SO:0000103
in_subset: SOFA

Axiom
annotated source: clone_insert_end
annotated property: definition
annotated target: The end of the clone insert.
database_cross_reference: SO:ke

polypeptide
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: derives_from
  some values from: CDS
definition: A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
has_alternative_id: SO:0000358
database_cross_reference: http://en.wikipedia.org/wiki/Polypeptide
has_exact_synonym: protein
has_obo_namespace: sequence
id: SO:0000104
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.

Axiom
annotated source: polypeptide
annotated property: definition
annotated target: A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: polypeptide
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Polypeptide

chromosome_arm
type: Class
subclass of: chromosome_part
definition: A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.
has_exact_synonym: chromosome arm
has_obo_namespace: sequence
id: SO:0000105

Axiom
annotated source: chromosome_arm
annotated property: definition
annotated target: A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.
database_cross_reference: http://www.medterms.com/script/main/art.asp

non_capped_primary_transcript
type: Class
has_obo_namespace: sequence
id: SO:0000106
deprecated: true

sequencing_primer
type: Class
subclass of: primer
definition: A single stranded oligo used for polymerase chain reaction.
has_exact_synonym: sequencing primer
has_obo_namespace: sequence
id: SO:0000107

mRNA_with_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: frameshift
subclass of: mRNA
subclass of: Restriction
  on property: has_quality
  some values from: frameshift
definition: An mRNA with a frameshift.
has_exact_synonym: frameshifted mRNA
has_exact_synonym: mRNA with frameshift
has_obo_namespace: sequence
id: SO:0000108

Axiom
annotated source: mRNA_with_frameshift
annotated property: definition
annotated target: An mRNA with a frameshift.
database_cross_reference: SO:xp

sequence_variant_obs
type: Class
definition: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
has_obo_namespace: sequence
has_related_synonym: mutation
id: SO:0000109
in_subset: SOFA
deprecated: true

Axiom
annotated source: sequence_variant_obs
annotated property: definition
annotated target: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
database_cross_reference: SO:ke

sequence_feature
type: Class
disjoint with: sequence_attribute
definition: Any extent of continuous biological sequence.
has_exact_synonym: INSDC_feature:misc_feature
has_exact_synonym: INSDC_note:other
has_exact_synonym: INSDC_note:sequence_feature
has_exact_synonym: located_sequence_feature
has_exact_synonym: sequence feature
has_obo_namespace: sequence
has_related_synonym: located sequence feature
id: SO:0000110
in_subset: SOFA

Axiom
annotated source: sequence_feature
annotated property: definition
annotated target: Any extent of continuous biological sequence.
database_cross_reference: LAMHDI:mb
database_cross_reference: SO:ke

transposable_element_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: part_of
    some values from: transposable_element
subclass of: gene
subclass of: Restriction
  on property: part_of
  some values from: transposable_element
definition: A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
has_exact_synonym: transposable element gene
has_obo_namespace: sequence
id: SO:0000111

Axiom
annotated source: transposable_element_gene
annotated property: definition
annotated target: A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
database_cross_reference: SO:ke

primer
type: Class
subclass of: ss_oligo
definition: An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
database_cross_reference: http://en.wikipedia.org/wiki/Primer_(molecular_biology)
has_exact_synonym: DNA primer
has_exact_synonym: primer oligonucleotide
has_exact_synonym: primer polynucleotide
has_exact_synonym: primer sequence
has_obo_namespace: sequence
id: SO:0000112
in_subset: SOFA

Axiom
annotated source: primer
annotated property: definition
annotated target: An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: primer
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Primer_(molecular_biology)

proviral_region
type: Class
subclass of: integrated_mobile_genetic_element
definition: A viral sequence which has integrated into a host genome.
has_exact_synonym: proviral region
has_obo_namespace: sequence
has_related_synonym: proviral sequence
id: SO:0000113
in_subset: SOFA

Axiom
annotated source: proviral_region
annotated property: definition
annotated target: A viral sequence which has integrated into a host genome.
database_cross_reference: SO:ke

methylated_cytosine
type: Class
subclass of: methylated_DNA_base_feature
subclass of: SO_0001963
definition: A methylated deoxy-cytosine.
has_exact_synonym: methylated C
has_exact_synonym: methylated cytosine
has_exact_synonym: methylated cytosine base
has_exact_synonym: methylated cytosine residue
has_exact_synonym: methylated_C
has_obo_namespace: sequence
id: SO:0000114
in_subset: SOFA

Axiom
annotated source: methylated_cytosine
annotated property: definition
annotated target: A methylated deoxy-cytosine.
database_cross_reference: SO:ke

transcript_feature
type: Class
has_obo_namespace: sequence
id: SO:0000115
deprecated: true

edited
type: Class
subclass of: transcript_attribute
definition: An attribute describing a sequence that is modified by editing.
has_obo_namespace: sequence
id: SO:0000116

Axiom
annotated source: edited
annotated property: definition
annotated target: An attribute describing a sequence that is modified by editing.
database_cross_reference: SO:ke

transcript_with_readthrough_stop_codon
type: Class
has_obo_namespace: sequence
id: SO:0000117
deprecated: true

transcript_with_translational_frameshift
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: translationally_frameshifted
subclass of: transcript
subclass of: Restriction
  on property: has_quality
  some values from: translationally_frameshifted
definition: A transcript with a translational frameshift.
has_exact_synonym: transcript with translational frameshift
has_obo_namespace: sequence
id: SO:0000118

Axiom
annotated source: transcript_with_translational_frameshift
annotated property: definition
annotated target: A transcript with a translational frameshift.
database_cross_reference: SO:xp

regulated
type: Class
subclass of: gene_attribute
definition: An attribute to describe a sequence that is regulated.
has_obo_namespace: sequence
id: SO:0000119

Axiom
annotated source: regulated
annotated property: definition
annotated target: An attribute to describe a sequence that is regulated.
database_cross_reference: SO:ke

protein_coding_primary_transcript
type: Class
subclass of: primary_transcript
definition: A primary transcript that, at least in part, encodes one or more proteins.
has_exact_synonym: protein coding primary transcript
has_obo_namespace: sequence
has_related_synonym: pre mRNA
id: SO:0000120
in_subset: SOFA
comment: May contain introns.

Axiom
annotated source: protein_coding_primary_transcript
annotated property: definition
annotated target: A primary transcript that, at least in part, encodes one or more proteins.
database_cross_reference: SO:ke

forward_primer
type: Class
equivalent class: Class
  intersection of: primer
  intersection of: Restriction
    on property: has_quality
    some values from: forward
subclass of: primer
subclass of: Restriction
  on property: has_quality
  some values from: forward
definition: A single stranded oligo used for polymerase chain reaction.
has_exact_synonym: DNA forward primer
has_exact_synonym: forward DNA primer
has_exact_synonym: forward primer
has_exact_synonym: forward primer oligo
has_exact_synonym: forward primer oligonucleotide
has_exact_synonym: forward primer polynucleotide
has_exact_synonym: forward primer sequence
has_obo_namespace: sequence
id: SO:0000121
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: forward_primer
annotated property: definition
annotated target: A single stranded oligo used for polymerase chain reaction.
database_cross_reference: http://mged.sourceforge.net/ontologies/MGEDontology.php

RNA_sequence_secondary_structure
type: Class
subclass of: sequence_secondary_structure
definition: A folded RNA sequence.
has_exact_synonym: RNA sequence secondary structure
has_obo_namespace: sequence
id: SO:0000122

Axiom
annotated source: RNA_sequence_secondary_structure
annotated property: definition
annotated target: A folded RNA sequence.
database_cross_reference: SO:ke

transcriptionally_regulated
type: Class
subclass of: regulated
definition: An attribute describing a gene that is regulated at transcription.
has_exact_synonym: transcriptionally regulated
has_obo_namespace: sequence
id: SO:0000123
comment: By:<protein_id>.

Axiom
annotated source: transcriptionally_regulated
annotated property: definition
annotated target: An attribute describing a gene that is regulated at transcription.
database_cross_reference: SO:ma

transcriptionally_constitutive
type: Class
subclass of: transcriptionally_regulated
definition: Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.
has_exact_synonym: transcriptionally constitutive
has_obo_namespace: sequence
id: SO:0000124

Axiom
annotated source: transcriptionally_constitutive
annotated property: definition
annotated target: Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.
database_cross_reference: SO:ke

transcriptionally_induced
type: Class
subclass of: transcriptionally_regulated
definition: An inducer molecule is required for transcription to occur.
has_exact_synonym: transcriptionally induced
has_obo_namespace: sequence
id: SO:0000125

Axiom
annotated source: transcriptionally_induced
annotated property: definition
annotated target: An inducer molecule is required for transcription to occur.
database_cross_reference: SO:ke

transcriptionally_repressed
type: Class
subclass of: transcriptionally_regulated
definition: A repressor molecule is required for transcription to stop.
has_exact_synonym: transcriptionally repressed
has_obo_namespace: sequence
id: SO:0000126

Axiom
annotated source: transcriptionally_repressed
annotated property: definition
annotated target: A repressor molecule is required for transcription to stop.
database_cross_reference: SO:ke

silenced_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: silenced
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: silenced
definition: A gene that is silenced.
has_exact_synonym: silenced gene
has_obo_namespace: sequence
id: SO:0000127

Axiom
annotated source: silenced_gene
annotated property: definition
annotated target: A gene that is silenced.
database_cross_reference: SO:xp

gene_silenced_by_DNA_modification
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_DNA_modification
subclass of: silenced_gene
subclass of: Restriction
  on property: has_quality
  some values from: silenced_by_DNA_modification
definition: A gene that is silenced by DNA modification.
has_exact_synonym: gene silenced by DNA modification
has_obo_namespace: sequence
id: SO:0000128

Axiom
annotated source: gene_silenced_by_DNA_modification
annotated property: definition
annotated target: A gene that is silenced by DNA modification.
database_cross_reference: SO:xp

gene_silenced_by_DNA_methylation
type: Class
equivalent class: Class
  intersection of: gene_silenced_by_DNA_modification
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_DNA_methylation
subclass of: gene_silenced_by_DNA_modification
subclass of: Restriction
  on property: has_quality
  some values from: silenced_by_DNA_methylation
definition: A gene that is silenced by DNA methylation.
has_exact_synonym: gene silenced by DNA methylation
has_exact_synonym: methylation-silenced gene
has_obo_namespace: sequence
id: SO:0000129

Axiom
annotated source: gene_silenced_by_DNA_methylation
annotated property: definition
annotated target: A gene that is silenced by DNA methylation.
database_cross_reference: SO:xp

post_translationally_regulated
type: Class
subclass of: regulated
definition: An attribute describing a gene that is regulated after it has been translated.
has_exact_synonym: post translationally regulated
has_exact_synonym: post-translationally regulated
has_obo_namespace: sequence
id: SO:0000130

Axiom
annotated source: post_translationally_regulated
annotated property: definition
annotated target: An attribute describing a gene that is regulated after it has been translated.
database_cross_reference: SO:ke

translationally_regulated
type: Class
subclass of: regulated
definition: An attribute describing a gene that is regulated as it is translated.
has_exact_synonym: translationally regulated
has_obo_namespace: sequence
id: SO:0000131

Axiom
annotated source: translationally_regulated
annotated property: definition
annotated target: An attribute describing a gene that is regulated as it is translated.
database_cross_reference: SO:ke

reverse_primer
type: Class
equivalent class: Class
  intersection of: primer
  intersection of: Restriction
    on property: has_quality
    some values from: reverse
subclass of: primer
subclass of: Restriction
  on property: has_quality
  some values from: reverse
definition: A single stranded oligo used for polymerase chain reaction.
has_exact_synonym: DNA reverse primer
has_exact_synonym: reverse DNA primer
has_exact_synonym: reverse primer
has_exact_synonym: reverse primer oligo
has_exact_synonym: reverse primer oligonucleotide
has_exact_synonym: reverse primer sequence
has_obo_namespace: sequence
id: SO:0000132
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: reverse_primer
annotated property: definition
annotated target: A single stranded oligo used for polymerase chain reaction.
database_cross_reference: http://mged.sourceforge.net/ontologies/MGEDontology.php

epigenetically_modified
type: Class
subclass of: gene_attribute
definition: This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones.
has_exact_synonym: epigenetically modified
has_obo_namespace: sequence
id: SO:0000133

Axiom
annotated source: epigenetically_modified
annotated property: definition
annotated target: This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones.
database_cross_reference: SO:ke

genomically_imprinted
type: Class
subclass of: regulated
subclass of: epigenetically_modified
definition: Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin.
has_broad_synonym: imprinted
database_cross_reference: http:http://en.wikipedia.org/wiki/Genomic_imprinting
has_exact_synonym: genomically imprinted
has_obo_namespace: sequence
id: SO:0000134

Axiom
annotated source: genomically_imprinted
annotated property: definition
annotated target: Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: genomically_imprinted
annotated property: database_cross_reference
annotated target: http:http://en.wikipedia.org/wiki/Genomic_imprinting

maternally_imprinted
type: Class
subclass of: genomically_imprinted
definition: The maternal copy of the gene is modified, rendering it transcriptionally silent.
has_exact_synonym: maternally imprinted
has_obo_namespace: sequence
id: SO:0000135

Axiom
annotated source: maternally_imprinted
annotated property: definition
annotated target: The maternal copy of the gene is modified, rendering it transcriptionally silent.
database_cross_reference: SO:ke

paternally_imprinted
type: Class
subclass of: genomically_imprinted
definition: The paternal copy of the gene is modified, rendering it transcriptionally silent.
has_exact_synonym: paternally imprinted
has_obo_namespace: sequence
id: SO:0000136

Axiom
annotated source: paternally_imprinted
annotated property: definition
annotated target: The paternal copy of the gene is modified, rendering it transcriptionally silent.
database_cross_reference: SO:ke

allelically_excluded
type: Class
subclass of: epigenetically_modified
definition: Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell.
has_exact_synonym: allelically excluded
has_obo_namespace: sequence
id: SO:0000137
comment: Examples are x-inactivation and immunoglobulin formation.

Axiom
annotated source: allelically_excluded
annotated property: definition
annotated target: Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell.
database_cross_reference: SO:ke

gene_rearranged_at_DNA_level
type: Class
equivalent class: Class
  intersection of: epigenetically_modified_gene
  intersection of: Restriction
    on property: has_quality
    some values from: rearranged_at_DNA_level
subclass of: epigenetically_modified_gene
subclass of: Restriction
  on property: has_quality
  some values from: rearranged_at_DNA_level
definition: An epigenetically modified gene, rearranged at the DNA level.
has_exact_synonym: gene rearranged at DNA level
has_obo_namespace: sequence
id: SO:0000138

Axiom
annotated source: gene_rearranged_at_DNA_level
annotated property: definition
annotated target: An epigenetically modified gene, rearranged at the DNA level.
database_cross_reference: SO:xp

ribosome_entry_site
type: Class
subclass of: mRNA_region
subclass of: Restriction
  on property: part_of
  some values from: five_prime_UTR
definition: Region in mRNA where ribosome assembles.
has_broad_synonym: INSDC_feature:regulatory
has_exact_synonym: INSDC_qualifier:ribosome_binding_site
has_exact_synonym: ribosome entry site
has_obo_namespace: sequence
id: SO:0000139
in_subset: SOFA

Axiom
annotated source: ribosome_entry_site
annotated property: definition
annotated target: Region in mRNA where ribosome assembles.
database_cross_reference: SO:ke

attenuator
type: Class
subclass of: translation_regulatory_region
subclass of: Restriction
  on property: part_of
  some values from: mRNA
definition: A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Attenuator
has_exact_synonym: INSDC_qualifier:attenuator
has_exact_synonym: attenuator sequence
has_obo_namespace: sequence
id: SO:0000140
in_subset: SOFA

Axiom
annotated source: attenuator
annotated property: definition
annotated target: A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
database_cross_reference: SO:as

wiki
type: Axiom
annotated source: attenuator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Attenuator

terminator
type: Class
subclass of: transcriptional_cis_regulatory_region
subclass of: Restriction
  on property: part_of
  some values from: transcript
definition: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Terminator_(genetics)
has_exact_synonym: INSDC_qualifier:terminator
has_exact_synonym: terminator sequence
has_obo_namespace: sequence
id: SO:0000141
in_subset: SOFA
comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: terminator
annotated property: definition
annotated target: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: terminator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Terminator_(genetics)

DNA_sequence_secondary_structure
type: Class
subclass of: sequence_secondary_structure
definition: A folded DNA sequence.
has_exact_synonym: DNA sequence secondary structure
has_obo_namespace: sequence
id: SO:0000142

Axiom
annotated source: DNA_sequence_secondary_structure
annotated property: definition
annotated target: A folded DNA sequence.
database_cross_reference: SO:ke

assembly_component
type: Class
subclass of: experimental_feature
definition: A region of known length which may be used to manufacture a longer region.
has_exact_synonym: assembly component
has_obo_namespace: sequence
id: SO:0000143
in_subset: SOFA

Axiom
annotated source: assembly_component
annotated property: definition
annotated target: A region of known length which may be used to manufacture a longer region.
database_cross_reference: SO:ke

primary_transcript_attribute
type: Class
has_obo_namespace: sequence
id: SO:0000144
deprecated: true

recoded_codon
type: Class
subclass of: codon
definition: A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.
has_exact_synonym: recoded codon
has_obo_namespace: sequence
id: SO:0000145

Axiom
annotated source: recoded_codon
annotated property: definition
annotated target: A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.
database_cross_reference: SO:xp

capped
type: Class
subclass of: transcript_attribute
definition: An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
has_obo_namespace: sequence
id: SO:0000146

Axiom
annotated source: capped
annotated property: definition
annotated target: An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
database_cross_reference: SO:ke

exon
type: Class
subclass of: transcript_region
definition: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
database_cross_reference: http://en.wikipedia.org/wiki/Exon
has_exact_synonym: INSDC_feature:exon
has_obo_namespace: sequence
id: SO:0000147
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: exon
annotated property: definition
annotated target: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: exon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Exon

supercontig
type: Class
subclass of: SO_0001876
subclass of: Restriction
  on property: part_of
  some values from: ultracontig
definition: One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
has_obo_namespace: sequence
has_related_synonym: scaffold
id: SO:0000148
in_subset: SOFA

Axiom
annotated source: supercontig
annotated property: definition
annotated target: One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
database_cross_reference: SO:ls

contig
type: Class
subclass of: assembly_component
subclass of: sequence_assembly
subclass of: Restriction
  on property: part_of
  some values from: supercontig
definition: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
database_cross_reference: http://en.wikipedia.org/wiki/Contig
has_obo_namespace: sequence
id: SO:0000149
in_subset: SOFA

Axiom
annotated source: contig
annotated property: definition
annotated target: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
database_cross_reference: SO:ls

wiki
type: Axiom
annotated source: contig
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Contig

read
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: contig
definition: A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
has_obo_namespace: sequence
id: SO:0000150
in_subset: SOFA

Axiom
annotated source: read
annotated property: definition
annotated target: A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
database_cross_reference: SO:rd

clone
type: Class
subclass of: reagent
definition: A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
database_cross_reference: http:http://en.wikipedia.org/wiki/Clone_(genetics)
has_obo_namespace: sequence
id: SO:0000151
in_subset: SOFA

Axiom
annotated source: clone
annotated property: definition
annotated target: A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: clone
annotated property: database_cross_reference
annotated target: http:http://en.wikipedia.org/wiki/Clone_(genetics)

YAC
type: Class
subclass of: vector_replicon
definition: Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.
has_exact_synonym: yeast artificial chromosome
has_obo_namespace: sequence
id: SO:0000152
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: YAC
annotated property: definition
annotated target: Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.
database_cross_reference: SO:ma

BAC
type: Class
subclass of: vector_replicon
definition: Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.
has_exact_synonym: bacterial artificial chromosome
has_obo_namespace: sequence
id: SO:0000153
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: BAC
annotated property: definition
annotated target: Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.
database_cross_reference: SO:ma

PAC
type: Class
subclass of: vector_replicon
definition: The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.
database_cross_reference: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
has_exact_synonym: P1
has_exact_synonym: P1 artificial chromosome
has_obo_namespace: sequence
id: SO:0000154
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.

Axiom
annotated source: PAC
annotated property: definition
annotated target: The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.
database_cross_reference: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome

wiki
type: Axiom
annotated source: PAC
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome

plasmid
type: Class
subclass of: replicon
definition: A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.
has_exact_synonym: plasmid sequence
has_obo_namespace: sequence
id: SO:0000155
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: plasmid
annotated property: definition
annotated target: A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.
database_cross_reference: SO:ma

cosmid
type: Class
subclass of: vector_replicon
definition: A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.
database_cross_reference: http://en.wikipedia.org/wiki/Cosmid
has_exact_synonym: cosmid vector
has_obo_namespace: sequence
id: SO:0000156
comment: Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: cosmid
annotated property: definition
annotated target: A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: cosmid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Cosmid

phagemid
type: Class
subclass of: vector_replicon
definition: A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids.
database_cross_reference: http://en.wikipedia.org/wiki/Phagemid
has_obo_namespace: sequence
has_related_synonym: phagemid vector
id: SO:0000157

Axiom
annotated source: phagemid
annotated property: definition
annotated target: A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: phagemid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Phagemid

fosmid
type: Class
subclass of: vector_replicon
definition: A cloning vector that utilizes the E. coli F factor.
database_cross_reference: http://en.wikipedia.org/wiki/Fosmid
has_obo_namespace: sequence
has_related_synonym: fosmid vector
id: SO:0000158
comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.

Axiom
annotated source: fosmid
annotated property: definition
annotated target: A cloning vector that utilizes the E. coli F factor.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: fosmid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Fosmid

deletion
type: Class
subclass of: sequence_alteration
subclass of: biological_region
definition: The point at which one or more contiguous nucleotides were excised.
has_alternative_id: SO:1000033
database_cross_reference: http://en.wikipedia.org/wiki/Nucleotide_deletion
database_cross_reference: loinc:LA6692-3
has_exact_synonym: deleted_sequence
has_exact_synonym: nucleotide deletion
has_exact_synonym: nucleotide_deletion
has_obo_namespace: sequence
id: SO:0000159
in_subset: SOFA

Axiom
annotated source: deletion
annotated property: definition
annotated target: The point at which one or more contiguous nucleotides were excised.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: deletion
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Nucleotide_deletion

Deletion
type: Axiom
annotated source: deletion
annotated property: database_cross_reference
annotated target: loinc:LA6692-3

lambda_clone
type: Class
definition: A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
has_obo_namespace: sequence
id: SO:0000160
deprecated: true

Axiom
annotated source: lambda_clone
annotated property: definition
annotated target: A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
database_cross_reference: ISBN:0-1767-2380-8

methylated_adenine
type: Class
subclass of: methylated_DNA_base_feature
subclass of: SO_0001962
definition: A modified base in which adenine has been methylated.
has_exact_synonym: methylated A
has_exact_synonym: methylated adenine
has_exact_synonym: methylated adenine base
has_exact_synonym: methylated adenine residue
has_exact_synonym: methylated_A
has_obo_namespace: sequence
id: SO:0000161
in_subset: SOFA

Axiom
annotated source: methylated_adenine
annotated property: definition
annotated target: A modified base in which adenine has been methylated.
database_cross_reference: SO:ke

splice_site
type: Class
subclass of: primary_transcript_region
definition: Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
database_cross_reference: http://en.wikipedia.org/wiki/Splice_site
has_exact_synonym: splice site
has_obo_namespace: sequence
id: SO:0000162
in_subset: SOFA
comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery.

Axiom
annotated source: splice_site
annotated property: definition
annotated target: Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
database_cross_reference: SO:cjm
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: splice_site
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Splice_site

five_prime_cis_splice_site
type: Class
subclass of: cis_splice_site
definition: Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
has_exact_synonym: 5' splice site
has_exact_synonym: donor splice site
has_exact_synonym: five prime splice site
has_exact_synonym: splice donor site
has_obo_namespace: sequence
has_related_synonym: donor
id: SO:0000163
in_subset: SOFA

Axiom
annotated source: five_prime_cis_splice_site
annotated property: definition
annotated target: Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
database_cross_reference: SO:cjm
database_cross_reference: SO:ke
database_cross_reference: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html

three_prime_cis_splice_site
type: Class
subclass of: cis_splice_site
definition: Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
has_exact_synonym: acceptor splice site
has_exact_synonym: splice acceptor site
has_exact_synonym: three prime splice site
has_obo_namespace: sequence
has_related_synonym: 3' splice site
has_related_synonym: acceptor
id: SO:0000164
in_subset: SOFA

Axiom
annotated source: three_prime_cis_splice_site
annotated property: definition
annotated target: Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
database_cross_reference: SO:cjm
database_cross_reference: SO:ke
database_cross_reference: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html

enhancer
type: Class
subclass of: cis_regulatory_module
definition: A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Enhancer_(genetics)
has_exact_synonym: INSDC_qualifier:enhancer
has_obo_namespace: sequence
id: SO:0000165
in_subset: SOFA
comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.

Axiom
annotated source: enhancer
annotated property: definition
annotated target: A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: enhancer
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Enhancer_(genetics)

enhancer_bound_by_factor
type: Class
equivalent class: Class
  intersection of: enhancer
  intersection of: Restriction
    on property: has_quality
    some values from: bound_by_factor
subclass of: enhancer
subclass of: Restriction
  on property: has_quality
  some values from: bound_by_factor
definition: An enhancer bound by a factor.
has_exact_synonym: enhancer bound by factor
has_obo_namespace: sequence
id: SO:0000166

Axiom
annotated source: enhancer_bound_by_factor
annotated property: definition
annotated target: An enhancer bound by a factor.
database_cross_reference: SO:xp

promoter
type: Class
subclass of: gene_component_region
subclass of: transcriptional_cis_regulatory_region
definition: A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Promoter
has_exact_synonym: INSDC_qualifier:promoter
has_exact_synonym: promoter sequence
has_obo_namespace: sequence
id: SO:0000167
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter.

Axiom
annotated source: promoter
annotated property: definition
annotated target: A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription.
database_cross_reference: SO:regcreative

wiki
type: Axiom
annotated source: promoter
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Promoter

restriction_enzyme_cut_site
type: Class
definition: A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.
has_obo_namespace: sequence
id: SO:0000168
deprecated: true

Axiom
annotated source: restriction_enzyme_cut_site
annotated property: definition
annotated target: A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.
database_cross_reference: SO:ma

RNApol_I_promoter
type: Class
subclass of: SO_0002221
definition: A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
has_exact_synonym: RNA polymerase A promoter
has_exact_synonym: RNApol I promoter
has_exact_synonym: pol I promoter
has_exact_synonym: polymerase I promoter
has_obo_namespace: sequence
id: SO:0000169
comment: parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.

Axiom
annotated source: RNApol_I_promoter
annotated property: definition
annotated target: A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
database_cross_reference: SO:ke

RNApol_II_promoter
type: Class
subclass of: SO_0002221
definition: A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
has_exact_synonym: RNA polymerase B promoter
has_exact_synonym: RNApol II promoter
has_exact_synonym: polymerase II promoter
has_obo_namespace: sequence
has_related_synonym: pol II promoter
id: SO:0000170
comment: parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.

Axiom
annotated source: RNApol_II_promoter
annotated property: definition
annotated target: A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
database_cross_reference: SO:ke

RNApol_III_promoter
type: Class
subclass of: SO_0002221
definition: A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
has_exact_synonym: RNA polymerase C promoter
has_exact_synonym: RNApol III promoter
has_exact_synonym: pol III promoter
has_exact_synonym: polymerase III promoter
has_obo_namespace: sequence
id: SO:0000171
comment: parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.

Axiom
annotated source: RNApol_III_promoter
annotated property: definition
annotated target: A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
database_cross_reference: SO:ke

CAAT_signal
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/CAAT_box
has_exact_synonym: CAAT box
has_exact_synonym: CAAT signal
has_exact_synonym: CAAT-box
has_exact_synonym: INSDC_qualifier:CAAT_signal
has_obo_namespace: sequence
id: SO:0000172

Axiom
annotated source: CAAT_signal
annotated property: definition
annotated target: Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: CAAT_signal
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/CAAT_box

GC_rich_promoter_region
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.
has_broad_synonym: INSDC_feature:regulatory
has_exact_synonym: GC rich promoter region
has_exact_synonym: GC-rich region
has_exact_synonym: INSDC_qualifier:GC_rich_promoter_region
has_obo_namespace: sequence
id: SO:0000173

Axiom
annotated source: GC_rich_promoter_region
annotated property: definition
annotated target: A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.
database_cross_reference: http://www.insdc.org/files/feature_table.html

TATA_box
type: Class
subclass of: core_eukaryotic_promoter_element
definition: A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/TATA_box
has_exact_synonym: Goldstein-Hogness box
has_exact_synonym: INSDC_qualifier:TATA_box
has_exact_synonym: TATA box
has_obo_namespace: sequence
id: SO:0000174
comment: Binds TBP.

Axiom
annotated source: TATA_box
annotated property: definition
annotated target: A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).
database_cross_reference: PMID:16858867
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: TATA_box
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/TATA_box

minus_10_signal
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: bacterial_RNApol_promoter_sigma_70_element
subclass of: Restriction
  on property: part_of
  some values from: SO_0001913
definition: A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Pribnow_box
has_exact_synonym: -10 signal
has_exact_synonym: INSDC_qualifier:minus_10_signal
has_exact_synonym: Pribnow Schaller box
has_exact_synonym: Pribnow box
has_exact_synonym: Pribnow-Schaller box
has_exact_synonym: minus 10 signal
has_obo_namespace: sequence
id: SO:0000175
comment: Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021.

Axiom
annotated source: minus_10_signal
annotated property: definition
annotated target: A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: minus_10_signal
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Pribnow_box

minus_35_signal
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: bacterial_RNApol_promoter_sigma_70_element
subclass of: Restriction
  on property: part_of
  some values from: SO_0001913
definition: A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.
has_broad_synonym: INSDC_feature:regulatory
has_exact_synonym: -35 signal
has_exact_synonym: INSDC_qualifier:minus_35_signal
has_exact_synonym: minus 35 signal
has_obo_namespace: sequence
id: SO:0000176
comment: Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021.

Axiom
annotated source: minus_35_signal
annotated property: definition
annotated target: A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.
database_cross_reference: http://www.insdc.org/files/feature_table.html

cross_genome_match
type: Class
subclass of: nucleotide_match
definition: A nucleotide match against a sequence from another organism.
has_exact_synonym: cross genome match
has_obo_namespace: sequence
id: SO:0000177
in_subset: SOFA

Axiom
annotated source: cross_genome_match
annotated property: definition
annotated target: A nucleotide match against a sequence from another organism.
database_cross_reference: SO:ma

operon
type: Class
subclass of: SO_0005855
definition: The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.
database_cross_reference: http://en.wikipedia.org/wiki/Operon
has_exact_synonym: INSDC_feature:operon
has_obo_namespace: sequence
id: SO:0000178
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Definition updated with per Mejia-Almonte et.al Redefining fundamental concepts of transcription initiation in prokaryotes Aug 5 2020.

Axiom
annotated source: operon
annotated property: definition
annotated target: The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: operon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Operon

clone_insert_start
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: clone_insert
definition: The start of the clone insert.
has_exact_synonym: clone insert start
has_obo_namespace: sequence
id: SO:0000179
in_subset: SOFA

Axiom
annotated source: clone_insert_start
annotated property: definition
annotated target: The start of the clone insert.
database_cross_reference: SO:ke

retrotransposon
type: Class
subclass of: transposable_element
definition: A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.
database_cross_reference: http://en.wikipedia.org/wiki/Retrotransposon
has_exact_synonym: class I transposon
has_exact_synonym: retrotransposon element
has_obo_namespace: sequence
has_related_synonym: class I
id: SO:0000180

Axiom
annotated source: retrotransposon
annotated property: definition
annotated target: A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.
database_cross_reference: http://www.dddmag.com/Glossary.aspx#r

wiki
type: Axiom
annotated source: retrotransposon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Retrotransposon

translated_nucleotide_match
type: Class
subclass of: nucleotide_match
definition: A match against a translated sequence.
has_exact_synonym: translated nucleotide match
has_obo_namespace: sequence
id: SO:0000181
in_subset: SOFA

Axiom
annotated source: translated_nucleotide_match
annotated property: definition
annotated target: A match against a translated sequence.
database_cross_reference: SO:ke

DNA_transposon
type: Class
subclass of: transposable_element
definition: A transposon where the mechanism of transposition is via a DNA intermediate.
has_exact_synonym: DNA transposon
has_exact_synonym: class II transposon
has_obo_namespace: sequence
has_related_synonym: class II
id: SO:0000182

Axiom
annotated source: DNA_transposon
annotated property: definition
annotated target: A transposon where the mechanism of transposition is via a DNA intermediate.
database_cross_reference: SO:ke

non_transcribed_region
type: Class
subclass of: gene_component_region
definition: A region of the gene which is not transcribed.
has_exact_synonym: non transcribed region
has_exact_synonym: non-transcribed sequence
has_exact_synonym: nontranscribed region
has_exact_synonym: nontranscribed sequence
has_obo_namespace: sequence
id: SO:0000183
in_subset: SOFA

Axiom
annotated source: non_transcribed_region
annotated property: definition
annotated target: A region of the gene which is not transcribed.
database_cross_reference: SO:ke

U2_intron
type: Class
subclass of: spliceosomal_intron
definition: A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
has_exact_synonym: U2 intron
has_obo_namespace: sequence
id: SO:0000184
comment: May have either GT-AG or AT-AG 5' and 3' boundaries.

Axiom
annotated source: U2_intron
annotated property: definition
annotated target: A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
database_cross_reference: PMID:9428511

primary_transcript
type: Class
subclass of: transcript
definition: A transcript that in its initial state requires modification to be functional.
database_cross_reference: http://en.wikipedia.org/wiki/Primary_transcript
has_exact_synonym: INSDC_feature:precursor_RNA
has_exact_synonym: INSDC_feature:prim_transcript
has_exact_synonym: precursor RNA
has_exact_synonym: primary transcript
has_obo_namespace: sequence
id: SO:0000185
in_subset: SOFA

Axiom
annotated source: primary_transcript
annotated property: definition
annotated target: A transcript that in its initial state requires modification to be functional.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: primary_transcript
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Primary_transcript

LTR_retrotransposon
type: Class
subclass of: retrotransposon
definition: A retrotransposon flanked by long terminal repeat sequences.
has_exact_synonym: LTR retrotransposon
has_exact_synonym: long terminal repeat retrotransposon
has_obo_namespace: sequence
id: SO:0000186

Axiom
annotated source: LTR_retrotransposon
annotated property: definition
annotated target: A retrotransposon flanked by long terminal repeat sequences.
database_cross_reference: SO:ke

repeat_family
type: Class
definition: A group of characterized repeat sequences.
has_obo_namespace: sequence
id: SO:0000187
in_subset: SOFA
deprecated: true

Axiom
annotated source: repeat_family
annotated property: definition
annotated target: A group of characterized repeat sequences.
database_cross_reference: SO:ke

intron
type: Class
subclass of: primary_transcript_region
definition: A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
database_cross_reference: http://en.wikipedia.org/wiki/Intron
has_exact_synonym: INSDC_feature:intron
has_obo_namespace: sequence
id: SO:0000188
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: intron
annotated property: definition
annotated target: A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: intron
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Intron

non_LTR_retrotransposon
type: Class
subclass of: retrotransposon
definition: A retrotransposon without long terminal repeat sequences.
has_exact_synonym: non LTR retrotransposon
has_obo_namespace: sequence
id: SO:0000189

Axiom
annotated source: non_LTR_retrotransposon
annotated property: definition
annotated target: A retrotransposon without long terminal repeat sequences.
database_cross_reference: SO:ke

five_prime_intron
type: Class
subclass of: intron
definition: An intron that is the most 5-prime in a given transcript.
has_exact_synonym: 5' intron
has_exact_synonym: 5' intron sequence
has_exact_synonym: five prime intron
has_obo_namespace: sequence
id: SO:0000190

interior_intron
type: Class
subclass of: intron
definition: An intron that is not the most 3-prime or the most 5-prime in a given transcript.
has_exact_synonym: interior intron
has_obo_namespace: sequence
id: SO:0000191

three_prime_intron
type: Class
subclass of: intron
definition: An intron that is the most 3-prime in a given transcript.
has_exact_synonym: 3' intron
has_exact_synonym: three prime intron
has_obo_namespace: sequence
has_related_synonym: 3' intron sequence
id: SO:0000192

RFLP_fragment
type: Class
subclass of: restriction_fragment
definition: A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
database_cross_reference: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism
has_exact_synonym: RFLP
has_exact_synonym: RFLP fragment
has_exact_synonym: restriction fragment length polymorphism
has_obo_namespace: sequence
id: SO:0000193
in_subset: SOFA

Axiom
annotated source: RFLP_fragment
annotated property: definition
annotated target: A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
database_cross_reference: GOC:pj

wiki
type: Axiom
annotated source: RFLP_fragment
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism

LINE_element
type: Class
subclass of: non_LTR_retrotransposon
definition: A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats.
has_exact_synonym: LINE
has_exact_synonym: LINE element
has_exact_synonym: Long interspersed element
has_exact_synonym: Long interspersed nuclear element
has_obo_namespace: sequence
id: SO:0000194

Axiom
annotated source: LINE_element
annotated property: definition
annotated target: A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats.
database_cross_reference: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html

coding_exon
type: Class
subclass of: exon
definition: An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
has_exact_synonym: coding exon
has_obo_namespace: sequence
id: SO:0000195
in_subset: SOFA

Axiom
annotated source: coding_exon
annotated property: definition
annotated target: An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
database_cross_reference: SO:ke

five_prime_coding_exon_coding_region
type: Class
subclass of: coding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: five_prime_coding_exon
definition: The sequence of the five_prime_coding_exon that codes for protein.
has_exact_synonym: five prime exon coding region
has_obo_namespace: sequence
id: SO:0000196
in_subset: SOFA

Axiom
annotated source: five_prime_coding_exon_coding_region
annotated property: definition
annotated target: The sequence of the five_prime_coding_exon that codes for protein.
database_cross_reference: SO:cjm

three_prime_coding_exon_coding_region
type: Class
subclass of: coding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: three_prime_coding_exon
definition: The sequence of the three_prime_coding_exon that codes for protein.
has_exact_synonym: three prime exon coding region
has_obo_namespace: sequence
id: SO:0000197
in_subset: SOFA

Axiom
annotated source: three_prime_coding_exon_coding_region
annotated property: definition
annotated target: The sequence of the three_prime_coding_exon that codes for protein.
database_cross_reference: SO:cjm

noncoding_exon
type: Class
subclass of: exon
definition: An exon that does not contain any codons.
has_exact_synonym: noncoding exon
has_obo_namespace: sequence
id: SO:0000198
in_subset: SOFA

Axiom
annotated source: noncoding_exon
annotated property: definition
annotated target: An exon that does not contain any codons.
database_cross_reference: SO:ke

translocation
type: Class
subclass of: SO_0001785
definition: A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions.
has_exact_synonym: translocated sequence
has_obo_namespace: sequence
has_related_synonym: transchr
id: SO:0000199
in_subset: DBVAR

Axiom
annotated source: translocation
annotated property: definition
annotated target: A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions.
database_cross_reference: NCBI:th
database_cross_reference: SO:ke

Axiom
annotated source: translocation
annotated property: has_related_synonym
annotated target: transchr
database_cross_reference: http://www.ncbi.nlm.nih.gov/dbvar/

five_prime_coding_exon
type: Class
subclass of: coding_exon
definition: The 5' most coding exon.
has_exact_synonym: 5' coding exon
has_exact_synonym: five prime coding exon
has_obo_namespace: sequence
id: SO:0000200
in_subset: SOFA

Axiom
annotated source: five_prime_coding_exon
annotated property: definition
annotated target: The 5' most coding exon.
database_cross_reference: SO:ke

interior_exon
type: Class
subclass of: exon
definition: An exon that is bounded by 5' and 3' splice sites.
has_exact_synonym: interior exon
has_obo_namespace: sequence
id: SO:0000201

Axiom
annotated source: interior_exon
annotated property: definition
annotated target: An exon that is bounded by 5' and 3' splice sites.
database_cross_reference: PMID:10373547

three_prime_coding_exon
type: Class
subclass of: coding_exon
definition: The coding exon that is most 3-prime on a given transcript.
has_exact_synonym: three prime coding exon
has_obo_namespace: sequence
has_related_synonym: 3' coding exon
id: SO:0000202

Axiom
annotated source: three_prime_coding_exon
annotated property: definition
annotated target: The coding exon that is most 3-prime on a given transcript.
database_cross_reference: SO:ma

UTR
type: Class
subclass of: mRNA_region
definition: Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
has_exact_synonym: untranslated region
has_obo_namespace: sequence
id: SO:0000203
in_subset: SOFA

Axiom
annotated source: UTR
annotated property: definition
annotated target: Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
database_cross_reference: SO:ke

five_prime_UTR
type: Class
subclass of: UTR
definition: A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
database_cross_reference: http://en.wikipedia.org/wiki/5'_UTR
has_exact_synonym: 5' UTR
has_exact_synonym: INSDC_feature:5'UTR
has_exact_synonym: five prime UTR
has_exact_synonym: five_prime_untranslated_region
has_obo_namespace: sequence
id: SO:0000204
in_subset: SOFA

Axiom
annotated source: five_prime_UTR
annotated property: definition
annotated target: A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: five_prime_UTR
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/5'_UTR

three_prime_UTR
type: Class
subclass of: UTR
definition: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
database_cross_reference: http://en.wikipedia.org/wiki/Three_prime_untranslated_region
has_exact_synonym: INSDC_feature:3'UTR
has_exact_synonym: three prime UTR
has_exact_synonym: three prime untranslated region
has_obo_namespace: sequence
id: SO:0000205
in_subset: SOFA

Axiom
annotated source: three_prime_UTR
annotated property: definition
annotated target: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: three_prime_UTR
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Three_prime_untranslated_region

SINE_element
type: Class
subclass of: non_LTR_retrotransposon
definition: A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.
database_cross_reference: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element
has_exact_synonym: SINE element
has_exact_synonym: Short interspersed element
has_exact_synonym: Short interspersed nuclear element
has_obo_namespace: sequence
id: SO:0000206

Axiom
annotated source: SINE_element
annotated property: definition
annotated target: A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: SINE_element
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element

simple_sequence_length_variation
type: Class
subclass of: sequence_length_alteration
definition: SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ.
database_cross_reference: http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism
has_exact_synonym: simple sequence length variation
has_obo_namespace: sequence
has_related_synonym: SSLP
has_related_synonym: simple sequence length polymorphism
id: SO:0000207

Axiom
annotated source: simple_sequence_length_variation
annotated property: definition
annotated target: SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ.
database_cross_reference: SO:ke

WIKI
type: Axiom
annotated source: simple_sequence_length_variation
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism

terminal_inverted_repeat_element
type: Class
subclass of: DNA_transposon
definition: A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.
has_exact_synonym: TIR element
has_exact_synonym: terminal inverted repeat element
has_obo_namespace: sequence
id: SO:0000208

Axiom
annotated source: terminal_inverted_repeat_element
annotated property: definition
annotated target: A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.
database_cross_reference: http://www.genetics.org/cgi/reprint/156/4/1983.pdf

rRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
definition: A primary transcript encoding a ribosomal RNA.
has_exact_synonym: rRNA primary transcript
has_exact_synonym: ribosomal RNA primary transcript
has_obo_namespace: sequence
id: SO:0000209
in_subset: SOFA

Axiom
annotated source: rRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a ribosomal RNA.
database_cross_reference: SO:ke

tRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
definition: A primary transcript encoding a transfer RNA (SO:0000253).
has_exact_synonym: tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000210

Axiom
annotated source: tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a transfer RNA (SO:0000253).
database_cross_reference: SO:ke

alanine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding alanyl tRNA.
has_exact_synonym: alanine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000211

Axiom
annotated source: alanine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding alanyl tRNA.
database_cross_reference: SO:ke

arginine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding arginyl tRNA (SO:0000255).
has_exact_synonym: arginine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000212

Axiom
annotated source: arginine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding arginyl tRNA (SO:0000255).
database_cross_reference: SO:ke

asparagine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding asparaginyl tRNA (SO:0000256).
has_exact_synonym: asparagine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000213

Axiom
annotated source: asparagine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding asparaginyl tRNA (SO:0000256).
database_cross_reference: SO:ke

aspartic_acid_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding aspartyl tRNA (SO:0000257).
has_exact_synonym: aspartic acid tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000214

Axiom
annotated source: aspartic_acid_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding aspartyl tRNA (SO:0000257).
database_cross_reference: SO:ke

cysteine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding cysteinyl tRNA (SO:0000258).
has_exact_synonym: cysteine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000215

Axiom
annotated source: cysteine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding cysteinyl tRNA (SO:0000258).
database_cross_reference: SO:ke

glutamic_acid_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding glutaminyl tRNA (SO:0000260).
has_exact_synonym: glutamic acid tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000216

Axiom
annotated source: glutamic_acid_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding glutaminyl tRNA (SO:0000260).
database_cross_reference: SO:ke

glutamine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding glutamyl tRNA (SO:0000260).
has_exact_synonym: glutamine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000217

Axiom
annotated source: glutamine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding glutamyl tRNA (SO:0000260).
database_cross_reference: SO:ke

glycine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding glycyl tRNA (SO:0000263).
has_exact_synonym: glycine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000218

Axiom
annotated source: glycine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding glycyl tRNA (SO:0000263).
database_cross_reference: SO:ke

histidine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding histidyl tRNA (SO:0000262).
has_exact_synonym: histidine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000219

Axiom
annotated source: histidine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding histidyl tRNA (SO:0000262).
database_cross_reference: SO:ke

isoleucine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding isoleucyl tRNA (SO:0000263).
has_exact_synonym: isoleucine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000220

Axiom
annotated source: isoleucine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding isoleucyl tRNA (SO:0000263).
database_cross_reference: SO:ke

leucine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding leucyl tRNA (SO:0000264).
has_exact_synonym: leucine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000221

Axiom
annotated source: leucine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding leucyl tRNA (SO:0000264).
database_cross_reference: SO:ke

lysine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding lysyl tRNA (SO:0000265).
has_exact_synonym: lysine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000222

Axiom
annotated source: lysine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding lysyl tRNA (SO:0000265).
database_cross_reference: SO:ke

methionine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding methionyl tRNA (SO:0000266).
has_exact_synonym: methionine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000223

Axiom
annotated source: methionine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding methionyl tRNA (SO:0000266).
database_cross_reference: SO:ke

phenylalanine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding phenylalanyl tRNA (SO:0000267).
has_exact_synonym: phenylalanine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000224

Axiom
annotated source: phenylalanine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding phenylalanyl tRNA (SO:0000267).
database_cross_reference: SO:ke

proline_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding prolyl tRNA (SO:0000268).
has_exact_synonym: proline tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000225

Axiom
annotated source: proline_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding prolyl tRNA (SO:0000268).
database_cross_reference: SO:ke

serine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding seryl tRNA (SO:000269).
has_exact_synonym: serine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000226

Axiom
annotated source: serine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding seryl tRNA (SO:000269).
database_cross_reference: SO:ke

threonine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding threonyl tRNA (SO:000270).
has_exact_synonym: threonine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000227

Axiom
annotated source: threonine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding threonyl tRNA (SO:000270).
database_cross_reference: SO:ke

tryptophan_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding tryptophanyl tRNA (SO:000271).
has_exact_synonym: tryptophan tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000228

Axiom
annotated source: tryptophan_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding tryptophanyl tRNA (SO:000271).
database_cross_reference: SO:ke

tyrosine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding tyrosyl tRNA (SO:000272).
has_exact_synonym: tyrosine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000229

Axiom
annotated source: tyrosine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding tyrosyl tRNA (SO:000272).
database_cross_reference: SO:ke

valine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding valyl tRNA (SO:000273).
has_exact_synonym: valine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0000230

Axiom
annotated source: valine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding valyl tRNA (SO:000273).
database_cross_reference: SO:ke

snRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
definition: A primary transcript encoding a small nuclear RNA (SO:0000274).
has_exact_synonym: snRNA primary transcript
has_obo_namespace: sequence
id: SO:0000231

Axiom
annotated source: snRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a small nuclear RNA (SO:0000274).
database_cross_reference: SO:ke

snoRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
definition: A primary transcript encoding one or more small nucleolar RNAs (SO:0000275).
has_exact_synonym: snoRNA primary transcript
has_obo_namespace: sequence
id: SO:0000232
comment: This definition was broadened 26 Jan 2021 to reflect that a single transcript can encode one or more snoRNAs. Brought to our attention by FlyBase. GitHub Issue #520 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/520).

Axiom
annotated source: snoRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding one or more small nucleolar RNAs (SO:0000275).
database_cross_reference: SO:ke

mature_transcript
type: Class
subclass of: transcript
subclass of: Restriction
  on property: derives_from
  some values from: primary_transcript
definition: A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
database_cross_reference: http://en.wikipedia.org/wiki/Mature_transcript
has_exact_synonym: mature transcript
has_obo_namespace: sequence
id: SO:0000233
in_subset: SOFA
comment: A processed transcript cannot contain introns.

Axiom
annotated source: mature_transcript
annotated property: definition
annotated target: A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: mature_transcript
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Mature_transcript

mRNA
type: Class
subclass of: mature_transcript
definition: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
database_cross_reference: http://en.wikipedia.org/wiki/MRNA
database_cross_reference: http://www.gencodegenes.org/gencode_biotypes.html
has_exact_synonym: INSDC_feature:mRNA
has_exact_synonym: messenger RNA
has_exact_synonym: protein_coding_transcript
has_obo_namespace: sequence
id: SO:0000234
in_subset: SOFA
comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: mRNA
annotated property: definition
annotated target: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: mRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/MRNA

GENCODE
type: Axiom
annotated source: mRNA
annotated property: database_cross_reference
annotated target: http://www.gencodegenes.org/gencode_biotypes.html

TF_binding_site
type: Class
subclass of: transcriptional_cis_regulatory_region
subclass of: nucleotide_to_protein_binding_site
subclass of: Restriction
  on property: part_of
  some values from: cis_regulatory_module
definition: A DNA site where a transcription factor binds.
has_exact_synonym: TF binding site
has_exact_synonym: transcription factor binding site
has_obo_namespace: sequence
id: SO:0000235
in_subset: SOFA
comment: Definition updated along with definitions in Mejia-Almonte et.al PMID:32665585. Added relationship part_of SO:0000727 CRM in place of previous CRM relationship has_part TF_binding_site August 2020 in response to requests from GREEKC initiative. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: TF_binding_site
annotated property: definition
annotated target: A DNA site where a transcription factor binds.
database_cross_reference: SO:ke

ORF
type: Class
subclass of: reading_frame
definition: The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
has_exact_synonym: open reading frame
has_obo_namespace: sequence
id: SO:0000236
in_subset: SOFA
comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: ORF
annotated property: definition
annotated target: The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
database_cross_reference: SGD:rb
database_cross_reference: SO:ma

transcript_attribute
type: Class
subclass of: feature_attribute
definition: An attribute describing a transcript.
has_exact_synonym: transcript attribute
has_obo_namespace: sequence
id: SO:0000237

foldback_element
type: Class
subclass of: DNA_transposon
definition: A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.
has_exact_synonym: foldback element
has_obo_namespace: sequence
has_related_synonym: LVR element
has_related_synonym: long inverted repeat element
id: SO:0000238

Axiom
annotated source: foldback_element
annotated property: definition
annotated target: A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.
database_cross_reference: http://www.genetics.org/cgi/reprint/156/4/1983.pdf

flanking_region
type: Class
subclass of: topologically_defined_region
definition: The sequences extending on either side of a specific region.
has_exact_synonym: flanking region
has_obo_namespace: sequence
id: SO:0000239
in_subset: SOFA

Axiom
annotated source: flanking_region
annotated property: definition
annotated target: The sequences extending on either side of a specific region.
database_cross_reference: SO:ke

chromosome_variation
type: Class
subclass of: variant_collection
subclass of: Restriction
  on property: part_of
  some values from: chromosomally_aberrant_genome
definition: A deviation in chromosome structure or number.
has_exact_synonym: chromosome variation
has_obo_namespace: sequence
id: SO:0000240

internal_UTR
type: Class
subclass of: UTR
definition: A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.
has_exact_synonym: internal UTR
has_obo_namespace: sequence
id: SO:0000241

Axiom
annotated source: internal_UTR
annotated property: definition
annotated target: A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.
database_cross_reference: SO:cjm

untranslated_region_polycistronic_mRNA
type: Class
subclass of: UTR
definition: The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
has_exact_synonym: untranslated region polycistronic mRNA
has_obo_namespace: sequence
id: SO:0000242

Axiom
annotated source: untranslated_region_polycistronic_mRNA
annotated property: definition
annotated target: The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
database_cross_reference: SO:ke

internal_ribosome_entry_site
type: Class
subclass of: ribosome_entry_site
definition: Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
database_cross_reference: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site
has_exact_synonym: IRES
has_exact_synonym: internal ribosomal entry sequence
has_exact_synonym: internal ribosomal entry site
has_exact_synonym: internal ribosome entry site
has_obo_namespace: sequence
has_related_synonym: internal ribosome entry sequence
id: SO:0000243

Axiom
annotated source: internal_ribosome_entry_site
annotated property: definition
annotated target: Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: internal_ribosome_entry_site
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site

four_cutter_restriction_site
type: Class
has_obo_namespace: sequence
has_related_synonym: 4-cutter_restriction_site
has_related_synonym: four-cutter_restriction_sit
id: SO:0000244
deprecated: true

mRNA_by_polyadenylation_status
type: Class
has_obo_namespace: sequence
id: SO:0000245
deprecated: true

polyadenylated
type: Class
subclass of: mRNA_attribute
definition: A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.
has_obo_namespace: sequence
id: SO:0000246

Axiom
annotated source: polyadenylated
annotated property: definition
annotated target: A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.
database_cross_reference: SO:ke

mRNA_not_polyadenylated
type: Class
has_obo_namespace: sequence
id: SO:0000247
deprecated: true

sequence_length_alteration
type: Class
subclass of: sequence_alteration
definition: A kind of kind of sequence alteration where the copies of a region present varies across a population.
has_exact_synonym: sequence length alteration
has_obo_namespace: sequence
id: SO:0000248

Axiom
annotated source: sequence_length_alteration
annotated property: definition
annotated target: A kind of kind of sequence alteration where the copies of a region present varies across a population.
database_cross_reference: SO:ke

six_cutter_restriction_site
type: Class
has_obo_namespace: sequence
has_related_synonym: 6-cutter_restriction_site
has_related_synonym: six-cutter_restriction_site
id: SO:0000249
deprecated: true

modified_RNA_base_feature
type: Class
subclass of: base
definition: A post_transcriptionally modified base.
has_exact_synonym: modified RNA base feature
has_obo_namespace: sequence
id: SO:0000250

Axiom
annotated source: modified_RNA_base_feature
annotated property: definition
annotated target: A post_transcriptionally modified base.
database_cross_reference: SO:ke

eight_cutter_restriction_site
type: Class
has_obo_namespace: sequence
has_related_synonym: 8-cutter_restriction_site
has_related_synonym: eight-cutter_restriction_site
id: SO:0000251
deprecated: true

rRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA_primary_transcript
definition: rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.
has_broad_synonym: INSDC_qualifier:unknown
database_cross_reference: http://en.wikipedia.org/wiki/RRNA
has_exact_synonym: INSDC_feature:rRNA
has_exact_synonym: ribosomal RNA
has_exact_synonym: ribosomal ribonucleic acid
has_obo_namespace: sequence
id: SO:0000252
in_subset: SOFA
comment: Definition updated 10 June 2021 as part of restructuring rRNA terms and reforming definitions to have similar structures. Request from EBI. See GitHub Issue #493

Axiom
annotated source: rRNA
annotated property: definition
annotated target: rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.
database_cross_reference: ISBN:0198506732
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/RRNA

tRNA
type: Class
subclass of: SO_0002247
subclass of: Restriction
  on property: derives_from
  some values from: tRNA_primary_transcript
definition: Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
has_broad_synonym: INSDC_qualifier:unknown
database_cross_reference: http://en.wikipedia.org/wiki/TRNA
has_exact_synonym: INSDC_feature:tRNA
has_obo_namespace: sequence
has_related_synonym: transfer RNA
has_related_synonym: transfer ribonucleic acid
id: SO:0000253
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: tRNA
annotated property: definition
annotated target: Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
database_cross_reference: ISBN:0198506732
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: tRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/TRNA

alanyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: alanine_tRNA_primary_transcript
definition: A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
has_exact_synonym: alanyl tRNA
has_exact_synonym: alanyl-transfer RNA
has_exact_synonym: alanyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000254

Axiom
annotated source: alanyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
database_cross_reference: SO:ke

rRNA_small_subunit_primary_transcript
type: Class
subclass of: rRNA_primary_transcript
definition: A primary transcript encoding a small ribosomal subunit RNA.
has_exact_synonym: rRNA small subunit primary transcript
has_obo_namespace: sequence
id: SO:0000255

Axiom
annotated source: rRNA_small_subunit_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a small ribosomal subunit RNA.
database_cross_reference: SO:ke

asparaginyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: asparagine_tRNA_primary_transcript
definition: A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
has_exact_synonym: asparaginyl tRNA
has_exact_synonym: asparaginyl-transfer RNA
has_exact_synonym: asparaginyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000256

Axiom
annotated source: asparaginyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
database_cross_reference: SO:ke

aspartyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: aspartic_acid_tRNA_primary_transcript
definition: A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
has_exact_synonym: aspartyl tRNA
has_exact_synonym: aspartyl-transfer RNA
has_exact_synonym: aspartyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000257

Axiom
annotated source: aspartyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
database_cross_reference: SO:ke

cysteinyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: cysteine_tRNA_primary_transcript
definition: A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
has_exact_synonym: cysteinyl tRNA
has_exact_synonym: cysteinyl-transfer RNA
has_exact_synonym: cysteinyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000258

Axiom
annotated source: cysteinyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
database_cross_reference: SO:ke

glutaminyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: glutamic_acid_tRNA_primary_transcript
definition: A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
has_exact_synonym: glutaminyl tRNA
has_exact_synonym: glutaminyl-transfer RNA
has_exact_synonym: glutaminyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000259

Axiom
annotated source: glutaminyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
database_cross_reference: SO:ke

glutamyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: glutamine_tRNA_primary_transcript
definition: A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
has_exact_synonym: glutamyl tRNA
has_exact_synonym: glutamyl-transfer ribonucleic acid
has_obo_namespace: sequence
has_related_synonym: glutamyl-transfer RNA
id: SO:0000260

Axiom
annotated source: glutamyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
database_cross_reference: SO:ke

glycyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: glycine_tRNA_primary_transcript
definition: A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
has_exact_synonym: glycyl tRNA
has_obo_namespace: sequence
has_related_synonym: glycyl-transfer RNA
has_related_synonym: glycyl-transfer ribonucleic acid
id: SO:0000261

Axiom
annotated source: glycyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
database_cross_reference: SO:ke

histidyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: histidine_tRNA_primary_transcript
definition: A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
has_exact_synonym: histidyl tRNA
has_exact_synonym: histidyl-transfer RNA
has_exact_synonym: histidyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000262

Axiom
annotated source: histidyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
database_cross_reference: SO:ke

isoleucyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: isoleucine_tRNA_primary_transcript
definition: A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
has_exact_synonym: isoleucyl tRNA
has_exact_synonym: isoleucyl-transfer RNA
has_exact_synonym: isoleucyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000263

Axiom
annotated source: isoleucyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
database_cross_reference: SO:ke

leucyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: leucine_tRNA_primary_transcript
definition: A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
has_exact_synonym: leucyl tRNA
has_exact_synonym: leucyl-transfer RNA
has_exact_synonym: leucyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000264

Axiom
annotated source: leucyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
database_cross_reference: SO:ke

lysyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: lysine_tRNA_primary_transcript
definition: A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
has_exact_synonym: lysyl tRNA
has_exact_synonym: lysyl-transfer RNA
has_exact_synonym: lysyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000265

Axiom
annotated source: lysyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
database_cross_reference: SO:ke

methionyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: methionine_tRNA_primary_transcript
definition: A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
has_exact_synonym: methionyl tRNA
has_exact_synonym: methionyl-transfer RNA
has_exact_synonym: methionyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000266

Axiom
annotated source: methionyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
database_cross_reference: SO:ke

phenylalanyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: phenylalanine_tRNA_primary_transcript
definition: A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
has_exact_synonym: phenylalanyl tRNA
has_exact_synonym: phenylalanyl-transfer RNA
has_exact_synonym: phenylalanyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000267

Axiom
annotated source: phenylalanyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
database_cross_reference: SO:ke

prolyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: proline_tRNA_primary_transcript
definition: A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
has_exact_synonym: prolyl tRNA
has_exact_synonym: prolyl-transfer RNA
has_exact_synonym: prolyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000268

Axiom
annotated source: prolyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
database_cross_reference: SO:ke

seryl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: serine_tRNA_primary_transcript
definition: A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
has_exact_synonym: seryl tRNA
has_exact_synonym: seryl-transfer RNA
has_obo_namespace: sequence
has_related_synonym: seryl-transfer ribonucleic acid
id: SO:0000269

Axiom
annotated source: seryl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
database_cross_reference: SO:ke

threonyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: threonine_tRNA_primary_transcript
definition: A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
has_exact_synonym: threonyl tRNA
has_exact_synonym: threonyl-transfer ribonucleic acid
has_obo_namespace: sequence
has_related_synonym: threonyl-transfer RNA
id: SO:0000270

Axiom
annotated source: threonyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
database_cross_reference: SO:ke

tryptophanyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: tryptophan_tRNA_primary_transcript
definition: A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
has_exact_synonym: tryptophanyl tRNA
has_exact_synonym: tryptophanyl-transfer RNA
has_exact_synonym: tryptophanyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000271

Axiom
annotated source: tryptophanyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
database_cross_reference: SO:ke

tyrosyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: tyrosine_tRNA_primary_transcript
definition: A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
has_exact_synonym: tyrosyl tRNA
has_exact_synonym: tyrosyl-transfer ribonucleic acid
has_obo_namespace: sequence
has_related_synonym: tyrosyl-transfer RNA
id: SO:0000272

Axiom
annotated source: tyrosyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
database_cross_reference: SO:ke

valyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: valine_tRNA_primary_transcript
definition: A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
has_exact_synonym: valyl tRNA
has_exact_synonym: valyl-transfer ribonucleic acid
has_obo_namespace: sequence
has_related_synonym: valyl-transfer RNA
id: SO:0000273

Axiom
annotated source: valyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
database_cross_reference: SO:ke

snRNA
type: Class
subclass of: SO_0002247
subclass of: Restriction
  on property: derives_from
  some values from: snRNA_primary_transcript
definition: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/SnRNA
has_exact_synonym: INSDC_qualifier:snRNA
has_exact_synonym: small nuclear RNA
has_obo_namespace: sequence
id: SO:0000274
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: snRNA
annotated property: definition
annotated target: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
database_cross_reference: PMID:11733745
database_cross_reference: WB:ems
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/SnRNA

snoRNA
type: Class
subclass of: SO_0002247
subclass of: Restriction
  on property: derives_from
  some values from: snoRNA_primary_transcript
definition: Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:snoRNA
has_exact_synonym: small nucleolar RNA
has_obo_namespace: sequence
id: SO:0000275
in_subset: SOFA
comment: Updated the definition of snoRNA (SO:0000275) from "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." to "Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing." to acknowledge that some snoRNAs functionally localize to other compartments (cytoplasm or even secreted). See GitHub Issue #578.

Axiom
annotated source: snoRNA
annotated property: definition
annotated target: Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing.
database_cross_reference: GOC:kgc
database_cross_reference: PMID:31828325

miRNA
type: Class
subclass of: small_regulatory_ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: pre_miRNA
definition: Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes). Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
has_alternative_id: SO:0000649
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/MiRNA
database_cross_reference: http://en.wikipedia.org/wiki/StRNA
has_exact_synonym: INSDC_qualifier:miRNA
has_exact_synonym: micro RNA
has_exact_synonym: microRNA
has_exact_synonym: small temporal RNA
has_exact_synonym: stRNA
has_obo_namespace: sequence
id: SO:0000276
in_subset: SOFA

Axiom
annotated source: miRNA
annotated property: definition
annotated target: Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes). Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
database_cross_reference: PMID:11081512
database_cross_reference: PMID:12592000

wiki
type: Axiom
annotated source: miRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/MiRNA

wiki
type: Axiom
annotated source: miRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/StRNA

bound_by_factor
type: Class
subclass of: feature_attribute
definition: An attribute describing a sequence that is bound by another molecule.
has_exact_synonym: bound by factor
has_obo_namespace: sequence
id: SO:0000277
comment: Formerly called transcript_by_bound_factor.

Axiom
annotated source: bound_by_factor
annotated property: definition
annotated target: An attribute describing a sequence that is bound by another molecule.
database_cross_reference: SO:ke

transcript_bound_by_nucleic_acid
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: bound_by_nucleic_acid
subclass of: transcript
subclass of: Restriction
  on property: has_quality
  some values from: bound_by_nucleic_acid
definition: A transcript that is bound by a nucleic acid.
has_exact_synonym: transcript bound by nucleic acid
has_obo_namespace: sequence
id: SO:0000278
comment: Formerly called transcript_by_bound_nucleic_acid.

Axiom
annotated source: transcript_bound_by_nucleic_acid
annotated property: definition
annotated target: A transcript that is bound by a nucleic acid.
database_cross_reference: SO:xp

transcript_bound_by_protein
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: bound_by_protein
subclass of: transcript
subclass of: Restriction
  on property: has_quality
  some values from: bound_by_protein
definition: A transcript that is bound by a protein.
has_exact_synonym: transcript bound by protein
has_obo_namespace: sequence
id: SO:0000279
comment: Formerly called transcript_by_bound_protein.

Axiom
annotated source: transcript_bound_by_protein
annotated property: definition
annotated target: A transcript that is bound by a protein.
database_cross_reference: SO:xp

engineered_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: gene
subclass of: engineered_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: A gene that is engineered.
has_exact_synonym: engineered gene
has_obo_namespace: sequence
id: SO:0000280

Axiom
annotated source: engineered_gene
annotated property: definition
annotated target: A gene that is engineered.
database_cross_reference: SO:xp

engineered_foreign_gene
type: Class
equivalent class: Class
  intersection of: engineered_gene
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: engineered_gene
subclass of: foreign_gene
subclass of: engineered_foreign_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
subclass of: Restriction
  on property: has_quality
  some values from: foreign
definition: A gene that is engineered and foreign.
has_exact_synonym: engineered foreign gene
has_obo_namespace: sequence
id: SO:0000281

Axiom
annotated source: engineered_foreign_gene
annotated property: definition
annotated target: A gene that is engineered and foreign.
database_cross_reference: SO:xp

mRNA_with_minus_1_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA_with_frameshift
  intersection of: Restriction
    on property: has_quality
    some values from: minus_1_frameshift
subclass of: mRNA_with_frameshift
subclass of: Restriction
  on property: has_quality
  some values from: minus_1_frameshift
definition: An mRNA with a minus 1 frameshift.
has_exact_synonym: mRNA with minus 1 frameshift
has_obo_namespace: sequence
id: SO:0000282

Axiom
annotated source: mRNA_with_minus_1_frameshift
annotated property: definition
annotated target: An mRNA with a minus 1 frameshift.
database_cross_reference: SO:xp

engineered_foreign_transposable_element_gene
type: Class
equivalent class: Class
  intersection of: transposable_element_gene
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: transposable_element_gene
subclass of: engineered_foreign_gene
subclass of: Restriction
  on property: has_quality
  some values from: engineered
subclass of: Restriction
  on property: has_quality
  some values from: foreign
definition: A transposable_element that is engineered and foreign.
has_exact_synonym: engineered foreign transposable element gene
has_obo_namespace: sequence
id: SO:0000283

Axiom
annotated source: engineered_foreign_transposable_element_gene
annotated property: definition
annotated target: A transposable_element that is engineered and foreign.
database_cross_reference: SO:xp

type_I_enzyme_restriction_site
type: Class
definition: The recognition site is bipartite and interrupted.
has_obo_namespace: sequence
id: SO:0000284
deprecated: true

Axiom
annotated source: type_I_enzyme_restriction_site
annotated property: definition
annotated target: The recognition site is bipartite and interrupted.
database_cross_reference: http://www.promega.com

foreign_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: foreign
definition: A gene that is foreign.
has_exact_synonym: foreign gene
has_obo_namespace: sequence
id: SO:0000285

Axiom
annotated source: foreign_gene
annotated property: definition
annotated target: A gene that is foreign.
database_cross_reference: SO:xp

long_terminal_repeat
type: Class
subclass of: repeat_region
subclass of: Restriction
  on property: part_of
  some values from: LTR_retrotransposon
definition: A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Long_terminal_repeat
has_exact_synonym: INSDC_qualifier:long_terminal_repeat
has_exact_synonym: LTR
has_exact_synonym: long terminal repeat
has_obo_namespace: sequence
has_related_synonym: direct terminal repeat
id: SO:0000286

Axiom
annotated source: long_terminal_repeat
annotated property: definition
annotated target: A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: long_terminal_repeat
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Long_terminal_repeat

fusion_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: fusion
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: fusion
definition: A gene that is a fusion.
database_cross_reference: http://en.wikipedia.org/wiki/Fusion_gene
has_exact_synonym: fusion gene
has_obo_namespace: sequence
id: SO:0000287

Axiom
annotated source: fusion_gene
annotated property: definition
annotated target: A gene that is a fusion.
database_cross_reference: SO:xp

wiki
type: Axiom
annotated source: fusion_gene
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Fusion_gene

engineered_fusion_gene
type: Class
equivalent class: Class
  intersection of: fusion_gene
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: engineered_gene
subclass of: fusion_gene
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: A fusion gene that is engineered.
has_exact_synonym: engineered fusion gene
has_obo_namespace: sequence
id: SO:0000288

Axiom
annotated source: engineered_fusion_gene
annotated property: definition
annotated target: A fusion gene that is engineered.
database_cross_reference: SO:xp

microsatellite
type: Class
subclass of: satellite_DNA
definition: A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Microsatellite
has_exact_synonym: INSDC_qualifier:microsatellite
has_exact_synonym: STR
has_exact_synonym: microsatellite locus
has_exact_synonym: microsatellite marker
has_exact_synonym: short tandem repeat
has_obo_namespace: sequence
id: SO:0000289
in_subset: SOFA

Axiom
annotated source: microsatellite
annotated property: definition
annotated target: A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
database_cross_reference: NCBI:th
database_cross_reference: http://www.informatics.jax.org/silver/glossary.shtml

wiki
type: Axiom
annotated source: microsatellite
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Microsatellite

Axiom
annotated source: microsatellite
annotated property: has_exact_synonym
annotated target: STR
database_cross_reference: http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/

dinucleotide_repeat_microsatellite_feature
type: Class
subclass of: microsatellite
definition: A region of a repeating dinucleotide sequence (two bases).
has_exact_synonym: dinucleotide repeat microsatellite
has_exact_synonym: dinucleotide repeat microsatellite feature
has_exact_synonym: dinucleotide repeat microsatellite locus
has_exact_synonym: dinucleotide repeat microsatellite marker
has_obo_namespace: sequence
id: SO:0000290

trinucleotide_repeat_microsatellite_feature
type: Class
subclass of: microsatellite
definition: A region of a repeating trinucleotide sequence (three bases).
has_exact_synonym: rinucleotide repeat microsatellite
has_exact_synonym: trinucleotide repeat microsatellite feature
has_exact_synonym: trinucleotide repeat microsatellite locus
has_obo_namespace: sequence
has_related_synonym: dinucleotide repeat microsatellite marker
id: SO:0000291

repetitive_element
type: Class
has_obo_namespace: sequence
id: SO:0000292
deprecated: true

engineered_foreign_repetitive_element
type: Class
equivalent class: Class
  intersection of: repeat_region
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: repeat_region
subclass of: engineered_foreign_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
subclass of: Restriction
  on property: has_quality
  some values from: foreign
definition: A repetitive element that is engineered and foreign.
has_exact_synonym: engineered foreign repetitive element
has_obo_namespace: sequence
id: SO:0000293

Axiom
annotated source: engineered_foreign_repetitive_element
annotated property: definition
annotated target: A repetitive element that is engineered and foreign.
database_cross_reference: SO:xp

inverted_repeat
type: Class
subclass of: repeat_region
definition: The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Inverted_repeat
has_exact_synonym: INSDC_qualifier:inverted
has_exact_synonym: inverted repeat
has_exact_synonym: inverted repeat sequence
has_obo_namespace: sequence
id: SO:0000294
in_subset: SOFA

Axiom
annotated source: inverted_repeat
annotated property: definition
annotated target: The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: inverted_repeat
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Inverted_repeat

U12_intron
type: Class
subclass of: spliceosomal_intron
definition: A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
has_exact_synonym: U12 intron
has_exact_synonym: U12-dependent intron
has_obo_namespace: sequence
id: SO:0000295
comment: May have either GT-AC or AT-AC 5' and 3' boundaries.

Axiom
annotated source: U12_intron
annotated property: definition
annotated target: A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
database_cross_reference: PMID:9428511

origin_of_replication
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: replicon
definition: A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites.
database_cross_reference: http://en.wikipedia.org/wiki/Origin_of_replication
has_exact_synonym: INSDC_feature:rep_origin
has_exact_synonym: ori
has_exact_synonym: origin of replication
has_obo_namespace: sequence
id: SO:0000296
in_subset: SOFA

Axiom
annotated source: origin_of_replication
annotated property: definition
annotated target: A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites.
database_cross_reference: NCBI:cf
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: origin_of_replication
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Origin_of_replication

D_loop
type: Class
subclass of: biological_region
definition: Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.
database_cross_reference: http://en.wikipedia.org/wiki/D_loop
has_exact_synonym: D-loop
has_exact_synonym: INSDC_feature:D-loop
has_obo_namespace: sequence
has_related_synonym: displacement loop
id: SO:0000297
comment: Moved from is_a: SO:0000296 origin_of_replication to is_a: SO:0001411 biological_region after Terrence Murphy (INSDC) pointed out that the D loop can also refer to a loop in DNA repair, which is not an origin of replication. See GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417)

Axiom
annotated source: D_loop
annotated property: definition
annotated target: Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: D_loop
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/D_loop

recombination_feature
type: Class
subclass of: biological_region
definition: A feature where there has been exchange of genetic material in the event of mitosis or meiosis
has_broad_synonym: INSDC_feature:misc_recomb
has_exact_synonym: INSDC_qualifier:other
has_exact_synonym: recombination feature
has_obo_namespace: sequence
id: SO:0000298

specific_recombination_site
type: Class
subclass of: sequence_rearrangement_feature
definition: A location where recombination or occurs during mitosis or meiosis.
has_exact_synonym: specific recombination site
has_obo_namespace: sequence
id: SO:0000299

recombination_feature_of_rearranged_gene
type: Class
subclass of: specific_recombination_site
definition: A location where a gene is rearranged due to recombination during mitosis or meiosis.
has_exact_synonym: recombination feature of rearranged gene
has_obo_namespace: sequence
id: SO:0000300

vertebrate_immune_system_gene_recombination_feature
type: Class
subclass of: recombination_feature_of_rearranged_gene
definition: A feature where recombination has occurred for the purpose of generating a diversity in the immune system.
has_exact_synonym: vertebrate immune system gene recombination feature
has_obo_namespace: sequence
id: SO:0000301

J_gene_recombination_feature
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
definition: Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.
has_exact_synonym: J gene recombination feature
has_exact_synonym: J-RS
has_obo_namespace: sequence
id: SO:0000302

Axiom
annotated source: J_gene_recombination_feature
annotated property: definition
annotated target: Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

clip
type: Class
subclass of: primary_transcript_region
definition: Part of the primary transcript that is clipped off during processing.
has_obo_namespace: sequence
id: SO:0000303
in_subset: SOFA

Axiom
annotated source: clip
annotated property: definition
annotated target: Part of the primary transcript that is clipped off during processing.
database_cross_reference: SO:ke

type_II_enzyme_restriction_site
type: Class
definition: The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.
has_obo_namespace: sequence
id: SO:0000304
deprecated: true

Axiom
annotated source: type_II_enzyme_restriction_site
annotated property: definition
annotated target: The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.
database_cross_reference: http://www.promega.com

modified_DNA_base
type: Class
subclass of: base
subclass of: epigenetically_modified_region
definition: A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
has_exact_synonym: INSDC_feature:modified_base
has_exact_synonym: modified base site
has_obo_namespace: sequence
id: SO:0000305
in_subset: SOFA
comment: Modified base:<modified_base>.

Axiom
annotated source: modified_DNA_base
annotated property: definition
annotated target: A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
database_cross_reference: http://www.insdc.org/files/feature_table.html

methylated_DNA_base_feature
type: Class
subclass of: modified_DNA_base
definition: A nucleotide modified by methylation.
has_exact_synonym: methylated base feature
has_obo_namespace: sequence
id: SO:0000306
in_subset: SOFA

Axiom
annotated source: methylated_DNA_base_feature
annotated property: definition
annotated target: A nucleotide modified by methylation.
database_cross_reference: SO:ke

CpG_island
type: Class
subclass of: biological_region
definition: Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
database_cross_reference: http://en.wikipedia.org/wiki/CpG_island
has_exact_synonym: CG island
has_exact_synonym: CpG island
has_obo_namespace: sequence
id: SO:0000307
in_subset: SOFA

Axiom
annotated source: CpG_island
annotated property: definition
annotated target: Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
database_cross_reference: SO:rd

wiki
type: Axiom
annotated source: CpG_island
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/CpG_island

sequence_feature_locating_method
type: Class
has_obo_namespace: sequence
id: SO:0000308
deprecated: true

computed_feature
type: Class
has_obo_namespace: sequence
id: SO:0000309
deprecated: true

predicted_ab_initio_computation
type: Class
has_obo_namespace: sequence
id: SO:0000310
deprecated: true

computed_feature_by_similarity
type: Class
definition: .
has_obo_namespace: sequence
id: SO:0000311
comment: similar to:<sequence_id>
deprecated: true

Axiom
annotated source: computed_feature_by_similarity
annotated property: definition
annotated target: .
database_cross_reference: SO:ma

experimentally_determined
type: Class
subclass of: validated
definition: Attribute to describe a feature that has been experimentally verified.
has_exact_synonym: experimentally determined
has_obo_namespace: sequence
id: SO:0000312

Axiom
annotated source: experimentally_determined
annotated property: definition
annotated target: Attribute to describe a feature that has been experimentally verified.
database_cross_reference: SO:ke

stem_loop
type: Class
subclass of: RNA_sequence_secondary_structure
definition: A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.
has_alternative_id: SO:0000019
database_cross_reference: http://en.wikipedia.org/wiki/Stem_loop
has_exact_synonym: INSDC_feature:stem_loop
has_exact_synonym: RNA_hairpin_loop
has_exact_synonym: stem loop
has_exact_synonym: stem-loop
has_obo_namespace: sequence
id: SO:0000313

Axiom
annotated source: stem_loop
annotated property: definition
annotated target: A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: stem_loop
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Stem_loop

direct_repeat
type: Class
subclass of: repeat_region
definition: A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Direct_repeat
has_exact_synonym: INSDC_qualifier:direct
has_exact_synonym: direct repeat
has_obo_namespace: sequence
id: SO:0000314
in_subset: SOFA

Axiom
annotated source: direct_repeat
annotated property: definition
annotated target: A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: direct_repeat
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Direct_repeat

TSS
type: Class
subclass of: primary_transcript_region
subclass of: SO_0002309
definition: The first base where RNA polymerase begins to synthesize the RNA transcript.
has_broad_synonym: INSDC_feature:misc_feature
has_exact_synonym: INSDC_note:transcription_start_site
has_exact_synonym: transcription start site
has_exact_synonym: transcription_start_site
has_obo_namespace: sequence
id: SO:0000315
in_subset: SOFA
comment: Added relationship is_a SO:0002309 core_promoter_element with the creation of core_promoter_element as part of GREEKC initiative August 2020 - Dave Sant.

Axiom
annotated source: TSS
annotated property: definition
annotated target: The first base where RNA polymerase begins to synthesize the RNA transcript.
database_cross_reference: SO:ke

CDS
type: Class
subclass of: mRNA_region
definition: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
has_exact_synonym: INSDC_feature:CDS
has_exact_synonym: coding sequence
has_exact_synonym: coding_sequence
has_obo_namespace: sequence
id: SO:0000316
in_subset: SOFA

Axiom
annotated source: CDS
annotated property: definition
annotated target: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
database_cross_reference: SO:ma

cDNA_clone
type: Class
equivalent class: Class
  intersection of: clone
  intersection of: Restriction
    on property: has_quality
    some values from: cDNA
subclass of: clone
subclass of: Restriction
  on property: has_quality
  some values from: cDNA
definition: Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
has_exact_synonym: cDNA clone
has_obo_namespace: sequence
id: SO:0000317
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: cDNA_clone
annotated property: definition
annotated target: Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
database_cross_reference: http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html

start_codon
type: Class
subclass of: codon
definition: First codon to be translated by a ribosome.
database_cross_reference: http://en.wikipedia.org/wiki/Start_codon
has_exact_synonym: initiation codon
has_exact_synonym: start codon
has_obo_namespace: sequence
id: SO:0000318
in_subset: SOFA

Axiom
annotated source: start_codon
annotated property: definition
annotated target: First codon to be translated by a ribosome.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: start_codon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Start_codon

stop_codon
type: Class
subclass of: codon
definition: In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
database_cross_reference: http://en.wikipedia.org/wiki/Stop_codon
has_exact_synonym: stop codon
has_obo_namespace: sequence
id: SO:0000319
in_subset: SOFA

Axiom
annotated source: stop_codon
annotated property: definition
annotated target: In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: stop_codon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Stop_codon

intronic_splice_enhancer
type: Class
subclass of: splice_enhancer
subclass of: Restriction
  on property: part_of
  some values from: spliceosomal_intron_region
definition: Sequences within the intron that modulate splice site selection for some introns.
has_exact_synonym: intronic splice enhancer
has_obo_namespace: sequence
id: SO:0000320

Axiom
annotated source: intronic_splice_enhancer
annotated property: definition
annotated target: Sequences within the intron that modulate splice site selection for some introns.
database_cross_reference: SO:ke

mRNA_with_plus_1_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA_with_frameshift
  intersection of: Restriction
    on property: has_quality
    some values from: plus_1_frameshift
subclass of: mRNA_with_frameshift
subclass of: Restriction
  on property: has_quality
  some values from: plus_1_frameshift
definition: An mRNA with a plus 1 frameshift.
has_exact_synonym: mRNA with plus 1 frameshift
has_obo_namespace: sequence
id: SO:0000321

Axiom
annotated source: mRNA_with_plus_1_frameshift
annotated property: definition
annotated target: An mRNA with a plus 1 frameshift.
database_cross_reference: SO:ke

nuclease_hypersensitive_site
type: Class
subclass of: nuclease_sensitive_site
subclass of: SO_0002331
definition: A region of nucleotide sequence targeted by a nuclease enzyme that is found cleaved more than would be expected by chance.
has_exact_synonym: nuclease hypersensitive site
has_obo_namespace: sequence
id: SO:0000322
comment: Relationship to accessible_DNA_region added 11 Feb 2021. GREEKC pointed out that this is an assay based term, but we need a biological term for the accessible DNA. See GitHub Issue #531.

coding_start
type: Class
subclass of: CDS_region
definition: The first base to be translated into protein.
has_exact_synonym: coding start
has_exact_synonym: translation initiation site
has_obo_namespace: sequence
has_related_synonym: translation start
id: SO:0000323

Axiom
annotated source: coding_start
annotated property: definition
annotated target: The first base to be translated into protein.
database_cross_reference: SO:ke

tag
type: Class
subclass of: oligo
definition: A nucleotide sequence that may be used to identify a larger sequence.
has_obo_namespace: sequence
id: SO:0000324
in_subset: SOFA

Axiom
annotated source: tag
annotated property: definition
annotated target: A nucleotide sequence that may be used to identify a larger sequence.
database_cross_reference: SO:ke

rRNA_large_subunit_primary_transcript
type: Class
subclass of: rRNA_primary_transcript
definition: A primary transcript encoding a large ribosomal subunit RNA.
has_exact_synonym: 35S rRNA primary transcript
has_exact_synonym: rRNA large subunit primary transcript
has_obo_namespace: sequence
id: SO:0000325
in_subset: SOFA

Axiom
annotated source: rRNA_large_subunit_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a large ribosomal subunit RNA.
database_cross_reference: SO:ke

SAGE_tag
type: Class
subclass of: tag
definition: A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
has_exact_synonym: SAGE tag
has_obo_namespace: sequence
id: SO:0000326
in_subset: SOFA

Axiom
annotated source: SAGE_tag
annotated property: definition
annotated target: A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
database_cross_reference: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

coding_end
type: Class
subclass of: CDS_region
definition: The last base to be translated into protein. It does not include the stop codon.
has_exact_synonym: coding end
has_exact_synonym: translation termination site
has_exact_synonym: translation_end
has_obo_namespace: sequence
id: SO:0000327

Axiom
annotated source: coding_end
annotated property: definition
annotated target: The last base to be translated into protein. It does not include the stop codon.
database_cross_reference: SO:ke

microarray_oligo
type: Class
subclass of: probe
definition: A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
has_exact_synonym: microarray oligo
has_exact_synonym: microarray oligonucleotide
has_obo_namespace: sequence
id: SO:0000328

mRNA_with_plus_2_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA_with_frameshift
  intersection of: Restriction
    on property: has_quality
    some values from: plus_2_framshift
subclass of: mRNA_with_frameshift
subclass of: Restriction
  on property: has_quality
  some values from: plus_2_framshift
definition: An mRNA with a plus 2 frameshift.
has_exact_synonym: mRNA with plus 2 frameshift
has_obo_namespace: sequence
id: SO:0000329

Axiom
annotated source: mRNA_with_plus_2_frameshift
annotated property: definition
annotated target: An mRNA with a plus 2 frameshift.
database_cross_reference: SO:xp

conserved_region
type: Class
subclass of: experimental_feature
definition: Region of sequence similarity by descent from a common ancestor.
has_broad_synonym: INSDC_feature:misc_feature
database_cross_reference: http://en.wikipedia.org/wiki/Conserved_region
has_exact_synonym: INSDC_note:conserved_region
has_exact_synonym: conserved region
has_obo_namespace: sequence
id: SO:0000330
in_subset: SOFA

Axiom
annotated source: conserved_region
annotated property: definition
annotated target: Region of sequence similarity by descent from a common ancestor.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: conserved_region
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Conserved_region

STS
type: Class
subclass of: tag
definition: Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
has_exact_synonym: INSDC_feature:STS
has_exact_synonym: sequence tag site
has_obo_namespace: sequence
id: SO:0000331
in_subset: SOFA

Axiom
annotated source: STS
annotated property: definition
annotated target: Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
database_cross_reference: http://www.biospace.com

coding_conserved_region
type: Class
subclass of: conserved_region
definition: Coding region of sequence similarity by descent from a common ancestor.
has_exact_synonym: coding conserved region
has_obo_namespace: sequence
id: SO:0000332
in_subset: SOFA

Axiom
annotated source: coding_conserved_region
annotated property: definition
annotated target: Coding region of sequence similarity by descent from a common ancestor.
database_cross_reference: SO:ke

exon_junction
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: mature_transcript
definition: The boundary between two exons in a processed transcript.
has_exact_synonym: exon junction
has_obo_namespace: sequence
id: SO:0000333
in_subset: SOFA

Axiom
annotated source: exon_junction
annotated property: definition
annotated target: The boundary between two exons in a processed transcript.
database_cross_reference: SO:ke

nc_conserved_region
type: Class
subclass of: conserved_region
definition: Non-coding region of sequence similarity by descent from a common ancestor.
has_exact_synonym: conserved non-coding element
has_exact_synonym: conserved non-coding sequence
has_exact_synonym: nc conserved region
has_exact_synonym: noncoding conserved region
has_obo_namespace: sequence
id: SO:0000334
in_subset: SOFA

Axiom
annotated source: nc_conserved_region
annotated property: definition
annotated target: Non-coding region of sequence similarity by descent from a common ancestor.
database_cross_reference: SO:ke

mRNA_with_minus_2_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA_with_frameshift
  intersection of: Restriction
    on property: has_quality
    some values from: minus_2_frameshift
subclass of: mRNA_with_frameshift
subclass of: Restriction
  on property: has_quality
  some values from: minus_2_frameshift
definition: A mRNA with a minus 2 frameshift.
has_exact_synonym: mRNA with minus 2 frameshift
has_obo_namespace: sequence
id: SO:0000335

Axiom
annotated source: mRNA_with_minus_2_frameshift
annotated property: definition
annotated target: A mRNA with a minus 2 frameshift.
database_cross_reference: SO:ke

pseudogene
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: gene
definition: A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog).
has_broad_synonym: INSDC_feature:gene
database_cross_reference: http://en.wikipedia.org/wiki/Pseudogene
has_exact_synonym: INSDC_qualifier:pseudo
has_exact_synonym: INSDC_qualifier:unknown
has_obo_namespace: sequence
id: SO:0000336
in_subset: Alliance of Genome Resources
in_subset: SOFA

Axiom
annotated source: pseudogene
annotated property: definition
annotated target: A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog).
database_cross_reference: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html

wiki
type: Axiom
annotated source: pseudogene
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Pseudogene

RNAi_reagent
type: Class
subclass of: ds_oligo
definition: A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
has_exact_synonym: RNAi reagent
has_obo_namespace: sequence
id: SO:0000337
in_subset: SOFA

Axiom
annotated source: RNAi_reagent
annotated property: definition
annotated target: A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
database_cross_reference: SO:rd

MITE
type: Class
subclass of: terminal_inverted_repeat_element
definition: A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins.
has_exact_synonym: miniature inverted repeat transposable element
has_obo_namespace: sequence
id: SO:0000338

Axiom
annotated source: MITE
annotated property: definition
annotated target: A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins.
database_cross_reference: http://www.pnas.org/cgi/content/full/97/18/10083

recombination_hotspot
type: Class
subclass of: recombination_feature
definition: A region in a genome which promotes recombination.
database_cross_reference: http://en.wikipedia.org/wiki/Recombination_hotspot
has_exact_synonym: recombination hotspot
has_obo_namespace: sequence
id: SO:0000339

Axiom
annotated source: recombination_hotspot
annotated property: definition
annotated target: A region in a genome which promotes recombination.
database_cross_reference: SO:rd

wiki
type: Axiom
annotated source: recombination_hotspot
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Recombination_hotspot

chromosome
type: Class
subclass of: replicon
definition: Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.
database_cross_reference: http://en.wikipedia.org/wiki/Chromosome
has_obo_namespace: sequence
id: SO:0000340
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: chromosome
annotated property: definition
annotated target: Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: chromosome
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Chromosome

chromosome_band
type: Class
subclass of: chromosome_part
definition: A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
database_cross_reference: http://en.wikipedia.org/wiki/Cytological_band
has_exact_synonym: chromosome band
has_exact_synonym: cytoband
has_exact_synonym: cytological band
has_obo_namespace: sequence
id: SO:0000341
in_subset: SOFA

Axiom
annotated source: chromosome_band
annotated property: definition
annotated target: A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: chromosome_band
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Cytological_band

site_specific_recombination_target_region
type: Class
subclass of: specific_recombination_site
definition: A region specifically recognised by a recombinase where recombination can occur during mitosis or meiosis.
has_exact_synonym: site specific recombination target region
has_obo_namespace: sequence
id: SO:0000342

match
type: Class
subclass of: experimental_feature
definition: A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
has_obo_namespace: sequence
id: SO:0000343
in_subset: SOFA

Axiom
annotated source: match
annotated property: definition
annotated target: A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
database_cross_reference: SO:ke

splice_enhancer
type: Class
subclass of: splicing_regulatory_region
definition: Region of a transcript that regulates splicing.
has_exact_synonym: splice enhancer
has_obo_namespace: sequence
id: SO:0000344
in_subset: SOFA

Axiom
annotated source: splice_enhancer
annotated property: definition
annotated target: Region of a transcript that regulates splicing.
database_cross_reference: SO:ke

EST
type: Class
subclass of: tag
subclass of: Restriction
  on property: derives_from
  some values from: mRNA
definition: A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
has_exact_synonym: expressed sequence tag
has_obo_namespace: sequence
id: SO:0000345
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: EST
annotated property: definition
annotated target: A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
database_cross_reference: SO:ke

loxP_site
type: Class
subclass of: resolution_site
definition: Cre-Recombination target sequence.
has_exact_synonym: loxP site
has_obo_namespace: sequence
has_related_synonym: Cre-recombination target region
id: SO:0000346

nucleotide_match
type: Class
subclass of: match
definition: A match against a nucleotide sequence.
has_exact_synonym: nucleotide match
has_obo_namespace: sequence
id: SO:0000347
in_subset: SOFA

Axiom
annotated source: nucleotide_match
annotated property: definition
annotated target: A match against a nucleotide sequence.
database_cross_reference: SO:ke

nucleic_acid
type: Class
subclass of: polymer_attribute
definition: An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.
database_cross_reference: http://en.wikipedia.org/wiki/Nucleic_acid
has_exact_synonym: nucleic acid
has_obo_namespace: sequence
id: SO:0000348

Axiom
annotated source: nucleic_acid
annotated property: definition
annotated target: An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.
database_cross_reference: CHEBI:33696
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: nucleic_acid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Nucleic_acid

protein_match
type: Class
subclass of: match
definition: A match against a protein sequence.
has_exact_synonym: protein match
has_obo_namespace: sequence
id: SO:0000349
in_subset: SOFA

Axiom
annotated source: protein_match
annotated property: definition
annotated target: A match against a protein sequence.
database_cross_reference: SO:ke

FRT_site
type: Class
subclass of: inversion_site
definition: An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.
has_exact_synonym: FLP recombination target region
has_exact_synonym: FRT site
has_obo_namespace: sequence
id: SO:0000350

Axiom
annotated source: FRT_site
annotated property: definition
annotated target: An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.
database_cross_reference: SO:ma

synthetic_sequence
type: Class
subclass of: polymer_attribute
definition: An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.
has_exact_synonym: synthetic sequence
has_obo_namespace: sequence
id: SO:0000351

Axiom
annotated source: synthetic_sequence
annotated property: definition
annotated target: An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.
database_cross_reference: SO:ma

DNA
type: Class
subclass of: nucleic_acid
definition: An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.
has_obo_namespace: sequence
id: SO:0000352

Axiom
annotated source: DNA
annotated property: definition
annotated target: An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.
database_cross_reference: RSC:cb

sequence_assembly
type: Class
subclass of: assembly
definition: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
database_cross_reference: http://en.wikipedia.org/wiki/Sequence_assembly
has_exact_synonym: sequence assembly
has_obo_namespace: sequence
id: SO:0000353
in_subset: SOFA

Axiom
annotated source: sequence_assembly
annotated property: definition
annotated target: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: sequence_assembly
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Sequence_assembly

group_1_intron_homing_endonuclease_target_region
type: Class
subclass of: nuclease_sensitive_site
definition: A region of intronic nucleotide sequence targeted by a nuclease enzyme.
has_exact_synonym: group 1 intron homing endonuclease target region
has_obo_namespace: sequence
id: SO:0000354

Axiom
annotated source: group_1_intron_homing_endonuclease_target_region
annotated property: definition
annotated target: A region of intronic nucleotide sequence targeted by a nuclease enzyme.
database_cross_reference: SO:ke

haplotype_block
type: Class
subclass of: recombination_feature
definition: A region of the genome which is co-inherited as the result of the lack of historic recombination within it.
has_exact_synonym: haplotype block
has_obo_namespace: sequence
id: SO:0000355

Axiom
annotated source: haplotype_block
annotated property: definition
annotated target: A region of the genome which is co-inherited as the result of the lack of historic recombination within it.
database_cross_reference: SO:ma

RNA
type: Class
subclass of: nucleic_acid
definition: An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.
has_obo_namespace: sequence
id: SO:0000356
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: RNA
annotated property: definition
annotated target: An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.
database_cross_reference: RSC:cb

flanked
type: Class
subclass of: feature_attribute
definition: An attribute describing a region that is bounded either side by a particular kind of region.
has_obo_namespace: sequence
id: SO:0000357

Axiom
annotated source: flanked
annotated property: definition
annotated target: An attribute describing a region that is bounded either side by a particular kind of region.
database_cross_reference: SO:ke

SO_0000358
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide
deprecated: true

floxed
type: Class
subclass of: flanked
definition: An attribute describing sequence that is flanked by Lox-P sites.
database_cross_reference: http://en.wikipedia.org/wiki/Floxed
has_obo_namespace: sequence
id: SO:0000359

Axiom
annotated source: floxed
annotated property: definition
annotated target: An attribute describing sequence that is flanked by Lox-P sites.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: floxed
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Floxed

codon
type: Class
subclass of: CDS_region
definition: A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
database_cross_reference: http://en.wikipedia.org/wiki/Codon
has_obo_namespace: sequence
id: SO:0000360
in_subset: SOFA

Axiom
annotated source: codon
annotated property: definition
annotated target: A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: codon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Codon

FRT_flanked
type: Class
subclass of: flanked
definition: An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.
has_exact_synonym: FRT flanked
has_obo_namespace: sequence
id: SO:0000361

Axiom
annotated source: FRT_flanked
annotated property: definition
annotated target: An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.
database_cross_reference: SO:ke

invalidated_by_chimeric_cDNA
type: Class
subclass of: invalidated
definition: A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.
has_exact_synonym: invalidated by chimeric cDNA
has_obo_namespace: sequence
id: SO:0000362

Axiom
annotated source: invalidated_by_chimeric_cDNA
annotated property: definition
annotated target: A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.
database_cross_reference: SO:ma

floxed_gene
type: Class
equivalent class: Class
  intersection of: transgene
  intersection of: Restriction
    on property: has_quality
    some values from: floxed
subclass of: transgene
subclass of: Restriction
  on property: has_quality
  some values from: floxed
definition: A transgene that is floxed.
has_exact_synonym: floxed gene
has_obo_namespace: sequence
id: SO:0000363

Axiom
annotated source: floxed_gene
annotated property: definition
annotated target: A transgene that is floxed.
database_cross_reference: SO:xp

transposable_element_flanking_region
type: Class
subclass of: flanking_region
definition: The region of sequence surrounding a transposable element.
has_exact_synonym: transposable element flanking region
has_obo_namespace: sequence
id: SO:0000364

Axiom
annotated source: transposable_element_flanking_region
annotated property: definition
annotated target: The region of sequence surrounding a transposable element.
database_cross_reference: SO:ke

integron
type: Class
subclass of: integrated_mobile_genetic_element
definition: A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.
database_cross_reference: http://en.wikipedia.org/wiki/Integron
has_obo_namespace: sequence
id: SO:0000365

Axiom
annotated source: integron
annotated property: definition
annotated target: A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.
database_cross_reference: SO:as

wiki
type: Axiom
annotated source: integron
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Integron

insertion_site
type: Class
subclass of: junction
definition: The junction where an insertion occurred.
has_exact_synonym: insertion site
has_obo_namespace: sequence
id: SO:0000366
in_subset: SOFA

Axiom
annotated source: insertion_site
annotated property: definition
annotated target: The junction where an insertion occurred.
database_cross_reference: SO:ke

attI_site
type: Class
subclass of: integration_excision_site
subclass of: Restriction
  on property: part_of
  some values from: integron
definition: A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
has_exact_synonym: attI site
has_obo_namespace: sequence
id: SO:0000367

Axiom
annotated source: attI_site
annotated property: definition
annotated target: A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
database_cross_reference: SO:as

transposable_element_insertion_site
type: Class
subclass of: insertion_site
definition: The junction in a genome where a transposable_element has inserted.
has_exact_synonym: transposable element insertion site
has_obo_namespace: sequence
id: SO:0000368
in_subset: SOFA

Axiom
annotated source: transposable_element_insertion_site
annotated property: definition
annotated target: The junction in a genome where a transposable_element has inserted.
database_cross_reference: SO:ke

integrase_coding_region
type: Class
has_obo_namespace: sequence
id: SO:0000369
deprecated: true

small_regulatory_ncRNA
type: Class
subclass of: SO_0002247
definition: A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others).
has_exact_synonym: small regulatory ncRNA
has_obo_namespace: sequence
id: SO:0000370
in_subset: SOFA

Axiom
annotated source: small_regulatory_ncRNA
annotated property: definition
annotated target: A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others).
database_cross_reference: PMID:28541282
database_cross_reference: PomBase:al
database_cross_reference: SO:ma

conjugative_transposon
type: Class
subclass of: DNA_transposon
definition: A transposon that encodes function required for conjugation.
has_exact_synonym: conjugative transposon
has_obo_namespace: sequence
id: SO:0000371

Axiom
annotated source: conjugative_transposon
annotated property: definition
annotated target: A transposon that encodes function required for conjugation.
database_cross_reference: http://www.sci.sdsu.edu/~smaloy/Glossary/C.html

enzymatic_RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: has_quality
  some values from: enzymatic
definition: An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
has_exact_synonym: enzymatic RNA
has_obo_namespace: sequence
id: SO:0000372
in_subset: SOFA
comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. Moved under ncRNA on 18 Nov 2021. See GitHub Issue #533.

Axiom
annotated source: enzymatic_RNA
annotated property: definition
annotated target: An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
database_cross_reference: RSC:cb

recombinationally_inverted_gene
type: Class
equivalent class: Class
  intersection of: recombinationally_rearranged_gene
  intersection of: Restriction
    on property: has_quality
    some values from: SO_1000036
subclass of: recombinationally_rearranged_gene
subclass of: Restriction
  on property: has_quality
  some values from: SO_1000036
definition: A recombinationally rearranged gene by inversion.
has_exact_synonym: recombinationally inverted gene
has_obo_namespace: sequence
id: SO:0000373

Axiom
annotated source: recombinationally_inverted_gene
annotated property: definition
annotated target: A recombinationally rearranged gene by inversion.
database_cross_reference: SO:xp

ribozyme
type: Class
equivalent class: Class
  intersection of: enzymatic_RNA
  intersection of: Restriction
    on property: has_quality
    some values from: ribozymic
subclass of: enzymatic_RNA
subclass of: Restriction
  on property: has_quality
  some values from: ribozymic
definition: An RNA with catalytic activity.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Ribozyme
has_exact_synonym: INSDC_qualifier:ribozyme
has_obo_namespace: sequence
id: SO:0000374
in_subset: SOFA

Axiom
annotated source: ribozyme
annotated property: definition
annotated target: An RNA with catalytic activity.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: ribozyme
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Ribozyme

cytosolic_5_8S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002240
definition: Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.
database_cross_reference: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
has_exact_synonym: cytosolic 5.8S LSU rRNA
has_exact_synonym: cytosolic 5.8S rRNA
has_exact_synonym: cytosolic 5.8S ribosomal RNA
has_exact_synonym: cytosolic rRNA 5 8S
has_obo_namespace: sequence
id: SO:0000375
in_subset: SOFA
comment: Dave Sant removed '5_8S rRNA is also found in archaea.' from definition due to lack of references mentioning this on 1 Feb 2021. See GitHub Issue #505. Renamed from rRNA_5_8S to cytosolic_5_8S_rRNA on 10 June 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_5_8S_rRNA
annotated property: definition
annotated target: Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.
database_cross_reference: https://rfam.xfam.org/family/RF00002

wiki
type: Axiom
annotated source: cytosolic_5_8S_rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA

RNA_6S
type: Class
subclass of: small_regulatory_ncRNA
definition: A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.
database_cross_reference: http://en.wikipedia.org/wiki/6S_RNA
has_exact_synonym: 6S RNA
has_exact_synonym: RNA 6S
has_obo_namespace: sequence
id: SO:0000376

Axiom
annotated source: RNA_6S
annotated property: definition
annotated target: A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: RNA_6S
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/6S_RNA

CsrB_RsmB_RNA
type: Class
subclass of: small_regulatory_ncRNA
definition: An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.
has_exact_synonym: CsrB RsmB RNA
has_exact_synonym: CsrB-RsmB RNA
has_obo_namespace: sequence
id: SO:0000377

Axiom
annotated source: CsrB_RsmB_RNA
annotated property: definition
annotated target: An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

DsrA_RNA
type: Class
subclass of: small_regulatory_ncRNA
definition: DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.
database_cross_reference: http://en.wikipedia.org/wiki/DsrA_RNA
has_exact_synonym: DsrA RNA
has_obo_namespace: sequence
id: SO:0000378

Axiom
annotated source: DsrA_RNA
annotated property: definition
annotated target: DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: DsrA_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/DsrA_RNA

GcvB_RNA
type: Class
subclass of: DsrA_RNA
definition: A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
database_cross_reference: http://en.wikipedia.org/wiki/GcvB_RNA
has_exact_synonym: GcvB RNA
has_obo_namespace: sequence
id: SO:0000379

Axiom
annotated source: GcvB_RNA
annotated property: definition
annotated target: A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: GcvB_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/GcvB_RNA

hammerhead_ribozyme
type: Class
equivalent class: Class
  intersection of: RNA_motif
  intersection of: Restriction
    on property: has_quality
    some values from: ribozymic
subclass of: RNA_motif
subclass of: Restriction
  on property: has_quality
  some values from: ribozymic
definition: A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Hammerhead_ribozyme
has_exact_synonym: INSDC_qualifier:hammerhead_ribozyme
has_exact_synonym: hammerhead ribozyme
has_obo_namespace: sequence
id: SO:0000380
in_subset: SOFA

Axiom
annotated source: hammerhead_ribozyme
annotated property: definition
annotated target: A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
database_cross_reference: PMID:2436805

wiki
type: Axiom
annotated source: hammerhead_ribozyme
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Hammerhead_ribozyme

group_IIA_intron
type: Class
subclass of: group_II_intron
definition: A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and gamma/gamma-prime for the 3-prime exon.
has_exact_synonym: group IIA intron
has_obo_namespace: sequence
id: SO:0000381

Axiom
annotated source: group_IIA_intron
annotated property: definition
annotated target: A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and gamma/gamma-prime for the 3-prime exon.
database_cross_reference: PMID:20463000

group_IIB_intron
type: Class
subclass of: group_II_intron
definition: A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon.
has_exact_synonym: group IIB intron
has_obo_namespace: sequence
id: SO:0000382

Axiom
annotated source: group_IIB_intron
annotated property: definition
annotated target: A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon.
database_cross_reference: PMID:20463000

MicF_RNA
type: Class
subclass of: antisense_RNA
definition: A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.
database_cross_reference: http://en.wikipedia.org/wiki/MicF_RNA
has_exact_synonym: MicF RNA
has_obo_namespace: sequence
id: SO:0000383

Axiom
annotated source: MicF_RNA
annotated property: definition
annotated target: A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: MicF_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/MicF_RNA

OxyS_RNA
type: Class
subclass of: small_regulatory_ncRNA
definition: A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.
database_cross_reference: http://en.wikipedia.org/wiki/OxyS_RNA
has_exact_synonym: OxyS RNA
has_obo_namespace: sequence
id: SO:0000384

Axiom
annotated source: OxyS_RNA
annotated property: definition
annotated target: A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: OxyS_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/OxyS_RNA

RNase_MRP_RNA
type: Class
subclass of: enzymatic_RNA
definition: The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:RNase_MRP_RNA
has_exact_synonym: RNase MRP RNA
has_obo_namespace: sequence
id: SO:0000385
in_subset: SOFA
comment: Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533.

Axiom
annotated source: RNase_MRP_RNA
annotated property: definition
annotated target: The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

RNase_P_RNA
type: Class
subclass of: enzymatic_RNA
definition: The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:RNase_P_RNA
has_exact_synonym: RNase P RNA
has_obo_namespace: sequence
id: SO:0000386
in_subset: SOFA
comment: Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533.

Axiom
annotated source: RNase_P_RNA
annotated property: definition
annotated target: The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

RprA_RNA
type: Class
subclass of: small_regulatory_ncRNA
definition: Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.
database_cross_reference: http://en.wikipedia.org/wiki/RprA_RNA
has_exact_synonym: RprA RNA
has_obo_namespace: sequence
id: SO:0000387

Axiom
annotated source: RprA_RNA
annotated property: definition
annotated target: Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: RprA_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/RprA_RNA

RRE_RNA
type: Class
subclass of: small_regulatory_ncRNA
definition: The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.
has_exact_synonym: RRE RNA
has_obo_namespace: sequence
id: SO:0000388

Axiom
annotated source: RRE_RNA
annotated property: definition
annotated target: The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

spot_42_RNA
type: Class
subclass of: small_regulatory_ncRNA
definition: A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.
database_cross_reference: http://en.wikipedia.org/wiki/Spot_42_RNA
has_exact_synonym: spot-42 RNA
has_obo_namespace: sequence
id: SO:0000389

Axiom
annotated source: spot_42_RNA
annotated property: definition
annotated target: A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: spot_42_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Spot_42_RNA

telomerase_RNA
type: Class
subclass of: ncRNA
definition: The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Telomerase_RNA
has_exact_synonym: INSDC_qualifier:telomerase_RNA
has_exact_synonym: telomerase RNA
has_obo_namespace: sequence
id: SO:0000390
in_subset: SOFA

Axiom
annotated source: telomerase_RNA
annotated property: definition
annotated target: The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: telomerase_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Telomerase_RNA

U1_snRNA
type: Class
subclass of: snRNA
definition: U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
database_cross_reference: http://en.wikipedia.org/wiki/U1_snRNA
has_exact_synonym: U1 small nuclear RNA
has_exact_synonym: U1 snRNA
has_exact_synonym: small nuclear RNA U1
has_exact_synonym: snRNA U1
has_obo_namespace: sequence
id: SO:0000391
in_subset: SOFA

Axiom
annotated source: U1_snRNA
annotated property: definition
annotated target: U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U1_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U1_snRNA

Axiom
annotated source: U1_snRNA
annotated property: has_exact_synonym
annotated target: U1 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U1_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U1
database_cross_reference: RSC:cb

Axiom
annotated source: U1_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U1
database_cross_reference: RSC:cb

U2_snRNA
type: Class
subclass of: snRNA
definition: U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
database_cross_reference: http://en.wikipedia.org/wiki/U2_snRNA
has_exact_synonym: U2 small nuclear RNA
has_exact_synonym: U2 snRNA
has_exact_synonym: small nuclear RNA U2
has_exact_synonym: snRNA U2
has_obo_namespace: sequence
id: SO:0000392
in_subset: SOFA

Axiom
annotated source: U2_snRNA
annotated property: definition
annotated target: U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U2_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U2_snRNA

Axiom
annotated source: U2_snRNA
annotated property: has_exact_synonym
annotated target: U2 small nuclear RNA
database_cross_reference: RSC:CB

Axiom
annotated source: U2_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U2
database_cross_reference: RSC:CB

Axiom
annotated source: U2_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U2
database_cross_reference: RSC:CB

U4_snRNA
type: Class
subclass of: snRNA
definition: U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
database_cross_reference: http://en.wikipedia.org/wiki/U4_snRNA
has_exact_synonym: U4 small nuclear RNA
has_exact_synonym: U4 snRNA
has_exact_synonym: small nuclear RNA U4
has_exact_synonym: snRNA U4
has_obo_namespace: sequence
id: SO:0000393
in_subset: SOFA

Axiom
annotated source: U4_snRNA
annotated property: definition
annotated target: U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U4_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U4_snRNA

Axiom
annotated source: U4_snRNA
annotated property: has_exact_synonym
annotated target: U4 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U4_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U4
database_cross_reference: RSC:cb

Axiom
annotated source: U4_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U4
database_cross_reference: RSC:cb

U4atac_snRNA
type: Class
subclass of: snRNA
definition: An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
has_exact_synonym: U4atac small nuclear RNA
has_exact_synonym: U4atac snRNA
has_exact_synonym: small nuclear RNA U4atac
has_exact_synonym: snRNA U4atac
has_obo_namespace: sequence
id: SO:0000394
in_subset: SOFA

Axiom
annotated source: U4atac_snRNA
annotated property: definition
annotated target: An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
database_cross_reference: PMID:12409455

Axiom
annotated source: U4atac_snRNA
annotated property: has_exact_synonym
annotated target: U4atac small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U4atac_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U4atac
database_cross_reference: RSC:cb

Axiom
annotated source: U4atac_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U4atac
database_cross_reference: RSC:cb

U5_snRNA
type: Class
subclass of: snRNA
definition: U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
database_cross_reference: http://en.wikipedia.org/wiki/U5_snRNA
has_exact_synonym: U5 small nuclear RNA
has_exact_synonym: U5 snRNA
has_exact_synonym: small nuclear RNA U5
has_exact_synonym: snRNA U5
has_obo_namespace: sequence
id: SO:0000395
in_subset: SOFA

Axiom
annotated source: U5_snRNA
annotated property: definition
annotated target: U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U5_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U5_snRNA

Axiom
annotated source: U5_snRNA
annotated property: has_exact_synonym
annotated target: U5 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U5_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U5
database_cross_reference: RSC:cb

Axiom
annotated source: U5_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U5
database_cross_reference: RSC:cb

U6_snRNA
type: Class
subclass of: snRNA
definition: U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
database_cross_reference: http://en.wikipedia.org/wiki/U6_snRNA
has_exact_synonym: U6 small nuclear RNA
has_exact_synonym: U6 snRNA
has_exact_synonym: small nuclear RNA U6
has_exact_synonym: snRNA U6
has_obo_namespace: sequence
id: SO:0000396
in_subset: SOFA

Axiom
annotated source: U6_snRNA
annotated property: definition
annotated target: U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U6_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U6_snRNA

Axiom
annotated source: U6_snRNA
annotated property: has_exact_synonym
annotated target: U6 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U6_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U6
database_cross_reference: RSC:cb

Axiom
annotated source: U6_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U6
database_cross_reference: RSC:cb

U6atac_snRNA
type: Class
subclass of: snRNA
definition: U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
has_exact_synonym: U6atac small nuclear RNA
has_exact_synonym: U6atac snRNA
has_exact_synonym: snRNA U6atac
has_obo_namespace: sequence
id: SO:0000397
in_subset: SOFA

Axiom
annotated source: U6atac_snRNA
annotated property: definition
annotated target: U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
database_cross_reference: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

Axiom
annotated source: U6atac_snRNA
annotated property: has_exact_synonym
annotated target: U6atac small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U6atac_snRNA
annotated property: has_exact_synonym
annotated target: U6atac snRNA
database_cross_reference: RSC:cb

Axiom
annotated source: U6atac_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U6atac
database_cross_reference: RSC:cb

U11_snRNA
type: Class
subclass of: snRNA
definition: U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
database_cross_reference: http://en.wikipedia.org/wiki/U11_snRNA
has_exact_synonym: U11 small nuclear RNA
has_exact_synonym: U11 snRNA
has_exact_synonym: small nuclear RNA U11
has_exact_synonym: snRNA U11
has_obo_namespace: sequence
id: SO:0000398
in_subset: SOFA

Axiom
annotated source: U11_snRNA
annotated property: definition
annotated target: U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
database_cross_reference: PMID:9622129

wiki
type: Axiom
annotated source: U11_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U11_snRNA

Axiom
annotated source: U11_snRNA
annotated property: has_exact_synonym
annotated target: U11 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U11_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U11
database_cross_reference: RSC:cb

Axiom
annotated source: U11_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U11
database_cross_reference: RSC:cb

U12_snRNA
type: Class
subclass of: snRNA
definition: The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
database_cross_reference: http://en.wikipedia.org/wiki/U12_snRNA
has_exact_synonym: U12 small nuclear RNA
has_exact_synonym: U12 snRNA
has_exact_synonym: small nuclear RNA U12
has_exact_synonym: snRNA U12
has_obo_namespace: sequence
id: SO:0000399
in_subset: SOFA

Axiom
annotated source: U12_snRNA
annotated property: definition
annotated target: The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U12_snRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/U12_snRNA

Axiom
annotated source: U12_snRNA
annotated property: has_exact_synonym
annotated target: U12 small nuclear RNA
database_cross_reference: RSC:cb

Axiom
annotated source: U12_snRNA
annotated property: has_exact_synonym
annotated target: small nuclear RNA U12
database_cross_reference: RSC:cb

Axiom
annotated source: U12_snRNA
annotated property: has_exact_synonym
annotated target: snRNA U12
database_cross_reference: RSC:cb

sequence_attribute
type: Class
definition: An attribute describes a quality of sequence.
has_exact_synonym: sequence attribute
has_obo_namespace: sequence
id: SO:0000400

Axiom
annotated source: sequence_attribute
annotated property: definition
annotated target: An attribute describes a quality of sequence.
database_cross_reference: SO:ke

gene_attribute
type: Class
subclass of: feature_attribute
definition: An attribute describing a gene.
has_exact_synonym: gene attribute
has_obo_namespace: sequence
id: SO:0000401

enhancer_attribute
type: Class
has_obo_namespace: sequence
id: SO:0000402
deprecated: true

U14_snoRNA
type: Class
subclass of: C_D_box_snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: SO_0005837
definition: U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
has_alternative_id: SO:0005839
has_exact_synonym: U14 small nucleolar RNA
has_exact_synonym: U14 snoRNA
has_exact_synonym: small nucleolar RNA U14
has_exact_synonym: snoRNA U14
has_obo_namespace: sequence
id: SO:0000403
in_subset: SOFA
comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.

Axiom
annotated source: U14_snoRNA
annotated property: definition
annotated target: U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
database_cross_reference: PMID:2551119
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

vault_RNA
type: Class
subclass of: ncRNA
definition: A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Vault_RNA
has_exact_synonym: INSDC_qualifier:vault_RNA
has_exact_synonym: vault RNA
has_obo_namespace: sequence
id: SO:0000404
in_subset: SOFA

Axiom
annotated source: vault_RNA
annotated property: definition
annotated target: A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: vault_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Vault_RNA

Y_RNA
type: Class
subclass of: ncRNA
definition: Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Y_RNA
has_exact_synonym: INSDC_qualifier:Y_RNA
has_exact_synonym: Y RNA
has_obo_namespace: sequence
id: SO:0000405
in_subset: SOFA

Axiom
annotated source: Y_RNA
annotated property: definition
annotated target: Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: Y_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Y_RNA

twintron
type: Class
subclass of: intron
definition: An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
database_cross_reference: http://en.wikipedia.org/wiki/Twintron
has_obo_namespace: sequence
id: SO:0000406

Axiom
annotated source: twintron
annotated property: definition
annotated target: An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
database_cross_reference: PMID:1899376
database_cross_reference: PMID:7823908

wiki
type: Axiom
annotated source: twintron
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Twintron

cytosolic_18S_rRNA
type: Class
subclass of: cytosolic_SSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002236
definition: Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes.
database_cross_reference: http://en.wikipedia.org/wiki/18S_ribosomal_RNA
has_exact_synonym: cytosolic 18S rRNA
has_exact_synonym: cytosolic 18S ribosomal RNA
has_exact_synonym: cytosolic rRNA 18S
has_obo_namespace: sequence
id: SO:0000407
in_subset: SOFA
comment: Renamed to cytosolic_18S_rRNA from rRNA_18S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_18S_rRNA
annotated property: definition
annotated target: Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: cytosolic_18S_rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/18S_ribosomal_RNA

site
type: Class
definition: The interbase position where something (eg an aberration) occurred.
has_obo_namespace: sequence
id: SO:0000408
deprecated: true

Axiom
annotated source: site
annotated property: definition
annotated target: The interbase position where something (eg an aberration) occurred.
database_cross_reference: SO:ke

binding_site
type: Class
subclass of: biological_region
definition: A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
has_alternative_id: BS:00033
database_cross_reference: http://en.wikipedia.org/wiki/Binding_site
has_exact_synonym: INSDC_feature:misc_binding
has_exact_synonym: binding site
has_exact_synonym: binding_or_interaction_site
has_obo_namespace: sequence
has_related_synonym: site
id: SO:0000409
in_subset: SOFA
in_subset: biosapiens
comment: See GO:0005488 : binding.

Axiom
annotated source: binding_site
annotated property: definition
annotated target: A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: binding_site
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Binding_site

protein_binding_site
type: Class
subclass of: binding_site
definition: A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
has_exact_synonym: INSDC_feature:protein_bind
has_exact_synonym: protein binding site
has_obo_namespace: sequence
id: SO:0000410
in_subset: SOFA
comment: See GO:0042277 : peptide binding.

Axiom
annotated source: protein_binding_site
annotated property: definition
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
database_cross_reference: SO:ke

rescue_region
type: Class
equivalent class: Class
  intersection of: reagent
  intersection of: Restriction
    on property: has_quality
    some values from: rescue
subclass of: reagent
subclass of: Restriction
  on property: has_quality
  some values from: rescue
definition: A region that rescues.
has_exact_synonym: rescue fragment
has_exact_synonym: rescue region
has_obo_namespace: sequence
has_related_synonym: rescue segment
id: SO:0000411

Axiom
annotated source: rescue_region
annotated property: definition
annotated target: A region that rescues.
database_cross_reference: SO:xp

restriction_fragment
type: Class
subclass of: assembly_component
definition: A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
database_cross_reference: http://en.wikipedia.org/wiki/Restriction_fragment
has_exact_synonym: restriction fragment
has_obo_namespace: sequence
id: SO:0000412
in_subset: SOFA

Axiom
annotated source: restriction_fragment
annotated property: definition
annotated target: A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: restriction_fragment
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Restriction_fragment

sequence_difference
type: Class
subclass of: remark
definition: A region where the sequence differs from that of a specified sequence.
has_exact_synonym: INSDC_feature:misc_difference
has_exact_synonym: sequence difference
has_obo_namespace: sequence
id: SO:0000413
in_subset: SOFA

Axiom
annotated source: sequence_difference
annotated property: definition
annotated target: A region where the sequence differs from that of a specified sequence.
database_cross_reference: SO:ke

invalidated_by_genomic_contamination
type: Class
subclass of: invalidated
definition: An attribute to describe a feature that is invalidated due to genomic contamination.
has_exact_synonym: invalidated by genomic contamination
has_obo_namespace: sequence
id: SO:0000414

Axiom
annotated source: invalidated_by_genomic_contamination
annotated property: definition
annotated target: An attribute to describe a feature that is invalidated due to genomic contamination.
database_cross_reference: SO:ke

invalidated_by_genomic_polyA_primed_cDNA
type: Class
subclass of: invalidated
definition: An attribute to describe a feature that is invalidated due to polyA priming.
has_exact_synonym: invalidated by genomic polyA primed cDNA
has_obo_namespace: sequence
id: SO:0000415

Axiom
annotated source: invalidated_by_genomic_polyA_primed_cDNA
annotated property: definition
annotated target: An attribute to describe a feature that is invalidated due to polyA priming.
database_cross_reference: SO:ke

invalidated_by_partial_processing
type: Class
subclass of: invalidated
definition: An attribute to describe a feature that is invalidated due to partial processing.
has_exact_synonym: invalidated by partial processing
has_obo_namespace: sequence
id: SO:0000416

Axiom
annotated source: invalidated_by_partial_processing
annotated property: definition
annotated target: An attribute to describe a feature that is invalidated due to partial processing.
database_cross_reference: SO:ke

polypeptide_domain
type: Class
subclass of: polypeptide_structural_region
subclass of: SO_0100021
definition: A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.
has_alternative_id: BS:00012
has_alternative_id: BS:00134
has_alternative_id: SO:0001069
has_broad_synonym: domain
has_broad_synonym: structural domain
has_exact_synonym: polypeptide domain
has_exact_synonym: polypeptide_structural_domain
has_obo_namespace: sequence
id: SO:0000417
in_subset: biosapiens
comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.

Axiom
annotated source: polypeptide_domain
annotated property: definition
annotated target: A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.
database_cross_reference: EBIBS:GAR

Axiom
annotated source: polypeptide_domain
annotated property: has_broad_synonym
annotated target: domain
database_cross_reference: uniprot:feature_type
has_synonym_type: biosapiens

Axiom
annotated source: polypeptide_domain
annotated property: has_broad_synonym
annotated target: structural domain
has_synonym_type: biosapiens

Axiom
annotated source: polypeptide_domain
annotated property: has_exact_synonym
annotated target: polypeptide_structural_domain
has_synonym_type: biosapiens

signal_peptide
type: Class
subclass of: peptide_localization_signal
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002251
subclass of: Restriction
  on property: part_of
  some values from: propeptide
definition: The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
has_alternative_id: BS:00159
database_cross_reference: http://en.wikipedia.org/wiki/Signal_peptide
has_exact_synonym: INSDC_feature:sig_peptide
has_exact_synonym: signal peptide
has_exact_synonym: signal peptide coding sequence
has_obo_namespace: sequence
has_related_synonym: signal
id: SO:0000418
in_subset: SOFA
in_subset: biosapiens
comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.

Axiom
annotated source: signal_peptide
annotated property: definition
annotated target: The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: signal_peptide
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Signal_peptide

Axiom
annotated source: signal_peptide
annotated property: has_related_synonym
annotated target: signal
database_cross_reference: uniprot:feature_type

mature_protein_region
type: Class
subclass of: polypeptide_region
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002249
subclass of: Restriction
  on property: part_of
  some values from: immature_peptide_region
definition: The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
has_alternative_id: BS:00149
has_exact_synonym: INSDC_feature:mat_peptide
has_exact_synonym: mature protein region
has_obo_namespace: sequence
has_related_synonym: chain
has_related_synonym: mature peptide
id: SO:0000419
in_subset: SOFA
in_subset: biosapiens
comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.

Axiom
annotated source: mature_protein_region
annotated property: definition
annotated target: The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb
database_cross_reference: http://www.insdc.org/files/feature_table.html

Axiom
annotated source: mature_protein_region
annotated property: has_related_synonym
annotated target: chain
database_cross_reference: uniprot:feature_type

five_prime_terminal_inverted_repeat
type: Class
subclass of: terminal_inverted_repeat
definition: An inverted repeat (SO:0000294) occurring at the 5-prime termini of a DNA transposon.
has_exact_synonym: 5' TIR
has_exact_synonym: five prime terminal inverted repeat
has_obo_namespace: sequence
id: SO:0000420

three_prime_terminal_inverted_repeat
type: Class
subclass of: terminal_inverted_repeat
definition: An inverted repeat (SO:0000294) occurring at the 3-prime termini of a DNA transposon.
has_exact_synonym: 3' TIR
has_exact_synonym: three prime terminal inverted repeat
has_obo_namespace: sequence
id: SO:0000421

U5_LTR_region
type: Class
subclass of: LTR_component
definition: The U5 segment of the long terminal repeats.
has_exact_synonym: U5 LTR region
has_exact_synonym: U5 long terminal repeat region
has_obo_namespace: sequence
id: SO:0000422

R_LTR_region
type: Class
subclass of: LTR_component
definition: The R segment of the long terminal repeats.
has_exact_synonym: R LTR region
has_exact_synonym: R long terminal repeat region
has_obo_namespace: sequence
id: SO:0000423

U3_LTR_region
type: Class
subclass of: LTR_component
definition: The U3 segment of the long terminal repeats.
has_exact_synonym: U3 LTR region
has_exact_synonym: U3 long terminal repeat region
has_obo_namespace: sequence
id: SO:0000424

five_prime_LTR
type: Class
subclass of: long_terminal_repeat
definition: The long terminal repeat found at the five-prime end of the sequence to be inserted into the host genome.
has_exact_synonym: 5' LTR
has_exact_synonym: 5' long terminal repeat
has_exact_synonym: five prime LTR
has_obo_namespace: sequence
id: SO:0000425

three_prime_LTR
type: Class
subclass of: long_terminal_repeat
definition: The long terminal repeat found at the three-prime end of the sequence to be inserted into the host genome.
has_exact_synonym: 3' LTR
has_exact_synonym: 3' long terminal repeat
has_exact_synonym: three prime LTR
has_obo_namespace: sequence
id: SO:0000426

R_five_prime_LTR_region
type: Class
subclass of: R_LTR_region
subclass of: five_prime_LTR_component
definition: The R segment of the three-prime long terminal repeat.
has_exact_synonym: R 5' long term repeat region
has_exact_synonym: R five prime LTR region
has_obo_namespace: sequence
id: SO:0000427

U5_five_prime_LTR_region
type: Class
subclass of: U5_LTR_region
subclass of: five_prime_LTR_component
definition: The U5 segment of the three-prime long terminal repeat.
has_exact_synonym: U5 5' long terminal repeat region
has_exact_synonym: U5 five prime LTR region
has_obo_namespace: sequence
id: SO:0000428

U3_five_prime_LTR_region
type: Class
subclass of: U3_LTR_region
subclass of: five_prime_LTR_component
definition: The U3 segment of the three-prime long terminal repeat.
has_exact_synonym: U3 5' long term repeat region
has_exact_synonym: U3 five prime LTR region
has_obo_namespace: sequence
id: SO:0000429

R_three_prime_LTR_region
type: Class
subclass of: three_prime_LTR_component
definition: The R segment of the three-prime long terminal repeat.
has_exact_synonym: R 3' long terminal repeat region
has_exact_synonym: R three prime LTR region
has_obo_namespace: sequence
id: SO:0000430

U3_three_prime_LTR_region
type: Class
subclass of: three_prime_LTR_component
definition: The U3 segment of the three-prime long terminal repeat.
has_exact_synonym: U3 3' long terminal repeat region
has_exact_synonym: U3 three prime LTR region
has_obo_namespace: sequence
id: SO:0000431

U5_three_prime_LTR_region
type: Class
subclass of: three_prime_LTR_component
definition: The U5 segment of the three-prime long terminal repeat.
has_exact_synonym: U5 3' long terminal repeat region
has_exact_synonym: U5 three prime LTR region
has_obo_namespace: sequence
id: SO:0000432

non_LTR_retrotransposon_polymeric_tract
type: Class
subclass of: repeat_region
subclass of: repeat_component
subclass of: Restriction
  on property: part_of
  some values from: non_LTR_retrotransposon
definition: A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
has_broad_synonym: INSDC_feature:repeat_region
has_exact_synonym: INSDC_qualifier:non_ltr_retrotransposon_polymeric_tract
has_exact_synonym: non LTR retrotransposon polymeric tract
has_obo_namespace: sequence
id: SO:0000433

Axiom
annotated source: non_LTR_retrotransposon_polymeric_tract
annotated property: definition
annotated target: A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
database_cross_reference: SO:ke

target_site_duplication
type: Class
equivalent class: Class
  intersection of: direct_repeat
  intersection of: Restriction
    on property: derives_from
    some values from: transposable_element
subclass of: direct_repeat
subclass of: Restriction
  on property: derives_from
  some values from: transposable_element
definition: A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.
has_exact_synonym: target site duplication
has_obo_namespace: sequence
id: SO:0000434

Axiom
annotated source: target_site_duplication
annotated property: definition
annotated target: A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.
database_cross_reference: http://www.koko.gov.my/CocoaBioTech/Glossaryt.html

RR_tract
type: Class
subclass of: conserved_region
subclass of: Restriction
  on property: part_of
  some values from: LTR_retrotransposon
definition: A polypurine tract within an LTR_retrotransposon.
has_exact_synonym: RR tract
has_obo_namespace: sequence
has_related_synonym: LTR retrotransposon poly purine tract
id: SO:0000435

Axiom
annotated source: RR_tract
annotated property: definition
annotated target: A polypurine tract within an LTR_retrotransposon.
database_cross_reference: SO:ke

ARS
type: Class
subclass of: origin_of_replication
definition: A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
has_exact_synonym: autonomously replicating sequence
has_obo_namespace: sequence
id: SO:0000436
in_subset: SOFA

Axiom
annotated source: ARS
annotated property: definition
annotated target: A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
database_cross_reference: SO:ma

assortment_derived_duplication
type: Class
has_obo_namespace: sequence
id: SO:0000437
deprecated: true

gene_not_polyadenylated
type: Class
has_obo_namespace: sequence
id: SO:0000438
deprecated: true

inverted_ring_chromosome
type: Class
subclass of: SO_1000030
subclass of: SO_1000045
definition: A ring chromosome is a chromosome whose arms have fused together to form a ring in an inverted fashion, often with the loss of the ends of the chromosome.
has_exact_synonym: inverted ring chromosome
has_obo_namespace: sequence
id: SO:0000439

vector_replicon
type: Class
subclass of: replicon
subclass of: Restriction
  on property: part_of
  some values from: clone
definition: A replicon that has been modified to act as a vector for foreign sequence.
database_cross_reference: http://en.wikipedia.org/wiki/Vector_(molecular_biology)
has_exact_synonym: vector
has_exact_synonym: vector replicon
has_obo_namespace: sequence
id: SO:0000440
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: vector_replicon
annotated property: definition
annotated target: A replicon that has been modified to act as a vector for foreign sequence.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: vector_replicon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Vector_(molecular_biology)

ss_oligo
type: Class
subclass of: oligo
definition: A single stranded oligonucleotide.
has_exact_synonym: single strand oligo
has_exact_synonym: single strand oligonucleotide
has_exact_synonym: single stranded oligonucleotide
has_exact_synonym: ss oligo
has_exact_synonym: ss oligonucleotide
has_obo_namespace: sequence
id: SO:0000441
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: ss_oligo
annotated property: definition
annotated target: A single stranded oligonucleotide.
database_cross_reference: SO:ke

ds_oligo
type: Class
subclass of: oligo
definition: A double stranded oligonucleotide.
has_exact_synonym: double stranded oligonucleotide
has_exact_synonym: ds oligo
has_exact_synonym: ds-oligonucleotide
has_obo_namespace: sequence
id: SO:0000442
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: ds_oligo
annotated property: definition
annotated target: A double stranded oligonucleotide.
database_cross_reference: SO:ke

polymer_attribute
type: Class
subclass of: sequence_attribute
definition: An attribute to describe the kind of biological sequence.
has_exact_synonym: polymer attribute
has_obo_namespace: sequence
id: SO:0000443

Axiom
annotated source: polymer_attribute
annotated property: definition
annotated target: An attribute to describe the kind of biological sequence.
database_cross_reference: SO:ke

three_prime_noncoding_exon
type: Class
subclass of: noncoding_exon
definition: Non-coding exon in the 3' UTR.
has_exact_synonym: three prime noncoding exon
has_obo_namespace: sequence
id: SO:0000444

Axiom
annotated source: three_prime_noncoding_exon
annotated property: definition
annotated target: Non-coding exon in the 3' UTR.
database_cross_reference: SO:ke

five_prime_noncoding_exon
type: Class
subclass of: noncoding_exon
definition: Non-coding exon in the 5' UTR.
has_exact_synonym: 5' nc exon
has_exact_synonym: 5' non coding exon
has_exact_synonym: five prime noncoding exon
has_obo_namespace: sequence
id: SO:0000445

Axiom
annotated source: five_prime_noncoding_exon
annotated property: definition
annotated target: Non-coding exon in the 5' UTR.
database_cross_reference: SO:ke

UTR_intron
type: Class
subclass of: intron
definition: Intron located in the untranslated region.
has_exact_synonym: UTR intron
has_obo_namespace: sequence
id: SO:0000446

Axiom
annotated source: UTR_intron
annotated property: definition
annotated target: Intron located in the untranslated region.
database_cross_reference: SO:ke

five_prime_UTR_intron
type: Class
subclass of: UTR_intron
definition: An intron located in the 5' UTR.
has_exact_synonym: five prime UTR intron
has_obo_namespace: sequence
id: SO:0000447

Axiom
annotated source: five_prime_UTR_intron
annotated property: definition
annotated target: An intron located in the 5' UTR.
database_cross_reference: SO:ke

three_prime_UTR_intron
type: Class
subclass of: UTR_intron
definition: An intron located in the 3' UTR.
has_exact_synonym: three prime UTR intron
has_obo_namespace: sequence
id: SO:0000448

Axiom
annotated source: three_prime_UTR_intron
annotated property: definition
annotated target: An intron located in the 3' UTR.
database_cross_reference: SO:ke

random_sequence
type: Class
subclass of: synthetic_sequence
definition: A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components.
has_exact_synonym: random sequence
has_obo_namespace: sequence
id: SO:0000449

Axiom
annotated source: random_sequence
annotated property: definition
annotated target: A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components.
database_cross_reference: SO:ma

interband
type: Class
subclass of: chromosome_part
definition: A light region between two darkly staining bands in a polytene chromosome.
has_obo_namespace: sequence
has_related_synonym: chromosome interband
id: SO:0000450

Axiom
annotated source: interband
annotated property: definition
annotated target: A light region between two darkly staining bands in a polytene chromosome.
database_cross_reference: SO:ma

gene_with_polyadenylated_mRNA
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: transcribed_to
    some values from: polyadenylated_mRNA
subclass of: protein_coding_gene
subclass of: Restriction
  on property: transcribed_to
  some values from: polyadenylated_mRNA
definition: A gene that encodes a polyadenylated mRNA.
has_exact_synonym: gene with polyadenylated mRNA
has_obo_namespace: sequence
id: SO:0000451

Axiom
annotated source: gene_with_polyadenylated_mRNA
annotated property: definition
annotated target: A gene that encodes a polyadenylated mRNA.
database_cross_reference: SO:xp

transgene_attribute
type: Class
has_obo_namespace: sequence
id: SO:0000452
deprecated: true

chromosomal_transposition
type: Class
subclass of: SO_1000183
definition: A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.
has_exact_synonym: chromosomal transposition
has_narrow_synonym: transposition
has_obo_namespace: sequence
id: SO:0000453

Axiom
annotated source: chromosomal_transposition
annotated property: definition
annotated target: A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.
database_cross_reference: FB:reference_manual
database_cross_reference: SO:ke

rasiRNA
type: Class
subclass of: piRNA
definition: A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:rasiRNA
has_exact_synonym: repeat associated small interfering RNA
has_obo_namespace: sequence
id: SO:0000454
in_subset: SOFA
comment: Changed parent term from ncRNA (SO:0000655) to piRNA (SO:0001035). See GitHub Issue #573.

Axiom
annotated source: rasiRNA
annotated property: definition
annotated target: A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
database_cross_reference: PMID:18032451
database_cross_reference: http://www.developmentalcell.com/content/article/abstract

gene_with_mRNA_with_frameshift
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: has_quality
    some values from: frameshift
subclass of: protein_coding_gene
subclass of: Restriction
  on property: has_quality
  some values from: frameshift
definition: A gene that encodes an mRNA with a frameshift.
has_exact_synonym: gene with mRNA with frameshift
has_obo_namespace: sequence
id: SO:0000455

Axiom
annotated source: gene_with_mRNA_with_frameshift
annotated property: definition
annotated target: A gene that encodes an mRNA with a frameshift.
database_cross_reference: SO:xp

recombinationally_rearranged_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: recombinationally_rearranged
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: recombinationally_rearranged
definition: A gene that is recombinationally rearranged.
has_exact_synonym: recombinationally rearranged gene
has_obo_namespace: sequence
id: SO:0000456

Axiom
annotated source: recombinationally_rearranged_gene
annotated property: definition
annotated target: A gene that is recombinationally rearranged.
database_cross_reference: SO:ke

interchromosomal_duplication
type: Class
subclass of: SO_1000037
definition: A chromosome duplication involving an insertion from another chromosome.
has_exact_synonym: interchromosomal duplication
has_obo_namespace: sequence
id: SO:0000457

Axiom
annotated source: interchromosomal_duplication
annotated property: definition
annotated target: A chromosome duplication involving an insertion from another chromosome.
database_cross_reference: SO:ke

D_gene_segment
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_segment
definition: Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
has_exact_synonym: D gene
has_exact_synonym: D-GENE
has_exact_synonym: INSDC_feature:D_segment
has_obo_namespace: sequence
id: SO:0000458

Axiom
annotated source: D_gene_segment
annotated property: definition
annotated target: Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

gene_with_trans_spliced_transcript
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: transcribed_to
    some values from: trans_spliced_transcript
subclass of: gene
subclass of: Restriction
  on property: transcribed_to
  some values from: trans_spliced_transcript
definition: A gene with a transcript that is trans-spliced.
has_exact_synonym: gene with trans spliced transcript
has_obo_namespace: sequence
id: SO:0000459

Axiom
annotated source: gene_with_trans_spliced_transcript
annotated property: definition
annotated target: A gene with a transcript that is trans-spliced.
database_cross_reference: SO:xp

vertebrate_immunoglobulin_T_cell_receptor_segment
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
definition: Germline genomic DNA with the sequence for a V, D, C, or J portion of an immunoglobulin/T-cell receptor.
has_exact_synonym: vertebrate immunoglobulin T cell receptor segment
has_exact_synonym: vertebrate_immunoglobulin/T-cell receptor gene
has_obo_namespace: sequence
id: SO:0000460
comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'.

inversion_derived_bipartite_deficiency
type: Class
subclass of: SO_1000029
definition: A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.
has_exact_synonym: inversion derived bipartite deficiency
has_obo_namespace: sequence
id: SO:0000461

Axiom
annotated source: inversion_derived_bipartite_deficiency
annotated property: definition
annotated target: A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.
database_cross_reference: FB:km

pseudogenic_region
type: Class
subclass of: biological_region
definition: A non-functional descendant of a functional entity.
has_exact_synonym: pseudogenic region
has_obo_namespace: sequence
id: SO:0000462
in_subset: SOFA

Axiom
annotated source: pseudogenic_region
annotated property: definition
annotated target: A non-functional descendant of a functional entity.
database_cross_reference: SO:cjm

encodes_alternately_spliced_transcripts
type: Class
subclass of: gene_attribute
definition: A gene that encodes more than one transcript.
has_exact_synonym: encodes alternately spliced transcripts
has_obo_namespace: sequence
id: SO:0000463

Axiom
annotated source: encodes_alternately_spliced_transcripts
annotated property: definition
annotated target: A gene that encodes more than one transcript.
database_cross_reference: SO:ke

decayed_exon
type: Class
subclass of: pseudogenic_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: exon
definition: A non-functional descendant of an exon.
has_exact_synonym: decayed exon
has_obo_namespace: sequence
id: SO:0000464
in_subset: SOFA
comment: Does not have to be part of a pseudogene.

Axiom
annotated source: decayed_exon
annotated property: definition
annotated target: A non-functional descendant of an exon.
database_cross_reference: SO:ke

inversion_derived_deficiency_plus_duplication
type: Class
subclass of: SO_1000029
subclass of: SO_1000038
definition: A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.
has_exact_synonym: inversion derived deficiency plus duplication
has_obo_namespace: sequence
id: SO:0000465

Axiom
annotated source: inversion_derived_deficiency_plus_duplication
annotated property: definition
annotated target: A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.
database_cross_reference: FB:km

V_gene_segment
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_segment
definition: Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.
has_exact_synonym: INSDC_feature:V_segment
has_exact_synonym: V gene
has_exact_synonym: V gene segment
has_exact_synonym: V-GENE
has_exact_synonym: variable_gene
has_obo_namespace: sequence
id: SO:0000466

Axiom
annotated source: V_gene_segment
annotated property: definition
annotated target: Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

post_translationally_regulated_by_protein_stability
type: Class
subclass of: post_translationally_regulated
definition: An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.
has_exact_synonym: post translationally regulated by protein stability
has_exact_synonym: post-translationally regulated by protein stability
has_obo_namespace: sequence
id: SO:0000467

Axiom
annotated source: post_translationally_regulated_by_protein_stability
annotated property: definition
annotated target: An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.
database_cross_reference: SO:ke

golden_path_fragment
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: golden_path
definition: One of the pieces of sequence that make up a golden path.
has_exact_synonym: golden path fragment
has_obo_namespace: sequence
id: SO:0000468
in_subset: SOFA

Axiom
annotated source: golden_path_fragment
annotated property: definition
annotated target: One of the pieces of sequence that make up a golden path.
database_cross_reference: SO:rd

post_translationally_regulated_by_protein_modification
type: Class
subclass of: post_translationally_regulated
definition: An attribute describing a gene sequence where the resulting protein is modified to regulate it.
has_exact_synonym: post translationally regulated by protein modification
has_exact_synonym: post-translationally regulated by protein modification
has_obo_namespace: sequence
id: SO:0000469

Axiom
annotated source: post_translationally_regulated_by_protein_modification
annotated property: definition
annotated target: An attribute describing a gene sequence where the resulting protein is modified to regulate it.
database_cross_reference: SO:ke

J_gene_segment
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_segment
definition: Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.
has_exact_synonym: INSDC_feature:J_segment
has_exact_synonym: J gene
has_exact_synonym: J-GENE
has_obo_namespace: sequence
id: SO:0000470

Axiom
annotated source: J_gene_segment
annotated property: definition
annotated target: Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

autoregulated
type: Class
subclass of: transcriptionally_regulated
definition: The gene product is involved in its own transcriptional regulation.
has_obo_namespace: sequence
id: SO:0000471

Axiom
annotated source: autoregulated
annotated property: definition
annotated target: The gene product is involved in its own transcriptional regulation.
database_cross_reference: SO:ke

tiling_path
type: Class
subclass of: sequence_assembly
definition: A set of regions which overlap with minimal polymorphism to form a linear sequence.
has_exact_synonym: tiling path
has_obo_namespace: sequence
id: SO:0000472
in_subset: SOFA

Axiom
annotated source: tiling_path
annotated property: definition
annotated target: A set of regions which overlap with minimal polymorphism to form a linear sequence.
database_cross_reference: SO:cjm

negatively_autoregulated
type: Class
subclass of: transcriptionally_repressed
subclass of: autoregulated
definition: The gene product is involved in its own transcriptional regulation where it decreases transcription.
has_exact_synonym: negatively autoregulated
has_obo_namespace: sequence
id: SO:0000473

Axiom
annotated source: negatively_autoregulated
annotated property: definition
annotated target: The gene product is involved in its own transcriptional regulation where it decreases transcription.
database_cross_reference: SO:ke

tiling_path_fragment
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: tiling_path
definition: A piece of sequence that makes up a tiling_path (SO:0000472).
has_exact_synonym: tiling path fragment
has_obo_namespace: sequence
id: SO:0000474
in_subset: SOFA

Axiom
annotated source: tiling_path_fragment
annotated property: definition
annotated target: A piece of sequence that makes up a tiling_path (SO:0000472).
database_cross_reference: SO:ke

positively_autoregulated
type: Class
subclass of: transcriptionally_induced
subclass of: autoregulated
definition: The gene product is involved in its own transcriptional regulation, where it increases transcription.
has_exact_synonym: positively autoregulated
has_obo_namespace: sequence
id: SO:0000475

Axiom
annotated source: positively_autoregulated
annotated property: definition
annotated target: The gene product is involved in its own transcriptional regulation, where it increases transcription.
database_cross_reference: SO:ke

contig_read
type: Class
subclass of: read
definition: A DNA sequencer read which is part of a contig.
has_exact_synonym: contig read
has_obo_namespace: sequence
id: SO:0000476

Axiom
annotated source: contig_read
annotated property: definition
annotated target: A DNA sequencer read which is part of a contig.
database_cross_reference: SO:ke

polycistronic_gene
type: Class
definition: A gene that is polycistronic.
has_obo_namespace: sequence
id: SO:0000477
deprecated: true

Axiom
annotated source: polycistronic_gene
annotated property: definition
annotated target: A gene that is polycistronic.
database_cross_reference: SO:ke

C_gene_segment
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
has_exact_synonym: C gene
has_exact_synonym: C_GENE
has_exact_synonym: INSDC_feature:C_region
has_exact_synonym: constant gene
has_obo_namespace: sequence
id: SO:0000478

Axiom
annotated source: C_gene_segment
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

trans_spliced_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: trans_spliced
subclass of: transcript
subclass of: Restriction
  on property: has_quality
  some values from: trans_spliced
definition: A transcript that is trans-spliced.
has_broad_synonym: INSDC_feature:tRNA
has_exact_synonym: INSDC_qualifier:trans_splicing
has_exact_synonym: trans spliced transcript
has_exact_synonym: trans-spliced transcript
has_obo_namespace: sequence
id: SO:0000479

Axiom
annotated source: trans_spliced_transcript
annotated property: definition
annotated target: A transcript that is trans-spliced.
database_cross_reference: SO:xp

tiling_path_clone
type: Class
subclass of: clone
subclass of: tiling_path_fragment
definition: A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.
has_exact_synonym: tiling path clone
has_obo_namespace: sequence
id: SO:0000480

Axiom
annotated source: tiling_path_clone
annotated property: definition
annotated target: A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.
database_cross_reference: SO:ke

terminal_inverted_repeat
type: Class
subclass of: inverted_repeat
subclass of: Restriction
  on property: part_of
  some values from: terminal_inverted_repeat_element
definition: An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.
has_exact_synonym: TIR
has_exact_synonym: terminal inverted repeat
has_obo_namespace: sequence
id: SO:0000481

Axiom
annotated source: terminal_inverted_repeat
annotated property: definition
annotated target: An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.
database_cross_reference: SO:ke

vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration.
has_exact_synonym: vertebrate immunoglobulin T cell receptor gene cluster
has_exact_synonym: vertebrate_immunoglobulin/T-cell receptor gene cluster
has_obo_namespace: sequence
id: SO:0000482

nc_primary_transcript
type: Class
subclass of: primary_transcript
definition: A primary transcript that is never translated into a protein.
has_exact_synonym: nc primary transcript
has_exact_synonym: noncoding primary transcript
has_obo_namespace: sequence
id: SO:0000483
in_subset: SOFA

Axiom
annotated source: nc_primary_transcript
annotated property: definition
annotated target: A primary transcript that is never translated into a protein.
database_cross_reference: SO:ke

three_prime_coding_exon_noncoding_region
type: Class
subclass of: noncoding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: three_prime_coding_exon
definition: The sequence of the 3' exon that is not coding.
has_exact_synonym: three prime coding exon noncoding region
has_exact_synonym: three_prime_exon_noncoding_region
has_obo_namespace: sequence
id: SO:0000484
in_subset: SOFA

Axiom
annotated source: three_prime_coding_exon_noncoding_region
annotated property: definition
annotated target: The sequence of the 3' exon that is not coding.
database_cross_reference: SO:ke

DJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.
has_exact_synonym: (DJ)-J-CLUSTER
has_exact_synonym: DJ J cluster
has_obo_namespace: sequence
id: SO:0000485

Axiom
annotated source: DJ_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

five_prime_coding_exon_noncoding_region
type: Class
subclass of: noncoding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: five_prime_coding_exon
definition: The sequence of the 5' exon preceding the start codon.
has_exact_synonym: five prime coding exon noncoding region
has_exact_synonym: five_prime_exon_noncoding_region
has_obo_namespace: sequence
id: SO:0000486
in_subset: SOFA

Axiom
annotated source: five_prime_coding_exon_noncoding_region
annotated property: definition
annotated target: The sequence of the 5' exon preceding the start codon.
database_cross_reference: SO:ke

VDJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.
has_exact_synonym: (VDJ)-J-C-CLUSTER
has_exact_synonym: VDJ J C cluster
has_obo_namespace: sequence
id: SO:0000487

Axiom
annotated source: VDJ_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

VDJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.
has_exact_synonym: (VDJ)-J-CLUSTER
has_exact_synonym: VDJ J cluster
has_obo_namespace: sequence
id: SO:0000488

Axiom
annotated source: VDJ_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

VJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.
has_exact_synonym: VJ C cluster
has_obo_namespace: sequence
has_related_synonym: (VJ)-C-CLUSTER
id: SO:0000489

Axiom
annotated source: VJ_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

VJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.
has_exact_synonym: (VJ)-J-C-CLUSTER
has_exact_synonym: VJ J C cluster
has_obo_namespace: sequence
id: SO:0000490

Axiom
annotated source: VJ_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

VJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.
has_exact_synonym: (VJ)-J-CLUSTER
has_exact_synonym: VJ J cluster
has_obo_namespace: sequence
id: SO:0000491

Axiom
annotated source: VJ_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

D_gene_recombination_feature
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
definition: Recombination signal including D-heptamer, D-spacer and D-nonamer in 5' of D-region of a D-gene or D-sequence.
has_exact_synonym: D gene recombination feature
has_obo_namespace: sequence
id: SO:0000492

three_prime_D_heptamer
type: Class
subclass of: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: three_prime_D_recombination_signal_sequence
definition: 7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: 3'D-HEPTAMER
has_exact_synonym: three prime D heptamer
has_obo_namespace: sequence
id: SO:0000493

Axiom
annotated source: three_prime_D_heptamer
annotated property: definition
annotated target: 7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

three_prime_D_nonamer
type: Class
subclass of: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: three_prime_D_recombination_signal_sequence
definition: A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: 3'D-NOMAMER
has_exact_synonym: three prime D nonamer
has_obo_namespace: sequence
id: SO:0000494

Axiom
annotated source: three_prime_D_nonamer
annotated property: definition
annotated target: A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

three_prime_D_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_spacer
subclass of: Restriction
  on property: part_of
  some values from: three_prime_D_recombination_signal_sequence
definition: A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.
has_exact_synonym: 3'D-SPACER
has_exact_synonym: three prime D spacer
has_obo_namespace: sequence
id: SO:0000495

Axiom
annotated source: three_prime_D_spacer
annotated property: definition
annotated target: A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

five_prime_D_heptamer
type: Class
subclass of: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: five_prime_D_recombination_signal_sequence
definition: 7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: 5'D-HEPTAMER
has_exact_synonym: five prime D heptamer
has_obo_namespace: sequence
id: SO:0000496

Axiom
annotated source: five_prime_D_heptamer
annotated property: definition
annotated target: 7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

five_prime_D_nonamer
type: Class
subclass of: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: five_prime_D_recombination_signal_sequence
definition: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: 5'D-NONAMER
has_exact_synonym: five prime D nonamer
has_obo_namespace: sequence
id: SO:0000497

Axiom
annotated source: five_prime_D_nonamer
annotated property: definition
annotated target: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

five_prime_D_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_spacer
subclass of: Restriction
  on property: part_of
  some values from: five_prime_D_recombination_signal_sequence
definition: 12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: 5'-SPACER
has_exact_synonym: five prime D spacer
has_exact_synonym: five prime D-spacer
has_obo_namespace: sequence
id: SO:0000498

Axiom
annotated source: five_prime_D_spacer
annotated property: definition
annotated target: 12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

virtual_sequence
type: Class
subclass of: sequence_assembly
definition: A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
has_exact_synonym: virtual sequence
has_obo_namespace: sequence
id: SO:0000499
in_subset: SOFA

Axiom
annotated source: virtual_sequence
annotated property: definition
annotated target: A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
database_cross_reference: SO:ke

Hoogsteen_base_pair
type: Class
subclass of: base_pair
definition: A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds.
database_cross_reference: http://en.wikipedia.org/wiki/Hoogsteen_base_pair
has_exact_synonym: Hoogsteen base pair
has_obo_namespace: sequence
id: SO:0000500

Axiom
annotated source: Hoogsteen_base_pair
annotated property: definition
annotated target: A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds.
database_cross_reference: PMID:12177293

wiki
type: Axiom
annotated source: Hoogsteen_base_pair
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Hoogsteen_base_pair

reverse_Hoogsteen_base_pair
type: Class
subclass of: base_pair
definition: A type of non-canonical base-pairing.
has_exact_synonym: reverse Hoogsteen base pair
has_obo_namespace: sequence
id: SO:0000501

Axiom
annotated source: reverse_Hoogsteen_base_pair
annotated property: definition
annotated target: A type of non-canonical base-pairing.
database_cross_reference: SO:ke

transcribed_region
type: Class
definition: A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
has_obo_namespace: sequence
id: SO:0000502
in_subset: SOFA
comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
deprecated: true

Axiom
annotated source: transcribed_region
annotated property: definition
annotated target: A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
database_cross_reference: SO:ke

alternately_spliced_gene_encodeing_one_transcript
type: Class
has_obo_namespace: sequence
id: SO:0000503
deprecated: true

D_DJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.
has_exact_synonym: D DJ C cluster
has_exact_synonym: D-(DJ)-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000504

Axiom
annotated source: D_DJ_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

D_DJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.
has_exact_synonym: D DJ cluster
has_exact_synonym: D-(DJ)-CLUSTER
has_obo_namespace: sequence
id: SO:0000505

Axiom
annotated source: D_DJ_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

D_DJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene.
has_exact_synonym: D DJ J C cluster
has_exact_synonym: D-(DJ)-J-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000506

Axiom
annotated source: D_DJ_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

pseudogenic_exon
type: Class
subclass of: pseudogenic_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: exon
subclass of: Restriction
  on property: part_of
  some values from: pseudogenic_transcript
definition: A non functional descendant of an exon, part of a pseudogene.
has_exact_synonym: pseudogenic exon
has_obo_namespace: sequence
id: SO:0000507
comment: This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.

Axiom
annotated source: pseudogenic_exon
annotated property: definition
annotated target: A non functional descendant of an exon, part of a pseudogene.
database_cross_reference: SO:ke

D_DJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.
has_exact_synonym: D DJ J cluster
has_exact_synonym: D-(DJ)-J-CLUSTER
has_obo_namespace: sequence
id: SO:0000508

Axiom
annotated source: D_DJ_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

D_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.
has_exact_synonym: D J C cluster
has_exact_synonym: D-J-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000509

Axiom
annotated source: D_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

VD_gene_segment
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
has_exact_synonym: VD gene
has_exact_synonym: V_D_GENE
has_obo_namespace: sequence
id: SO:0000510

Axiom
annotated source: VD_gene_segment
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.
has_exact_synonym: J C cluster
has_exact_synonym: J-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000511

Axiom
annotated source: J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

inversion_derived_deficiency_plus_aneuploid
type: Class
subclass of: SO_1000029
definition: A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.
has_exact_synonym: inversion derived deficiency plus aneuploid
has_obo_namespace: sequence
id: SO:0000512

Axiom
annotated source: inversion_derived_deficiency_plus_aneuploid
annotated property: definition
annotated target: A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.
database_cross_reference: FB:km

J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.
has_exact_synonym: J cluster
has_exact_synonym: J-CLUSTER
has_obo_namespace: sequence
id: SO:0000513

Axiom
annotated source: J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

J_nonamer
type: Class
subclass of: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: J_gene_recombination_feature
definition: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: J nonamer
has_exact_synonym: J-NONAMER
has_obo_namespace: sequence
id: SO:0000514

Axiom
annotated source: J_nonamer
annotated property: definition
annotated target: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

J_heptamer
type: Class
subclass of: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: J_gene_recombination_feature
definition: 7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: J heptamer
has_exact_synonym: J-HEPTAMER
has_obo_namespace: sequence
id: SO:0000515

Axiom
annotated source: J_heptamer
annotated property: definition
annotated target: 7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

pseudogenic_transcript
type: Class
subclass of: pseudogenic_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: transcript
subclass of: Restriction
  on property: part_of
  some values from: pseudogene
definition: A non functional descendant of a transcript, part of a pseudogene.
has_broad_synonym: INSDC_feature:misc_RNA
has_exact_synonym: INSDC_qualifier:pseudo
has_exact_synonym: pseudogenic transcript
has_obo_namespace: sequence
id: SO:0000516
comment: This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.

Axiom
annotated source: pseudogenic_transcript
annotated property: definition
annotated target: A non functional descendant of a transcript, part of a pseudogene.
database_cross_reference: SO:ke

J_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_spacer
subclass of: Restriction
  on property: part_of
  some values from: J_gene_recombination_feature
definition: 12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: J spacer
has_exact_synonym: J-SPACER
has_obo_namespace: sequence
id: SO:0000517

Axiom
annotated source: J_spacer
annotated property: definition
annotated target: 12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_DJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.
has_exact_synonym: V DJ cluster
has_exact_synonym: V-(DJ)-CLUSTER
has_obo_namespace: sequence
id: SO:0000518

Axiom
annotated source: V_DJ_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_DJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.
has_exact_synonym: V DJ J cluster
has_obo_namespace: sequence
has_related_synonym: V-(DJ)-J-CLUSTER
id: SO:0000519

Axiom
annotated source: V_DJ_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_VDJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.
has_exact_synonym: V VDJ C cluster
has_exact_synonym: V-(VDJ)-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000520

Axiom
annotated source: V_VDJ_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_VDJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.
has_exact_synonym: V VDJ cluster
has_exact_synonym: V-(VDJ)-CLUSTER
has_obo_namespace: sequence
id: SO:0000521

Axiom
annotated source: V_VDJ_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_VDJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.
has_exact_synonym: V VDJ J cluster
has_obo_namespace: sequence
has_related_synonym: V-(VDJ)-J-CLUSTER
id: SO:0000522

Axiom
annotated source: V_VDJ_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_VJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.
has_exact_synonym: V VJ C cluster
has_exact_synonym: V-(VJ)-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000523

Axiom
annotated source: V_VJ_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_VJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.
has_exact_synonym: V VJ cluster
has_exact_synonym: V-(VJ)-CLUSTER
has_obo_namespace: sequence
id: SO:0000524

Axiom
annotated source: V_VJ_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_VJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.
has_exact_synonym: V VJ J cluster
has_exact_synonym: V-(VJ)-J-CLUSTER
has_obo_namespace: sequence
id: SO:0000525

Axiom
annotated source: V_VJ_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.
has_exact_synonym: V cluster
has_exact_synonym: V-CLUSTER
has_obo_namespace: sequence
id: SO:0000526

Axiom
annotated source: V_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_D_DJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.
has_exact_synonym: V D DJ C cluster
has_exact_synonym: V-D-(DJ)-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000527

Axiom
annotated source: V_D_DJ_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_D_DJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.
has_exact_synonym: V D DJ cluster
has_exact_synonym: V-D-(DJ)-CLUSTER
has_obo_namespace: sequence
id: SO:0000528

Axiom
annotated source: V_D_DJ_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_D_DJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.
has_exact_synonym: V D DJ J C cluster
has_exact_synonym: V-D-(DJ)-J-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000529

Axiom
annotated source: V_D_DJ_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_D_DJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.
has_exact_synonym: V D DJ J cluster
has_exact_synonym: V-D-(DJ)-J-CLUSTER
has_obo_namespace: sequence
id: SO:0000530

Axiom
annotated source: V_D_DJ_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_D_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene.
has_exact_synonym: V D J C cluster
has_exact_synonym: V-D-J-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000531

Axiom
annotated source: V_D_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_D_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.
has_exact_synonym: V D J cluster
has_exact_synonym: V-D-J-CLUSTER
has_obo_namespace: sequence
id: SO:0000532

Axiom
annotated source: V_D_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_heptamer
type: Class
subclass of: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: V_gene_recombination_feature
definition: 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: V heptamer
has_exact_synonym: V-HEPTAMER
has_obo_namespace: sequence
id: SO:0000533

Axiom
annotated source: V_heptamer
annotated property: definition
annotated target: 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.
has_exact_synonym: V J cluster
has_exact_synonym: V-J-CLUSTER
has_obo_namespace: sequence
id: SO:0000534

Axiom
annotated source: V_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.
has_exact_synonym: V J C cluster
has_exact_synonym: V-J-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000535

Axiom
annotated source: V_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_nonamer
type: Class
subclass of: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: V_gene_recombination_feature
definition: 9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: V nonamer
has_exact_synonym: V-NONAMER
has_obo_namespace: sequence
id: SO:0000536

Axiom
annotated source: V_nonamer
annotated property: definition
annotated target: 9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_spacer
subclass of: Restriction
  on property: part_of
  some values from: V_gene_recombination_feature
definition: 12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: V spacer
has_exact_synonym: V-SPACER
has_obo_namespace: sequence
id: SO:0000537

Axiom
annotated source: V_spacer
annotated property: definition
annotated target: 12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_gene_recombination_feature
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
definition: Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.
has_exact_synonym: V gene recombination feature
has_exact_synonym: V-RS
has_obo_namespace: sequence
id: SO:0000538

Axiom
annotated source: V_gene_recombination_feature
annotated property: definition
annotated target: Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

DJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.
has_exact_synonym: (DJ)-C-CLUSTER
has_exact_synonym: DJ C cluster
has_obo_namespace: sequence
id: SO:0000539

Axiom
annotated source: DJ_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

DJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.
has_exact_synonym: (DJ)-J-C-CLUSTER
has_exact_synonym: DJ J C cluster
has_obo_namespace: sequence
id: SO:0000540

Axiom
annotated source: DJ_J_C_cluster
annotated property: definition
annotated target: Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

VDJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.
has_exact_synonym: (VDJ)-C-CLUSTER
has_exact_synonym: VDJ C cluster
has_obo_namespace: sequence
id: SO:0000541

Axiom
annotated source: VDJ_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_DJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.
has_exact_synonym: V DJ C cluster
has_exact_synonym: V-(DJ)-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000542

Axiom
annotated source: V_DJ_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

alternately_spliced_gene_encoding_greater_than_one_transcript
type: Class
has_obo_namespace: sequence
id: SO:0000543
deprecated: true

helitron
type: Class
subclass of: DNA_transposon
definition: A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons.
database_cross_reference: http://en.wikipedia.org/wiki/Helitron
has_obo_namespace: sequence
has_related_synonym: ISCR
id: SO:0000544

Axiom
annotated source: helitron
annotated property: definition
annotated target: A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons.
database_cross_reference: http://www.pnas.org/cgi/content/full/100/11/6569

wiki
type: Axiom
annotated source: helitron
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Helitron

recoding_pseudoknot
type: Class
subclass of: pseudoknot
subclass of: Restriction
  on property: part_of
  some values from: SO_1001268
definition: The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding.
has_exact_synonym: recoding pseudoknot
has_obo_namespace: sequence
id: SO:0000545

Axiom
annotated source: recoding_pseudoknot
annotated property: definition
annotated target: The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding.
database_cross_reference: http://www.pubmedcentral.nih.gov/articlerender.fcgi

designed_sequence
type: Class
subclass of: synthetic_sequence
definition: An oligonucleotide sequence that was designed by an experimenter that may or may not correspond with any natural sequence.
has_exact_synonym: designed sequence
has_obo_namespace: sequence
id: SO:0000546

inversion_derived_bipartite_duplication
type: Class
subclass of: SO_1000038
definition: A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.
has_exact_synonym: inversion derived bipartite duplication
has_obo_namespace: sequence
id: SO:0000547

Axiom
annotated source: inversion_derived_bipartite_duplication
annotated property: definition
annotated target: A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.
database_cross_reference: FB:km

gene_with_edited_transcript
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: transcribed_to
    some values from: edited_transcript
subclass of: protein_coding_gene
subclass of: Restriction
  on property: transcribed_to
  some values from: edited_transcript
definition: A gene that encodes a transcript that is edited.
has_exact_synonym: gene with edited transcript
has_obo_namespace: sequence
id: SO:0000548

Axiom
annotated source: gene_with_edited_transcript
annotated property: definition
annotated target: A gene that encodes a transcript that is edited.
database_cross_reference: SO:xp

inversion_derived_duplication_plus_aneuploid
type: Class
subclass of: SO_1000038
definition: A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion.
has_exact_synonym: inversion derived duplication plus aneuploid
has_obo_namespace: sequence
id: SO:0000549

Axiom
annotated source: inversion_derived_duplication_plus_aneuploid
annotated property: definition
annotated target: A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion.
database_cross_reference: FB:km

aneuploid_chromosome
type: Class
subclass of: SO_1000183
definition: A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking.
has_exact_synonym: aneuploid chromosome
has_obo_namespace: sequence
id: SO:0000550
comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.

Axiom
annotated source: aneuploid_chromosome
annotated property: definition
annotated target: A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking.
database_cross_reference: SO:ke

polyA_signal_sequence
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
has_broad_synonym: INSDC_feature:regulatory
has_exact_synonym: INSDC_qualifier:polyA_signal_sequence
has_exact_synonym: poly(A) signal
has_exact_synonym: polyA signal sequence
has_exact_synonym: polyadenylation termination signal
has_obo_namespace: sequence
id: SO:0000551
in_subset: SOFA
comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: polyA_signal_sequence
annotated property: definition
annotated target: The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
database_cross_reference: http://www.insdc.org/files/feature_table.html

Shine_Dalgarno_sequence
type: Class
subclass of: ribosome_entry_site
definition: A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
database_cross_reference: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence
has_exact_synonym: Shine Dalgarno sequence
has_exact_synonym: Shine-Dalgarno sequence
has_exact_synonym: five prime ribosome binding site
has_obo_namespace: sequence
has_related_synonym: RBS
id: SO:0000552
comment: Not found in Eukaryotic sequence.

Axiom
annotated source: Shine_Dalgarno_sequence
annotated property: definition
annotated target: A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
database_cross_reference: SO:jh

wiki
type: Axiom
annotated source: Shine_Dalgarno_sequence
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence

polyA_site
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: three_prime_UTR
subclass of: Restriction
  on property: part_of
  some values from: mature_transcript
definition: The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
has_alternative_id: SO:0001430
has_exact_synonym: INSDC_feature:polyA_site
has_exact_synonym: polyA cleavage site
has_exact_synonym: polyA junction
has_exact_synonym: polyA site
has_exact_synonym: polyA_junction
has_obo_namespace: sequence
has_related_synonym: polyadenylation site
id: SO:0000553
in_subset: SOFA

Axiom
annotated source: polyA_site
annotated property: definition
annotated target: The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
database_cross_reference: http://www.insdc.org/files/feature_table.html

assortment_derived_deficiency_plus_duplication
type: Class
has_obo_namespace: sequence
id: SO:0000554
deprecated: true

five_prime_clip
type: Class
subclass of: clip
definition: 5' most region of a precursor transcript that is clipped off during processing.
has_exact_synonym: five prime clip
has_obo_namespace: sequence
has_related_synonym: 5' clip
id: SO:0000555

Axiom
annotated source: five_prime_clip
annotated property: definition
annotated target: 5' most region of a precursor transcript that is clipped off during processing.
database_cross_reference: http://www.insdc.org/files/feature_table.html

five_prime_D_recombination_signal_sequence
type: Class
subclass of: D_gene_recombination_feature
definition: Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene.
has_exact_synonym: 5'RS
has_exact_synonym: five prime D recombination signal sequence
has_exact_synonym: five prime D-recombination signal sequence
has_obo_namespace: sequence
id: SO:0000556

Axiom
annotated source: five_prime_D_recombination_signal_sequence
annotated property: definition
annotated target: Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

three_prime_clip
type: Class
subclass of: clip
definition: 3'-most region of a precursor transcript that is clipped off during processing.
has_exact_synonym: 3'-clip
has_exact_synonym: three prime clip
has_obo_namespace: sequence
id: SO:0000557

Axiom
annotated source: three_prime_clip
annotated property: definition
annotated target: 3'-most region of a precursor transcript that is clipped off during processing.
database_cross_reference: http://www.insdc.org/files/feature_table.html

C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.
has_exact_synonym: C cluster
has_exact_synonym: C-CLUSTER
has_obo_namespace: sequence
id: SO:0000558

Axiom
annotated source: C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

D_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.
has_exact_synonym: D cluster
has_exact_synonym: D-CLUSTER
has_obo_namespace: sequence
id: SO:0000559

Axiom
annotated source: D_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

D_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.
has_exact_synonym: D J cluster
has_exact_synonym: D-J-CLUSTER
has_obo_namespace: sequence
id: SO:0000560

Axiom
annotated source: D_J_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
definition: Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.
has_exact_synonym: heptamer of recombination feature of vertebrate immune system gene
has_obo_namespace: sequence
has_related_synonym: HEPTAMER
id: SO:0000561

Axiom
annotated source: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
annotated property: definition
annotated target: Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
definition: Nine nucleotide recombination site, part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.
has_exact_synonym: nonamer of recombination feature of vertebrate immune system gene
has_obo_namespace: sequence
id: SO:0000562

vertebrate_immune_system_gene_recombination_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
definition: A 12 or 23 nucleotide spacer between two regions of an immunoglobulin/T-cell receptor gene that may be rearranged by recombinase.
has_exact_synonym: vertebrate immune system gene recombination spacer
has_obo_namespace: sequence
id: SO:0000563

V_DJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene.
has_exact_synonym: V DJ J C cluster
has_exact_synonym: V-(DJ)-J-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000564

Axiom
annotated source: V_DJ_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_VDJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene.
has_exact_synonym: V VDJ J C cluster
has_exact_synonym: V-(VDJ)-J-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000565

Axiom
annotated source: V_VDJ_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

V_VJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: J_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: C_gene_segment
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene.
has_exact_synonym: V VJ J C cluster
has_exact_synonym: V-(VJ)-J-C-CLUSTER
has_obo_namespace: sequence
id: SO:0000566

Axiom
annotated source: V_VJ_J_C_cluster
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

inversion_derived_aneuploid_chromosome
type: Class
subclass of: aneuploid_chromosome
definition: A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.
has_exact_synonym: inversion derived aneuploid chromosome
has_obo_namespace: sequence
id: SO:0000567

Axiom
annotated source: inversion_derived_aneuploid_chromosome
annotated property: definition
annotated target: A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.
database_cross_reference: FB:km

bidirectional_promoter
type: Class
subclass of: promoter
definition: A promoter that can allow for transcription in both directions.
has_exact_synonym: bidirectional promoter
has_obo_namespace: sequence
id: SO:0000568
comment: Definition updated in Aug 2020 by Dave Sant.

Axiom
annotated source: bidirectional_promoter
annotated property: definition
annotated target: A promoter that can allow for transcription in both directions.
database_cross_reference: PMID:21601935
database_cross_reference: SO:ke

retrotransposed
type: Class
subclass of: feature_attribute
definition: An attribute of a feature that occurred as the product of a reverse transcriptase mediated event.
has_alternative_id: SO:0100042
database_cross_reference: http://en.wikipedia.org/wiki/Retrotransposed
has_obo_namespace: sequence
id: SO:0000569
comment: GO:0003964 RNA-directed DNA polymerase activity.

Axiom
annotated source: retrotransposed
annotated property: definition
annotated target: An attribute of a feature that occurred as the product of a reverse transcriptase mediated event.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: retrotransposed
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Retrotransposed

three_prime_D_recombination_signal_sequence
type: Class
subclass of: D_gene_recombination_feature
definition: Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene.
has_exact_synonym: 3'D-RS
has_exact_synonym: three prime D recombination signal sequence
has_exact_synonym: three_prime_D-recombination_signal_sequence
has_obo_namespace: sequence
id: SO:0000570

Axiom
annotated source: three_prime_D_recombination_signal_sequence
annotated property: definition
annotated target: Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

miRNA_encoding
type: Class
subclass of: non_protein_coding
definition: A region that can be transcribed into a microRNA (miRNA).
has_exact_synonym: miRNA encoding
has_obo_namespace: sequence
id: SO:0000571

DJ_gene_segment
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment.
has_exact_synonym: D-J-GENE
has_exact_synonym: DJ gene
has_obo_namespace: sequence
id: SO:0000572

Axiom
annotated source: DJ_gene_segment
annotated property: definition
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment.
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

rRNA_encoding
type: Class
subclass of: non_protein_coding
definition: A region that can be transcribed into a ribosomal RNA (rRNA).
has_exact_synonym: rRNA encoding
has_obo_namespace: sequence
id: SO:0000573

VDJ_gene_segment
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
definition: Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
has_exact_synonym: V-D-J-GENE
has_exact_synonym: VDJ gene
has_obo_namespace: sequence
id: SO:0000574

Axiom
annotated source: VDJ_gene_segment
annotated property: definition
annotated target: Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

scRNA_encoding
type: Class
subclass of: non_protein_coding
definition: A region that can be transcribed into a small cytoplasmic RNA (scRNA).
has_exact_synonym: scRNA encoding
has_obo_namespace: sequence
id: SO:0000575

VJ_gene_segment
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
definition: Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
has_exact_synonym: V-J-GENE
has_exact_synonym: VJ gene
has_obo_namespace: sequence
id: SO:0000576

Axiom
annotated source: VJ_gene_segment
annotated property: definition
annotated target: Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
database_cross_reference: http://www.imgt.org/cgi-bin/IMGTlect.jv#

centromere
type: Class
subclass of: chromosomal_structural_element
definition: A region of chromosome where the spindle fibers attach during mitosis and meiosis.
database_cross_reference: http://en.wikipedia.org/wiki/Centromere
has_exact_synonym: INSDC_feature:centromere
has_obo_namespace: sequence
id: SO:0000577
in_subset: SOFA

Axiom
annotated source: centromere
annotated property: definition
annotated target: A region of chromosome where the spindle fibers attach during mitosis and meiosis.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: centromere
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Centromere

snoRNA_encoding
type: Class
subclass of: non_protein_coding
definition: A region that can be transcribed into a small nucleolar RNA (snoRNA).
has_exact_synonym: snoRNA encoding
has_obo_namespace: sequence
id: SO:0000578

edited_transcript_feature
type: Class
subclass of: transcript_region
definition: A locatable feature on a transcript that is edited.
has_exact_synonym: edited transcript feature
has_obo_namespace: sequence
id: SO:0000579

Axiom
annotated source: edited_transcript_feature
annotated property: definition
annotated target: A locatable feature on a transcript that is edited.
database_cross_reference: SO:ma

methylation_guide_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
definition: A primary transcript encoding a methylation guide small nucleolar RNA.
has_exact_synonym: methylation guide snoRNA primary transcript
has_obo_namespace: sequence
id: SO:0000580

Axiom
annotated source: methylation_guide_snoRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a methylation guide small nucleolar RNA.
database_cross_reference: SO:ke

cap
type: Class
subclass of: biological_region
definition: A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
database_cross_reference: http://en.wikipedia.org/wiki/5%27_cap
has_obo_namespace: sequence
id: SO:0000581
in_subset: SOFA

Axiom
annotated source: cap
annotated property: definition
annotated target: A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
database_cross_reference: http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html

wiki
type: Axiom
annotated source: cap
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/5%27_cap

rRNA_cleavage_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
definition: A primary transcript encoding an rRNA cleavage snoRNA.
has_exact_synonym: rRNA cleavage snoRNA primary transcript
has_obo_namespace: sequence
id: SO:0000582

Axiom
annotated source: rRNA_cleavage_snoRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding an rRNA cleavage snoRNA.
database_cross_reference: SO:ke

pre_edited_region
type: Class
subclass of: edited_transcript_feature
definition: The region of a transcript that will be edited.
has_exact_synonym: pre edited region
has_exact_synonym: pre-edited region
has_obo_namespace: sequence
id: SO:0000583

Axiom
annotated source: pre_edited_region
annotated property: definition
annotated target: The region of a transcript that will be edited.
database_cross_reference: http://dna.kdna.ucla.edu/rna/index.aspx

tmRNA
type: Class
subclass of: small_regulatory_ncRNA
definition: A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.
database_cross_reference: http://en.wikipedia.org/wiki/TmRNA
has_exact_synonym: INSDC_feature:tmRNA
has_obo_namespace: sequence
has_related_synonym: 10Sa RNA
has_related_synonym: ssrA
id: SO:0000584

Axiom
annotated source: tmRNA
annotated property: definition
annotated target: A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: tmRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/TmRNA

C_D_box_snoRNA_encoding
type: Class
subclass of: snoRNA_encoding
definition: snoRNA that is associated with guiding methylation of nucleotides. It contains two short conserved sequence motifs: C (RUGAUGA) near the 5-prime end and D (CUGA) near the 3-prime end.
has_exact_synonym: C/D box snoRNA encoding
has_obo_namespace: sequence
id: SO:0000585

tmRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
definition: A primary transcript encoding a tmRNA (SO:0000584).
has_exact_synonym: tmRNA primary transcript
has_obo_namespace: sequence
has_related_synonym: 10Sa RNA primary transcript
has_related_synonym: ssrA RNA primary transcript
id: SO:0000586

Axiom
annotated source: tmRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a tmRNA (SO:0000584).
database_cross_reference: SO:ke

group_I_intron
type: Class
subclass of: autocatalytically_spliced_intron
definition: Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.
database_cross_reference: http://en.wikipedia.org/wiki/Group_I_intron
has_exact_synonym: group I intron
has_obo_namespace: sequence
id: SO:0000587
in_subset: SOFA
comment: GO:0000372.

Axiom
annotated source: group_I_intron
annotated property: definition
annotated target: Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: group_I_intron
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Group_I_intron

autocatalytically_spliced_intron
type: Class
equivalent class: Class
  intersection of: intron
  intersection of: Restriction
    on property: has_quality
    some values from: ribozymic
subclass of: intron
subclass of: Restriction
  on property: has_quality
  some values from: ribozymic
definition: A self spliced intron.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:autocatalytically_spliced_intron
has_exact_synonym: autocatalytically spliced intron
has_obo_namespace: sequence
id: SO:0000588
in_subset: SOFA

Axiom
annotated source: autocatalytically_spliced_intron
annotated property: definition
annotated target: A self spliced intron.
database_cross_reference: SO:ke

SRP_RNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
definition: A primary transcript encoding a signal recognition particle RNA.
has_exact_synonym: SRP RNA primary transcript
has_obo_namespace: sequence
id: SO:0000589

Axiom
annotated source: SRP_RNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a signal recognition particle RNA.
database_cross_reference: SO:ke

SRP_RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: SRP_RNA_primary_transcript
definition: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
has_broad_synonym: INSDC_feature:ncRNA
has_exact_synonym: INSDC_qualifier:SRP_RNA
has_exact_synonym: SRP RNA
has_obo_namespace: sequence
has_related_synonym: 7S RNA
has_related_synonym: signal recognition particle RNA
id: SO:0000590
in_subset: SOFA

Axiom
annotated source: SRP_RNA
annotated property: definition
annotated target: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

pseudoknot
type: Class
subclass of: sequence_secondary_structure
definition: A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop.
database_cross_reference: http://en.wikipedia.org/wiki/Pseudoknot
has_obo_namespace: sequence
id: SO:0000591

Axiom
annotated source: pseudoknot
annotated property: definition
annotated target: A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: pseudoknot
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Pseudoknot

H_pseudoknot
type: Class
subclass of: pseudoknot
definition: A pseudoknot which contains two stems and at least two loops.
has_exact_synonym: H pseudoknot
has_exact_synonym: H-pseudoknot
has_exact_synonym: H-type pseudoknot
has_exact_synonym: classical pseudoknot
has_exact_synonym: hairpin-type pseudoknot
has_obo_namespace: sequence
id: SO:0000592

Axiom
annotated source: H_pseudoknot
annotated property: definition
annotated target: A pseudoknot which contains two stems and at least two loops.
database_cross_reference: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi

C_D_box_snoRNA
type: Class
subclass of: snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: C_D_box_snoRNA_primary_transcript
definition: Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.
has_exact_synonym: C D box snoRNA
has_exact_synonym: C/D box snoRNA
has_exact_synonym: SNORD
has_exact_synonym: box C/D snoRNA
has_obo_namespace: sequence
id: SO:0000593
in_subset: SOFA
comment: Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577.

Axiom
annotated source: C_D_box_snoRNA
annotated property: definition
annotated target: Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.
database_cross_reference: http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html

Axiom
annotated source: C_D_box_snoRNA
annotated property: has_exact_synonym
annotated target: SNORD
database_cross_reference: PMID:31828325

H_ACA_box_snoRNA
type: Class
subclass of: snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: H_ACA_box_snoRNA_primary_transcript
definition: Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.
has_exact_synonym: H ACA box snoRNA
has_exact_synonym: H/ACA box snoRNA
has_exact_synonym: SNORA
has_exact_synonym: box H/ACA snoRNA
has_obo_namespace: sequence
id: SO:0000594
comment: Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577.

Axiom
annotated source: H_ACA_box_snoRNA
annotated property: definition
annotated target: Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.
database_cross_reference: http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html

Axiom
annotated source: H_ACA_box_snoRNA
annotated property: has_exact_synonym
annotated target: SNORA
database_cross_reference: PMID:31828325

C_D_box_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
definition: A primary transcript encoding a small nucleolar RNA of the box C/D family.
has_exact_synonym: C/D box snoRNA primary transcript
has_obo_namespace: sequence
id: SO:0000595

Axiom
annotated source: C_D_box_snoRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a small nucleolar RNA of the box C/D family.
database_cross_reference: SO:ke

H_ACA_box_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
definition: A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
has_exact_synonym: H ACA box snoRNA primary transcript
has_obo_namespace: sequence
id: SO:0000596

Axiom
annotated source: H_ACA_box_snoRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
database_cross_reference: SO:ke

transcript_edited_by_U_insertion/deletion
type: Class
definition: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
has_obo_namespace: sequence
id: SO:0000597
deprecated: true

Axiom
annotated source: transcript_edited_by_U_insertion/deletion
annotated property: definition
annotated target: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
database_cross_reference: http://www.rna.ucla.edu/index.html

edited_by_C_insertion_and_dinucleotide_insertion
type: Class
has_obo_namespace: sequence
has_related_synonym: transcript_edited_by_C-insertion_and_dinucleotide_insertion
id: SO:0000598
deprecated: true

edited_by_C_to_U_substitution
type: Class
has_obo_namespace: sequence
id: SO:0000599
deprecated: true

edited_by_A_to_I_substitution
type: Class
has_obo_namespace: sequence
id: SO:0000600
deprecated: true

edited_by_G_addition
type: Class
has_obo_namespace: sequence
id: SO:0000601
deprecated: true

guide_RNA
type: Class
subclass of: ncRNA
definition: A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Guide_RNA
has_exact_synonym: INSDC_qualifier:guide_RNA
has_exact_synonym: gRNA
has_exact_synonym: guide RNA
has_obo_namespace: sequence
id: SO:0000602
in_subset: SOFA

Axiom
annotated source: guide_RNA
annotated property: definition
annotated target: A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
database_cross_reference: http://www.rna.ucla.edu/index.html

wiki
type: Axiom
annotated source: guide_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Guide_RNA

group_II_intron
type: Class
subclass of: autocatalytically_spliced_intron
definition: Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
database_cross_reference: http://en.wikipedia.org/wiki/Group_II_intron
has_exact_synonym: group II intron
has_obo_namespace: sequence
id: SO:0000603
in_subset: SOFA
comment: GO:0000373.

Axiom
annotated source: group_II_intron
annotated property: definition
annotated target: Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
database_cross_reference: http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml

wiki
type: Axiom
annotated source: group_II_intron
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Group_II_intron

editing_block
type: Class
subclass of: edited_transcript_feature
definition: Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
has_exact_synonym: editing block
has_obo_namespace: sequence
id: SO:0000604

Axiom
annotated source: editing_block
annotated property: definition
annotated target: Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
database_cross_reference: http://dna.kdna.ucla.edu/rna/index.aspx

intergenic_region
type: Class
subclass of: biological_region
definition: A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
database_cross_reference: http://en.wikipedia.org/wiki/Intergenic_region
has_exact_synonym: intergenic region
has_obo_namespace: sequence
id: SO:0000605
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: intergenic_region
annotated property: definition
annotated target: A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
database_cross_reference: SO:cjm

wiki
type: Axiom
annotated source: intergenic_region
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Intergenic_region

editing_domain
type: Class
subclass of: edited_transcript_feature
definition: Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
has_exact_synonym: editing domain
has_obo_namespace: sequence
id: SO:0000606

Axiom
annotated source: editing_domain
annotated property: definition
annotated target: Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
database_cross_reference: http://dna.kdna.ucla.edu/rna/index.aspx

unedited_region
type: Class
subclass of: edited_transcript_feature
definition: The region of an edited transcript that will not be edited.
has_exact_synonym: unedited region
has_obo_namespace: sequence
id: SO:0000607

Axiom
annotated source: unedited_region
annotated property: definition
annotated target: The region of an edited transcript that will not be edited.
database_cross_reference: http://dna.kdna.ucla.edu/rna/index.aspx

H_ACA_box_snoRNA_encoding
type: Class
subclass of: snoRNA_encoding
definition: snoRNA that is associated with guiding polyuridylation. It contains two short conserved sequence motifs: H box (ANANNA) and ACA (ACA).
has_exact_synonym: H ACA box snoRNA encoding
has_obo_namespace: sequence
id: SO:0000608

oligo_U_tail
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: adjacent_to
  some values from: guide_RNA
definition: The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
has_exact_synonym: oligo U tail
has_obo_namespace: sequence
id: SO:0000609

Axiom
annotated source: oligo_U_tail
annotated property: definition
annotated target: The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
database_cross_reference: http://www.rna.ucla.edu/

polyA_sequence
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: adjacent_to
  some values from: mRNA
definition: Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
has_exact_synonym: polyA sequence
has_obo_namespace: sequence
id: SO:0000610
in_subset: SOFA

Axiom
annotated source: polyA_sequence
annotated property: definition
annotated target: Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
database_cross_reference: SO:ke

branch_site
type: Class
subclass of: spliceosomal_intron_region
definition: A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
has_exact_synonym: branch point
has_exact_synonym: branch site
has_exact_synonym: branch_point
has_obo_namespace: sequence
id: SO:0000611
in_subset: SOFA

Axiom
annotated source: branch_site
annotated property: definition
annotated target: A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
database_cross_reference: SO:ke

polypyrimidine_tract
type: Class
subclass of: spliceosomal_intron_region
definition: The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
database_cross_reference: http://en.wikipedia.org/wiki/Polypyrimidine_tract
has_exact_synonym: polypyrimidine tract
has_obo_namespace: sequence
id: SO:0000612
in_subset: SOFA

Axiom
annotated source: polypyrimidine_tract
annotated property: definition
annotated target: The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
database_cross_reference: http://nar.oupjournals.org/cgi/content/full/25/4/888

wiki
type: Axiom
annotated source: polypyrimidine_tract
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Polypyrimidine_tract

bacterial_RNApol_promoter
type: Class
subclass of: SO_0002222
definition: A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
has_exact_synonym: bacterial RNApol promoter
has_obo_namespace: sequence
id: SO:0000613
comment: former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.

Axiom
annotated source: bacterial_RNApol_promoter
annotated property: definition
annotated target: A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
database_cross_reference: SO:ke

bacterial_terminator
type: Class
subclass of: terminator
definition: A terminator signal for bacterial transcription.
has_exact_synonym: bacterial terminator
has_obo_namespace: sequence
id: SO:0000614
comment: Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.

Axiom
annotated source: bacterial_terminator
annotated property: definition
annotated target: A terminator signal for bacterial transcription.
database_cross_reference: SO:ke

terminator_of_type_2_RNApol_III_promoter
type: Class
subclass of: eukaryotic_terminator
definition: A terminator signal for RNA polymerase III transcription.
has_exact_synonym: terminator of type 2 RNApol III promoter
has_obo_namespace: sequence
id: SO:0000615

Axiom
annotated source: terminator_of_type_2_RNApol_III_promoter
annotated property: definition
annotated target: A terminator signal for RNA polymerase III transcription.
database_cross_reference: SO:ke

transcription_end_site
type: Class
subclass of: primary_transcript_region
definition: The base where transcription ends.
has_exact_synonym: transcription end site
has_obo_namespace: sequence
id: SO:0000616
in_subset: SOFA

Axiom
annotated source: transcription_end_site
annotated property: definition
annotated target: The base where transcription ends.
database_cross_reference: SO:ke

RNApol_III_promoter_type_1
type: Class
subclass of: RNApol_III_promoter
definition: This type of promoter recruits RNA pol III. This promoter is intragenic and includes an A box, an intermediate element, and a C box. This is well conserved in the 5s rRNA promoters across species.
has_exact_synonym: RNApol III promoter type 1
has_obo_namespace: sequence
id: SO:0000617

Axiom
annotated source: RNApol_III_promoter_type_1
annotated property: definition
annotated target: This type of promoter recruits RNA pol III. This promoter is intragenic and includes an A box, an intermediate element, and a C box. This is well conserved in the 5s rRNA promoters across species.
database_cross_reference: PMID:12381659

RNApol_III_promoter_type_2
type: Class
subclass of: RNApol_III_promoter
definition: This type of promoter recruits RNA pol III to transcribe genes mainly for t-RNA. This promoter is intragenic and includes an A box and a B box.
has_exact_synonym: RNApol III promoter type 2
has_obo_namespace: sequence
has_related_synonym: tRNA promoter
id: SO:0000618

Axiom
annotated source: RNApol_III_promoter_type_2
annotated property: definition
annotated target: This type of promoter recruits RNA pol III to transcribe genes mainly for t-RNA. This promoter is intragenic and includes an A box and a B box.
database_cross_reference: PMID:12381659

A_box
type: Class
subclass of: core_eukaryotic_promoter_element
definition: A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.
database_cross_reference: http://en.wikipedia.org/wiki/A-box
has_exact_synonym: A-box
has_obo_namespace: sequence
id: SO:0000619
comment: Binds TFIIIC.

Axiom
annotated source: A_box
annotated property: definition
annotated target: A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: A_box
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/A-box

B_box
type: Class
subclass of: core_eukaryotic_promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_III_promoter_type_2
definition: A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.
has_exact_synonym: B-box
has_obo_namespace: sequence
id: SO:0000620
comment: Binds TFIIIC.

Axiom
annotated source: B_box
annotated property: definition
annotated target: A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.
database_cross_reference: SO:ke

RNApol_III_promoter_type_3
type: Class
subclass of: RNApol_III_promoter
definition: This type of promoter recruits RNA pol III to transcribe predominantly noncoding RNAs. This promoter contains a proximal sequence element (PSE) and a TATA box upstream of the gene that it regulates. Transcription can also be activated by a distal sequence element (DSE), which is located further upstream.
has_exact_synonym: RNApol III promoter type 3
has_obo_namespace: sequence
id: SO:0000621

Axiom
annotated source: RNApol_III_promoter_type_3
annotated property: definition
annotated target: This type of promoter recruits RNA pol III to transcribe predominantly noncoding RNAs. This promoter contains a proximal sequence element (PSE) and a TATA box upstream of the gene that it regulates. Transcription can also be activated by a distal sequence element (DSE), which is located further upstream.
database_cross_reference: PMID:12381659

C_box
type: Class
subclass of: core_eukaryotic_promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_III_promoter_type_1
definition: An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.
has_exact_synonym: C-box
has_obo_namespace: sequence
id: SO:0000622

Axiom
annotated source: C_box
annotated property: definition
annotated target: An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.
database_cross_reference: SO:ke

snRNA_encoding
type: Class
subclass of: non_protein_coding
definition: A region that can be transcribed into a small nuclear RNA (snRNA).
has_exact_synonym: snRNA encoding
has_obo_namespace: sequence
id: SO:0000623

telomere
type: Class
subclass of: chromosomal_structural_element
definition: A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
database_cross_reference: http://en.wikipedia.org/wiki/Telomere
has_exact_synonym: INSDC_feature:telomere
has_exact_synonym: telomeric DNA
has_exact_synonym: telomeric sequence
has_obo_namespace: sequence
id: SO:0000624
in_subset: SOFA

Axiom
annotated source: telomere
annotated property: definition
annotated target: A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: telomere
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Telomere

silencer
type: Class
subclass of: cis_regulatory_module
definition: A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Silencer_(DNA)
has_exact_synonym: INSDC_qualifier:silencer
has_obo_namespace: sequence
id: SO:0000625
in_subset: SOFA

Axiom
annotated source: silencer
annotated property: definition
annotated target: A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: silencer
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Silencer_(DNA)

chromosomal_regulatory_element
type: Class
subclass of: chromosome_part
definition: Regions of the chromosome that are important for regulating binding of chromosomes to the nuclear matrix.
has_exact_synonym: chromosomal regulatory element
has_obo_namespace: sequence
id: SO:0000626

insulator
type: Class
subclass of: cis_regulatory_module
definition: A regulatory region that 1) when located between a CRM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Insulator_(genetics)
has_exact_synonym: INSDC_qualifier:insulator
has_exact_synonym: insulator element
has_obo_namespace: sequence
id: SO:0000627
in_subset: SOFA
comment: moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.

Axiom
annotated source: insulator
annotated property: definition
annotated target: A regulatory region that 1) when located between a CRM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region.
database_cross_reference: NCBI:cf
database_cross_reference: PMID:12154228
database_cross_reference: SO:regcreative

wiki
type: Axiom
annotated source: insulator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Insulator_(genetics)

chromosomal_structural_element
type: Class
subclass of: chromosome_part
definition: Regions of the chromosome that are important for structural elements.
has_exact_synonym: chromosomal structural element
has_obo_namespace: sequence
id: SO:0000628
in_subset: SOFA

five_prime_open_reading_frame
type: Class
subclass of: mRNA_region
subclass of: Restriction
  on property: part_of
  some values from: five_prime_UTR
definition: An open reading frame found within the 5' UTR that can be translated and stall the translation of the downstream open reading frame.
has_exact_synonym: five prime open reading frame
has_obo_namespace: sequence
id: SO:0000629

Axiom
annotated source: five_prime_open_reading_frame
annotated property: definition
annotated target: An open reading frame found within the 5' UTR that can be translated and stall the translation of the downstream open reading frame.
database_cross_reference: PMID:12890013

upstream_AUG_codon
type: Class
subclass of: UTR_region
subclass of: Restriction
  on property: part_of
  some values from: UTR
definition: A start codon upstream of the ORF.
has_exact_synonym: upstream AUG codon
has_obo_namespace: sequence
id: SO:0000630

Axiom
annotated source: upstream_AUG_codon
annotated property: definition
annotated target: A start codon upstream of the ORF.
database_cross_reference: SO:ke

polycistronic_primary_transcript
type: Class
equivalent class: Class
  intersection of: primary_transcript
  intersection of: Restriction
    on property: has_quality
    some values from: polycistronic
subclass of: polycistronic_transcript
subclass of: primary_transcript
subclass of: Restriction
  on property: has_quality
  some values from: polycistronic
definition: A primary transcript encoding for more than one gene product.
has_exact_synonym: polycistronic primary transcript
has_obo_namespace: sequence
id: SO:0000631

Axiom
annotated source: polycistronic_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding for more than one gene product.
database_cross_reference: SO:ke

monocistronic_primary_transcript
type: Class
equivalent class: Class
  intersection of: primary_transcript
  intersection of: Restriction
    on property: has_quality
    some values from: monocistronic
subclass of: primary_transcript
subclass of: monocistronic_transcript
subclass of: Restriction
  on property: has_quality
  some values from: monocistronic
definition: A primary transcript encoding for one gene product.
has_exact_synonym: monocistronic primary transcript
has_obo_namespace: sequence
id: SO:0000632

Axiom
annotated source: monocistronic_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding for one gene product.
database_cross_reference: SO:ke

monocistronic_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: monocistronic
subclass of: mRNA
subclass of: monocistronic_transcript
subclass of: Restriction
  on property: has_quality
  some values from: monocistronic
definition: An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
database_cross_reference: http://en.wikipedia.org/wiki/Monocistronic_mRNA
has_exact_synonym: monocistronic mRNA
has_exact_synonym: monocistronic processed transcript
has_obo_namespace: sequence
id: SO:0000633

Axiom
annotated source: monocistronic_mRNA
annotated property: definition
annotated target: An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
database_cross_reference: SO:rd

wiki
type: Axiom
annotated source: monocistronic_mRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Monocistronic_mRNA

polycistronic_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: polycistronic
subclass of: polycistronic_transcript
subclass of: mRNA
subclass of: Restriction
  on property: has_quality
  some values from: polycistronic
definition: An mRNA that encodes multiple proteins from at least two non-overlapping regions.
database_cross_reference: http://en.wikipedia.org/wiki/Polycistronic_mRNA
has_exact_synonym: polycistronic mRNA
has_obo_namespace: sequence
has_related_synonym: polycistronic processed transcript
id: SO:0000634

Axiom
annotated source: polycistronic_mRNA
annotated property: definition
annotated target: An mRNA that encodes multiple proteins from at least two non-overlapping regions.
database_cross_reference: SO:rd

wiki
type: Axiom
annotated source: polycistronic_mRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Polycistronic_mRNA

mini_exon_donor_RNA
type: Class
subclass of: primary_transcript
definition: A primary transcript that donates the spliced leader to other mRNA.
has_exact_synonym: mini exon donor RNA
has_exact_synonym: mini-exon donor RNA
has_obo_namespace: sequence
id: SO:0000635

Axiom
annotated source: mini_exon_donor_RNA
annotated property: definition
annotated target: A primary transcript that donates the spliced leader to other mRNA.
database_cross_reference: SO:ke

spliced_leader_RNA
type: Class
subclass of: primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: mini_exon_donor_RNA
definition: Snall nuclear RNAs that are incorporated into the pre-mRNAs to replace the 5' end in some eukaryotes.
has_exact_synonym: spliced leader RNA
has_obo_namespace: sequence
has_related_synonym: mini-exon
id: SO:0000636

Axiom
annotated source: spliced_leader_RNA
annotated property: definition
annotated target: Snall nuclear RNAs that are incorporated into the pre-mRNAs to replace the 5' end in some eukaryotes.
database_cross_reference: PMID:24130571

engineered_plasmid
type: Class
equivalent class: Class
  intersection of: plasmid
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: plasmid
subclass of: engineered_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: A plasmid that is engineered.
has_exact_synonym: engineered plasmid
has_obo_namespace: sequence
has_related_synonym: engineered plasmid gene
id: SO:0000637

Axiom
annotated source: engineered_plasmid
annotated property: definition
annotated target: A plasmid that is engineered.
database_cross_reference: SO:xp

transcribed_spacer_region
type: Class
subclass of: rRNA_primary_transcript_region
definition: Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
has_exact_synonym: transcribed spacer region
has_obo_namespace: sequence
id: SO:0000638

Axiom
annotated source: transcribed_spacer_region
annotated property: definition
annotated target: Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
database_cross_reference: http://oregonstate.edu/instruction/bb492/general/glossary.html

internal_transcribed_spacer_region
type: Class
subclass of: transcribed_spacer_region
definition: Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
has_exact_synonym: internal transcribed spacer region
has_obo_namespace: sequence
id: SO:0000639

Axiom
annotated source: internal_transcribed_spacer_region
annotated property: definition
annotated target: Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
database_cross_reference: SO:ke

external_transcribed_spacer_region
type: Class
subclass of: transcribed_spacer_region
definition: Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
has_exact_synonym: external transcribed spacer region
has_obo_namespace: sequence
id: SO:0000640

Axiom
annotated source: external_transcribed_spacer_region
annotated property: definition
annotated target: Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
database_cross_reference: SO:ke

tetranucleotide_repeat_microsatellite_feature
type: Class
subclass of: microsatellite
definition: A region of a repeating tetranucleotide sequence (four bases).
has_exact_synonym: tetranucleotide repeat microsatellite feature
has_obo_namespace: sequence
id: SO:0000641

SRP_RNA_encoding
type: Class
subclass of: non_protein_coding
definition: A region that can be transcribed into a signal recognition particle RNA (SRP RNA).
has_exact_synonym: SRP RNA encoding
has_obo_namespace: sequence
id: SO:0000642

minisatellite
type: Class
subclass of: satellite_DNA
definition: A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Minisatellite
has_exact_synonym: INSDC_qualifier:minisatellite
has_exact_synonym: VNTR
has_obo_namespace: sequence
id: SO:0000643
in_subset: SOFA

Axiom
annotated source: minisatellite
annotated property: definition
annotated target: A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
database_cross_reference: http://www.informatics.jax.org/silver/glossary.shtml

wiki
type: Axiom
annotated source: minisatellite
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Minisatellite

Axiom
annotated source: minisatellite
annotated property: has_exact_synonym
annotated target: VNTR
database_cross_reference: http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/

antisense_RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: antisense_primary_transcript
definition: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/Antisense_RNA
has_exact_synonym: INSDC_qualifier:antisense_RNA
has_exact_synonym: antisense RNA
has_obo_namespace: sequence
id: SO:0000644
in_subset: SOFA

Axiom
annotated source: antisense_RNA
annotated property: definition
annotated target: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: antisense_RNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Antisense_RNA

antisense_primary_transcript
type: Class
subclass of: primary_transcript
definition: The reverse complement of the primary transcript.
has_exact_synonym: antisense primary transcript
has_obo_namespace: sequence
id: SO:0000645
in_subset: SOFA

Axiom
annotated source: antisense_primary_transcript
annotated property: definition
annotated target: The reverse complement of the primary transcript.
database_cross_reference: SO:ke

siRNA
type: Class
subclass of: small_regulatory_ncRNA
definition: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. siRNAs trigger the cleavage of their target molecules.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/SiRNA
has_exact_synonym: INSDC_qualifier:siRNA
has_exact_synonym: small interfering RNA
has_obo_namespace: sequence
id: SO:0000646
in_subset: SOFA

Axiom
annotated source: siRNA
annotated property: definition
annotated target: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. siRNAs trigger the cleavage of their target molecules.
database_cross_reference: PMID:12592000

wiki
type: Axiom
annotated source: siRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/SiRNA

miRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
subclass of: Restriction
  on property: has_part
  some values from: pre_miRNA
definition: A primary transcript encoding a micro RNA.
has_alternative_id: SO:0000648
has_exact_synonym: miRNA primary transcript
has_exact_synonym: micro RNA primary transcript
has_exact_synonym: small temporal RNA primary transcript
has_exact_synonym: stRNA primary transcript
has_exact_synonym: stRNA_primary_transcript
has_obo_namespace: sequence
id: SO:0000647

Axiom
annotated source: miRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding a micro RNA.
database_cross_reference: SO:ke

SO_0000648
type: Class
IAO_0000231: IAO_0000227
term replaced by: miRNA_primary_transcript
deprecated: true

SO_0000649
type: Class
IAO_0000231: IAO_0000227
term replaced by: miRNA
deprecated: true

cytosolic_SSU_rRNA
type: Class
subclass of: SO_0002343
subclass of: Restriction
  on property: derives_from
  some values from: rRNA_small_subunit_primary_transcript
definition: Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes.
has_exact_synonym: cytosolic SSU rRNA
has_exact_synonym: cytosolic SSU ribosomal RNA
has_exact_synonym: cytosolic small subunit rRNA
has_obo_namespace: sequence
id: SO:0000650
in_subset: SOFA
comment: Renamed to cytosolic_SSU_rRNA from small_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_SSU_rRNA
annotated property: definition
annotated target: Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes.
database_cross_reference: SO:ke

cytosolic_LSU_rRNA
type: Class
subclass of: SO_0002343
subclass of: Restriction
  on property: derives_from
  some values from: rRNA_large_subunit_primary_transcript
definition: Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.
has_exact_synonym: cytosolic LSU RNA
has_exact_synonym: cytosolic LSU rRNA
has_exact_synonym: cytosolic large subunit rRNA
has_obo_namespace: sequence
id: SO:0000651
in_subset: SOFA
comment: Renamed to cytosolic_LSU_rRNA from large_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_LSU_rRNA
annotated property: definition
annotated target: Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.
database_cross_reference: SO:ke

cytosolic_5S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002238
definition: Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes.
database_cross_reference: http://en.wikipedia.org/wiki/5S_ribosomal_RNA
has_exact_synonym: cytosolic 5S LSU rRNA
has_exact_synonym: cytosolic 5S rRNA
has_exact_synonym: cytosolic 5S ribosomal RNA
has_exact_synonym: cytosolic rRNA 5S
has_obo_namespace: sequence
id: SO:0000652
in_subset: SOFA
comment: Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_5S_rRNA
annotated property: definition
annotated target: Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: cytosolic_5S_rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/5S_ribosomal_RNA

cytosolic_28S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002239
definition: Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes.
database_cross_reference: http://en.wikipedia.org/wiki/28S_ribosomal_RNA
has_exact_synonym: cytosolic 28S LSU rRNA
has_exact_synonym: cytosolic 28S rRNA
has_exact_synonym: cytosolic 28S ribosomal RNA
has_exact_synonym: cytosolic rRNA 28S
has_obo_namespace: sequence
id: SO:0000653
in_subset: SOFA
comment: Renamed from rRNA_28S to cytosolic_28S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_28S_rRNA
annotated property: definition
annotated target: Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: cytosolic_28S_rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/28S_ribosomal_RNA

maxicircle_gene
type: Class
equivalent class: Class
  intersection of: kinetoplast_gene
  intersection of: Restriction
    on property: part_of
    some values from: maxicircle
subclass of: kinetoplast_gene
subclass of: Restriction
  on property: part_of
  some values from: maxicircle
definition: A mitochondrial gene located in a maxicircle.
has_exact_synonym: maxi-circle gene
has_exact_synonym: maxicircle gene
has_obo_namespace: sequence
id: SO:0000654

Axiom
annotated source: maxicircle_gene
annotated property: definition
annotated target: A mitochondrial gene located in a maxicircle.
database_cross_reference: SO:xp

ncRNA
type: Class
subclass of: mature_transcript
definition: An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
has_broad_synonym: INSDC_qualifier:other
database_cross_reference: http://en.wikipedia.org/wiki/NcRNA
database_cross_reference: http://www.gencodegenes.org/gencode_biotypes.html
has_exact_synonym: known_ncrna
has_exact_synonym: noncoding RNA
has_obo_namespace: sequence
id: SO:0000655
in_subset: SOFA
comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.

Axiom
annotated source: ncRNA
annotated property: definition
annotated target: An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: ncRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/NcRNA

GENCODE
type: Axiom
annotated source: ncRNA
annotated property: database_cross_reference
annotated target: http://www.gencodegenes.org/gencode_biotypes.html

stRNA_encoding
type: Class
subclass of: non_protein_coding
definition: A region that can be transcribed into a small temporal RNA (stRNA). Found in roundworm development.
has_exact_synonym: stRNA encoding
has_obo_namespace: sequence
id: SO:0000656

repeat_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: has_part
  some values from: repeat_unit
definition: A region of sequence containing one or more repeat units.
has_broad_synonym: INSDC_feature:repeat_region
has_exact_synonym: INSDC_qualifier:other
has_exact_synonym: repeat region
has_obo_namespace: sequence
id: SO:0000657
in_subset: SOFA

Axiom
annotated source: repeat_region
annotated property: definition
annotated target: A region of sequence containing one or more repeat units.
database_cross_reference: SO:ke

dispersed_repeat
type: Class
subclass of: repeat_region
definition: A repeat that is located at dispersed sites in the genome.
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Interspersed_repeat
has_exact_synonym: INSDC_qualifier:dispersed
has_exact_synonym: dispersed repeat
has_exact_synonym: interspersed repeat
has_obo_namespace: sequence
id: SO:0000658
in_subset: SOFA

Axiom
annotated source: dispersed_repeat
annotated property: definition
annotated target: A repeat that is located at dispersed sites in the genome.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: dispersed_repeat
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Interspersed_repeat

tmRNA_encoding
type: Class
subclass of: non_protein_coding
definition: A region that can be transcribed into a transfer-messenger RNA (tmRNA).
has_exact_synonym: tmRNA encoding
has_obo_namespace: sequence
id: SO:0000659

DNA_invertase_target_sequence
type: Class
has_obo_namespace: sequence
id: SO:0000660
deprecated: true

intron_attribute
type: Class
has_obo_namespace: sequence
id: SO:0000661
deprecated: true

spliceosomal_intron
type: Class
subclass of: intron
definition: An intron which is spliced by the spliceosome.
has_exact_synonym: spliceosomal intron
has_obo_namespace: sequence
id: SO:0000662
in_subset: SOFA
comment: GO:0000398.

Axiom
annotated source: spliceosomal_intron
annotated property: definition
annotated target: An intron which is spliced by the spliceosome.
database_cross_reference: SO:ke

tRNA_encoding
type: Class
subclass of: non_protein_coding
definition: A region that can be transcribed into a transfer RNA (tRNA).
has_exact_synonym: tRNA encoding
has_obo_namespace: sequence
id: SO:0000663

introgressed_chromosome_region
type: Class
subclass of: chromosome_part
definition: A region of a chromosome that has been introduced by backcrossing with a separate species.
has_exact_synonym: introgressed chromosome region
has_obo_namespace: sequence
id: SO:0000664

Axiom
annotated source: introgressed_chromosome_region
annotated property: definition
annotated target: A region of a chromosome that has been introduced by backcrossing with a separate species.
database_cross_reference: PMID:11454782

monocistronic_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: monocistronic
subclass of: transcript
subclass of: Restriction
  on property: has_quality
  some values from: monocistronic
definition: A transcript that is monocistronic.
has_exact_synonym: monocistronic transcript
has_obo_namespace: sequence
id: SO:0000665

Axiom
annotated source: monocistronic_transcript
annotated property: definition
annotated target: A transcript that is monocistronic.
database_cross_reference: SO:xp

mobile_intron
type: Class
equivalent class: Class
  intersection of: intron
  intersection of: Restriction
    on property: has_quality
    some values from: mobile
subclass of: intron
subclass of: mobile_genetic_element
subclass of: Restriction
  on property: has_quality
  some values from: mobile
definition: An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
has_exact_synonym: mobile intron
has_obo_namespace: sequence
id: SO:0000666

Axiom
annotated source: mobile_intron
annotated property: definition
annotated target: An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
database_cross_reference: SO:ke

insertion
type: Class
subclass of: sequence_alteration
subclass of: biological_region
definition: The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
has_alternative_id: SO:1000034
database_cross_reference: loinc:LA6687-3
has_exact_synonym: insertion
has_exact_synonym: nucleotide insertion
has_exact_synonym: nucleotide_insertion
has_obo_namespace: sequence
id: SO:0000667
in_subset: DBVAR
in_subset: SOFA

Axiom
annotated source: insertion
annotated property: definition
annotated target: The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
database_cross_reference: SO:ke

Insertion
type: Axiom
annotated source: insertion
annotated property: database_cross_reference
annotated target: loinc:LA6687-3

Axiom
annotated source: insertion
annotated property: has_exact_synonym
annotated target: insertion
database_cross_reference: http://www.ncbi.nlm.nih.gov/dbvar/
has_synonym_type: DBVAR

EST_match
type: Class
subclass of: expressed_sequence_match
definition: A match against an EST sequence.
has_exact_synonym: EST match
has_obo_namespace: sequence
id: SO:0000668
in_subset: SOFA

Axiom
annotated source: EST_match
annotated property: definition
annotated target: A match against an EST sequence.
database_cross_reference: SO:ke

sequence_rearrangement_feature
type: Class
subclass of: recombination_feature
definition: A feature where a segment of DNA has been rearranged from what it was in the parent cell.
has_exact_synonym: sequence rearrangement feature
has_obo_namespace: sequence
id: SO:0000669

chromosome_breakage_sequence
type: Class
subclass of: sequence_rearrangement_feature
definition: A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.
has_exact_synonym: chromosome breakage sequence
has_obo_namespace: sequence
id: SO:0000670

Axiom
annotated source: chromosome_breakage_sequence
annotated property: definition
annotated target: A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.
database_cross_reference: SO:ma

internal_eliminated_sequence
type: Class
subclass of: sequence_rearrangement_feature
definition: A sequence eliminated from the genome of ciliates during nuclear differentiation.
has_exact_synonym: internal eliminated sequence
has_obo_namespace: sequence
id: SO:0000671

Axiom
annotated source: internal_eliminated_sequence
annotated property: definition
annotated target: A sequence eliminated from the genome of ciliates during nuclear differentiation.
database_cross_reference: SO:ma

macronucleus_destined_segment
type: Class
subclass of: sequence_rearrangement_feature
definition: A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.
has_exact_synonym: macronucleus destined segment
has_obo_namespace: sequence
id: SO:0000672

Axiom
annotated source: macronucleus_destined_segment
annotated property: definition
annotated target: A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.
database_cross_reference: SO:ma

transcript
type: Class
subclass of: gene_member_region
subclass of: Restriction
  on property: overlaps
  some values from: SO_0002300
definition: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
has_broad_synonym: INSDC_feature:misc_RNA
database_cross_reference: http://en.wikipedia.org/wiki/RNA
has_obo_namespace: sequence
id: SO:0000673
in_subset: SOFA
comment: Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020.

Axiom
annotated source: transcript
annotated property: definition
annotated target: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: transcript
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/RNA

non_canonical_splice_site
type: Class
definition: A splice site where the donor and acceptor sites differ from the canonical form.
consider: non_canonical_three_prime_splice_site
consider: non_canonical_five_prime_splice_site
has_exact_synonym: non canonical splice site
has_exact_synonym: non-canonical splice site
has_obo_namespace: sequence
id: SO:0000674
deprecated: true

Axiom
annotated source: non_canonical_splice_site
annotated property: definition
annotated target: A splice site where the donor and acceptor sites differ from the canonical form.
database_cross_reference: SO:ke

canonical_splice_site
type: Class
definition: The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.
consider: canonical_three_prime_splice_site
consider: canonical_five_prime_splice_site
has_exact_synonym: canonical splice site
has_obo_namespace: sequence
id: SO:0000675
deprecated: true

Axiom
annotated source: canonical_splice_site
annotated property: definition
annotated target: The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.
database_cross_reference: SO:ke

canonical_three_prime_splice_site
type: Class
subclass of: three_prime_cis_splice_site
definition: The canonical 3' splice site has the sequence "AG".
has_exact_synonym: canonical 3' splice site
has_exact_synonym: canonical three prime splice site
has_obo_namespace: sequence
id: SO:0000676

Axiom
annotated source: canonical_three_prime_splice_site
annotated property: definition
annotated target: The canonical 3' splice site has the sequence "AG".
database_cross_reference: SO:ke

canonical_five_prime_splice_site
type: Class
subclass of: five_prime_cis_splice_site
definition: The canonical 5' splice site has the sequence "GT".
has_exact_synonym: canonical 5' splice site
has_exact_synonym: canonical five prime splice site
has_obo_namespace: sequence
id: SO:0000677

Axiom
annotated source: canonical_five_prime_splice_site
annotated property: definition
annotated target: The canonical 5' splice site has the sequence "GT".
database_cross_reference: SO:ke

non_canonical_three_prime_splice_site
type: Class
subclass of: three_prime_cis_splice_site
definition: A 3' splice site that does not have the sequence "AG".
has_exact_synonym: non canonical three prime splice site
has_exact_synonym: non-canonical three prime splice site
has_obo_namespace: sequence
has_related_synonym: non canonical 3' splice site
id: SO:0000678

Axiom
annotated source: non_canonical_three_prime_splice_site
annotated property: definition
annotated target: A 3' splice site that does not have the sequence "AG".
database_cross_reference: SO:ke

non_canonical_five_prime_splice_site
type: Class
subclass of: five_prime_cis_splice_site
definition: A 5' splice site which does not have the sequence "GT".
has_exact_synonym: non canonical 5' splice site
has_exact_synonym: non canonical five prime splice site
has_exact_synonym: non-canonical five prime splice site
has_obo_namespace: sequence
id: SO:0000679

Axiom
annotated source: non_canonical_five_prime_splice_site
annotated property: definition
annotated target: A 5' splice site which does not have the sequence "GT".
database_cross_reference: SO:ke

non_canonical_start_codon
type: Class
subclass of: start_codon
definition: A start codon that is not the usual AUG sequence.
has_exact_synonym: non ATG start codon
has_exact_synonym: non canonical start codon
has_exact_synonym: non-canonical start codon
has_obo_namespace: sequence
id: SO:0000680

Axiom
annotated source: non_canonical_start_codon
annotated property: definition
annotated target: A start codon that is not the usual AUG sequence.
database_cross_reference: SO:ke

aberrant_processed_transcript
type: Class
subclass of: transcript
definition: A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
has_exact_synonym: aberrant processed transcript
has_obo_namespace: sequence
id: SO:0000681

Axiom
annotated source: aberrant_processed_transcript
annotated property: definition
annotated target: A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
database_cross_reference: SO:ke

splicing_feature
type: Class
has_obo_namespace: sequence
id: SO:0000682
deprecated: true

exonic_splice_enhancer
type: Class
subclass of: splice_enhancer
definition: Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.
has_exact_synonym: exonic splice enhancer
has_obo_namespace: sequence
id: SO:0000683

Axiom
annotated source: exonic_splice_enhancer
annotated property: definition
annotated target: Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.
database_cross_reference: http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi

nuclease_sensitive_site
type: Class
subclass of: nuclease_binding_site
definition: A region of nucleotide sequence targeted by a nuclease enzyme.
has_exact_synonym: nuclease sensitive site
has_obo_namespace: sequence
id: SO:0000684
in_subset: SOFA

Axiom
annotated source: nuclease_sensitive_site
annotated property: definition
annotated target: A region of nucleotide sequence targeted by a nuclease enzyme.
database_cross_reference: SO:ma

DNaseI_hypersensitive_site
type: Class
subclass of: nuclease_hypersensitive_site
definition: DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I.
has_broad_synonym: INSDC_feature:regulatory
has_exact_synonym: DHS
has_exact_synonym: DNaseI hypersensitive site
has_exact_synonym: INSDC_qualifier:DNase_I_hypersensitive_site
has_obo_namespace: sequence
id: SO:0000685

translocation_element
type: Class
subclass of: SO_1000044
definition: A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations.
has_exact_synonym: translocation element
has_obo_namespace: sequence
id: SO:0000686

Axiom
annotated source: translocation_element
annotated property: definition
annotated target: A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations.
database_cross_reference: SO:ma

deletion_junction
type: Class
subclass of: junction
definition: The space between two bases in a sequence which marks the position where a deletion has occurred.
has_exact_synonym: deletion junction
has_obo_namespace: sequence
id: SO:0000687
in_subset: SOFA

Axiom
annotated source: deletion_junction
annotated property: definition
annotated target: The space between two bases in a sequence which marks the position where a deletion has occurred.
database_cross_reference: SO:ke

golden_path
type: Class
subclass of: sequence_assembly
definition: A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
has_exact_synonym: golden path
has_obo_namespace: sequence
id: SO:0000688
in_subset: SOFA

Axiom
annotated source: golden_path
annotated property: definition
annotated target: A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
database_cross_reference: SO:ls

cDNA_match
type: Class
subclass of: expressed_sequence_match
definition: A match against cDNA sequence.
has_exact_synonym: cDNA match
has_obo_namespace: sequence
id: SO:0000689
in_subset: SOFA

Axiom
annotated source: cDNA_match
annotated property: definition
annotated target: A match against cDNA sequence.
database_cross_reference: SO:ke

gene_with_polycistronic_transcript
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: transcribed_to
    some values from: polycistronic_transcript
subclass of: gene
subclass of: Restriction
  on property: transcribed_to
  some values from: polycistronic_transcript
definition: A gene that encodes a polycistronic transcript.
has_exact_synonym: gene with polycistronic transcript
has_obo_namespace: sequence
id: SO:0000690

Axiom
annotated source: gene_with_polycistronic_transcript
annotated property: definition
annotated target: A gene that encodes a polycistronic transcript.
database_cross_reference: SO:xp

cleaved_initiator_methionine
type: Class
subclass of: SO_0100011
definition: The initiator methionine that has been cleaved from a mature polypeptide sequence.
has_alternative_id: BS:00067
has_exact_synonym: cleaved initiator methionine
has_obo_namespace: sequence
has_related_synonym: init_met
has_related_synonym: initiator methionine
id: SO:0000691
in_subset: biosapiens

Axiom
annotated source: cleaved_initiator_methionine
annotated property: definition
annotated target: The initiator methionine that has been cleaved from a mature polypeptide sequence.
database_cross_reference: EBIBS:GAR

Axiom
annotated source: cleaved_initiator_methionine
annotated property: has_related_synonym
annotated target: init_met
database_cross_reference: uniprot:feature_type

gene_with_dicistronic_transcript
type: Class
equivalent class: Class
  intersection of: gene_with_polycistronic_transcript
  intersection of: Restriction
    on property: transcribed_to
    some values from: dicistronic_transcript
subclass of: gene_with_polycistronic_transcript
subclass of: Restriction
  on property: transcribed_to
  some values from: dicistronic_transcript
definition: A gene that encodes a dicistronic transcript.
has_exact_synonym: gene with dicistronic transcript
has_obo_namespace: sequence
id: SO:0000692

Axiom
annotated source: gene_with_dicistronic_transcript
annotated property: definition
annotated target: A gene that encodes a dicistronic transcript.
database_cross_reference: SO:xp

gene_with_recoded_mRNA
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: has_quality
    some values from: recoded
subclass of: protein_coding_gene
subclass of: Restriction
  on property: has_quality
  some values from: recoded
definition: A gene that encodes an mRNA that is recoded.
has_exact_synonym: gene with recoded mRNA
has_obo_namespace: sequence
id: SO:0000693

Axiom
annotated source: gene_with_recoded_mRNA
annotated property: definition
annotated target: A gene that encodes an mRNA that is recoded.
database_cross_reference: SO:xp

SNP
type: Class
subclass of: SNV
definition: SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
has_exact_synonym: single nucleotide polymorphism
has_obo_namespace: sequence
id: SO:0000694
in_subset: SOFA

Axiom
annotated source: SNP
annotated property: definition
annotated target: SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
database_cross_reference: SO:cb

reagent
type: Class
subclass of: biomaterial_region
definition: A sequence used in experiment.
has_obo_namespace: sequence
id: SO:0000695
in_subset: SOFA
comment: Requested by Lynn Crosby, jan 2006.

Axiom
annotated source: reagent
annotated property: definition
annotated target: A sequence used in experiment.
database_cross_reference: SO:ke

oligo
type: Class
subclass of: reagent
definition: A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
database_cross_reference: http://en.wikipedia.org/wiki/Oligonucleotide
has_exact_synonym: oligonucleotide
has_obo_namespace: sequence
id: SO:0000696
in_subset: SOFA

Axiom
annotated source: oligo
annotated property: definition
annotated target: A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: oligo
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Oligonucleotide

gene_with_stop_codon_read_through
type: Class
equivalent class: Class
  intersection of: gene_with_recoded_mRNA
  intersection of: Restriction
    on property: has_part
    some values from: stop_codon_read_through
subclass of: gene_with_recoded_mRNA
subclass of: Restriction
  on property: has_part
  some values from: stop_codon_read_through
definition: A gene that encodes a transcript with stop codon readthrough.
has_exact_synonym: gene with stop codon read through
has_obo_namespace: sequence
id: SO:0000697

Axiom
annotated source: gene_with_stop_codon_read_through
annotated property: definition
annotated target: A gene that encodes a transcript with stop codon readthrough.
database_cross_reference: SO:xp

gene_with_stop_codon_redefined_as_pyrrolysine
type: Class
equivalent class: Class
  intersection of: gene_with_recoded_mRNA
  intersection of: Restriction
    on property: has_part
    some values from: stop_codon_redefined_as_pyrrolysine
subclass of: gene_with_stop_codon_read_through
subclass of: Restriction
  on property: has_part
  some values from: stop_codon_redefined_as_pyrrolysine
definition: A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
has_exact_synonym: gene with stop codon redefined as pyrrolysine
has_obo_namespace: sequence
id: SO:0000698

Axiom
annotated source: gene_with_stop_codon_redefined_as_pyrrolysine
annotated property: definition
annotated target: A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
database_cross_reference: SO:xp

junction
type: Class
subclass of: sequence_feature
definition: A sequence_feature with an extent of zero.
has_exact_synonym: boundary
has_exact_synonym: breakpoint
has_obo_namespace: sequence
id: SO:0000699
in_subset: SOFA
comment: A junction is a boundary between regions. A boundary has an extent of zero.

Axiom
annotated source: junction
annotated property: definition
annotated target: A sequence_feature with an extent of zero.
database_cross_reference: SO:ke

remark
type: Class
subclass of: experimental_feature
definition: A comment about the sequence.
has_obo_namespace: sequence
id: SO:0000700
in_subset: SOFA

Axiom
annotated source: remark
annotated property: definition
annotated target: A comment about the sequence.
database_cross_reference: SO:ke

possible_base_call_error
type: Class
subclass of: sequence_difference
definition: A region of sequence where the validity of the base calling is questionable.
has_exact_synonym: possible base call error
has_obo_namespace: sequence
id: SO:0000701
in_subset: SOFA

Axiom
annotated source: possible_base_call_error
annotated property: definition
annotated target: A region of sequence where the validity of the base calling is questionable.
database_cross_reference: SO:ke

possible_assembly_error
type: Class
subclass of: sequence_difference
definition: A region of sequence where there may have been an error in the assembly.
has_exact_synonym: possible assembly error
has_obo_namespace: sequence
id: SO:0000702
in_subset: SOFA

Axiom
annotated source: possible_assembly_error
annotated property: definition
annotated target: A region of sequence where there may have been an error in the assembly.
database_cross_reference: SO:ke

experimental_result_region
type: Class
subclass of: remark
definition: A region of sequence implicated in an experimental result.
has_exact_synonym: experimental result region
has_obo_namespace: sequence
id: SO:0000703
in_subset: SOFA

Axiom
annotated source: experimental_result_region
annotated property: definition
annotated target: A region of sequence implicated in an experimental result.
database_cross_reference: SO:ke

gene
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: member_of
  some values from: SO_0005855
definition: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
database_cross_reference: http://en.wikipedia.org/wiki/Gene
has_exact_synonym: INSDC_feature:gene
has_obo_namespace: sequence
id: SO:0000704
in_subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.

Axiom
annotated source: gene
annotated property: definition
annotated target: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
database_cross_reference: SO:immuno_workshop

wiki
type: Axiom
annotated source: gene
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Gene

tandem_repeat
type: Class
subclass of: repeat_region
definition: Two or more adjacent copies of a region (of length greater than 1).
has_broad_synonym: INSDC_feature:repeat_region
database_cross_reference: http://en.wikipedia.org/wiki/Tandem_repeat
database_cross_reference: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
has_exact_synonym: INSDC_qualifier:tandem
has_exact_synonym: tandem repeat
has_obo_namespace: sequence
id: SO:0000705
in_subset: SOFA

Axiom
annotated source: tandem_repeat
annotated property: definition
annotated target: Two or more adjacent copies of a region (of length greater than 1).
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: tandem_repeat
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Tandem_repeat

trans_splice_acceptor_site
type: Class
subclass of: trans_splice_site
definition: The 3' splice site of the acceptor primary transcript.
has_exact_synonym: trans splice acceptor site
has_obo_namespace: sequence
has_related_synonym: 3' trans splice site
id: SO:0000706
in_subset: SOFA
comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.

Axiom
annotated source: trans_splice_acceptor_site
annotated property: definition
annotated target: The 3' splice site of the acceptor primary transcript.
database_cross_reference: SO:ke

trans_splice_donor_site
type: Class
subclass of: trans_splice_site
definition: The 5' five prime splice site region of the donor RNA.
has_exact_synonym: trans splice donor site
has_exact_synonym: trans-splice donor site
has_obo_namespace: sequence
has_related_synonym: 5 prime trans splice site
id: SO:0000707
comment: SL RNA contains a donor site.

Axiom
annotated source: trans_splice_donor_site
annotated property: definition
annotated target: The 5' five prime splice site region of the donor RNA.
database_cross_reference: SO:ke

SL1_acceptor_site
type: Class
subclass of: trans_splice_acceptor_site
definition: A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
has_exact_synonym: SL1 acceptor site
has_obo_namespace: sequence
id: SO:0000708

Axiom
annotated source: SL1_acceptor_site
annotated property: definition
annotated target: A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
database_cross_reference: SO:nlw

SL2_acceptor_site
type: Class
subclass of: trans_splice_acceptor_site
definition: A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.
has_exact_synonym: SL2 acceptor site
has_obo_namespace: sequence
id: SO:0000709

Axiom
annotated source: SL2_acceptor_site
annotated property: definition
annotated target: A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.
database_cross_reference: SO:nlw

gene_with_stop_codon_redefined_as_selenocysteine
type: Class
equivalent class: Class
  intersection of: gene_with_stop_codon_read_through
  intersection of: Restriction
    on property: has_part
    some values from: stop_codon_redefined_as_selenocysteine
subclass of: gene_with_stop_codon_read_through
subclass of: Restriction
  on property: has_part
  some values from: stop_codon_redefined_as_selenocysteine
definition: A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
has_exact_synonym: gene with stop codon redefined as selenocysteine
has_obo_namespace: sequence
id: SO:0000710

Axiom
annotated source: gene_with_stop_codon_redefined_as_selenocysteine
annotated property: definition
annotated target: A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
database_cross_reference: SO:xp

gene_with_mRNA_recoded_by_translational_bypass
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: has_quality
    some values from: recoded_by_translational_bypass
subclass of: gene_with_recoded_mRNA
subclass of: Restriction
  on property: has_quality
  some values from: recoded_by_translational_bypass
definition: A gene with mRNA recoded by translational bypass.
has_exact_synonym: gene with mRNA recoded by translational bypass
has_obo_namespace: sequence
id: SO:0000711

Axiom
annotated source: gene_with_mRNA_recoded_by_translational_bypass
annotated property: definition
annotated target: A gene with mRNA recoded by translational bypass.
database_cross_reference: SO:xp

gene_with_transcript_with_translational_frameshift
type: Class
equivalent class: Class
  intersection of: gene_with_recoded_mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: translationally_frameshifted
subclass of: gene_with_recoded_mRNA
subclass of: Restriction
  on property: has_quality
  some values from: translationally_frameshifted
definition: A gene encoding a transcript that has a translational frameshift.
has_exact_synonym: gene with transcript with translational frameshift
has_obo_namespace: sequence
id: SO:0000712

Axiom
annotated source: gene_with_transcript_with_translational_frameshift
annotated property: definition
annotated target: A gene encoding a transcript that has a translational frameshift.
database_cross_reference: SO:xp

DNA_motif
type: Class
subclass of: nucleotide_motif
definition: A motif that is active in the DNA form of the sequence.
database_cross_reference: http://en.wikipedia.org/wiki/DNA_motif
has_exact_synonym: DNA motif
has_obo_namespace: sequence
id: SO:0000713

Axiom
annotated source: DNA_motif
annotated property: definition
annotated target: A motif that is active in the DNA form of the sequence.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: DNA_motif
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/DNA_motif

nucleotide_motif
type: Class
subclass of: sequence_motif
definition: A region of nucleotide sequence corresponding to a known motif.
has_broad_synonym: INSDC_feature:misc_feature
has_exact_synonym: INSDC_note:nucleotide_motif
has_exact_synonym: nucleotide motif
has_obo_namespace: sequence
id: SO:0000714
in_subset: SOFA

Axiom
annotated source: nucleotide_motif
annotated property: definition
annotated target: A region of nucleotide sequence corresponding to a known motif.
database_cross_reference: SO:ke

RNA_motif
type: Class
subclass of: nucleotide_motif
definition: A motif that is active in RNA sequence.
has_exact_synonym: RNA motif
has_obo_namespace: sequence
id: SO:0000715
in_subset: SOFA

Axiom
annotated source: RNA_motif
annotated property: definition
annotated target: A motif that is active in RNA sequence.
database_cross_reference: SO:ke

dicistronic_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: dicistronic
subclass of: dicistronic_transcript
subclass of: polycistronic_mRNA
subclass of: Restriction
  on property: has_quality
  some values from: dicistronic
definition: An mRNA that has the quality dicistronic.
has_exact_synonym: dicistronic mRNA
has_obo_namespace: sequence
has_related_synonym: dicistronic processed transcript
id: SO:0000716

Axiom
annotated source: dicistronic_mRNA
annotated property: definition
annotated target: An mRNA that has the quality dicistronic.
database_cross_reference: SO:ke

reading_frame
type: Class
subclass of: experimental_feature
definition: A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
database_cross_reference: http://en.wikipedia.org/wiki/Reading_frame
has_exact_synonym: reading frame
has_obo_namespace: sequence
id: SO:0000717
in_subset: SOFA
comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.

Axiom
annotated source: reading_frame
annotated property: definition
annotated target: A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
database_cross_reference: SGD:rb

wiki
type: Axiom
annotated source: reading_frame
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Reading_frame

blocked_reading_frame
type: Class
subclass of: reading_frame
definition: A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons.
has_exact_synonym: blocked reading frame
has_obo_namespace: sequence
id: SO:0000718
comment: Term requested by Rama from SGD.

Axiom
annotated source: blocked_reading_frame
annotated property: definition
annotated target: A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons.
database_cross_reference: SGD:rb

ultracontig
type: Class
subclass of: SO_0001876
definition: An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
has_exact_synonym: pseudochromosome
has_obo_namespace: sequence
has_related_synonym: superscaffold
id: SO:0000719
in_subset: SOFA

Axiom
annotated source: ultracontig
annotated property: definition
annotated target: An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
database_cross_reference: FB:WG

foreign_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: transposable_element
subclass of: Restriction
  on property: has_quality
  some values from: foreign
definition: A transposable element that is foreign.
has_exact_synonym: foreign transposable element
has_obo_namespace: sequence
id: SO:0000720
comment: requested by Michael on 19 Nov 2004.

Axiom
annotated source: foreign_transposable_element
annotated property: definition
annotated target: A transposable element that is foreign.
database_cross_reference: SO:ke

gene_with_dicistronic_primary_transcript
type: Class
equivalent class: Class
  intersection of: gene_with_dicistronic_transcript
  intersection of: Restriction
    on property: transcribed_to
    some values from: SO_1001197
subclass of: gene_with_dicistronic_transcript
subclass of: Restriction
  on property: transcribed_to
  some values from: SO_1001197
definition: A gene that encodes a dicistronic primary transcript.
has_exact_synonym: gene with dicistronic primary transcript
has_obo_namespace: sequence
id: SO:0000721
comment: Requested by Michael, 19 nov 2004.

Axiom
annotated source: gene_with_dicistronic_primary_transcript
annotated property: definition
annotated target: A gene that encodes a dicistronic primary transcript.
database_cross_reference: SO:xp

gene_with_dicistronic_mRNA
type: Class
equivalent class: Class
  intersection of: gene_with_dicistronic_transcript
  intersection of: Restriction
    on property: transcribed_to
    some values from: dicistronic_mRNA
subclass of: gene_with_dicistronic_transcript
subclass of: Restriction
  on property: transcribed_to
  some values from: dicistronic_mRNA
definition: A gene that encodes a polycistronic mRNA.
has_exact_synonym: gene with dicistronic mRNA
has_exact_synonym: gene with dicistronic processed transcript
has_obo_namespace: sequence
id: SO:0000722
comment: Requested by MA nov 19 2004.

Axiom
annotated source: gene_with_dicistronic_mRNA
annotated property: definition
annotated target: A gene that encodes a polycistronic mRNA.
database_cross_reference: SO:xp

iDNA
type: Class
subclass of: recombination_feature
definition: Genomic sequence removed from the genome, as a normal event, by a process of recombination.
has_exact_synonym: INSDC_feature:iDNA
has_exact_synonym: intervening DNA
has_obo_namespace: sequence
id: SO:0000723

Axiom
annotated source: iDNA
annotated property: definition
annotated target: Genomic sequence removed from the genome, as a normal event, by a process of recombination.
database_cross_reference: SO:ma

oriT
type: Class
subclass of: origin_of_replication
definition: A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
database_cross_reference: http://en.wikipedia.org/wiki/Origin_of_transfer
has_exact_synonym: INSDC_feature:oriT
has_exact_synonym: origin of transfer
has_obo_namespace: sequence
id: SO:0000724
in_subset: SOFA

Axiom
annotated source: oriT
annotated property: definition
annotated target: A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: oriT
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Origin_of_transfer

transit_peptide
type: Class
subclass of: peptide_localization_signal
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002252
definition: The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
has_alternative_id: BS:00055
has_exact_synonym: INSDC_feature:transit_peptide
has_exact_synonym: transit peptide
has_obo_namespace: sequence
has_related_synonym: signal
has_related_synonym: transit
id: SO:0000725
in_subset: SOFA
in_subset: biosapiens
comment: Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.

Axiom
annotated source: transit_peptide
annotated property: definition
annotated target: The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
database_cross_reference: http://www.insdc.org/files/feature_table.html

Axiom
annotated source: transit_peptide
annotated property: has_related_synonym
annotated target: transit
database_cross_reference: uniprot:feature_type

repeat_unit
type: Class
subclass of: biological_region
definition: The simplest repeated component of a repeat region. A single repeat.
database_cross_reference: http://www.insdc.org/files/feature_table.html
has_exact_synonym: repeat unit
has_obo_namespace: sequence
id: SO:0000726
comment: Added to comply with the feature table. A single repeat.

Axiom
annotated source: repeat_unit
annotated property: definition
annotated target: The simplest repeated component of a repeat region. A single repeat.
database_cross_reference: SO:ke

cis_regulatory_module
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs.
has_exact_synonym: CRM
has_exact_synonym: TF module
has_exact_synonym: cis regulatory module
has_exact_synonym: transcription factor module
has_obo_namespace: sequence
id: SO:0000727
in_subset: SOFA
comment: Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534.

Axiom
annotated source: cis_regulatory_module
annotated property: definition
annotated target: A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs.
database_cross_reference: PMID:19660565
database_cross_reference: SO:SG

intein
type: Class
subclass of: SO_0100011
definition: A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.
database_cross_reference: http://en.wikipedia.org/wiki/Intein
has_obo_namespace: sequence
has_related_synonym: protein intron
id: SO:0000728
comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein.

Axiom
annotated source: intein
annotated property: definition
annotated target: A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: intein
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Intein

intein_containing
type: Class
subclass of: protein_coding
definition: An attribute of protein-coding genes where the initial protein product contains an intein.
has_exact_synonym: intein containing
has_obo_namespace: sequence
id: SO:0000729

Axiom
annotated source: intein_containing
annotated property: definition
annotated target: An attribute of protein-coding genes where the initial protein product contains an intein.
database_cross_reference: SO:ke

gap
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: sequence_assembly
definition: A gap in the sequence of known length. The unknown bases are filled in with N's.
has_exact_synonym: INSDC_feature:gap
has_narrow_synonym: INSDC_feature:assembly_gap
has_obo_namespace: sequence
id: SO:0000730
in_subset: SOFA

Axiom
annotated source: gap
annotated property: definition
annotated target: A gap in the sequence of known length. The unknown bases are filled in with N's.
database_cross_reference: SO:ke

fragmentary
type: Class
subclass of: status
definition: An attribute to describe a feature that is incomplete.
has_exact_synonym: fragment
has_obo_namespace: sequence
id: SO:0000731
comment: Term added because of request by MO people.

Axiom
annotated source: fragmentary
annotated property: definition
annotated target: An attribute to describe a feature that is incomplete.
database_cross_reference: SO:ke

predicted
type: Class
subclass of: status
definition: An attribute describing an unverified region.
database_cross_reference: http://en.wikipedia.org/wiki/Predicted
has_obo_namespace: sequence
id: SO:0000732

Axiom
annotated source: predicted
annotated property: definition
annotated target: An attribute describing an unverified region.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: predicted
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Predicted

feature_attribute
type: Class
subclass of: sequence_attribute
definition: An attribute describing a located_sequence_feature.
has_exact_synonym: feature attribute
has_obo_namespace: sequence
id: SO:0000733

Axiom
annotated source: feature_attribute
annotated property: definition
annotated target: An attribute describing a located_sequence_feature.
database_cross_reference: SO:ke

exemplar_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: exemplar
subclass of: mRNA
subclass of: Restriction
  on property: has_quality
  some values from: exemplar
definition: An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
has_exact_synonym: exemplar mRNA
has_obo_namespace: sequence
id: SO:0000734
comment: Added for the MO people.

Axiom
annotated source: exemplar_mRNA
annotated property: definition
annotated target: An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
database_cross_reference: http://mged.sourceforge.net/ontologies/MGEDontology.php

sequence_location
type: Class
subclass of: sequence_attribute
definition: The location of a sequence.
has_exact_synonym: sequence location
has_obo_namespace: sequence
id: SO:0000735

organelle_sequence
type: Class
subclass of: sequence_location
definition: A sequence of DNA that originates from a an organelle.
has_exact_synonym: organelle sequence
has_obo_namespace: sequence
id: SO:0000736

mitochondrial_sequence
type: Class
subclass of: organelle_sequence
definition: DNA belonging to the genome of a mitochondria.
has_exact_synonym: mitochondrial sequence
has_obo_namespace: sequence
id: SO:0000737
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

nuclear_sequence
type: Class
subclass of: sequence_location
definition: DNA belonging to the nuclear genome of cell.
has_exact_synonym: nuclear sequence
has_obo_namespace: sequence
id: SO:0000738
comment: Moved from is_a SO:0000736 (organelle_sequence) when brought to our attention by GitHub issue #489.

nucleomorphic_sequence
type: Class
subclass of: organelle_sequence
definition: DNA belonging to the genome of a plastid such as a chloroplast. The nucleomorph is the nuclei of the plastic.
has_exact_synonym: nucleomorphic sequence
has_obo_namespace: sequence
id: SO:0000739

plastid_sequence
type: Class
subclass of: organelle_sequence
definition: DNA belonging to the genome of a plastid such as a chloroplast.
has_exact_synonym: plastid sequence
has_obo_namespace: sequence
id: SO:0000740

kinetoplast
type: Class
equivalent class: Class
  intersection of: sequence_collection
  intersection of: Restriction
    on property: has_part
    some values from: maxicircle
  intersection of: Restriction
    on property: has_part
    some values from: minicircle
subclass of: genome
subclass of: Restriction
  on property: has_part
  some values from: maxicircle
subclass of: Restriction
  on property: has_part
  some values from: minicircle
definition: A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species.
has_alternative_id: SO:0000826
database_cross_reference: http://en.wikipedia.org/wiki/Kinetoplast
has_exact_synonym: kinetoplast_chromosome
has_obo_namespace: sequence
id: SO:0000741

Axiom
annotated source: kinetoplast
annotated property: definition
annotated target: A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species.
database_cross_reference: PMID:8395055

wiki
type: Axiom
annotated source: kinetoplast
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Kinetoplast

maxicircle
type: Class
subclass of: replicon
definition: A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.
has_alternative_id: SO:0000827
has_exact_synonym: maxicircle_chromosome
has_obo_namespace: sequence
id: SO:0000742

Axiom
annotated source: maxicircle
annotated property: definition
annotated target: A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.
database_cross_reference: PMID:8395055

apicoplast_sequence
type: Class
subclass of: plastid_sequence
definition: DNA belonging to the genome of an apicoplast, a non-photosynthetic plastid.
has_exact_synonym: apicoplast sequence
has_obo_namespace: sequence
id: SO:0000743

chromoplast_sequence
type: Class
subclass of: plastid_sequence
definition: DNA belonging to the genome of a chromoplast, a colored plastid for synthesis and storage of pigments.
has_exact_synonym: chromoplast sequence
has_obo_namespace: sequence
id: SO:0000744

chloroplast_sequence
type: Class
subclass of: plastid_sequence
definition: DNA belonging to the genome of a chloroplast, a green plastid for photosynthesis.
has_exact_synonym: chloroplast sequence
has_obo_namespace: sequence
id: SO:0000745

cyanelle_sequence
type: Class
subclass of: plastid_sequence
definition: DNA belonging to the genome of a cyanelle, a photosynthetic plastid found in algae.
has_exact_synonym: cyanelle sequence
has_obo_namespace: sequence
id: SO:0000746

leucoplast_sequence
type: Class
subclass of: plastid_sequence
definition: DNA belonging to the genome of a leucoplast, a colorless plastid generally containing starch or oil.
has_exact_synonym: leucoplast sequence
has_obo_namespace: sequence
id: SO:0000747

proplastid_sequence
type: Class
subclass of: plastid_sequence
definition: DNA belonging to the genome of a proplastid such as an immature chloroplast.
has_exact_synonym: proplastid sequence
has_obo_namespace: sequence
id: SO:0000748

plasmid_location
type: Class
subclass of: sequence_location
definition: The location of DNA that has come from a plasmid sequence.
has_exact_synonym: plasmid location
has_obo_namespace: sequence
id: SO:0000749

amplification_origin
type: Class
subclass of: origin_of_replication
definition: An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.
has_exact_synonym: amplification origin
has_obo_namespace: sequence
id: SO:0000750

Axiom
annotated source: amplification_origin
annotated property: definition
annotated target: An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.
database_cross_reference: SO:ma

proviral_location
type: Class
subclass of: sequence_location
definition: The location of DNA that has come from a viral origin.
has_exact_synonym: proviral location
has_obo_namespace: sequence
id: SO:0000751

gene_group_regulatory_region
type: Class
definition: A region that is involved in the regulation of transcription of a group of regulated genes.
term replaced by: transcriptional_cis_regulatory_region
has_exact_synonym: gene group regulatory region
has_obo_namespace: sequence
id: SO:0000752
in_subset: SOFA
comment: Merged into transcriptional_cis_regulatory_region (SO:0001055) on 11 Feb 2021 as part of GREEKC reducing redundancy as we prepare to submit several terms to Ensembl. See GitHub Issue #529.
deprecated: true

clone_insert
type: Class
subclass of: reagent
subclass of: Restriction
  on property: part_of
  some values from: clone
definition: The region of sequence that has been inserted and is being propagated by the clone.
has_exact_synonym: clone insert
has_obo_namespace: sequence
id: SO:0000753
in_subset: SOFA

Axiom
annotated source: clone_insert
annotated property: definition
annotated target: The region of sequence that has been inserted and is being propagated by the clone.
database_cross_reference: SO:ke

lambda_vector
type: Class
subclass of: vector_replicon
definition: The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
has_exact_synonym: lambda vector
has_obo_namespace: sequence
id: SO:0000754

Axiom
annotated source: lambda_vector
annotated property: definition
annotated target: The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
database_cross_reference: ISBN:0-1767-2380-8

plasmid_vector
type: Class
equivalent class: Class
  intersection of: replicon
  intersection of: Restriction
    on property: derives_from
    some values from: plasmid
subclass of: vector_replicon
subclass of: Restriction
  on property: derives_from
  some values from: plasmid
definition: A plasmid that has been generated to act as a vector for foreign sequence.
database_cross_reference: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors
has_exact_synonym: plasmid vector
has_obo_namespace: sequence
id: SO:0000755

wiki
type: Axiom
annotated source: plasmid_vector
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors

cDNA
type: Class
subclass of: DNA
definition: DNA synthesized by reverse transcriptase using RNA as a template.
database_cross_reference: http://en.wikipedia.org/wiki/CDNA
has_exact_synonym: complementary DNA
has_obo_namespace: sequence
id: SO:0000756

Axiom
annotated source: cDNA
annotated property: definition
annotated target: DNA synthesized by reverse transcriptase using RNA as a template.
database_cross_reference: SO:ma

wiki
type: Axiom
annotated source: cDNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/CDNA

single_stranded_cDNA
type: Class
subclass of: cDNA
definition: DNA synthesized from RNA by reverse transcriptase, single stranded.
has_exact_synonym: single strand cDNA
has_exact_synonym: single stranded cDNA
has_obo_namespace: sequence
has_related_synonym: single-strand cDNA
id: SO:0000757

double_stranded_cDNA
type: Class
subclass of: cDNA
definition: DNA synthesized from RNA by reverse transcriptase that has been copied by PCR to make it double stranded.
has_exact_synonym: double stranded cDNA
has_obo_namespace: sequence
has_related_synonym: double strand cDNA
has_related_synonym: double-strand cDNA
id: SO:0000758

plasmid_clone
type: Class
has_obo_namespace: sequence
id: SO:0000759
deprecated: true

YAC_clone
type: Class
has_obo_namespace: sequence
id: SO:0000760
deprecated: true

phagemid_clone
type: Class
has_obo_namespace: sequence
id: SO:0000761
deprecated: true

PAC_clone
type: Class
has_obo_namespace: sequence
has_related_synonym: P1_clone
id: SO:0000762
deprecated: true

fosmid_clone
type: Class
has_obo_namespace: sequence
id: SO:0000763
deprecated: true

BAC_clone
type: Class
has_obo_namespace: sequence
id: SO:0000764
deprecated: true

cosmid_clone
type: Class
has_obo_namespace: sequence
id: SO:0000765
deprecated: true

pyrrolysyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: pyrrolysine_tRNA_primary_transcript
definition: A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
has_exact_synonym: pyrrolysyl tRNA
has_exact_synonym: pyrrolysyl-transfer RNA
has_exact_synonym: pyrrolysyl-transfer ribonucleic acid
has_obo_namespace: sequence
id: SO:0000766

Axiom
annotated source: pyrrolysyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
database_cross_reference: SO:ke

clone_insert_start
type: Class
has_obo_namespace: sequence
id: SO:0000767
deprecated: true

episome
type: Class
subclass of: plasmid
definition: A plasmid that may integrate with a chromosome.
has_obo_namespace: sequence
id: SO:0000768

Axiom
annotated source: episome
annotated property: definition
annotated target: A plasmid that may integrate with a chromosome.
database_cross_reference: SO:ma

tmRNA_coding_piece
type: Class
subclass of: tmRNA_region
definition: The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
has_exact_synonym: tmRNA coding piece
has_obo_namespace: sequence
id: SO:0000769
comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005.

Axiom
annotated source: tmRNA_coding_piece
annotated property: definition
annotated target: The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
database_cross_reference: Indiana:kw
database_cross_reference: doi:10.1093/nar/gkh795
database_cross_reference: issn:1362-4962

tmRNA_acceptor_piece
type: Class
subclass of: tmRNA_region
definition: The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
has_exact_synonym: tmRNA acceptor piece
has_obo_namespace: sequence
id: SO:0000770
comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005.

Axiom
annotated source: tmRNA_acceptor_piece
annotated property: definition
annotated target: The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
database_cross_reference: Indiana:kw
database_cross_reference: doi:10.1093/nar/gkh795

QTL
type: Class
subclass of: biological_region
definition: A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
has_exact_synonym: quantitative trait locus
has_obo_namespace: sequence
id: SO:0000771
comment: Added in respose to request by Simon Twigger November 14th 2005.

Axiom
annotated source: QTL
annotated property: definition
annotated target: A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
database_cross_reference: http://rgd.mcw.edu/tu/qtls/

genomic_island
type: Class
subclass of: integrated_mobile_genetic_element
definition: A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
database_cross_reference: http://en.wikipedia.org/wiki/Genomic_island
has_exact_synonym: genomic island
has_obo_namespace: sequence
id: SO:0000772
comment: Genomic islands are transmissible elements characterized by large size (>10kb).

Axiom
annotated source: genomic_island
annotated property: definition
annotated target: A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
database_cross_reference: Phigo:at
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: genomic_island
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Genomic_island

pathogenic_island
type: Class
subclass of: genomic_island
definition: Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.
has_exact_synonym: pathogenic island
has_obo_namespace: sequence
id: SO:0000773
comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.

Axiom
annotated source: pathogenic_island
annotated property: definition
annotated target: Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.
database_cross_reference: SO:ke

metabolic_island
type: Class
subclass of: genomic_island
definition: A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.
has_exact_synonym: metabolic island
has_obo_namespace: sequence
id: SO:0000774
comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.

Axiom
annotated source: metabolic_island
annotated property: definition
annotated target: A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.
database_cross_reference: SO:ke

adaptive_island
type: Class
subclass of: genomic_island
definition: An adaptive island is a genomic island that provides an adaptive advantage to the host.
has_exact_synonym: adaptive island
has_obo_namespace: sequence
id: SO:0000775
comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.

Axiom
annotated source: adaptive_island
annotated property: definition
annotated target: An adaptive island is a genomic island that provides an adaptive advantage to the host.
database_cross_reference: SO:ke

symbiosis_island
type: Class
subclass of: genomic_island
definition: A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.
has_exact_synonym: symbiosis island
has_obo_namespace: sequence
id: SO:0000776
comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.

Axiom
annotated source: symbiosis_island
annotated property: definition
annotated target: A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.
database_cross_reference: SO:ke

pseudogenic_rRNA
type: Class
subclass of: pseudogenic_transcript
definition: A non functional descendant of an rRNA.
has_broad_synonym: INSDC_feature:rRNA
has_exact_synonym: INSDC_qualifier:pseudo
has_exact_synonym: pseudogenic rRNA
has_obo_namespace: sequence
id: SO:0000777
in_subset: SOFA
comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.

Axiom
annotated source: pseudogenic_rRNA
annotated property: definition
annotated target: A non functional descendant of an rRNA.
database_cross_reference: SO:ke

pseudogenic_tRNA
type: Class
subclass of: pseudogenic_transcript
definition: A non functional descendent of a tRNA.
has_broad_synonym: INSDC_feature:tRNA
has_exact_synonym: INSDC_qualifier:pseudo
has_exact_synonym: pseudogenic tRNA
has_obo_namespace: sequence
id: SO:0000778
in_subset: SOFA
comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.

Axiom
annotated source: pseudogenic_tRNA
annotated property: definition
annotated target: A non functional descendent of a tRNA.
database_cross_reference: SO:ke

engineered_episome
type: Class
equivalent class: Class
  intersection of: episome
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: engineered_plasmid
subclass of: episome
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: An episome that is engineered.
has_exact_synonym: engineered episome
has_obo_namespace: sequence
id: SO:0000779
comment: Requested by Lynn Crosby Jan 2006.

Axiom
annotated source: engineered_episome
annotated property: definition
annotated target: An episome that is engineered.
database_cross_reference: SO:xp

transposable_element_attribute
type: Class
has_obo_namespace: sequence
id: SO:0000780
comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs
deprecated: true

transgenic
type: Class
subclass of: feature_attribute
definition: Attribute describing sequence that has been integrated with foreign sequence.
has_obo_namespace: sequence
id: SO:0000781

Axiom
annotated source: transgenic
annotated property: definition
annotated target: Attribute describing sequence that has been integrated with foreign sequence.
database_cross_reference: SO:ke

natural
type: Class
subclass of: feature_attribute
definition: An attribute describing a feature that occurs in nature.
has_obo_namespace: sequence
id: SO:0000782

Axiom
annotated source: natural
annotated property: definition
annotated target: An attribute describing a feature that occurs in nature.
database_cross_reference: SO:ke

engineered
type: Class
subclass of: feature_attribute
definition: An attribute to describe a region that was modified in vitro.
has_obo_namespace: sequence
id: SO:0000783

Axiom
annotated source: engineered
annotated property: definition
annotated target: An attribute to describe a region that was modified in vitro.
database_cross_reference: SO:ke

foreign
type: Class
subclass of: feature_attribute
definition: An attribute to describe a region from another species.
has_obo_namespace: sequence
id: SO:0000784

Axiom
annotated source: foreign
annotated property: definition
annotated target: An attribute to describe a region from another species.
database_cross_reference: SO:ke

cloned_region
type: Class
subclass of: reagent
subclass of: Restriction
  on property: part_of
  some values from: clone_insert
definition: The region of sequence that has been inserted and is being propagated by the clone.
has_exact_synonym: cloned region
has_exact_synonym: cloned segment
has_obo_namespace: sequence
id: SO:0000785
comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.

reagent_attribute
type: Class
has_exact_synonym: reagent attribute
has_obo_namespace: sequence
id: SO:0000786
comment: Added jan 2006 by KE.
deprecated: true

clone_attribute
type: Class
has_obo_namespace: sequence
id: SO:0000787
deprecated: true

cloned
type: Class
has_obo_namespace: sequence
id: SO:0000788
deprecated: true

validated
type: Class
subclass of: status
definition: An attribute to describe a feature that has been proven.
has_obo_namespace: sequence
id: SO:0000789

Axiom
annotated source: validated
annotated property: definition
annotated target: An attribute to describe a feature that has been proven.
database_cross_reference: SO:ke

invalidated
type: Class
subclass of: status
definition: An attribute describing a feature that is invalidated.
has_obo_namespace: sequence
id: SO:0000790

Axiom
annotated source: invalidated
annotated property: definition
annotated target: An attribute describing a feature that is invalidated.
database_cross_reference: SO:ke

cloned_genomic
type: Class
has_obo_namespace: sequence
id: SO:0000791
deprecated: true

cloned_cDNA
type: Class
has_obo_namespace: sequence
id: SO:0000792
deprecated: true

engineered_DNA
type: Class
has_obo_namespace: sequence
id: SO:0000793
deprecated: true

engineered_rescue_region
type: Class
equivalent class: Class
  intersection of: rescue_region
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: rescue_region
subclass of: engineered_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: A rescue region that is engineered.
has_exact_synonym: engineered rescue fragment
has_exact_synonym: engineered rescue region
has_exact_synonym: engineered rescue segment
has_obo_namespace: sequence
id: SO:0000794

Axiom
annotated source: engineered_rescue_region
annotated property: definition
annotated target: A rescue region that is engineered.
database_cross_reference: SO:xp

rescue_mini_gene
type: Class
equivalent class: Class
  intersection of: mini_gene
  intersection of: Restriction
    on property: has_quality
    some values from: rescue
subclass of: mini_gene
subclass of: Restriction
  on property: has_quality
  some values from: rescue
definition: A mini_gene that rescues.
has_exact_synonym: rescue mini gene
has_exact_synonym: rescue mini-gene
has_obo_namespace: sequence
id: SO:0000795

Axiom
annotated source: rescue_mini_gene
annotated property: definition
annotated target: A mini_gene that rescues.
database_cross_reference: SO:xp

transgenic_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: derives_from
    some values from: clone
  intersection of: Restriction
    on property: has_quality
    some values from: transgenic
subclass of: transposable_element
subclass of: Restriction
  on property: derives_from
  some values from: clone
subclass of: Restriction
  on property: has_quality
  some values from: transgenic
definition: TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.
has_exact_synonym: transgenic transposable element
has_obo_namespace: sequence
id: SO:0000796
comment: Modified as requested by Lynn - FB. May 2007.

Axiom
annotated source: transgenic_transposable_element
annotated property: definition
annotated target: TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.
database_cross_reference: FB:mc

natural_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: has_quality
    some values from: natural
subclass of: transposable_element
subclass of: extrachromosomal_mobile_genetic_element
subclass of: Restriction
  on property: has_quality
  some values from: natural
definition: TE that exists (or existed) in nature.
has_exact_synonym: natural transposable element
has_obo_namespace: sequence
id: SO:0000797

Axiom
annotated source: natural_transposable_element
annotated property: definition
annotated target: TE that exists (or existed) in nature.
database_cross_reference: FB:mc

engineered_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: transposable_element
subclass of: engineered_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: TE that has been modified by manipulations in vitro.
has_exact_synonym: engineered transposable element
has_obo_namespace: sequence
id: SO:0000798

Axiom
annotated source: engineered_transposable_element
annotated property: definition
annotated target: TE that has been modified by manipulations in vitro.
database_cross_reference: FB:mc

engineered_foreign_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: foreign_transposable_element
subclass of: engineered_transposable_element
subclass of: engineered_foreign_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
subclass of: Restriction
  on property: has_quality
  some values from: foreign
definition: A transposable_element that is engineered and foreign.
has_exact_synonym: engineered foreign transposable element
has_obo_namespace: sequence
id: SO:0000799

Axiom
annotated source: engineered_foreign_transposable_element
annotated property: definition
annotated target: A transposable_element that is engineered and foreign.
database_cross_reference: FB:mc

assortment_derived_duplication
type: Class
subclass of: assortment_derived_variation
definition: A multi-chromosome duplication aberration generated by reassortment of other aberration components.
has_exact_synonym: assortment derived duplication
has_obo_namespace: sequence
id: SO:0000800

Axiom
annotated source: assortment_derived_duplication
annotated property: definition
annotated target: A multi-chromosome duplication aberration generated by reassortment of other aberration components.
database_cross_reference: FB:gm

assortment_derived_deficiency_plus_duplication
type: Class
subclass of: assortment_derived_variation
definition: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
has_exact_synonym: assortment derived deficiency plus duplication
has_obo_namespace: sequence
id: SO:0000801

Axiom
annotated source: assortment_derived_deficiency_plus_duplication
annotated property: definition
annotated target: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
database_cross_reference: FB:gm

assortment_derived_deficiency
type: Class
subclass of: assortment_derived_variation
definition: A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
has_exact_synonym: assortment-derived deficiency
has_obo_namespace: sequence
id: SO:0000802

Axiom
annotated source: assortment_derived_deficiency
annotated property: definition
annotated target: A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
database_cross_reference: FB:gm

assortment_derived_aneuploid
type: Class
subclass of: assortment_derived_variation
definition: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
has_exact_synonym: assortment derived aneuploid
has_obo_namespace: sequence
id: SO:0000803

Axiom
annotated source: assortment_derived_aneuploid
annotated property: definition
annotated target: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
database_cross_reference: FB:gm

engineered_region
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: biomaterial_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: A region that is engineered.
has_exact_synonym: construct
has_exact_synonym: engineered region
has_exact_synonym: engineered sequence
has_obo_namespace: sequence
id: SO:0000804

Axiom
annotated source: engineered_region
annotated property: definition
annotated target: A region that is engineered.
database_cross_reference: SO:xp

engineered_foreign_region
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: engineered_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
subclass of: Restriction
  on property: has_quality
  some values from: foreign
definition: A region that is engineered and foreign.
has_exact_synonym: engineered foreign region
has_obo_namespace: sequence
id: SO:0000805

Axiom
annotated source: engineered_foreign_region
annotated property: definition
annotated target: A region that is engineered and foreign.
database_cross_reference: SO:xp

fusion
type: Class
subclass of: feature_attribute
definition: When two regions of DNA are joined together that are not normally together.
has_obo_namespace: sequence
id: SO:0000806

engineered_tag
type: Class
equivalent class: Class
  intersection of: tag
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: tag
subclass of: engineered_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: A tag that is engineered.
has_exact_synonym: engineered tag
has_obo_namespace: sequence
id: SO:0000807

Axiom
annotated source: engineered_tag
annotated property: definition
annotated target: A tag that is engineered.
database_cross_reference: SO:xp

validated_cDNA_clone
type: Class
equivalent class: Class
  intersection of: cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: validated
subclass of: cDNA_clone
subclass of: Restriction
  on property: has_quality
  some values from: validated
definition: A cDNA clone that has been validated.
has_exact_synonym: validated cDNA clone
has_obo_namespace: sequence
id: SO:0000808

Axiom
annotated source: validated_cDNA_clone
annotated property: definition
annotated target: A cDNA clone that has been validated.
database_cross_reference: SO:xp

invalidated_cDNA_clone
type: Class
equivalent class: Class
  intersection of: cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated
subclass of: cDNA_clone
subclass of: Restriction
  on property: has_quality
  some values from: invalidated
definition: A cDNA clone that is invalid.
has_exact_synonym: invalidated cDNA clone
has_obo_namespace: sequence
id: SO:0000809

Axiom
annotated source: invalidated_cDNA_clone
annotated property: definition
annotated target: A cDNA clone that is invalid.
database_cross_reference: SO:xp

chimeric_cDNA_clone
type: Class
equivalent class: Class
  intersection of: invalidated_cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated_by_chimeric_cDNA
subclass of: invalidated_cDNA_clone
subclass of: Restriction
  on property: has_quality
  some values from: invalidated_by_chimeric_cDNA
definition: A cDNA clone invalidated because it is chimeric.
has_exact_synonym: chimeric cDNA clone
has_obo_namespace: sequence
id: SO:0000810

Axiom
annotated source: chimeric_cDNA_clone
annotated property: definition
annotated target: A cDNA clone invalidated because it is chimeric.
database_cross_reference: SO:xp

genomically_contaminated_cDNA_clone
type: Class
equivalent class: Class
  intersection of: invalidated_cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated_by_genomic_contamination
subclass of: invalidated_cDNA_clone
subclass of: Restriction
  on property: has_quality
  some values from: invalidated_by_genomic_contamination
definition: A cDNA clone invalidated by genomic contamination.
has_exact_synonym: genomically contaminated cDNA clone
has_obo_namespace: sequence
id: SO:0000811

Axiom
annotated source: genomically_contaminated_cDNA_clone
annotated property: definition
annotated target: A cDNA clone invalidated by genomic contamination.
database_cross_reference: SO:xp

polyA_primed_cDNA_clone
type: Class
equivalent class: Class
  intersection of: invalidated_cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated_by_genomic_polyA_primed_cDNA
subclass of: invalidated_cDNA_clone
subclass of: Restriction
  on property: has_quality
  some values from: invalidated_by_genomic_polyA_primed_cDNA
definition: A cDNA clone invalidated by polyA priming.
has_exact_synonym: polyA primed cDNA clone
has_obo_namespace: sequence
id: SO:0000812

Axiom
annotated source: polyA_primed_cDNA_clone
annotated property: definition
annotated target: A cDNA clone invalidated by polyA priming.
database_cross_reference: SO:xp

partially_processed_cDNA_clone
type: Class
equivalent class: Class
  intersection of: invalidated_cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated_by_partial_processing
subclass of: invalidated_cDNA_clone
subclass of: Restriction
  on property: has_quality
  some values from: invalidated_by_partial_processing
definition: A cDNA invalidated clone by partial processing.
has_exact_synonym: partially processed cDNA clone
has_obo_namespace: sequence
id: SO:0000813

Axiom
annotated source: partially_processed_cDNA_clone
annotated property: definition
annotated target: A cDNA invalidated clone by partial processing.
database_cross_reference: SO:xp

rescue
type: Class
subclass of: feature_attribute
definition: An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.
has_obo_namespace: sequence
id: SO:0000814

Axiom
annotated source: rescue
annotated property: definition
annotated target: An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.
database_cross_reference: SO:ke

mini_gene
type: Class
subclass of: ORF
definition: By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.
has_exact_synonym: mini gene
has_obo_namespace: sequence
id: SO:0000815

Axiom
annotated source: mini_gene
annotated property: definition
annotated target: By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.
database_cross_reference: PMID:15992143

rescue_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: rescue
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: rescue
definition: A gene that rescues.
has_exact_synonym: rescue gene
has_obo_namespace: sequence
id: SO:0000816

Axiom
annotated source: rescue_gene
annotated property: definition
annotated target: A gene that rescues.
database_cross_reference: SO:xp

wild_type
type: Class
subclass of: feature_attribute
definition: An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.
database_cross_reference: http://en.wikipedia.org/wiki/Wild_type
database_cross_reference: loinc:LA9658-1
has_exact_synonym: wild type
has_obo_namespace: sequence
id: SO:0000817

Axiom
annotated source: wild_type
annotated property: definition
annotated target: An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: wild_type
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Wild_type

wild type
type: Axiom
annotated source: wild_type
annotated property: database_cross_reference
annotated target: loinc:LA9658-1

wild_type_rescue_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: wild_type
subclass of: rescue_gene
subclass of: Restriction
  on property: has_quality
  some values from: wild_type
definition: A gene that rescues.
has_exact_synonym: wild type rescue gene
has_obo_namespace: sequence
id: SO:0000818

Axiom
annotated source: wild_type_rescue_gene
annotated property: definition
annotated target: A gene that rescues.
database_cross_reference: SO:xp

mitochondrial_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: mitochondrial_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: mitochondrial_sequence
definition: A chromosome originating in a mitochondria.
has_exact_synonym: mitochondrial chromosome
has_obo_namespace: sequence
id: SO:0000819

Axiom
annotated source: mitochondrial_chromosome
annotated property: definition
annotated target: A chromosome originating in a mitochondria.
database_cross_reference: SO:xp

chloroplast_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: chloroplast_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: chloroplast_sequence
definition: A chromosome originating in a chloroplast.
has_exact_synonym: chloroplast chromosome
has_obo_namespace: sequence
id: SO:0000820

Axiom
annotated source: chloroplast_chromosome
annotated property: definition
annotated target: A chromosome originating in a chloroplast.
database_cross_reference: SO:xp

chromoplast_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: chromoplast_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: chromoplast_sequence
definition: A chromosome originating in a chromoplast.
has_exact_synonym: chromoplast chromosome
has_obo_namespace: sequence
id: SO:0000821

Axiom
annotated source: chromoplast_chromosome
annotated property: definition
annotated target: A chromosome originating in a chromoplast.
database_cross_reference: SO:xp

cyanelle_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: cyanelle_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: cyanelle_sequence
definition: A chromosome originating in a cyanelle.
has_exact_synonym: cyanelle chromosome
has_obo_namespace: sequence
id: SO:0000822

Axiom
annotated source: cyanelle_chromosome
annotated property: definition
annotated target: A chromosome originating in a cyanelle.
database_cross_reference: SO:xp

leucoplast_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: leucoplast_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: leucoplast_sequence
definition: A chromosome with origin in a leucoplast.
has_exact_synonym: leucoplast chromosome
has_obo_namespace: sequence
id: SO:0000823

Axiom
annotated source: leucoplast_chromosome
annotated property: definition
annotated target: A chromosome with origin in a leucoplast.
database_cross_reference: SO:xp

macronuclear_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: macronuclear_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: macronuclear_sequence
definition: A chromosome originating in a macronucleus.
has_exact_synonym: macronuclear chromosome
has_obo_namespace: sequence
id: SO:0000824

Axiom
annotated source: macronuclear_chromosome
annotated property: definition
annotated target: A chromosome originating in a macronucleus.
database_cross_reference: SO:xp

micronuclear_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: micronuclear_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: micronuclear_sequence
definition: A chromosome originating in a micronucleus.
has_exact_synonym: micronuclear chromosome
has_obo_namespace: sequence
id: SO:0000825

Axiom
annotated source: micronuclear_chromosome
annotated property: definition
annotated target: A chromosome originating in a micronucleus.
database_cross_reference: SO:xp

SO_0000826
type: Class
IAO_0000231: IAO_0000227
term replaced by: kinetoplast
deprecated: true

SO_0000827
type: Class
IAO_0000231: IAO_0000227
term replaced by: maxicircle
deprecated: true

nuclear_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: nuclear_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: nuclear_sequence
definition: A chromosome originating in a nucleus.
has_exact_synonym: nuclear chromosome
has_obo_namespace: sequence
id: SO:0000828

Axiom
annotated source: nuclear_chromosome
annotated property: definition
annotated target: A chromosome originating in a nucleus.
database_cross_reference: SO:xp

nucleomorphic_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: nucleomorphic_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: nucleomorphic_sequence
definition: A chromosome originating in a nucleomorph.
has_exact_synonym: nucleomorphic chromosome
has_obo_namespace: sequence
id: SO:0000829

Axiom
annotated source: nucleomorphic_chromosome
annotated property: definition
annotated target: A chromosome originating in a nucleomorph.
database_cross_reference: SO:xp

chromosome_part
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: chromosome
definition: A region of a chromosome.
has_exact_synonym: chromosomal region
has_exact_synonym: chromosomal_region
has_exact_synonym: chromosome part
has_obo_namespace: sequence
id: SO:0000830
in_subset: SOFA
comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.

Axiom
annotated source: chromosome_part
annotated property: definition
annotated target: A region of a chromosome.
database_cross_reference: SO:ke

gene_member_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: member_of
  some values from: gene
definition: A region of a gene.
has_exact_synonym: gene member region
has_obo_namespace: sequence
id: SO:0000831
in_subset: SOFA
comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root.

Axiom
annotated source: gene_member_region
annotated property: definition
annotated target: A region of a gene.
database_cross_reference: SO:ke

promoter_region
type: Class
definition: A region of sequence which is part of a promoter.
has_obo_namespace: sequence
id: SO:0000832
comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.
deprecated: true

Axiom
annotated source: promoter_region
annotated property: definition
annotated target: A region of sequence which is part of a promoter.
database_cross_reference: SO:ke

transcript_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: transcript
definition: A region of a transcript.
has_exact_synonym: transcript region
has_obo_namespace: sequence
id: SO:0000833
in_subset: SOFA
comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.

Axiom
annotated source: transcript_region
annotated property: definition
annotated target: A region of a transcript.
database_cross_reference: SO:ke

mature_transcript_region
type: Class
subclass of: transcript_region
definition: A region of a mature transcript.
has_exact_synonym: mature transcript region
has_obo_namespace: sequence
id: SO:0000834
in_subset: SOFA
comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.

Axiom
annotated source: mature_transcript_region
annotated property: definition
annotated target: A region of a mature transcript.
database_cross_reference: SO:ke

primary_transcript_region
type: Class
subclass of: transcript_region
subclass of: Restriction
  on property: part_of
  some values from: primary_transcript
definition: A part of a primary transcript.
has_exact_synonym: primary transcript region
has_obo_namespace: sequence
id: SO:0000835
in_subset: SOFA
comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.

Axiom
annotated source: primary_transcript_region
annotated property: definition
annotated target: A part of a primary transcript.
database_cross_reference: SO:ke

mRNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: mRNA
definition: A region of an mRNA.
has_exact_synonym: mRNA region
has_obo_namespace: sequence
id: SO:0000836
in_subset: SOFA
comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.

Axiom
annotated source: mRNA_region
annotated property: definition
annotated target: A region of an mRNA.
database_cross_reference: SO:cb

UTR_region
type: Class
subclass of: mRNA_region
definition: A region of UTR.
has_exact_synonym: UTR region
has_obo_namespace: sequence
id: SO:0000837
in_subset: SOFA
comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.

Axiom
annotated source: UTR_region
annotated property: definition
annotated target: A region of UTR.
database_cross_reference: SO:ke

rRNA_primary_transcript_region
type: Class
subclass of: primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: rRNA_primary_transcript
definition: A region of an rRNA primary transcript.
has_exact_synonym: rRNA primary transcript region
has_obo_namespace: sequence
id: SO:0000838
comment: To allow transcribed_spacer_region to have a path to the root.

Axiom
annotated source: rRNA_primary_transcript_region
annotated property: definition
annotated target: A region of an rRNA primary transcript.
database_cross_reference: SO:ke

polypeptide_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: polypeptide
definition: Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
has_alternative_id: BS:00124
has_alternative_id: BS:00331
has_narrow_synonym: region
has_narrow_synonym: site
has_obo_namespace: sequence
has_related_synonym: positional
has_related_synonym: positional polypeptide feature
has_related_synonym: region or site annotation
id: SO:0000839
in_subset: SOFA
in_subset: biosapiens
comment: Added to allow the polypeptide regions to have is_a paths back to the root.

Axiom
annotated source: polypeptide_region
annotated property: definition
annotated target: Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
database_cross_reference: SO:GAR
database_cross_reference: SO:ke

Axiom
annotated source: polypeptide_region
annotated property: has_narrow_synonym
annotated target: region
database_cross_reference: uniprot:feature_type

Axiom
annotated source: polypeptide_region
annotated property: has_narrow_synonym
annotated target: site
database_cross_reference: uniprot:feature_type

repeat_component
type: Class
subclass of: topologically_defined_region
definition: A region of a repeated sequence.
has_exact_synonym: repeat component
has_obo_namespace: sequence
id: SO:0000840
comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root.

Axiom
annotated source: repeat_component
annotated property: definition
annotated target: A region of a repeated sequence.
database_cross_reference: SO:ke

spliceosomal_intron_region
type: Class
subclass of: primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: spliceosomal_intron
definition: A region within an intron.
has_exact_synonym: spliceosomal intron region
has_obo_namespace: sequence
id: SO:0000841
in_subset: SOFA
comment: A terms added to allow the parts of introns to have is_a paths to the root.

Axiom
annotated source: spliceosomal_intron_region
annotated property: definition
annotated target: A region within an intron.
database_cross_reference: SO:ke

gene_component_region
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: gene
definition: A region of a gene that has a specific function.
has_exact_synonym: gene component region
has_obo_namespace: sequence
id: SO:0000842
in_subset: SOFA

bacterial_RNApol_promoter_region
type: Class
definition: A region which is part of a bacterial RNA polymerase promoter.
has_obo_namespace: sequence
id: SO:0000843
comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.
deprecated: true

Axiom
annotated source: bacterial_RNApol_promoter_region
annotated property: definition
annotated target: A region which is part of a bacterial RNA polymerase promoter.
database_cross_reference: SO:ke

RNApol_II_promoter_region
type: Class
definition: A region of sequence which is a promoter for RNA polymerase II.
has_obo_namespace: sequence
id: SO:0000844
comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.
deprecated: true

Axiom
annotated source: RNApol_II_promoter_region
annotated property: definition
annotated target: A region of sequence which is a promoter for RNA polymerase II.
database_cross_reference: SO:ke

RNApol_III_promoter_type_1_region
type: Class
definition: A region of sequence which is a promoter for RNA polymerase III type 1.
has_obo_namespace: sequence
id: SO:0000845
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.
deprecated: true

Axiom
annotated source: RNApol_III_promoter_type_1_region
annotated property: definition
annotated target: A region of sequence which is a promoter for RNA polymerase III type 1.
database_cross_reference: SO:ke

RNApol_III_promoter_type_2_region
type: Class
definition: A region of sequence which is a promoter for RNA polymerase III type 2.
has_obo_namespace: sequence
id: SO:0000846
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.
deprecated: true

Axiom
annotated source: RNApol_III_promoter_type_2_region
annotated property: definition
annotated target: A region of sequence which is a promoter for RNA polymerase III type 2.
database_cross_reference: SO:ke

tmRNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: tmRNA
definition: A region of a tmRNA.
has_exact_synonym: tmRNA region
has_obo_namespace: sequence
id: SO:0000847
comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.

Axiom
annotated source: tmRNA_region
annotated property: definition
annotated target: A region of a tmRNA.
database_cross_reference: SO:cb

LTR_component
type: Class
subclass of: repeat_component
subclass of: Restriction
  on property: part_of
  some values from: long_terminal_repeat
definition: The long terminal repeat found at the ends of the sequence to be inserted into the host genome.
has_exact_synonym: LTR component
has_exact_synonym: long term repeat component
has_obo_namespace: sequence
id: SO:0000848

three_prime_LTR_component
type: Class
subclass of: LTR_component
subclass of: Restriction
  on property: part_of
  some values from: three_prime_LTR
definition: A component of the three-prime long terminal repeat.
has_exact_synonym: 3' long terminal repeat component
has_exact_synonym: three prime LTR component
has_obo_namespace: sequence
id: SO:0000849

Axiom
annotated source: three_prime_LTR_component
annotated property: definition
annotated target: A component of the three-prime long terminal repeat.
database_cross_reference: PMID:8649407

five_prime_LTR_component
type: Class
subclass of: LTR_component
subclass of: Restriction
  on property: part_of
  some values from: five_prime_LTR
definition: A component of the five-prime long terminal repeat.
has_exact_synonym: 5' long term repeat component
has_exact_synonym: five prime LTR component
has_obo_namespace: sequence
id: SO:0000850

Axiom
annotated source: five_prime_LTR_component
annotated property: definition
annotated target: A component of the five-prime long terminal repeat.
database_cross_reference: PMID:8649407

CDS_region
type: Class
subclass of: mRNA_region
subclass of: Restriction
  on property: part_of
  some values from: CDS
definition: A region of a CDS.
has_exact_synonym: CDS region
has_obo_namespace: sequence
id: SO:0000851
in_subset: SOFA

Axiom
annotated source: CDS_region
annotated property: definition
annotated target: A region of a CDS.
database_cross_reference: SO:cb

exon_region
type: Class
subclass of: transcript_region
subclass of: Restriction
  on property: part_of
  some values from: exon
definition: A region of an exon.
has_exact_synonym: exon region
has_obo_namespace: sequence
id: SO:0000852
in_subset: SOFA

Axiom
annotated source: exon_region
annotated property: definition
annotated target: A region of an exon.
database_cross_reference: RSC:cb

homologous_region
type: Class
equivalent class: Class
  intersection of: conserved_region
  intersection of: Restriction
    on property: has_quality
    some values from: homologous
subclass of: conserved_region
subclass of: Restriction
  on property: has_quality
  some values from: homologous
definition: A region that is homologous to another region.
database_cross_reference: http://en.wikipedia.org/wiki/Homology_(biology)
has_exact_synonym: homolog
has_exact_synonym: homologous region
has_exact_synonym: homologue
has_obo_namespace: sequence
id: SO:0000853

Axiom
annotated source: homologous_region
annotated property: definition
annotated target: A region that is homologous to another region.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: homologous_region
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Homology_(biology)

paralogous_region
type: Class
equivalent class: Class
  intersection of: homologous_region
  intersection of: Restriction
    on property: has_quality
    some values from: paralogous
subclass of: homologous_region
subclass of: Restriction
  on property: has_quality
  some values from: paralogous
definition: A homologous_region that is paralogous to another region.
database_cross_reference: http://en.wikipedia.org/wiki/Paralog#Paralogy
has_exact_synonym: paralog
has_exact_synonym: paralogous region
has_exact_synonym: paralogue
has_obo_namespace: sequence
id: SO:0000854
comment: A term to be used in conjunction with the paralogous_to relationship.

Axiom
annotated source: paralogous_region
annotated property: definition
annotated target: A homologous_region that is paralogous to another region.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: paralogous_region
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Paralog#Paralogy

orthologous_region
type: Class
equivalent class: Class
  intersection of: homologous_region
  intersection of: Restriction
    on property: has_quality
    some values from: orthologous
subclass of: homologous_region
subclass of: Restriction
  on property: has_quality
  some values from: orthologous
definition: A homologous_region that is orthologous to another region.
database_cross_reference: http://en.wikipedia.org/wiki/Ortholog#Orthology
has_exact_synonym: ortholog
has_exact_synonym: orthologous region
has_exact_synonym: orthologue
has_obo_namespace: sequence
id: SO:0000855
comment: This term should be used in conjunction with the similarity relationships defined in SO.

Axiom
annotated source: orthologous_region
annotated property: definition
annotated target: A homologous_region that is orthologous to another region.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: orthologous_region
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Ortholog#Orthology

conserved
type: Class
subclass of: feature_attribute
definition: A region that is similar or identical across more than one species.
has_obo_namespace: sequence
id: SO:0000856

homologous
type: Class
subclass of: conserved
definition: Similarity due to common ancestry.
has_obo_namespace: sequence
id: SO:0000857

Axiom
annotated source: homologous
annotated property: definition
annotated target: Similarity due to common ancestry.
database_cross_reference: SO:ke

orthologous
type: Class
subclass of: homologous
definition: An attribute describing a kind of homology where divergence occurred after a speciation event.
has_obo_namespace: sequence
id: SO:0000858

Axiom
annotated source: orthologous
annotated property: definition
annotated target: An attribute describing a kind of homology where divergence occurred after a speciation event.
database_cross_reference: SO:ke

paralogous
type: Class
subclass of: homologous
definition: An attribute describing a kind of homology where divergence occurred after a duplication event.
has_obo_namespace: sequence
id: SO:0000859

Axiom
annotated source: paralogous
annotated property: definition
annotated target: An attribute describing a kind of homology where divergence occurred after a duplication event.
database_cross_reference: SO:ke

syntenic
type: Class
subclass of: conserved
definition: Attribute describing sequence regions occurring in same order on chromosome of different species.
database_cross_reference: http://en.wikipedia.org/wiki/Syntenic
has_obo_namespace: sequence
id: SO:0000860

Axiom
annotated source: syntenic
annotated property: definition
annotated target: Attribute describing sequence regions occurring in same order on chromosome of different species.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: syntenic
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Syntenic

capped_primary_transcript
type: Class
equivalent class: Class
  intersection of: primary_transcript
  intersection of: Restriction
    on property: adjacent_to
    some values from: cap
  intersection of: Restriction
    on property: has_quality
    some values from: capped
subclass of: primary_transcript
subclass of: Restriction
  on property: adjacent_to
  some values from: cap
subclass of: Restriction
  on property: has_quality
  some values from: capped
definition: A primary transcript that is capped.
has_exact_synonym: capped primary transcript
has_obo_namespace: sequence
id: SO:0000861

Axiom
annotated source: capped_primary_transcript
annotated property: definition
annotated target: A primary transcript that is capped.
database_cross_reference: SO:xp

capped_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: adjacent_to
    some values from: cap
  intersection of: Restriction
    on property: has_quality
    some values from: capped
subclass of: mRNA
subclass of: Restriction
  on property: adjacent_to
  some values from: cap
subclass of: Restriction
  on property: has_quality
  some values from: capped
definition: An mRNA that is capped.
has_exact_synonym: capped mRNA
has_obo_namespace: sequence
id: SO:0000862

Axiom
annotated source: capped_mRNA
annotated property: definition
annotated target: An mRNA that is capped.
database_cross_reference: SO:xp

mRNA_attribute
type: Class
subclass of: transcript_attribute
definition: An attribute describing an mRNA feature.
has_exact_synonym: mRNA attribute
has_obo_namespace: sequence
id: SO:0000863

Axiom
annotated source: mRNA_attribute
annotated property: definition
annotated target: An attribute describing an mRNA feature.
database_cross_reference: SO:ke

exemplar
type: Class
subclass of: mRNA_attribute
definition: An attribute describing a sequence is representative of a class of similar sequences.
has_obo_namespace: sequence
id: SO:0000864

Axiom
annotated source: exemplar
annotated property: definition
annotated target: An attribute describing a sequence is representative of a class of similar sequences.
database_cross_reference: SO:ke

frameshift
type: Class
subclass of: mRNA_attribute
definition: An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.
database_cross_reference: http://en.wikipedia.org/wiki/Frameshift
has_obo_namespace: sequence
id: SO:0000865

Axiom
annotated source: frameshift
annotated property: definition
annotated target: An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: frameshift
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Frameshift

minus_1_frameshift
type: Class
subclass of: frameshift
definition: A frameshift caused by deleting one base.
has_exact_synonym: minus 1 frameshift
has_obo_namespace: sequence
id: SO:0000866

Axiom
annotated source: minus_1_frameshift
annotated property: definition
annotated target: A frameshift caused by deleting one base.
database_cross_reference: SO:ke

minus_2_frameshift
type: Class
subclass of: frameshift
definition: A frameshift caused by deleting two bases.
has_exact_synonym: minus 2 frameshift
has_obo_namespace: sequence
id: SO:0000867

Axiom
annotated source: minus_2_frameshift
annotated property: definition
annotated target: A frameshift caused by deleting two bases.
database_cross_reference: SO:ke

plus_1_frameshift
type: Class
subclass of: frameshift
definition: A frameshift caused by inserting one base.
has_exact_synonym: plus 1 frameshift
has_obo_namespace: sequence
id: SO:0000868

Axiom
annotated source: plus_1_frameshift
annotated property: definition
annotated target: A frameshift caused by inserting one base.
database_cross_reference: SO:ke

plus_2_framshift
type: Class
subclass of: frameshift
definition: A frameshift caused by inserting two bases.
has_exact_synonym: plus 2 framshift
has_obo_namespace: sequence
id: SO:0000869

Axiom
annotated source: plus_2_framshift
annotated property: definition
annotated target: A frameshift caused by inserting two bases.
database_cross_reference: SO:ke

trans_spliced
type: Class
subclass of: transcript_attribute
definition: An attribute describing transcript sequence that is created by splicing exons from diferent genes.
has_exact_synonym: trans-spliced
has_obo_namespace: sequence
id: SO:0000870

Axiom
annotated source: trans_spliced
annotated property: definition
annotated target: An attribute describing transcript sequence that is created by splicing exons from diferent genes.
database_cross_reference: SO:ke

polyadenylated_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: adjacent_to
    some values from: polyA_sequence
  intersection of: Restriction
    on property: has_quality
    some values from: polyadenylated
subclass of: mRNA
subclass of: Restriction
  on property: adjacent_to
  some values from: polyA_sequence
subclass of: Restriction
  on property: has_quality
  some values from: polyadenylated
definition: An mRNA that is polyadenylated.
has_exact_synonym: polyadenylated mRNA
has_obo_namespace: sequence
id: SO:0000871

Axiom
annotated source: polyadenylated_mRNA
annotated property: definition
annotated target: An mRNA that is polyadenylated.
database_cross_reference: SO:xp

trans_spliced_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: adjacent_to
    some values from: spliced_leader_RNA
  intersection of: Restriction
    on property: has_quality
    some values from: trans_spliced
subclass of: mRNA
subclass of: trans_spliced_transcript
subclass of: Restriction
  on property: adjacent_to
  some values from: spliced_leader_RNA
subclass of: Restriction
  on property: has_quality
  some values from: trans_spliced
definition: An mRNA that is trans-spliced.
has_exact_synonym: trans-spliced mRNA
has_obo_namespace: sequence
id: SO:0000872

Axiom
annotated source: trans_spliced_mRNA
annotated property: definition
annotated target: An mRNA that is trans-spliced.
database_cross_reference: SO:xp

edited_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: edited
subclass of: transcript
subclass of: Restriction
  on property: guided_by
  some values from: guide_RNA
subclass of: Restriction
  on property: has_part
  some values from: anchor_binding_site
subclass of: Restriction
  on property: has_quality
  some values from: edited
definition: A transcript that is edited.
has_exact_synonym: edited transcript
has_obo_namespace: sequence
id: SO:0000873

Axiom
annotated source: edited_transcript
annotated property: definition
annotated target: A transcript that is edited.
database_cross_reference: SO:ke

edited_transcript_by_A_to_I_substitution
type: Class
subclass of: edited_transcript
definition: A transcript that has been edited by A to I substitution.
has_exact_synonym: edited transcript by A to I substitution
has_obo_namespace: sequence
id: SO:0000874

Axiom
annotated source: edited_transcript_by_A_to_I_substitution
annotated property: definition
annotated target: A transcript that has been edited by A to I substitution.
database_cross_reference: SO:ke

bound_by_protein
type: Class
subclass of: bound_by_factor
definition: An attribute describing a sequence that is bound by a protein.
has_exact_synonym: bound by protein
has_obo_namespace: sequence
id: SO:0000875

Axiom
annotated source: bound_by_protein
annotated property: definition
annotated target: An attribute describing a sequence that is bound by a protein.
database_cross_reference: SO:ke

bound_by_nucleic_acid
type: Class
subclass of: bound_by_factor
definition: An attribute describing a sequence that is bound by a nucleic acid.
has_exact_synonym: bound by nucleic acid
has_obo_namespace: sequence
id: SO:0000876

Axiom
annotated source: bound_by_nucleic_acid
annotated property: definition
annotated target: An attribute describing a sequence that is bound by a nucleic acid.
database_cross_reference: SO:ke

alternatively_spliced
type: Class
subclass of: transcript_attribute
definition: An attribute describing a situation where a gene may encode for more than 1 transcript.
has_exact_synonym: alternatively spliced
has_obo_namespace: sequence
id: SO:0000877

Axiom
annotated source: alternatively_spliced
annotated property: definition
annotated target: An attribute describing a situation where a gene may encode for more than 1 transcript.
database_cross_reference: SO:ke

monocistronic
type: Class
subclass of: transcript_attribute
definition: An attribute describing a sequence that contains the code for one gene product.
has_obo_namespace: sequence
id: SO:0000878

Axiom
annotated source: monocistronic
annotated property: definition
annotated target: An attribute describing a sequence that contains the code for one gene product.
database_cross_reference: SO:ke

dicistronic
type: Class
subclass of: polycistronic
definition: An attribute describing a sequence that contains the code for two gene products.
has_obo_namespace: sequence
id: SO:0000879

Axiom
annotated source: dicistronic
annotated property: definition
annotated target: An attribute describing a sequence that contains the code for two gene products.
database_cross_reference: SO:ke

polycistronic
type: Class
subclass of: transcript_attribute
definition: An attribute describing a sequence that contains the code for more than one gene product.
has_obo_namespace: sequence
id: SO:0000880

Axiom
annotated source: polycistronic
annotated property: definition
annotated target: An attribute describing a sequence that contains the code for more than one gene product.
database_cross_reference: SO:ke

recoded
type: Class
subclass of: mRNA_attribute
definition: An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.
has_obo_namespace: sequence
id: SO:0000881

Axiom
annotated source: recoded
annotated property: definition
annotated target: An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.
database_cross_reference: SO:ke

codon_redefined
type: Class
subclass of: recoded
definition: An attribute describing the alteration of codon meaning.
has_exact_synonym: codon redefined
has_obo_namespace: sequence
id: SO:0000882

Axiom
annotated source: codon_redefined
annotated property: definition
annotated target: An attribute describing the alteration of codon meaning.
database_cross_reference: SO:ke

stop_codon_read_through
type: Class
subclass of: recoded_codon
definition: A stop codon redefined to be a new amino acid.
has_exact_synonym: stop codon read through
has_obo_namespace: sequence
has_related_synonym: stop codon readthrough
id: SO:0000883

Axiom
annotated source: stop_codon_read_through
annotated property: definition
annotated target: A stop codon redefined to be a new amino acid.
database_cross_reference: SO:ke

stop_codon_redefined_as_pyrrolysine
type: Class
subclass of: stop_codon_read_through
definition: A stop codon redefined to be the new amino acid, pyrrolysine.
has_exact_synonym: stop codon redefined as pyrrolysine
has_obo_namespace: sequence
id: SO:0000884

Axiom
annotated source: stop_codon_redefined_as_pyrrolysine
annotated property: definition
annotated target: A stop codon redefined to be the new amino acid, pyrrolysine.
database_cross_reference: SO:ke

stop_codon_redefined_as_selenocysteine
type: Class
subclass of: stop_codon_read_through
definition: A stop codon redefined to be the new amino acid, selenocysteine.
has_exact_synonym: stop codon redefined as selenocysteine
has_obo_namespace: sequence
id: SO:0000885

Axiom
annotated source: stop_codon_redefined_as_selenocysteine
annotated property: definition
annotated target: A stop codon redefined to be the new amino acid, selenocysteine.
database_cross_reference: SO:ke

recoded_by_translational_bypass
type: Class
subclass of: recoded
definition: Recoded mRNA where a block of nucleotides is not translated.
has_exact_synonym: recoded by translational bypass
has_obo_namespace: sequence
id: SO:0000886

Axiom
annotated source: recoded_by_translational_bypass
annotated property: definition
annotated target: Recoded mRNA where a block of nucleotides is not translated.
database_cross_reference: SO:ke

translationally_frameshifted
type: Class
subclass of: recoded
definition: Recoding by frameshifting a particular site.
has_exact_synonym: translationally frameshifted
has_obo_namespace: sequence
id: SO:0000887

Axiom
annotated source: translationally_frameshifted
annotated property: definition
annotated target: Recoding by frameshifting a particular site.
database_cross_reference: SO:ke

maternally_imprinted_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: maternally_imprinted
subclass of: epigenetically_modified_gene
subclass of: Restriction
  on property: has_quality
  some values from: maternally_imprinted
definition: A gene that is maternally_imprinted.
has_exact_synonym: maternally imprinted gene
has_obo_namespace: sequence
id: SO:0000888

Axiom
annotated source: maternally_imprinted_gene
annotated property: definition
annotated target: A gene that is maternally_imprinted.
database_cross_reference: SO:xp

paternally_imprinted_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: paternally_imprinted
subclass of: epigenetically_modified_gene
subclass of: Restriction
  on property: has_quality
  some values from: paternally_imprinted
definition: A gene that is paternally imprinted.
has_exact_synonym: paternally imprinted gene
has_obo_namespace: sequence
id: SO:0000889

Axiom
annotated source: paternally_imprinted_gene
annotated property: definition
annotated target: A gene that is paternally imprinted.
database_cross_reference: SO:xp

post_translationally_regulated_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: post_translationally_regulated
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: post_translationally_regulated
definition: A gene that is post translationally regulated.
has_exact_synonym: post translationally regulated gene
has_obo_namespace: sequence
id: SO:0000890

Axiom
annotated source: post_translationally_regulated_gene
annotated property: definition
annotated target: A gene that is post translationally regulated.
database_cross_reference: SO:xp

negatively_autoregulated_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: negatively_autoregulated
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: negatively_autoregulated
definition: A gene that is negatively autoreguated.
has_exact_synonym: negatively autoregulated gene
has_obo_namespace: sequence
id: SO:0000891

Axiom
annotated source: negatively_autoregulated_gene
annotated property: definition
annotated target: A gene that is negatively autoreguated.
database_cross_reference: SO:xp

positively_autoregulated_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: positively_autoregulated
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: positively_autoregulated
definition: A gene that is positively autoregulated.
has_exact_synonym: positively autoregulated gene
has_obo_namespace: sequence
id: SO:0000892

Axiom
annotated source: positively_autoregulated_gene
annotated property: definition
annotated target: A gene that is positively autoregulated.
database_cross_reference: SO:xp

silenced
type: Class
subclass of: transcriptionally_repressed
definition: An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.
database_cross_reference: http://en.wikipedia.org/wiki/Silenced
has_obo_namespace: sequence
id: SO:0000893

Axiom
annotated source: silenced
annotated property: definition
annotated target: An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: silenced
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Silenced

silenced_by_DNA_modification
type: Class
subclass of: silenced
definition: An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.
has_exact_synonym: silenced by DNA modification
has_obo_namespace: sequence
id: SO:0000894

Axiom
annotated source: silenced_by_DNA_modification
annotated property: definition
annotated target: An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.
database_cross_reference: SO:ke

silenced_by_DNA_methylation
type: Class
subclass of: silenced_by_DNA_modification
definition: An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.
has_exact_synonym: silenced by DNA methylation
has_obo_namespace: sequence
id: SO:0000895

Axiom
annotated source: silenced_by_DNA_methylation
annotated property: definition
annotated target: An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.
database_cross_reference: SO:ke

translationally_regulated_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: translationally_regulated
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: translationally_regulated
definition: A gene that is translationally regulated.
has_exact_synonym: translationally regulated gene
has_obo_namespace: sequence
id: SO:0000896

Axiom
annotated source: translationally_regulated_gene
annotated property: definition
annotated target: A gene that is translationally regulated.
database_cross_reference: SO:xp

allelically_excluded_gene
type: Class
equivalent class: Class
  intersection of: epigenetically_modified_gene
  intersection of: Restriction
    on property: has_quality
    some values from: allelically_excluded
subclass of: epigenetically_modified_gene
subclass of: Restriction
  on property: has_quality
  some values from: allelically_excluded
definition: A gene that is allelically_excluded.
has_exact_synonym: allelically excluded gene
has_obo_namespace: sequence
id: SO:0000897

Axiom
annotated source: allelically_excluded_gene
annotated property: definition
annotated target: A gene that is allelically_excluded.
database_cross_reference: SO:xp

epigenetically_modified_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: epigenetically_modified
subclass of: gene
subclass of: epigenetically_modified_region
subclass of: Restriction
  on property: has_quality
  some values from: epigenetically_modified
definition: A gene that is epigenetically modified.
has_exact_synonym: epigenetically modified gene
has_obo_namespace: sequence
id: SO:0000898

Axiom
annotated source: epigenetically_modified_gene
annotated property: definition
annotated target: A gene that is epigenetically modified.
database_cross_reference: SO:ke

nuclear_mitochondrial
type: Class
definition: An attribute describing a nuclear pseudogene of a mitochndrial gene.
has_exact_synonym: nuclear mitochondrial
has_obo_namespace: sequence
id: SO:0000899
deprecated: true

Axiom
annotated source: nuclear_mitochondrial
annotated property: definition
annotated target: An attribute describing a nuclear pseudogene of a mitochndrial gene.
database_cross_reference: SO:ke

processed
type: Class
definition: An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.
has_obo_namespace: sequence
id: SO:0000900
deprecated: true

Axiom
annotated source: processed
annotated property: definition
annotated target: An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.
database_cross_reference: SO:ke

unequally_crossed_over
type: Class
definition: An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.
has_exact_synonym: unequally crossed over
has_obo_namespace: sequence
id: SO:0000901
deprecated: true

Axiom
annotated source: unequally_crossed_over
annotated property: definition
annotated target: An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.
database_cross_reference: SO:ke

transgene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: transgenic
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: transgenic
definition: A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
database_cross_reference: http://en.wikipedia.org/wiki/Transgene
has_obo_namespace: sequence
id: SO:0000902

Axiom
annotated source: transgene
annotated property: definition
annotated target: A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
database_cross_reference: SO:xp

wiki
type: Axiom
annotated source: transgene
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Transgene

endogenous_retroviral_sequence
type: Class
subclass of: proviral_location
definition: Endogenous DNA sequence that are likely to have arisen from retroviruses.
has_exact_synonym: endogenous retroviral sequence
has_obo_namespace: sequence
id: SO:0000903

rearranged_at_DNA_level
type: Class
subclass of: epigenetically_modified
definition: An attribute to describe the sequence of a feature, where the DNA is rearranged.
has_exact_synonym: rearranged at DNA level
has_obo_namespace: sequence
id: SO:0000904

Axiom
annotated source: rearranged_at_DNA_level
annotated property: definition
annotated target: An attribute to describe the sequence of a feature, where the DNA is rearranged.
database_cross_reference: SO:ke

status
type: Class
subclass of: feature_attribute
definition: An attribute describing the status of a feature, based on the available evidence.
has_obo_namespace: sequence
id: SO:0000905
comment: This term is the hypernym of attributes and should not be annotated to.

Axiom
annotated source: status
annotated property: definition
annotated target: An attribute describing the status of a feature, based on the available evidence.
database_cross_reference: SO:ke

independently_known
type: Class
subclass of: status
definition: Attribute to describe a feature that is independently known - not predicted.
has_exact_synonym: independently known
has_obo_namespace: sequence
id: SO:0000906

Axiom
annotated source: independently_known
annotated property: definition
annotated target: Attribute to describe a feature that is independently known - not predicted.
database_cross_reference: SO:ke

supported_by_sequence_similarity
type: Class
subclass of: predicted
definition: An attribute to describe a feature that has been predicted using sequence similarity techniques.
has_exact_synonym: supported by sequence similarity
has_obo_namespace: sequence
id: SO:0000907

Axiom
annotated source: supported_by_sequence_similarity
annotated property: definition
annotated target: An attribute to describe a feature that has been predicted using sequence similarity techniques.
database_cross_reference: SO:ke

supported_by_domain_match
type: Class
subclass of: supported_by_sequence_similarity
definition: An attribute to describe a feature that has been predicted using sequence similarity of a known domain.
has_exact_synonym: supported by domain match
has_obo_namespace: sequence
id: SO:0000908

Axiom
annotated source: supported_by_domain_match
annotated property: definition
annotated target: An attribute to describe a feature that has been predicted using sequence similarity of a known domain.
database_cross_reference: SO:ke

supported_by_EST_or_cDNA
type: Class
subclass of: supported_by_sequence_similarity
definition: An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.
has_exact_synonym: supported by EST or cDNA
has_obo_namespace: sequence
id: SO:0000909

Axiom
annotated source: supported_by_EST_or_cDNA
annotated property: definition
annotated target: An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.
database_cross_reference: SO:ke

orphan
type: Class
subclass of: predicted
definition: A gene whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.
has_obo_namespace: sequence
id: SO:0000910

predicted_by_ab_initio_computation
type: Class
subclass of: predicted
definition: An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.
has_exact_synonym: predicted by ab initio computation
has_obo_namespace: sequence
id: SO:0000911

Axiom
annotated source: predicted_by_ab_initio_computation
annotated property: definition
annotated target: An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.
database_cross_reference: SO:ke

asx_turn
type: Class
subclass of: polypeptide_turn_motif
definition: A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
has_alternative_id: BS:00203
has_exact_synonym: asx turn
has_obo_namespace: sequence
id: SO:0000912
in_subset: biosapiens

Axiom
annotated source: asx_turn
annotated property: definition
annotated target: A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

cloned_cDNA_insert
type: Class
equivalent class: Class
  intersection of: clone_insert
  intersection of: Restriction
    on property: has_quality
    some values from: cDNA
subclass of: clone_insert
subclass of: Restriction
  on property: has_quality
  some values from: cDNA
definition: A clone insert made from cDNA.
has_exact_synonym: cloned cDNA insert
has_obo_namespace: sequence
id: SO:0000913

Axiom
annotated source: cloned_cDNA_insert
annotated property: definition
annotated target: A clone insert made from cDNA.
database_cross_reference: SO:xp

cloned_genomic_insert
type: Class
equivalent class: Class
  intersection of: clone_insert
  intersection of: Restriction
    on property: has_quality
    some values from: genomic_DNA
subclass of: clone_insert
subclass of: Restriction
  on property: has_quality
  some values from: genomic_DNA
definition: A clone insert made from genomic DNA.
has_exact_synonym: cloned genomic insert
has_obo_namespace: sequence
id: SO:0000914

Axiom
annotated source: cloned_genomic_insert
annotated property: definition
annotated target: A clone insert made from genomic DNA.
database_cross_reference: SO:xp

engineered_insert
type: Class
equivalent class: Class
  intersection of: clone_insert
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: clone_insert
subclass of: engineered_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: A clone insert that is engineered.
has_exact_synonym: engineered insert
has_obo_namespace: sequence
id: SO:0000915

Axiom
annotated source: engineered_insert
annotated property: definition
annotated target: A clone insert that is engineered.
database_cross_reference: SO:xp

edit_operation
type: Class
has_exact_synonym: edit operation
has_obo_namespace: sequence
id: SO:0000916
deprecated: true

insert_U
type: Class
definition: An edit to insert a U.
has_exact_synonym: insert U
has_obo_namespace: sequence
id: SO:0000917
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
deprecated: true

Axiom
annotated source: insert_U
annotated property: definition
annotated target: An edit to insert a U.
database_cross_reference: SO:ke

delete_U
type: Class
definition: An edit to delete a uridine.
has_exact_synonym: delete U
has_obo_namespace: sequence
id: SO:0000918
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
deprecated: true

Axiom
annotated source: delete_U
annotated property: definition
annotated target: An edit to delete a uridine.
database_cross_reference: SO:ke

substitute_A_to_I
type: Class
definition: An edit to substitute an I for an A.
has_exact_synonym: substitute A to I
has_obo_namespace: sequence
id: SO:0000919
deprecated: true

Axiom
annotated source: substitute_A_to_I
annotated property: definition
annotated target: An edit to substitute an I for an A.
database_cross_reference: SO:ke

insert_C
type: Class
definition: An edit to insert a cytidine.
has_exact_synonym: insert C
has_obo_namespace: sequence
id: SO:0000920
deprecated: true

Axiom
annotated source: insert_C
annotated property: definition
annotated target: An edit to insert a cytidine.
database_cross_reference: SO:ke

insert_dinucleotide
type: Class
definition: An edit to insert a dinucleotide.
has_exact_synonym: insert dinucleotide
has_obo_namespace: sequence
id: SO:0000921
deprecated: true

Axiom
annotated source: insert_dinucleotide
annotated property: definition
annotated target: An edit to insert a dinucleotide.
database_cross_reference: SO:ke

substitute_C_to_U
type: Class
definition: An edit to substitute an U for a C.
has_exact_synonym: substitute C to U
has_obo_namespace: sequence
id: SO:0000922
deprecated: true

Axiom
annotated source: substitute_C_to_U
annotated property: definition
annotated target: An edit to substitute an U for a C.
database_cross_reference: SO:ke

insert_G
type: Class
definition: An edit to insert a G.
has_exact_synonym: insert G
has_obo_namespace: sequence
id: SO:0000923
deprecated: true

Axiom
annotated source: insert_G
annotated property: definition
annotated target: An edit to insert a G.
database_cross_reference: SO:ke

insert_GC
type: Class
definition: An edit to insert a GC dinucleotide.
has_exact_synonym: insert GC
has_obo_namespace: sequence
id: SO:0000924
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
deprecated: true

Axiom
annotated source: insert_GC
annotated property: definition
annotated target: An edit to insert a GC dinucleotide.
database_cross_reference: SO:ke

insert_GU
type: Class
definition: An edit to insert a GU dinucleotide.
has_exact_synonym: insert GU
has_obo_namespace: sequence
id: SO:0000925
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
deprecated: true

Axiom
annotated source: insert_GU
annotated property: definition
annotated target: An edit to insert a GU dinucleotide.
database_cross_reference: SO:ke

insert_CU
type: Class
definition: An edit to insert a CU dinucleotide.
has_exact_synonym: insert CU
has_obo_namespace: sequence
id: SO:0000926
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
deprecated: true

Axiom
annotated source: insert_CU
annotated property: definition
annotated target: An edit to insert a CU dinucleotide.
database_cross_reference: SO:ke

insert_AU
type: Class
definition: An edit to insert a AU dinucleotide.
has_exact_synonym: insert AU
has_obo_namespace: sequence
id: SO:0000927
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
deprecated: true

Axiom
annotated source: insert_AU
annotated property: definition
annotated target: An edit to insert a AU dinucleotide.
database_cross_reference: SO:ke

insert_AA
type: Class
definition: An edit to insert a AA dinucleotide.
has_exact_synonym: insert AA
has_obo_namespace: sequence
id: SO:0000928
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
deprecated: true

Axiom
annotated source: insert_AA
annotated property: definition
annotated target: An edit to insert a AA dinucleotide.
database_cross_reference: SO:ke

edited_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: edited
subclass of: mRNA
subclass of: edited_transcript
subclass of: Restriction
  on property: has_quality
  some values from: edited
definition: An mRNA that is edited.
has_exact_synonym: edited mRNA
has_obo_namespace: sequence
id: SO:0000929

Axiom
annotated source: edited_mRNA
annotated property: definition
annotated target: An mRNA that is edited.
database_cross_reference: SO:xp

guide_RNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: guide_RNA
definition: A region of guide RNA.
has_exact_synonym: guide RNA region
has_obo_namespace: sequence
id: SO:0000930

Axiom
annotated source: guide_RNA_region
annotated property: definition
annotated target: A region of guide RNA.
database_cross_reference: SO:ma

anchor_region
type: Class
subclass of: guide_RNA_region
definition: A region of a guide_RNA that base-pairs to a target mRNA.
has_exact_synonym: anchor region
has_obo_namespace: sequence
id: SO:0000931

Axiom
annotated source: anchor_region
annotated property: definition
annotated target: A region of a guide_RNA that base-pairs to a target mRNA.
database_cross_reference: SO:jk

pre_edited_mRNA
type: Class
subclass of: protein_coding_primary_transcript
definition: A primary transcript that, at least in part, encodes one or more proteins that has not been edited.
has_exact_synonym: pre-edited mRNA
has_obo_namespace: sequence
id: SO:0000932

intermediate
type: Class
subclass of: feature_attribute
definition: An attribute to describe a feature between stages of processing.
has_obo_namespace: sequence
id: SO:0000933

Axiom
annotated source: intermediate
annotated property: definition
annotated target: An attribute to describe a feature between stages of processing.
database_cross_reference: SO:ke

miRNA_target_site
type: Class
subclass of: nucleotide_binding_site
definition: A miRNA target site is a binding site where the molecule is a micro RNA.
has_exact_synonym: miRNA target site
has_obo_namespace: sequence
id: SO:0000934

Axiom
annotated source: miRNA_target_site
annotated property: definition
annotated target: A miRNA target site is a binding site where the molecule is a micro RNA.
database_cross_reference: FB:cds

edited_CDS
type: Class
equivalent class: Class
  intersection of: CDS
  intersection of: Restriction
    on property: has_quality
    some values from: edited
subclass of: CDS
subclass of: Restriction
  on property: has_quality
  some values from: edited
definition: A CDS that is edited.
has_exact_synonym: edited CDS
has_obo_namespace: sequence
id: SO:0000935

Axiom
annotated source: edited_CDS
annotated property: definition
annotated target: A CDS that is edited.
database_cross_reference: SO:xp

vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA.
has_exact_synonym: vertebrate immunoglobulin T cell receptor rearranged segment
has_obo_namespace: sequence
id: SO:0000936

vertebrate_immune_system_feature
type: Class
has_obo_namespace: sequence
id: SO:0000937
deprecated: true

vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration.
has_exact_synonym: vertebrate immunoglobulin T cell receptor rearranged gene cluster
has_obo_namespace: sequence
id: SO:0000938

vertebrate_immune_system_gene_recombination_signal_feature
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
definition: Feature used for the recombination of genomic material for the purpose of generating diversity of the immune system.
has_exact_synonym: vertebrate immune system gene recombination signal feature
has_obo_namespace: sequence
id: SO:0000939

recombinationally_rearranged
type: Class
subclass of: feature_attribute
definition: A gene that is recombinationally rearranged.
has_exact_synonym: recombinationally rearranged
has_obo_namespace: sequence
id: SO:0000940

recombinationally_rearranged_vertebrate_immune_system_gene
type: Class
subclass of: recombinationally_rearranged_gene
definition: A recombinationally rearranged gene of the vertebrate immune system.
has_exact_synonym: recombinationally rearranged vertebrate immune system gene
has_obo_namespace: sequence
id: SO:0000941

Axiom
annotated source: recombinationally_rearranged_vertebrate_immune_system_gene
annotated property: definition
annotated target: A recombinationally rearranged gene of the vertebrate immune system.
database_cross_reference: SO:xp

attP_site
type: Class
subclass of: integration_excision_site
subclass of: Restriction
  on property: part_of
  some values from: phage_sequence
definition: An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome.
has_exact_synonym: attP site
has_obo_namespace: sequence
id: SO:0000942

Axiom
annotated source: attP_site
annotated property: definition
annotated target: An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome.
database_cross_reference: SO:as

attB_site
type: Class
subclass of: integration_excision_site
definition: An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
has_exact_synonym: attB site
has_obo_namespace: sequence
id: SO:0000943

Axiom
annotated source: attB_site
annotated property: definition
annotated target: An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
database_cross_reference: SO:as

attL_site
type: Class
subclass of: integration_excision_site
definition: A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site.
has_obo_namespace: sequence
has_related_synonym: attBP'
has_related_synonym: attL site
id: SO:0000944

Axiom
annotated source: attL_site
annotated property: definition
annotated target: A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site.
database_cross_reference: SO:as

attR_site
type: Class
subclass of: integration_excision_site
definition: A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site.
has_exact_synonym: attR site
has_obo_namespace: sequence
has_related_synonym: attPB'
id: SO:0000945

Axiom
annotated source: attR_site
annotated property: definition
annotated target: A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site.
database_cross_reference: SO:as

integration_excision_site
type: Class
subclass of: site_specific_recombination_target_region
definition: A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site.
has_exact_synonym: integration excision site
has_obo_namespace: sequence
has_related_synonym: attachment site
id: SO:0000946

Axiom
annotated source: integration_excision_site
annotated property: definition
annotated target: A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site.
database_cross_reference: SO:as

resolution_site
type: Class
subclass of: site_specific_recombination_target_region
definition: A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles.
has_exact_synonym: res site
has_exact_synonym: resolution site
has_obo_namespace: sequence
id: SO:0000947

Axiom
annotated source: resolution_site
annotated property: definition
annotated target: A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles.
database_cross_reference: SO:as

inversion_site
type: Class
subclass of: site_specific_recombination_target_region
definition: A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.
has_exact_synonym: inversion site
has_obo_namespace: sequence
id: SO:0000948
comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.

Axiom
annotated source: inversion_site
annotated property: definition
annotated target: A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.
database_cross_reference: SO:ma

dif_site
type: Class
subclass of: resolution_site
definition: A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase.
has_exact_synonym: dif site
has_obo_namespace: sequence
id: SO:0000949

Axiom
annotated source: dif_site
annotated property: definition
annotated target: A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase.
database_cross_reference: SO:as

attC_site
type: Class
subclass of: integration_excision_site
subclass of: Restriction
  on property: part_of
  some values from: integron
definition: An attC site is a sequence required for the integration of a DNA of an integron.
has_exact_synonym: attC site
has_obo_namespace: sequence
id: SO:0000950

Axiom
annotated source: attC_site
annotated property: definition
annotated target: An attC site is a sequence required for the integration of a DNA of an integron.
database_cross_reference: SO:as

eukaryotic_terminator
type: Class
subclass of: terminator
definition: A signal for RNA polymerase to terminate transcription.
has_exact_synonym: eukaryotic terminator
has_obo_namespace: sequence
id: SO:0000951

oriV
type: Class
subclass of: origin_of_replication
definition: An origin of vegetative replication in plasmids and phages.
has_exact_synonym: origin of vegetative replication
has_obo_namespace: sequence
id: SO:0000952

Axiom
annotated source: oriV
annotated property: definition
annotated target: An origin of vegetative replication in plasmids and phages.
database_cross_reference: SO:as

oriC
type: Class
subclass of: origin_of_replication
definition: An origin of bacterial chromosome replication.
has_exact_synonym: origin of bacterial chromosome replication
has_obo_namespace: sequence
id: SO:0000953

Axiom
annotated source: oriC
annotated property: definition
annotated target: An origin of bacterial chromosome replication.
database_cross_reference: SO:as

DNA_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: DNA
subclass of: chromosome
subclass of: Restriction
  on property: has_quality
  some values from: DNA
definition: Structural unit composed of a self-replicating, DNA molecule.
has_exact_synonym: DNA chromosome
has_obo_namespace: sequence
id: SO:0000954

Axiom
annotated source: DNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, DNA molecule.
database_cross_reference: SO:ma

double_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: double
subclass of: DNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: double
definition: Structural unit composed of a self-replicating, double-stranded DNA molecule.
has_exact_synonym: double stranded DNA chromosome
has_obo_namespace: sequence
id: SO:0000955

Axiom
annotated source: double_stranded_DNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, double-stranded DNA molecule.
database_cross_reference: SO:ma

single_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: single
subclass of: DNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: single
definition: Structural unit composed of a self-replicating, single-stranded DNA molecule.
has_exact_synonym: single stranded DNA chromosome
has_obo_namespace: sequence
id: SO:0000956

Axiom
annotated source: single_stranded_DNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, single-stranded DNA molecule.
database_cross_reference: SO:ma

linear_double_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: double_stranded_DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: linear
subclass of: double_stranded_DNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: linear
definition: Structural unit composed of a self-replicating, double-stranded, linear DNA molecule.
has_exact_synonym: linear double stranded DNA chromosome
has_obo_namespace: sequence
id: SO:0000957

Axiom
annotated source: linear_double_stranded_DNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, double-stranded, linear DNA molecule.
database_cross_reference: SO:ma

circular_double_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: double_stranded_DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: circular
subclass of: double_stranded_DNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: circular
definition: Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.
has_exact_synonym: circular double stranded DNA chromosome
has_obo_namespace: sequence
id: SO:0000958

Axiom
annotated source: circular_double_stranded_DNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.
database_cross_reference: SO:ma

linear_single_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: single_stranded_DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: linear
subclass of: single_stranded_DNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: linear
definition: Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.
has_exact_synonym: linear single stranded DNA chromosome
has_obo_namespace: sequence
id: SO:0000959

Axiom
annotated source: linear_single_stranded_DNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.
database_cross_reference: SO:ma

circular_single_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: single_stranded_DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: circular
subclass of: single_stranded_DNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: circular
definition: Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
has_exact_synonym: circular single stranded DNA chromosome
has_obo_namespace: sequence
id: SO:0000960

Axiom
annotated source: circular_single_stranded_DNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
database_cross_reference: SO:ma

RNA_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: RNA
subclass of: chromosome
subclass of: Restriction
  on property: has_quality
  some values from: RNA
definition: Structural unit composed of a self-replicating, RNA molecule.
has_exact_synonym: RNA chromosome
has_obo_namespace: sequence
id: SO:0000961

Axiom
annotated source: RNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, RNA molecule.
database_cross_reference: SO:ma

single_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: single
subclass of: RNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: single
definition: Structural unit composed of a self-replicating, single-stranded RNA molecule.
has_exact_synonym: single stranded RNA chromosome
has_obo_namespace: sequence
id: SO:0000962

Axiom
annotated source: single_stranded_RNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, single-stranded RNA molecule.
database_cross_reference: SO:ma

linear_single_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: single_stranded_RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: linear
subclass of: single_stranded_RNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: linear
definition: Structural unit composed of a self-replicating, single-stranded, linear RNA molecule.
has_exact_synonym: linear single stranded RNA chromosome
has_obo_namespace: sequence
id: SO:0000963

Axiom
annotated source: linear_single_stranded_RNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, single-stranded, linear RNA molecule.
database_cross_reference: SO:ma

linear_double_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: double_stranded_RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: linear
subclass of: double_stranded_RNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: linear
definition: Structural unit composed of a self-replicating, double-stranded, linear RNA molecule.
has_exact_synonym: linear double stranded RNA chromosome
has_obo_namespace: sequence
id: SO:0000964

Axiom
annotated source: linear_double_stranded_RNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, double-stranded, linear RNA molecule.
database_cross_reference: SO:ma

double_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: double
subclass of: RNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: double
definition: Structural unit composed of a self-replicating, double-stranded RNA molecule.
has_exact_synonym: double stranded RNA chromosome
has_obo_namespace: sequence
id: SO:0000965

Axiom
annotated source: double_stranded_RNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, double-stranded RNA molecule.
database_cross_reference: SO:ma

circular_single_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: single_stranded_RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: circular
subclass of: single_stranded_RNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: circular
definition: Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
has_exact_synonym: circular single stranded RNA chromosome
has_obo_namespace: sequence
id: SO:0000966

Axiom
annotated source: circular_single_stranded_RNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
database_cross_reference: SO:ma

circular_double_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: double_stranded_RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: circular
subclass of: double_stranded_RNA_chromosome
subclass of: Restriction
  on property: has_quality
  some values from: circular
definition: Structural unit composed of a self-replicating, double-stranded, circular RNA molecule.
has_exact_synonym: circular double stranded RNA chromosome
has_obo_namespace: sequence
id: SO:0000967

Axiom
annotated source: circular_double_stranded_RNA_chromosome
annotated property: definition
annotated target: Structural unit composed of a self-replicating, double-stranded, circular RNA molecule.
database_cross_reference: SO:ma

sequence_replication_mode
type: Class
has_exact_synonym: sequence replication mode
has_obo_namespace: sequence
id: SO:0000968
comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
deprecated: true

rolling_circle
type: Class
database_cross_reference: http://en.wikipedia.org/wiki/Rolling_circle
has_exact_synonym: rolling circle
has_obo_namespace: sequence
id: SO:0000969
comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581.
deprecated: true

wiki
type: Axiom
annotated source: rolling_circle
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Rolling_circle

theta_replication
type: Class
has_exact_synonym: theta replication
has_obo_namespace: sequence
id: SO:0000970
comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582
deprecated: true

DNA_replication_mode
type: Class
has_exact_synonym: DNA replication mode
has_obo_namespace: sequence
id: SO:0000971
comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260.
deprecated: true

RNA_replication_mode
type: Class
has_exact_synonym: RNA replication mode
has_obo_namespace: sequence
id: SO:0000972
comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
deprecated: true

insertion_sequence
type: Class
subclass of: terminal_inverted_repeat_element
definition: A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.
database_cross_reference: http://en.wikipedia.org/wiki/Insertion_sequence
has_exact_synonym: insertion sequence
has_obo_namespace: sequence
has_related_synonym: IS
id: SO:0000973

Axiom
annotated source: insertion_sequence
annotated property: definition
annotated target: A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.
database_cross_reference: SO:as

wiki
type: Axiom
annotated source: insertion_sequence
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Insertion_sequence

SO_0000974
type: Class
IAO_0000231: IAO_0000227
term replaced by: minicircle
deprecated: true

minicircle_gene
type: Class
equivalent class: Class
  intersection of: kinetoplast_gene
  intersection of: Restriction
    on property: part_of
    some values from: minicircle
subclass of: kinetoplast_gene
subclass of: Restriction
  on property: part_of
  some values from: minicircle
definition: A gene found within a minicircle.
has_exact_synonym: minicircle gene
has_obo_namespace: sequence
id: SO:0000975

cryptic
type: Class
subclass of: feature_attribute
definition: A feature_attribute describing a feature that is not manifest under normal conditions.
has_obo_namespace: sequence
id: SO:0000976

Axiom
annotated source: cryptic
annotated property: definition
annotated target: A feature_attribute describing a feature that is not manifest under normal conditions.
database_cross_reference: SO:ke

anchor_binding_site
type: Class
subclass of: transcript_region
has_exact_synonym: anchor binding site
has_obo_namespace: sequence
id: SO:0000977
comment: Part of an edited transcript only.

template_region
type: Class
subclass of: guide_RNA_region
definition: A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
has_exact_synonym: information region
has_exact_synonym: template region
has_obo_namespace: sequence
id: SO:0000978

Axiom
annotated source: template_region
annotated property: definition
annotated target: A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
database_cross_reference: SO:jk

gRNA_encoding
type: Class
subclass of: non_protein_coding
definition: A non-protein_coding gene that encodes a guide_RNA.
has_exact_synonym: gRNA encoding
has_obo_namespace: sequence
id: SO:0000979

Axiom
annotated source: gRNA_encoding
annotated property: definition
annotated target: A non-protein_coding gene that encodes a guide_RNA.
database_cross_reference: SO:ma

minicircle
type: Class
subclass of: replicon
definition: A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs.
has_alternative_id: SO:0000974
database_cross_reference: http://en.wikipedia.org/wiki/Minicircle
has_exact_synonym: minicircle_chromosome
has_obo_namespace: sequence
id: SO:0000980

Axiom
annotated source: minicircle
annotated property: definition
annotated target: A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs.
database_cross_reference: PMID:8395055

wiki
type: Axiom
annotated source: minicircle
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Minicircle

rho_dependent_bacterial_terminator
type: Class
subclass of: bacterial_terminator
definition: A transcription terminator that is dependent upon Rho.
has_exact_synonym: rho dependent bacterial terminator
has_obo_namespace: sequence
id: SO:0000981

rho_independent_bacterial_terminator
type: Class
subclass of: bacterial_terminator
definition: A transcription terminator that is not dependent upon Rho. Rather, the mRNA contains a sequence that allows it to base-pair with itself and make a stem-loop structure.
has_exact_synonym: rho independent bacterial terminator
has_obo_namespace: sequence
id: SO:0000982

strand_attribute
type: Class
subclass of: feature_attribute
definition: The attribute of how many strands are present in a nucleotide polymer.
has_exact_synonym: strand attribute
has_obo_namespace: sequence
id: SO:0000983
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.

single
type: Class
subclass of: strand_attribute
definition: When a nucleotide polymer has only one strand.
has_obo_namespace: sequence
id: SO:0000984
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.

double
type: Class
subclass of: strand_attribute
definition: When a nucleotide polymer has two strands that are reverse-complement to one another and pair together.
has_obo_namespace: sequence
id: SO:0000985
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.

topology_attribute
type: Class
subclass of: polymer_attribute
definition: The attribute of whether a nucleotide polymer is linear or circular.
has_exact_synonym: topology attribute
has_obo_namespace: sequence
id: SO:0000986
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.

linear
type: Class
subclass of: topology_attribute
disjoint with: circular
definition: A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.
has_obo_namespace: sequence
has_related_synonym: two-ended
id: SO:0000987
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.

Axiom
annotated source: linear
annotated property: definition
annotated target: A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.
database_cross_reference: SO:cb

circular
type: Class
subclass of: topology_attribute
definition: A quality of a nucleotide polymer that has no terminal nucleotide residues.
has_obo_namespace: sequence
has_related_synonym: zero-ended
id: SO:0000988
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.

Axiom
annotated source: circular
annotated property: definition
annotated target: A quality of a nucleotide polymer that has no terminal nucleotide residues.
database_cross_reference: SO:cb

class_II_RNA
type: Class
subclass of: ncRNA
definition: Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
has_exact_synonym: class II RNA
has_obo_namespace: sequence
id: SO:0000989

Axiom
annotated source: class_II_RNA
annotated property: definition
annotated target: Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
database_cross_reference: PMID:15333696

class_I_RNA
type: Class
subclass of: ncRNA
definition: Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
has_exact_synonym: class I RNA
has_obo_namespace: sequence
id: SO:0000990
comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.

Axiom
annotated source: class_I_RNA
annotated property: definition
annotated target: Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
database_cross_reference: PMID:15333696

genomic_DNA
type: Class
subclass of: DNA
definition: DNA located in the genome and able to be transmitted to the offspring.
has_exact_synonym: gDNA
has_exact_synonym: genomic DNA
has_obo_namespace: sequence
id: SO:0000991
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated source: genomic_DNA
annotated property: definition
annotated target: DNA located in the genome and able to be transmitted to the offspring.
database_cross_reference: BCS:etrwz

BAC_cloned_genomic_insert
type: Class
equivalent class: Class
  intersection of: cloned_genomic_insert
  intersection of: Restriction
    on property: derives_from
    some values from: BAC
subclass of: cloned_genomic_insert
subclass of: Restriction
  on property: derives_from
  some values from: BAC
definition: A region of DNA that has been inserted into the bacterial genome using a bacterial artificial chromosome.
has_exact_synonym: BAC cloned genomic insert
has_obo_namespace: sequence
id: SO:0000992
comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006.

consensus
type: Class
subclass of: status
definition: A sequence produced from an aligment algorithm that uses multiple sequences as input.
has_obo_namespace: sequence
id: SO:0000993
comment: Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.

consensus_region
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: consensus
subclass of: experimental_feature
subclass of: Restriction
  on property: has_quality
  some values from: consensus
definition: A region that has a known consensus sequence.
has_exact_synonym: consensus region
has_obo_namespace: sequence
id: SO:0000994
comment: DO not obsolete without considering MGED mapping.

consensus_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: consensus
subclass of: mRNA
subclass of: consensus_region
subclass of: Restriction
  on property: has_quality
  some values from: consensus
definition: An mRNA sequence produced from an aligment algorithm that uses multiple sequences as input.
has_exact_synonym: consensus mRNA
has_obo_namespace: sequence
id: SO:0000995
comment: DO not obsolete without considering MGED mapping.

predicted_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: predicted
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: predicted
definition: A region of the genome that has been predicted to be a gene but has not been confirmed by laboratory experiments.
has_exact_synonym: predicted gene
has_obo_namespace: sequence
id: SO:0000996
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

gene_fragment
type: Class
equivalent class: Class
  intersection of: gene_component_region
  intersection of: Restriction
    on property: has_quality
    some values from: fragmentary
subclass of: gene_component_region
subclass of: Restriction
  on property: has_quality
  some values from: fragmentary
definition: A portion of a gene that is not the complete gene.
has_exact_synonym: gene fragment
has_obo_namespace: sequence
id: SO:0000997
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

recursive_splice_site
type: Class
subclass of: cis_splice_site
definition: A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.
has_exact_synonym: recursive splice site
has_obo_namespace: sequence
id: SO:0000998

Axiom
annotated source: recursive_splice_site
annotated property: definition
annotated target: A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.
database_cross_reference: http://www.genetics.org/cgi/content/full/170/2/661

BAC_end
type: Class
subclass of: read
subclass of: Restriction
  on property: part_of
  some values from: BAC
definition: A region of sequence from the end of a BAC clone that may provide a highly specific marker.
has_exact_synonym: BAC end
has_exact_synonym: BAC end sequence
has_exact_synonym: BES
has_obo_namespace: sequence
id: SO:0000999
comment: Requested by Keith Boroevich December, 2006.

Axiom
annotated source: BAC_end
annotated property: definition
annotated target: A region of sequence from the end of a BAC clone that may provide a highly specific marker.
database_cross_reference: SO:ke

cytosolic_16S_rRNA
type: Class
subclass of: cytosolic_SSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002237
definition: Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes.
database_cross_reference: http://en.wikipedia.org/wiki/16S_ribosomal_RNA
has_exact_synonym: cytosolic 16S SSU RNA
has_exact_synonym: cytosolic 16S ribosomal RNA
has_exact_synonym: cytosolic rRNA 16S
has_obo_namespace: sequence
has_related_synonym: cytosolic 16S rRNA
id: SO:0001000
in_subset: SOFA
comment: Renamed to cytosolic_16S_rRNA from rRNA_16S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_16S_rRNA
annotated property: definition
annotated target: Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: cytosolic_16S_rRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/16S_ribosomal_RNA

cytosolic_23S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002243
definition: Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes.
has_exact_synonym: cytosolic 23S LSU rRNA
has_exact_synonym: cytosolic 23S rRNA
has_exact_synonym: cytosolic rRNA 23S
has_obo_namespace: sequence
has_related_synonym: cytosolic 23S ribosomal RNA
id: SO:0001001
in_subset: SOFA
comment: Renamed from rRNA_23S to cytosolic_23S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_23S_rRNA
annotated property: definition
annotated target: Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes.
database_cross_reference: SO:ke

cytosolic_25S_rRNA
type: Class
subclass of: cytosolic_LSU_rRNA
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002242
definition: Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes.
has_exact_synonym: cytosolic 25S LSU rRNA
has_exact_synonym: cytosolic 25S rRNA
has_exact_synonym: cytosolic 25S ribosomal RNA
has_exact_synonym: cytosolic rRNA 25S
has_obo_namespace: sequence
id: SO:0001002
in_subset: SOFA
comment: Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.

Axiom
annotated source: cytosolic_25S_rRNA
annotated property: definition
annotated target: Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes.
database_cross_reference: PMID:15493135
database_cross_reference: PMID:2100998
database_cross_reference: RSC:cb

solo_LTR
type: Class
subclass of: long_terminal_repeat
definition: A recombination product between the 2 LTR of the same element.
has_exact_synonym: solo LTR
has_obo_namespace: sequence
id: SO:0001003
comment: Requested by Hadi Quesneville January 2007.

Axiom
annotated source: solo_LTR
annotated property: definition
annotated target: A recombination product between the 2 LTR of the same element.
database_cross_reference: SO:ke

low_complexity
type: Class
subclass of: status
definition: When a sequence does not contain an equal distribution of all four possible nucleotide bases or does not contain all nucleotide bases.
has_exact_synonym: low complexity
has_obo_namespace: sequence
id: SO:0001004

low_complexity_region
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: low_complexity
subclass of: experimental_feature
subclass of: Restriction
  on property: has_quality
  some values from: low_complexity
definition: A region where the DNA does not contain an equal distrubution of all four possible nucleotides or does not contain all four nucleotides.
has_exact_synonym: low complexity region
has_obo_namespace: sequence
id: SO:0001005

prophage
type: Class
subclass of: proviral_region
definition: A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island".
database_cross_reference: http://en.wikipedia.org/wiki/Prophage
has_obo_namespace: sequence
id: SO:0001006

Axiom
annotated source: prophage
annotated property: definition
annotated target: A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island".
database_cross_reference: GOC:jl

wiki
type: Axiom
annotated source: prophage
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Prophage

cryptic_prophage
type: Class
subclass of: genomic_island
definition: A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.
database_cross_reference: http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w
has_exact_synonym: cryptic prophage
has_obo_namespace: sequence
id: SO:0001007
comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site.

Axiom
annotated source: cryptic_prophage
annotated property: definition
annotated target: A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.
database_cross_reference: GOC:jl

tetraloop
type: Class
subclass of: stem_loop
definition: A base-paired stem with loop of 4 non-hydrogen bonded nucleotides.
database_cross_reference: http://en.wikipedia.org/wiki/Tetraloop
has_obo_namespace: sequence
id: SO:0001008

Axiom
annotated source: tetraloop
annotated property: definition
annotated target: A base-paired stem with loop of 4 non-hydrogen bonded nucleotides.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: tetraloop
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Tetraloop

DNA_constraint_sequence
type: Class
subclass of: ds_oligo
definition: A double-stranded DNA used to control macromolecular structure and function.
has_exact_synonym: DNA constraint
has_exact_synonym: DNA constraint sequence
has_obo_namespace: sequence
id: SO:0001009

Axiom
annotated source: DNA_constraint_sequence
annotated property: definition
annotated target: A double-stranded DNA used to control macromolecular structure and function.

i_motif
type: Class
subclass of: DNA_sequence_secondary_structure
definition: A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.
has_exact_synonym: i motif
has_exact_synonym: short intercalated motif
has_obo_namespace: sequence
id: SO:0001010

Axiom
annotated source: i_motif
annotated property: definition
annotated target: A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.
database_cross_reference: PMID:9753739

PNA_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: PNA
subclass of: synthetic_oligo
subclass of: Restriction
  on property: has_quality
  some values from: PNA
definition: Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
database_cross_reference: http://en.wikipedia.org/wiki/Peptide_nucleic_acid
has_exact_synonym: PNA oligo
has_exact_synonym: peptide nucleic acid
has_obo_namespace: sequence
id: SO:0001011

Axiom
annotated source: PNA_oligo
annotated property: definition
annotated target: Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: PNA_oligo
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Peptide_nucleic_acid

DNAzyme
type: Class
equivalent class: Class
  intersection of: oligo
  intersection of: Restriction
    on property: has_quality
    some values from: enzymatic
subclass of: oligo
subclass of: Restriction
  on property: has_quality
  some values from: enzymatic
definition: A DNA sequence with catalytic activity.
has_exact_synonym: DNA enzyme
has_exact_synonym: catalytic DNA
has_obo_namespace: sequence
has_related_synonym: deoxyribozyme
id: SO:0001012
comment: Added by request from Colin Batchelor.

Axiom
annotated source: DNAzyme
annotated property: definition
annotated target: A DNA sequence with catalytic activity.
database_cross_reference: SO:cb

MNP
type: Class
subclass of: SO_0002007
definition: A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.
has_obo_namespace: sequence
has_related_synonym: multiple nucleotide polymorphism
id: SO:0001013

Axiom
annotated source: MNP
annotated property: definition
annotated target: A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.
database_cross_reference: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi

intron_domain
type: Class
subclass of: primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: intron
definition: An intronic region that has an attribute.
has_exact_synonym: intron domain
has_obo_namespace: sequence
id: SO:0001014
comment: Requested by Colin Batchelor, Feb 2007.

wobble_base_pair
type: Class
subclass of: base_pair
definition: A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.
database_cross_reference: http://en.wikipedia.org/wiki/Wobble_base_pair
has_exact_synonym: wobble base pair
has_exact_synonym: wobble pair
has_obo_namespace: sequence
id: SO:0001015

Axiom
annotated source: wobble_base_pair
annotated property: definition
annotated target: A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.
database_cross_reference: PMID:11256617

wiki
type: Axiom
annotated source: wobble_base_pair
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Wobble_base_pair

internal_guide_sequence
type: Class
subclass of: intron_domain
subclass of: Restriction
  on property: part_of
  some values from: group_I_intron
definition: A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.
has_exact_synonym: IGS
has_exact_synonym: internal guide sequence
has_obo_namespace: sequence
id: SO:0001016

Axiom
annotated source: internal_guide_sequence
annotated property: definition
annotated target: A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.
database_cross_reference: SO:cb

silent_mutation
type: Class
subclass of: SO_0001878
definition: A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation.
database_cross_reference: http://en.wikipedia.org/wiki/Silent_mutation
database_cross_reference: loinc:LA6700-4
has_exact_synonym: silent mutation
has_obo_namespace: sequence
id: SO:0001017
comment: Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc.

Axiom
annotated source: silent_mutation
annotated property: definition
annotated target: A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: silent_mutation
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Silent_mutation

Silent
type: Axiom
annotated source: silent_mutation
annotated property: database_cross_reference
annotated target: loinc:LA6700-4

epitope
type: Class
subclass of: binding_site
definition: A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.
database_cross_reference: http://en.wikipedia.org/wiki/Epitope
has_obo_namespace: sequence
id: SO:0001018
comment: Requested by Trish Whetzel.

Axiom
annotated source: epitope
annotated property: definition
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.
database_cross_reference: SO:cb
database_cross_reference: http://en.wikipedia.org/wiki/Epitope

wiki
type: Axiom
annotated source: epitope
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Epitope

copy_number_variation
type: Class
subclass of: sequence_length_alteration
definition: A variation that increases or decreases the copy number of a given region.
database_cross_reference: http://en.wikipedia.org/wiki/Copy_number_variation
has_exact_synonym: CNP
has_exact_synonym: CNV
has_exact_synonym: copy number polymorphism
has_exact_synonym: copy number variation
has_obo_namespace: sequence
id: SO:0001019
in_subset: SOFA

Axiom
annotated source: copy_number_variation
annotated property: definition
annotated target: A variation that increases or decreases the copy number of a given region.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: copy_number_variation
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Copy_number_variation

sequence_variant_affecting_copy_number
type: Class
term replaced by: copy_number_change
has_exact_synonym: mutation affecting copy number
has_exact_synonym: sequence variant affecting copy number
has_obo_namespace: sequence
id: SO:0001020
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
deprecated: true

chromosome_breakpoint
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: chromosome
definition: A chromosomal region that may sustain a double-strand break, resulting in a recombination event.
has_alternative_id: SO:0001242
has_broad_synonym: INSDC_feature:misc_recomb
has_exact_synonym: INSDC_qualifier:chromosome_breakpoint
has_exact_synonym: aberration breakpoint
has_exact_synonym: aberration_junction
has_exact_synonym: chromosome breakpoint
has_obo_namespace: sequence
id: SO:0001021

inversion_breakpoint
type: Class
subclass of: chromosome_breakpoint
definition: The point within a chromosome where an inversion begins or ends.
has_exact_synonym: inversion breakpoint
has_obo_namespace: sequence
id: SO:0001022

Axiom
annotated source: inversion_breakpoint
annotated property: definition
annotated target: The point within a chromosome where an inversion begins or ends.
database_cross_reference: SO:cb

allele
type: Class
subclass of: variant_collection
subclass of: Restriction
  on property: variant_of
  some values from: gene
definition: An allele is one of a set of coexisting sequence variants of a gene.
database_cross_reference: http://en.wikipedia.org/wiki/Allele
has_exact_synonym: allelomorph
has_obo_namespace: sequence
id: SO:0001023

Axiom
annotated source: allele
annotated property: definition
annotated target: An allele is one of a set of coexisting sequence variants of a gene.
database_cross_reference: SO:immuno_workshop

wiki
type: Axiom
annotated source: allele
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Allele

haplotype
type: Class
subclass of: variant_collection
subclass of: Restriction
  on property: variant_of
  some values from: haplotype_block
definition: A haplotype is one of a set of coexisting sequence variants of a haplotype block.
database_cross_reference: http://en.wikipedia.org/wiki/Haplotype
has_obo_namespace: sequence
id: SO:0001024

Axiom
annotated source: haplotype
annotated property: definition
annotated target: A haplotype is one of a set of coexisting sequence variants of a haplotype block.
database_cross_reference: SO:immuno_workshop

wiki
type: Axiom
annotated source: haplotype
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Haplotype

polymorphic_sequence_variant
type: Class
subclass of: allele
definition: A sequence variant that is segregating in one or more natural populations of a species.
has_exact_synonym: polymorphic sequence variant
has_obo_namespace: sequence
id: SO:0001025

Axiom
annotated source: polymorphic_sequence_variant
annotated property: definition
annotated target: A sequence variant that is segregating in one or more natural populations of a species.
database_cross_reference: SO:immuno_workshop

genome
type: Class
equivalent class: Class
  intersection of: sequence_collection
  intersection of: Restriction
    on property: has_part
    some values from: replicon
subclass of: sequence_collection
subclass of: Restriction
  on property: has_part
  some values from: replicon
definition: A genome is the sum of genetic material within a cell or virion.
database_cross_reference: http://en.wikipedia.org/wiki/Genome
has_obo_namespace: sequence
id: SO:0001026

Axiom
annotated source: genome
annotated property: definition
annotated target: A genome is the sum of genetic material within a cell or virion.
database_cross_reference: SO:immuno_workshop

wiki
type: Axiom
annotated source: genome
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Genome

genotype
type: Class
subclass of: variant_collection
subclass of: Restriction
  on property: variant_of
  some values from: genome
definition: A genotype is a variant genome, complete or incomplete.
database_cross_reference: http://en.wikipedia.org/wiki/Genotype
has_obo_namespace: sequence
id: SO:0001027

Axiom
annotated source: genotype
annotated property: definition
annotated target: A genotype is a variant genome, complete or incomplete.
database_cross_reference: SO:immuno_workshop

wiki
type: Axiom
annotated source: genotype
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Genotype

diplotype
type: Class
subclass of: variant_collection
definition: A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.
has_obo_namespace: sequence
id: SO:0001028

Axiom
annotated source: diplotype
annotated property: definition
annotated target: A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.
database_cross_reference: SO:immuno_workshop

direction_attribute
type: Class
subclass of: feature_attribute
definition: The attribute of whether the sequence is the same direction as a feature (forward) or the opposite direction as a feature (reverse).
has_exact_synonym: direction attribute
has_obo_namespace: sequence
id: SO:0001029

forward
type: Class
subclass of: direction_attribute
definition: Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.
has_obo_namespace: sequence
id: SO:0001030

Axiom
annotated source: forward
annotated property: definition
annotated target: Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.
database_cross_reference: SO:ke

reverse
type: Class
subclass of: direction_attribute
definition: Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.
has_obo_namespace: sequence
id: SO:0001031

Axiom
annotated source: reverse
annotated property: definition
annotated target: Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.
database_cross_reference: SO:ke

mitochondrial_DNA
type: Class
equivalent class: Class
  intersection of: mitochondrial_sequence
  intersection of: Restriction
    on property: has_quality
    some values from: DNA
subclass of: mitochondrial_sequence
subclass of: Restriction
  on property: has_quality
  some values from: DNA
definition: DNA belonging to the genome of a mitochondria.
database_cross_reference: http://en.wikipedia.org/wiki/Mitochondrial_DNA
has_exact_synonym: mitochondrial DNA
has_exact_synonym: mtDNA
has_obo_namespace: sequence
id: SO:0001032
comment: This terms is used by MO.

wiki
type: Axiom
annotated source: mitochondrial_DNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Mitochondrial_DNA

chloroplast_DNA
type: Class
equivalent class: Class
  intersection of: chloroplast_sequence
  intersection of: Restriction
    on property: has_quality
    some values from: DNA
subclass of: chloroplast_sequence
subclass of: Restriction
  on property: has_quality
  some values from: DNA
definition: DNA belonging to the genome of a chloroplast, a photosynthetic plastid.
has_exact_synonym: chloroplast DNA
has_obo_namespace: sequence
id: SO:0001033
comment: This term is used by MO.

miRtron
type: Class
subclass of: intron_domain
subclass of: Restriction
  on property: has_part
  some values from: pre_miRNA
definition: A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
has_obo_namespace: sequence
id: SO:0001034
comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.

Axiom
annotated source: miRtron
annotated property: definition
annotated target: A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
database_cross_reference: PMID:17589500
database_cross_reference: SO:ma

piRNA
type: Class
subclass of: small_regulatory_ncRNA
definition: A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
has_broad_synonym: INSDC_feature:ncRNA
database_cross_reference: http://en.wikipedia.org/wiki/PiRNA
has_exact_synonym: INSDC_qualifier:piRNA
has_exact_synonym: piwi-associated RNA
has_obo_namespace: sequence
id: SO:0001035

Axiom
annotated source: piRNA
annotated property: definition
annotated target: A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: piRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/PiRNA

arginyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: arginine_tRNA_primary_transcript
definition: A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
has_exact_synonym: arginyl tRNA
has_obo_namespace: sequence
id: SO:0001036

Axiom
annotated source: arginyl_tRNA
annotated property: definition
annotated target: A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
database_cross_reference: SO:ke

mobile_genetic_element
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: mobile
subclass of: biological_region
subclass of: Restriction
  on property: has_quality
  some values from: mobile
definition: A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
database_cross_reference: http://en.wikipedia.org/wiki/Mobile_genetic_element
has_exact_synonym: INSDC_feature:mobile_element
has_exact_synonym: MGE
has_exact_synonym: mobile genetic element
has_obo_namespace: sequence
id: SO:0001037
in_subset: SOFA

Axiom
annotated source: mobile_genetic_element
annotated property: definition
annotated target: A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
database_cross_reference: PMID:14681355

wiki
type: Axiom
annotated source: mobile_genetic_element
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Mobile_genetic_element

extrachromosomal_mobile_genetic_element
type: Class
subclass of: mobile_genetic_element
definition: An MGE that is not integrated into the host chromosome.
has_exact_synonym: extrachromosomal mobile genetic element
has_obo_namespace: sequence
id: SO:0001038

Axiom
annotated source: extrachromosomal_mobile_genetic_element
annotated property: definition
annotated target: An MGE that is not integrated into the host chromosome.
database_cross_reference: SO:ke

integrated_mobile_genetic_element
type: Class
subclass of: mobile_genetic_element
definition: An MGE that is integrated into the host chromosome.
has_exact_synonym: integrated mobile genetic element
has_obo_namespace: sequence
id: SO:0001039
in_subset: SOFA

Axiom
annotated source: integrated_mobile_genetic_element
annotated property: definition
annotated target: An MGE that is integrated into the host chromosome.
database_cross_reference: SO:ke

integrated_plasmid
type: Class
equivalent class: Class
  intersection of: integrated_mobile_genetic_element
  intersection of: Restriction
    on property: derives_from
    some values from: plasmid
subclass of: integrated_mobile_genetic_element
subclass of: Restriction
  on property: derives_from
  some values from: plasmid
definition: A plasmid sequence that is integrated within the host chromosome.
has_exact_synonym: integrated plasmid
has_obo_namespace: sequence
id: SO:0001040

Axiom
annotated source: integrated_plasmid
annotated property: definition
annotated target: A plasmid sequence that is integrated within the host chromosome.
database_cross_reference: SO:ke

viral_sequence
type: Class
subclass of: extrachromosomal_mobile_genetic_element
subclass of: replicon
definition: The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.
has_exact_synonym: viral sequence
has_exact_synonym: virus sequence
has_obo_namespace: sequence
id: SO:0001041
comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.

Axiom
annotated source: viral_sequence
annotated property: definition
annotated target: The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.
database_cross_reference: SO:ke

phage_sequence
type: Class
subclass of: viral_sequence
definition: The nucleotide sequence of a virus that infects bacteria.
database_cross_reference: http://en.wikipedia.org/wiki/Bacteriophage
has_exact_synonym: bacteriophage
has_exact_synonym: phage
has_exact_synonym: phage sequence
has_obo_namespace: sequence
id: SO:0001042

Axiom
annotated source: phage_sequence
annotated property: definition
annotated target: The nucleotide sequence of a virus that infects bacteria.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: phage_sequence
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Bacteriophage

attCtn_site
type: Class
subclass of: integration_excision_site
subclass of: Restriction
  on property: part_of
  some values from: conjugative_transposon
definition: An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
has_exact_synonym: attCtn site
has_obo_namespace: sequence
id: SO:0001043

Axiom
annotated source: attCtn_site
annotated property: definition
annotated target: An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
database_cross_reference: Phigo:at

nuclear_mt_pseudogene
type: Class
subclass of: SO_0001760
definition: A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.
database_cross_reference: http://en.wikipedia.org/wiki/Numt
has_exact_synonym: NUMT
has_exact_synonym: nuclear mitochondrial pseudogene
has_exact_synonym: nuclear mt pseudogene
has_obo_namespace: sequence
id: SO:0001044
comment: Definition change requested by Val, 3172757.

Axiom
annotated source: nuclear_mt_pseudogene
annotated property: definition
annotated target: A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.
database_cross_reference: SO:xp

wikipedia
type: Axiom
annotated source: nuclear_mt_pseudogene
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Numt

cointegrated_plasmid
type: Class
subclass of: integrated_mobile_genetic_element
definition: A MGE region consisting of two fused plasmids resulting from a replicative transposition event.
has_exact_synonym: cointegrated plasmid
has_exact_synonym: cointegrated replicon
has_obo_namespace: sequence
id: SO:0001045

Axiom
annotated source: cointegrated_plasmid
annotated property: definition
annotated target: A MGE region consisting of two fused plasmids resulting from a replicative transposition event.
database_cross_reference: phigo:at

IRLinv_site
type: Class
subclass of: inversion_site_part
subclass of: Restriction
  on property: part_of
  some values from: inversion_site
definition: Component of the inversion site located at the left of a region susceptible to site-specific inversion.
has_exact_synonym: IRLinv site
has_obo_namespace: sequence
id: SO:0001046

Axiom
annotated source: IRLinv_site
annotated property: definition
annotated target: Component of the inversion site located at the left of a region susceptible to site-specific inversion.
database_cross_reference: Phigo:at

IRRinv_site
type: Class
subclass of: inversion_site_part
subclass of: Restriction
  on property: part_of
  some values from: inversion_site
definition: Component of the inversion site located at the right of a region susceptible to site-specific inversion.
has_exact_synonym: IRRinv site
has_obo_namespace: sequence
id: SO:0001047

Axiom
annotated source: IRRinv_site
annotated property: definition
annotated target: Component of the inversion site located at the right of a region susceptible to site-specific inversion.
database_cross_reference: Phigo:at

inversion_site_part
type: Class
subclass of: site_specific_recombination_target_region
definition: A region located within an inversion site.
has_exact_synonym: inversion site part
has_obo_namespace: sequence
id: SO:0001048
comment: A term created to allow the parts of an inversion site have an is_a path back to the root.

Axiom
annotated source: inversion_site_part
annotated property: definition
annotated target: A region located within an inversion site.
database_cross_reference: SO:ke

defective_conjugative_transposon
type: Class
subclass of: genomic_island
definition: An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
has_exact_synonym: defective conjugative transposon
has_obo_namespace: sequence
id: SO:0001049

Axiom
annotated source: defective_conjugative_transposon
annotated property: definition
annotated target: An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
database_cross_reference: Phigo:ariane

repeat_fragment
type: Class
subclass of: repeat_component
subclass of: Restriction
  on property: part_of
  some values from: nested_repeat
definition: A portion of a repeat, interrupted by the insertion of another element.
has_exact_synonym: repeat fragment
has_obo_namespace: sequence
id: SO:0001050
comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats.

Axiom
annotated source: repeat_fragment
annotated property: definition
annotated target: A portion of a repeat, interrupted by the insertion of another element.
database_cross_reference: SO:ke

nested_region
type: Class
has_obo_namespace: sequence
id: SO:0001051
deprecated: true

nested_repeat
type: Class
has_obo_namespace: sequence
id: SO:0001052
deprecated: true

nested_transposon
type: Class
has_obo_namespace: sequence
id: SO:0001053
deprecated: true

transposon_fragment
type: Class
subclass of: repeat_component
subclass of: Restriction
  on property: part_of
  some values from: nested_transposon
definition: A portion of a transposon, interrupted by the insertion of another element.
has_exact_synonym: transposon fragment
has_obo_namespace: sequence
id: SO:0001054

Axiom
annotated source: transposon_fragment
annotated property: definition
annotated target: A portion of a transposon, interrupted by the insertion of another element.
database_cross_reference: SO:ke

transcriptional_cis_regulatory_region
type: Class
subclass of: SO_0005836
definition: A regulatory_region that modulates the transcription of a gene or genes.
has_broad_synonym: INSDC_feature:regulatory
has_exact_synonym: INSDC_qualifier:transcriptional_cis_regulatory_region
has_exact_synonym: transcription-control region
has_exact_synonym: transcriptional cis regulatory region
has_obo_namespace: sequence
id: SO:0001055
in_subset: SOFA
comment: Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: transcriptional_cis_regulatory_region
annotated property: definition
annotated target: A regulatory_region that modulates the transcription of a gene or genes.
database_cross_reference: PMID:9679020
database_cross_reference: SO:regcreative

splicing_regulatory_region
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: A regulatory_region that modulates splicing.
has_exact_synonym: splicing regulatory region
has_obo_namespace: sequence
id: SO:0001056
in_subset: SOFA
comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: splicing_regulatory_region
annotated property: definition
annotated target: A regulatory_region that modulates splicing.
database_cross_reference: SO:ke

enhanceosome
type: Class
has_obo_namespace: sequence
id: SO:0001057
deprecated: true

promoter_targeting_sequence
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.
has_exact_synonym: promoter targeting sequence
has_obo_namespace: sequence
id: SO:0001058
comment: Obsoleted Jan 21, 2021 by Dave Sant. GREEKC consortium individuals pointed out that this did not fit with the other child terms of transcriptional_cis_regulatory_region (SO:0001055), which are currently promoter, CRM and promoter flanking region. No comments about when this term was created exist, no references are listed. GREEKC members assume that this was previously under enhansosome (SO:0001057), which was probably created along with this term but has since been obsoleted. This term can be resurrected as non-obsolete if we can find a reference publication and/or change the name to a term that is commonly used in the field.
deprecated: true

Axiom
annotated source: promoter_targeting_sequence
annotated property: definition
annotated target: A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.
database_cross_reference: SO:regcreative

sequence_alteration
type: Class
subclass of: SO_0002072
definition: A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
has_alternative_id: SO:1000004
has_alternative_id: SO:1000007
has_broad_synonym: INSDC_feature:misc_feature
has_exact_synonym: INSDC_feature:variation
has_exact_synonym: INSDC_note:sequence_alteration
has_exact_synonym: sequence alteration
has_narrow_synonym: partially characterised change in DNA sequence
has_narrow_synonym: partially_characterised_change_in_DNA_sequence
has_narrow_synonym: uncharacterised_change_in_nucleotide_sequence
has_obo_namespace: sequence
has_related_synonym: sequence variation
id: SO:0001059
in_subset: SOFA
comment: Merged with partially characterized change in nucleotide sequence.

Axiom
annotated source: sequence_alteration
annotated property: definition
annotated target: A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
database_cross_reference: SO:ke

sequence_variant
type: Class
definition: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
has_exact_synonym: Jannovar:sequence_variant
has_exact_synonym: VAAST:sequence_variant
has_exact_synonym: sequence variant
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:unknown
id: SO:0001060

Axiom
annotated source: sequence_variant
annotated property: definition
annotated target: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
database_cross_reference: SO:ke

Axiom
annotated source: sequence_variant
annotated property: has_exact_synonym
annotated target: Jannovar:sequence_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: sequence_variant
annotated property: has_exact_synonym
annotated target: VAAST:sequence_variant
has_synonym_type: variant annotation term

Axiom
annotated source: sequence_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:unknown
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

propeptide_cleavage_site
type: Class
subclass of: SO_0100011
subclass of: Restriction
  on property: part_of
  some values from: propeptide
definition: The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.
has_alternative_id: BS:00063
has_exact_synonym: propeptide cleavage site
has_obo_namespace: sequence
id: SO:0001061
in_subset: biosapiens
comment: Discrete.

Axiom
annotated source: propeptide_cleavage_site
annotated property: definition
annotated target: The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.
database_cross_reference: EBIBS:GAR

propeptide
type: Class
subclass of: SO_0100011
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002250
definition: Part of a peptide chain which is cleaved off during the formation of the mature protein.
has_alternative_id: BS:00077
database_cross_reference: http://en.wikipedia.org/wiki/Propeptide
has_exact_synonym: INSDC_feature:propeptide
has_obo_namespace: sequence
has_related_synonym: propep
id: SO:0001062
in_subset: biosapiens
comment: Range.

Axiom
annotated source: propeptide
annotated property: definition
annotated target: Part of a peptide chain which is cleaved off during the formation of the mature protein.
database_cross_reference: EBIBS:GAR

wiki
type: Axiom
annotated source: propeptide
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Propeptide

Axiom
annotated source: propeptide
annotated property: has_related_synonym
annotated target: propep
database_cross_reference: uniprot:feature_type

immature_peptide_region
type: Class
subclass of: polypeptide_region
definition: An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
has_alternative_id: BS:00129
has_exact_synonym: immature peptide region
has_obo_namespace: sequence
id: SO:0001063
in_subset: SOFA
in_subset: biosapiens
comment: Range.

Axiom
annotated source: immature_peptide_region
annotated property: definition
annotated target: An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
database_cross_reference: EBIBS:GAR

active_peptide
type: Class
subclass of: mature_protein_region
definition: Active peptides are proteins which are biologically active, released from a precursor molecule.
has_alternative_id: BS:00076
has_broad_synonym: peptide
database_cross_reference: http://en.wikipedia.org/wiki/Peptide
has_exact_synonym: active peptide
has_obo_namespace: sequence
id: SO:0001064
in_subset: biosapiens
comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.

Axiom
annotated source: active_peptide
annotated property: definition
annotated target: Active peptides are proteins which are biologically active, released from a precursor molecule.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: active_peptide
annotated property: has_broad_synonym
annotated target: peptide
database_cross_reference: uniprot:feature_type

wiki
type: Axiom
annotated source: active_peptide
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Peptide

SO_0001065
type: Class
IAO_0000231: IAO_0000227
term replaced by: alternate_sequence_site
deprecated: true

compositionally_biased_region_of_peptide
type: Class
subclass of: polypeptide_region
definition: Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.
has_alternative_id: BS:00068
has_exact_synonym: compositionally_biased_region
has_obo_namespace: sequence
has_related_synonym: compbias
has_related_synonym: compositional bias
has_related_synonym: compositionally biased
has_related_synonym: compositionally biased region of peptide
id: SO:0001066
in_subset: biosapiens
comment: Range.

Axiom
annotated source: compositionally_biased_region_of_peptide
annotated property: definition
annotated target: Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: compositionally_biased_region_of_peptide
annotated property: has_related_synonym
annotated target: compbias
database_cross_reference: uniprot:feature_type

polypeptide_motif
type: Class
subclass of: SO_0100021
definition: A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.).
has_alternative_id: BS:00032
has_broad_synonym: motif
has_exact_synonym: polypeptide motif
has_obo_namespace: sequence
id: SO:0001067
in_subset: biosapiens
comment: Range.

Axiom
annotated source: polypeptide_motif
annotated property: definition
annotated target: A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.).
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: polypeptide_motif
annotated property: has_broad_synonym
annotated target: motif
database_cross_reference: uniprot:feature_type

polypeptide_repeat
type: Class
subclass of: SO_0100021
definition: A polypeptide_repeat is a single copy of an internal sequence repetition.
has_alternative_id: BS:00070
has_exact_synonym: polypeptide repeat
has_obo_namespace: sequence
has_related_synonym: repeat
id: SO:0001068
in_subset: biosapiens
comment: Range.

Axiom
annotated source: polypeptide_repeat
annotated property: definition
annotated target: A polypeptide_repeat is a single copy of an internal sequence repetition.
database_cross_reference: EBIBS:GAR

Axiom
annotated source: polypeptide_repeat
annotated property: has_related_synonym
annotated target: repeat
database_cross_reference: uniprot:feature_type

SO_0001069
type: Class
IAO_0000231: IAO_0000227
term replaced by: polypeptide_domain
deprecated: true

polypeptide_structural_region
type: Class
subclass of: polypeptide_region
definition: Region of polypeptide with a given structural property.
has_alternative_id: BS:00337
has_exact_synonym: polypeptide structural region
has_obo_namespace: sequence
has_related_synonym: structural_region
id: SO:0001070
in_subset: biosapiens
comment: Range.

Axiom
annotated source: polypeptide_structural_region
annotated property: definition
annotated target: Region of polypeptide with a given structural property.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

membrane_structure
type: Class
subclass of: polypeptide_structural_region
definition: Arrangement of the polypeptide with respect to the lipid bilayer.
has_alternative_id: BS:00128
has_exact_synonym: membrane structure
has_obo_namespace: sequence
id: SO:0001071
in_subset: biosapiens
comment: Range.

Axiom
annotated source: membrane_structure
annotated property: definition
annotated target: Arrangement of the polypeptide with respect to the lipid bilayer.
database_cross_reference: EBIBS:GAR

extramembrane_polypeptide_region
type: Class
subclass of: polypeptide_structural_region
subclass of: Restriction
  on property: part_of
  some values from: membrane_structure
definition: Polypeptide region that is localized outside of a lipid bilayer.
has_alternative_id: BS:00154
has_exact_synonym: extramembrane polypeptide region
has_obo_namespace: sequence
has_related_synonym: extramembrane
has_related_synonym: extramembrane_region
has_related_synonym: topo_dom
id: SO:0001072
in_subset: biosapiens
comment: Range.

Axiom
annotated source: extramembrane_polypeptide_region
annotated property: definition
annotated target: Polypeptide region that is localized outside of a lipid bilayer.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

Axiom
annotated source: extramembrane_polypeptide_region
annotated property: has_related_synonym
annotated target: extramembrane
has_synonym_type: biosapiens

Axiom
annotated source: extramembrane_polypeptide_region
annotated property: has_related_synonym
annotated target: extramembrane_region
has_synonym_type: biosapiens

Axiom
annotated source: extramembrane_polypeptide_region
annotated property: has_related_synonym
annotated target: topo_dom
database_cross_reference: uniprot:feature_type
has_synonym_type: biosapiens

cytoplasmic_polypeptide_region
type: Class
subclass of: extramembrane_polypeptide_region
definition: Polypeptide region that is localized inside the cytoplasm.
has_alternative_id: BS:00145
has_exact_synonym: cytoplasm_location
has_exact_synonym: cytoplasmic polypeptide region
has_obo_namespace: sequence
has_related_synonym: inside
id: SO:0001073
in_subset: biosapiens

Axiom
annotated source: cytoplasmic_polypeptide_region
annotated property: definition
annotated target: Polypeptide region that is localized inside the cytoplasm.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

Axiom
annotated source: cytoplasmic_polypeptide_region
annotated property: has_exact_synonym
annotated target: cytoplasm_location
has_synonym_type: biosapiens

Axiom
annotated source: cytoplasmic_polypeptide_region
annotated property: has_related_synonym
annotated target: inside
has_synonym_type: biosapiens

non_cytoplasmic_polypeptide_region
type: Class
subclass of: extramembrane_polypeptide_region
definition: Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.
has_alternative_id: BS:00144
has_exact_synonym: non cytoplasmic polypeptide region
has_exact_synonym: non_cytoplasm_location
has_obo_namespace: sequence
has_related_synonym: outside
id: SO:0001074
in_subset: biosapiens
comment: This could be inside an organelle within the cell.

Axiom
annotated source: non_cytoplasmic_polypeptide_region
annotated property: definition
annotated target: Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

Axiom
annotated source: non_cytoplasmic_polypeptide_region
annotated property: has_exact_synonym
annotated target: non_cytoplasm_location
has_synonym_type: biosapiens

Axiom
annotated source: non_cytoplasmic_polypeptide_region
annotated property: has_related_synonym
annotated target: outside
has_synonym_type: biosapiens

intramembrane_polypeptide_region
type: Class
subclass of: polypeptide_structural_region
subclass of: Restriction
  on property: part_of
  some values from: membrane_structure
definition: Polypeptide region present in the lipid bilayer.
has_alternative_id: BS:00156
has_exact_synonym: intramembrane polypeptide region
has_obo_namespace: sequence
has_related_synonym: intramembrane
id: SO:0001075
in_subset: biosapiens

Axiom
annotated source: intramembrane_polypeptide_region
annotated property: definition
annotated target: Polypeptide region present in the lipid bilayer.
database_cross_reference: EBIBS:GAR

Axiom
annotated source: intramembrane_polypeptide_region
annotated property: has_related_synonym
annotated target: intramembrane
has_synonym_type: biosapiens

membrane_peptide_loop
type: Class
subclass of: intramembrane_polypeptide_region
definition: Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.
has_alternative_id: BS:00155
has_exact_synonym: membrane peptide loop
has_obo_namespace: sequence
has_related_synonym: membrane_loop
id: SO:0001076
in_subset: biosapiens

Axiom
annotated source: membrane_peptide_loop
annotated property: definition
annotated target: Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

Axiom
annotated source: membrane_peptide_loop
annotated property: has_related_synonym
annotated target: membrane_loop
has_synonym_type: biosapiens

transmembrane_polypeptide_region
type: Class
subclass of: intramembrane_polypeptide_region
definition: Polypeptide region traversing the lipid bilayer.
has_alternative_id: BS:00158
has_exact_synonym: transmembrane polypeptide region
has_obo_namespace: sequence
has_related_synonym: transmem
has_related_synonym: transmembrane
id: SO:0001077
in_subset: biosapiens

Axiom
annotated source: transmembrane_polypeptide_region
annotated property: definition
annotated target: Polypeptide region traversing the lipid bilayer.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curator_manual

Axiom
annotated source: transmembrane_polypeptide_region
annotated property: has_related_synonym
annotated target: transmem
database_cross_reference: uniprot:feature_type
has_synonym_type: biosapiens

Axiom
annotated source: transmembrane_polypeptide_region
annotated property: has_related_synonym
annotated target: transmembrane
has_synonym_type: biosapiens

polypeptide_secondary_structure
type: Class
subclass of: polypeptide_structural_region
definition: A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.
has_alternative_id: BS:00003
database_cross_reference: http://en.wikipedia.org/wiki/Secondary_structure
has_exact_synonym: polypeptide secondary structure
has_obo_namespace: sequence
has_related_synonym: 2nary structure
has_related_synonym: secondary structure
has_related_synonym: secondary structure region
has_related_synonym: secondary_structure
id: SO:0001078
in_subset: biosapiens
comment: Biosapien term was secondary_structure.

Axiom
annotated source: polypeptide_secondary_structure
annotated property: definition
annotated target: A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.
database_cross_reference: EBIBS:GAR

wiki
type: Axiom
annotated source: polypeptide_secondary_structure
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Secondary_structure

Axiom
annotated source: polypeptide_secondary_structure
annotated property: has_related_synonym
annotated target: 2nary structure
has_synonym_type: biosapiens

Axiom
annotated source: polypeptide_secondary_structure
annotated property: has_related_synonym
annotated target: secondary structure
has_synonym_type: biosapiens

Axiom
annotated source: polypeptide_secondary_structure
annotated property: has_related_synonym
annotated target: secondary structure region
has_synonym_type: biosapiens

Axiom
annotated source: polypeptide_secondary_structure
annotated property: has_related_synonym
annotated target: secondary_structure
has_synonym_type: biosapiens

polypeptide_structural_motif
type: Class
subclass of: polypeptide_structural_region
definition: Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit.
has_alternative_id: BS:0000338
database_cross_reference: http://en.wikipedia.org/wiki/Structural_motif
has_obo_namespace: sequence
has_related_synonym: polypeptide structural motif
has_related_synonym: structural_motif
id: SO:0001079
in_subset: biosapiens

Axiom
annotated source: polypeptide_structural_motif
annotated property: definition
annotated target: Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit.
database_cross_reference: EBIBS:GAR

wiki
type: Axiom
annotated source: polypeptide_structural_motif
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Structural_motif

Axiom
annotated source: polypeptide_structural_motif
annotated property: has_related_synonym
annotated target: structural_motif
has_synonym_type: biosapiens

coiled_coil
type: Class
subclass of: polypeptide_structural_motif
definition: A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.
has_alternative_id: BS:00041
database_cross_reference: http://en.wikipedia.org/wiki/Coiled_coil
has_exact_synonym: coiled coil
has_obo_namespace: sequence
has_related_synonym: coiled
id: SO:0001080
in_subset: biosapiens
comment: Range.

Axiom
annotated source: coiled_coil
annotated property: definition
annotated target: A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

wiki
type: Axiom
annotated source: coiled_coil
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Coiled_coil

Axiom
annotated source: coiled_coil
annotated property: has_related_synonym
annotated target: coiled
database_cross_reference: uniprot:feature_type
has_synonym_type: biosapiens

helix_turn_helix
type: Class
subclass of: polypeptide_structural_motif
subclass of: Restriction
  on property: has_part
  some values from: peptide_helix
subclass of: Restriction
  on property: has_part
  some values from: polypeptide_turn_motif
definition: A motif comprising two helices separated by a turn.
has_alternative_id: BS:00147
has_exact_synonym: helix turn helix
has_exact_synonym: helix-turn-helix
has_obo_namespace: sequence
has_related_synonym: HTH
id: SO:0001081
in_subset: biosapiens

Axiom
annotated source: helix_turn_helix
annotated property: definition
annotated target: A motif comprising two helices separated by a turn.
database_cross_reference: EBIBS:GAR

Axiom
annotated source: helix_turn_helix
annotated property: has_related_synonym
annotated target: HTH
has_synonym_type: biosapiens

polypeptide_sequencing_information
type: Class
subclass of: remark
definition: Incompatibility in the sequence due to some experimental problem.
has_alternative_id: BS:00125
has_exact_synonym: sequencing_information
has_obo_namespace: sequence
id: SO:0001082
in_subset: biosapiens
comment: Range.

Axiom
annotated source: polypeptide_sequencing_information
annotated property: definition
annotated target: Incompatibility in the sequence due to some experimental problem.
database_cross_reference: EBIBS:GAR

non_adjacent_residues
type: Class
subclass of: polypeptide_sequencing_information
definition: Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them.
has_alternative_id: BS:00182
has_exact_synonym: non consecutive
has_exact_synonym: non_cons
has_obo_namespace: sequence
id: SO:0001083
in_subset: biosapiens

Axiom
annotated source: non_adjacent_residues
annotated property: definition
annotated target: Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: non_adjacent_residues
annotated property: has_exact_synonym
annotated target: non_cons
database_cross_reference: uniprot:feature_type

non_terminal_residue
type: Class
subclass of: polypeptide_sequencing_information
definition: The residue at an extremity of the sequence is not the terminal residue.
has_alternative_id: BS:00072
has_exact_synonym: non terminal
has_exact_synonym: non_ter
has_obo_namespace: sequence
id: SO:0001084
in_subset: biosapiens
comment: Discrete.

Axiom
annotated source: non_terminal_residue
annotated property: definition
annotated target: The residue at an extremity of the sequence is not the terminal residue.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: non_terminal_residue
annotated property: has_exact_synonym
annotated target: non_ter
database_cross_reference: uniprot:feature_type

sequence_conflict
type: Class
subclass of: polypeptide_sequencing_information
definition: Different sources report differing sequences.
has_alternative_id: BS:00069
has_exact_synonym: conflict
has_obo_namespace: sequence
id: SO:0001085
in_subset: biosapiens
comment: Discrete.

Axiom
annotated source: sequence_conflict
annotated property: definition
annotated target: Different sources report differing sequences.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: sequence_conflict
annotated property: has_exact_synonym
annotated target: conflict
database_cross_reference: uniprot:feature_type

sequence_uncertainty
type: Class
subclass of: polypeptide_sequencing_information
definition: Describes the positions in a sequence where the authors are unsure about the sequence assignment.
has_alternative_id: BS:00181
has_exact_synonym: INSDC_feature:unsure
has_exact_synonym: unsure
has_obo_namespace: sequence
id: SO:0001086
in_subset: biosapiens

Axiom
annotated source: sequence_uncertainty
annotated property: definition
annotated target: Describes the positions in a sequence where the authors are unsure about the sequence assignment.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: sequence_uncertainty
annotated property: has_exact_synonym
annotated target: unsure
database_cross_reference: uniprot:feature_type

cross_link
type: Class
definition: Posttranslationally formed amino acid bonds.
has_alternative_id: BS:00178
has_exact_synonym: cross link
has_obo_namespace: sequence
has_related_synonym: crosslink
id: SO:0001087
in_subset: biosapiens
deprecated: true

Axiom
annotated source: cross_link
annotated property: definition
annotated target: Posttranslationally formed amino acid bonds.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

disulfide_bond
type: Class
definition: The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.
has_alternative_id: BS:00028
has_exact_synonym: disulphide
has_obo_namespace: sequence
has_related_synonym: disulfid
has_related_synonym: disulfide
has_related_synonym: disulfide bond
has_related_synonym: disulphide bond
id: SO:0001088
in_subset: biosapiens
comment: 2 discreet & joined.
deprecated: true

Axiom
annotated source: disulfide_bond
annotated property: definition
annotated target: The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

post_translationally_modified_region
type: Class
subclass of: SO_0100001
definition: A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein.
has_alternative_id: BS:00052
database_cross_reference: http://en.wikipedia.org/wiki/Post_translational_modification
has_exact_synonym: mod_res
has_exact_synonym: modified residue
has_exact_synonym: post_translational_modification
has_obo_namespace: sequence
id: SO:0001089
in_subset: biosapiens
comment: Discrete.

Axiom
annotated source: post_translationally_modified_region
annotated property: definition
annotated target: A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

wiki
type: Axiom
annotated source: post_translationally_modified_region
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Post_translational_modification

Axiom
annotated source: post_translationally_modified_region
annotated property: has_exact_synonym
annotated target: mod_res
database_cross_reference: uniprot:feature_type

covalent_binding_site
type: Class
definition: Binding involving a covalent bond.
has_alternative_id: BS:00246
has_exact_synonym: covalent binding site
has_obo_namespace: sequence
id: SO:0001090
in_subset: biosapiens
deprecated: true

Axiom
annotated source: covalent_binding_site
annotated property: definition
annotated target: Binding involving a covalent bond.
database_cross_reference: EBIBS:GAR

non_covalent_binding_site
type: Class
definition: Binding site for any chemical group (co-enzyme, prosthetic group, etc.).
has_alternative_id: BS:00029
has_exact_synonym: non covalent binding site
has_obo_namespace: sequence
has_related_synonym: binding
has_related_synonym: binding site
id: SO:0001091
in_subset: biosapiens
comment: Discrete.
deprecated: true

Axiom
annotated source: non_covalent_binding_site
annotated property: definition
annotated target: Binding site for any chemical group (co-enzyme, prosthetic group, etc.).
database_cross_reference: EBIBS:GAR

Axiom
annotated source: non_covalent_binding_site
annotated property: has_related_synonym
annotated target: binding
database_cross_reference: uniprot:curation

polypeptide_metal_contact
type: Class
subclass of: metal_binding_site
subclass of: SO_0100002
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions.
has_alternative_id: BS:00027
has_obo_namespace: sequence
has_related_synonym: metal_binding
id: SO:0001092
in_subset: biosapiens
comment: Residue is part of a binding site for a metal ion.

Axiom
annotated source: polypeptide_metal_contact
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb
database_cross_reference: UniProt:curation_manual

protein_protein_contact
type: Class
subclass of: protein_binding_site
subclass of: SO_0100002
definition: A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues.
has_alternative_id: BS:00131
database_cross_reference: http://en.wikipedia.org/wiki/Protein_protein_interaction
has_exact_synonym: protein protein contact
has_exact_synonym: protein protein contact site
has_obo_namespace: sequence
has_related_synonym: protein_protein_interaction
id: SO:0001093
in_subset: biosapiens

Axiom
annotated source: protein_protein_contact
annotated property: definition
annotated target: A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:Curation_manual

wiki
type: Axiom
annotated source: protein_protein_contact
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Protein_protein_interaction

polypeptide_calcium_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions.
has_alternative_id: BS:00186
has_exact_synonym: Ca_contact_site
has_exact_synonym: ca_bind
has_exact_synonym: polypeptide calcium ion contact site
has_obo_namespace: sequence
has_related_synonym: ca bind
id: SO:0001094
in_subset: biosapiens
comment: Residue involved in contact with calcium.

Axiom
annotated source: polypeptide_calcium_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions.
database_cross_reference: EBIBS:GAR

Axiom
annotated source: polypeptide_calcium_ion_contact_site
annotated property: has_exact_synonym
annotated target: ca_bind
database_cross_reference: uniprot:feature_type
has_synonym_type: biosapiens

polypeptide_cobalt_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions.
has_alternative_id: BS:00136
has_exact_synonym: Co_contact_site
has_exact_synonym: polypeptide cobalt ion contact site
has_obo_namespace: sequence
id: SO:0001095
in_subset: biosapiens

Axiom
annotated source: polypeptide_cobalt_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

polypeptide_copper_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions.
has_alternative_id: BS:00146
has_exact_synonym: Cu_contact_site
has_exact_synonym: polypeptide copper ion contact site
has_obo_namespace: sequence
id: SO:0001096
in_subset: biosapiens

Axiom
annotated source: polypeptide_copper_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

polypeptide_iron_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions.
has_alternative_id: BS:00137
has_exact_synonym: Fe_contact_site
has_exact_synonym: polypeptide iron ion contact site
has_obo_namespace: sequence
id: SO:0001097
in_subset: biosapiens

Axiom
annotated source: polypeptide_iron_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

polypeptide_magnesium_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions.
has_alternative_id: BS:00187
has_exact_synonym: Mg_contact_site
has_exact_synonym: polypeptide magnesium ion contact site
has_obo_namespace: sequence
id: SO:0001098
in_subset: biosapiens

Axiom
annotated source: polypeptide_magnesium_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

polypeptide_manganese_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions.
has_alternative_id: BS:00140
has_exact_synonym: Mn_contact_site
has_exact_synonym: polypeptide manganese ion contact site
has_obo_namespace: sequence
id: SO:0001099
in_subset: biosapiens

Axiom
annotated source: polypeptide_manganese_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

polypeptide_molybdenum_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.
has_alternative_id: BS:00141
has_exact_synonym: Mo_contact_site
has_exact_synonym: polypeptide molybdenum ion contact site
has_obo_namespace: sequence
id: SO:0001100
in_subset: biosapiens

Axiom
annotated source: polypeptide_molybdenum_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

polypeptide_nickel_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.
has_alternative_id: BS:00142
has_exact_synonym: Ni_contact_site
has_exact_synonym: polypeptide nickel ion contact site
has_obo_namespace: sequence
id: SO:0001101
in_subset: biosapiens

Axiom
annotated source: polypeptide_nickel_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.
database_cross_reference: EBIBS:GAR

polypeptide_tungsten_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.
has_alternative_id: BS:00143
has_exact_synonym: W_contact_site
has_exact_synonym: polypeptide tungsten ion contact site
has_obo_namespace: sequence
id: SO:0001102
in_subset: biosapiens

Axiom
annotated source: polypeptide_tungsten_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

polypeptide_zinc_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
definition: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions.
has_alternative_id: BS:00185
has_exact_synonym: Zn_contact_site
has_exact_synonym: polypeptide zinc ion contact site
has_obo_namespace: sequence
id: SO:0001103
in_subset: biosapiens

Axiom
annotated source: polypeptide_zinc_ion_contact_site
annotated property: definition
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:cb

catalytic_residue
type: Class
subclass of: amino_acid
subclass of: Restriction
  on property: part_of
  some values from: SO_0100019
definition: Amino acid involved in the activity of an enzyme.
has_alternative_id: BS:00026
has_exact_synonym: active site residue
has_exact_synonym: catalytic residue
has_obo_namespace: sequence
has_related_synonym: act_site
id: SO:0001104
in_subset: biosapiens
comment: Discrete.

Axiom
annotated source: catalytic_residue
annotated property: definition
annotated target: Amino acid involved in the activity of an enzyme.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: catalytic_residue
annotated property: has_related_synonym
annotated target: act_site
database_cross_reference: uniprot:feature_type

polypeptide_ligand_contact
type: Class
subclass of: ligand_binding_site
subclass of: SO_0100002
definition: Residues which interact with a ligand.
has_alternative_id: BS:00157
has_exact_synonym: polypeptide ligand contact
has_obo_namespace: sequence
has_related_synonym: protein-ligand interaction
id: SO:0001105
in_subset: biosapiens

Axiom
annotated source: polypeptide_ligand_contact
annotated property: definition
annotated target: Residues which interact with a ligand.
database_cross_reference: EBIBS:GAR

asx_motif
type: Class
subclass of: polypeptide_secondary_structure
definition: A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
has_alternative_id: BS:00202
has_exact_synonym: asx motif
has_obo_namespace: sequence
id: SO:0001106
in_subset: biosapiens

Axiom
annotated source: asx_motif
annotated property: definition
annotated target: A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

beta_bulge
type: Class
subclass of: polypeptide_secondary_structure
definition: A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
has_alternative_id: BS:00208
database_cross_reference: http://en.wikipedia.org/wiki/Beta_bulge
has_exact_synonym: beta bulge
has_obo_namespace: sequence
id: SO:0001107
in_subset: biosapiens

Axiom
annotated source: beta_bulge
annotated property: definition
annotated target: A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

wiki
type: Axiom
annotated source: beta_bulge
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Beta_bulge

beta_bulge_loop
type: Class
subclass of: polypeptide_secondary_structure
definition: A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins.
has_alternative_id: BS:00209
has_exact_synonym: beta bulge loop
has_obo_namespace: sequence
id: SO:0001108
in_subset: biosapiens

Axiom
annotated source: beta_bulge_loop
annotated property: definition
annotated target: A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins.
database_cross_reference: EBIBS:GAR
database_cross_reference: Http://www.ebi.ac.uk/msd-srv/msdmotif/

beta_bulge_loop_five
type: Class
subclass of: beta_bulge_loop
definition: A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.
has_alternative_id: BS:00210
has_exact_synonym: beta bulge loop five
has_obo_namespace: sequence
id: SO:0001109
in_subset: biosapiens

Axiom
annotated source: beta_bulge_loop_five
annotated property: definition
annotated target: A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

beta_bulge_loop_six
type: Class
subclass of: beta_bulge_loop
definition: A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.
has_alternative_id: BS:00211
has_exact_synonym: beta bulge loop six
has_obo_namespace: sequence
id: SO:0001110
in_subset: biosapiens

Axiom
annotated source: beta_bulge_loop_six
annotated property: definition
annotated target: A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

beta_strand
type: Class
subclass of: polypeptide_secondary_structure
definition: A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.
has_alternative_id: BS:00042
database_cross_reference: http://en.wikipedia.org/wiki/Beta_sheet
has_obo_namespace: sequence
has_related_synonym: strand
id: SO:0001111
in_subset: biosapiens
comment: Range.

Axiom
annotated source: beta_strand
annotated property: definition
annotated target: A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

wiki
type: Axiom
annotated source: beta_strand
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Beta_sheet

Axiom
annotated source: beta_strand
annotated property: has_related_synonym
annotated target: strand
database_cross_reference: uniprot:feature_type
has_synonym_type: biosapiens

antiparallel_beta_strand
type: Class
subclass of: beta_strand
definition: A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.
has_alternative_id: BS:0000341
has_exact_synonym: antiparallel beta strand
has_obo_namespace: sequence
id: SO:0001112
in_subset: biosapiens
comment: Range.

Axiom
annotated source: antiparallel_beta_strand
annotated property: definition
annotated target: A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

parallel_beta_strand
type: Class
subclass of: beta_strand
definition: A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.
has_alternative_id: BS:00151
has_exact_synonym: parallel beta strand
has_obo_namespace: sequence
id: SO:0001113
in_subset: biosapiens
comment: Range.

Axiom
annotated source: parallel_beta_strand
annotated property: definition
annotated target: A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

peptide_helix
type: Class
subclass of: polypeptide_secondary_structure
definition: A helix is a secondary_structure conformation where the peptide backbone forms a coil.
has_alternative_id: BS:00152
has_obo_namespace: sequence
has_related_synonym: helix
id: SO:0001114
in_subset: biosapiens
comment: Range.

Axiom
annotated source: peptide_helix
annotated property: definition
annotated target: A helix is a secondary_structure conformation where the peptide backbone forms a coil.
database_cross_reference: EBIBS:GAR

Axiom
annotated source: peptide_helix
annotated property: has_related_synonym
annotated target: helix
has_synonym_type: biosapiens

left_handed_peptide_helix
type: Class
subclass of: peptide_helix
definition: A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.
has_alternative_id: BS:00222
has_exact_synonym: left handed helix
has_obo_namespace: sequence
has_related_synonym: helix-l
id: SO:0001115
in_subset: biosapiens

Axiom
annotated source: left_handed_peptide_helix
annotated property: definition
annotated target: A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.
database_cross_reference: EBIBS:GAR

right_handed_peptide_helix
type: Class
subclass of: peptide_helix
definition: A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.
has_alternative_id: BS:0000339
has_exact_synonym: right handed helix
has_obo_namespace: sequence
has_related_synonym: helix
id: SO:0001116
in_subset: biosapiens

Axiom
annotated source: right_handed_peptide_helix
annotated property: definition
annotated target: A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.
database_cross_reference: EBIBS:GAR

Axiom
annotated source: right_handed_peptide_helix
annotated property: has_related_synonym
annotated target: helix
has_synonym_type: biosapiens

alpha_helix
type: Class
subclass of: right_handed_peptide_helix
definition: The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
has_alternative_id: BS:00040
database_cross_reference: http://en.wikipedia.org/wiki/Alpha_helix
has_obo_namespace: sequence
has_related_synonym: a-helix
has_related_synonym: helix
id: SO:0001117
in_subset: biosapiens
comment: Range.

Axiom
annotated source: alpha_helix
annotated property: definition
annotated target: The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
database_cross_reference: EBIBS:GAR

wiki
type: Axiom
annotated source: alpha_helix
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Alpha_helix

Axiom
annotated source: alpha_helix
annotated property: has_related_synonym
annotated target: a-helix
has_synonym_type: biosapiens

Axiom
annotated source: alpha_helix
annotated property: has_related_synonym
annotated target: helix
database_cross_reference: uniprot:feature_type
has_synonym_type: biosapiens

pi_helix
type: Class
subclass of: right_handed_peptide_helix
definition: The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
has_alternative_id: BS:00153
database_cross_reference: http://en.wikipedia.org/wiki/Pi_helix
has_exact_synonym: pi helix
has_obo_namespace: sequence
id: SO:0001118
in_subset: biosapiens
comment: Range.

Axiom
annotated source: pi_helix
annotated property: definition
annotated target: The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
database_cross_reference: EBIBS:GAR

wiki
type: Axiom
annotated source: pi_helix
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Pi_helix

three_ten_helix
type: Class
subclass of: right_handed_peptide_helix
definition: The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
has_alternative_id: BS:0000340
database_cross_reference: http://en.wikipedia.org/wiki/310_helix
has_exact_synonym: 3(10) helix
has_exact_synonym: 3-10 helix
has_exact_synonym: 310 helix
has_exact_synonym: three ten helix
has_obo_namespace: sequence
id: SO:0001119
in_subset: biosapiens
comment: Range.

Axiom
annotated source: three_ten_helix
annotated property: definition
annotated target: The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
database_cross_reference: EBIBS:GAR

wiki
type: Axiom
annotated source: three_ten_helix
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/310_helix

polypeptide_nest_motif
type: Class
subclass of: polypeptide_secondary_structure
definition: A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.
has_alternative_id: BS:00223
has_exact_synonym: nest_motif
has_obo_namespace: sequence
has_related_synonym: nest
has_related_synonym: polypeptide nest motif
id: SO:0001120
in_subset: biosapiens

Axiom
annotated source: polypeptide_nest_motif
annotated property: definition
annotated target: A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

Axiom
annotated source: polypeptide_nest_motif
annotated property: has_related_synonym
annotated target: nest
has_synonym_type: biosapiens

polypeptide_nest_left_right_motif
type: Class
subclass of: polypeptide_nest_motif
definition: A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
has_alternative_id: BS:00224
has_exact_synonym: nest_left_right
has_exact_synonym: nest_lr
has_exact_synonym: polypeptide nest left right motif
has_obo_namespace: sequence
id: SO:0001121
in_subset: biosapiens

Axiom
annotated source: polypeptide_nest_left_right_motif
annotated property: definition
annotated target: A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

polypeptide_nest_right_left_motif
type: Class
subclass of: polypeptide_nest_motif
definition: A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
has_alternative_id: BS:00225
has_exact_synonym: nest_right_left
has_exact_synonym: nest_rl
has_exact_synonym: polypeptide nest right left motif
has_obo_namespace: sequence
id: SO:0001122
in_subset: biosapiens

Axiom
annotated source: polypeptide_nest_right_left_motif
annotated property: definition
annotated target: A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

schellmann_loop
type: Class
subclass of: polypeptide_secondary_structure
definition: A motif of six or seven consecutive residues that contains two H-bonds.
has_alternative_id: BS:00226
has_exact_synonym: schellmann loop
has_obo_namespace: sequence
has_related_synonym: paperclip
has_related_synonym: paperclip loop
id: SO:0001123
in_subset: biosapiens

Axiom
annotated source: schellmann_loop
annotated property: definition
annotated target: A motif of six or seven consecutive residues that contains two H-bonds.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

Axiom
annotated source: schellmann_loop
annotated property: has_related_synonym
annotated target: paperclip
has_synonym_type: biosapiens

schellmann_loop_seven
type: Class
subclass of: schellmann_loop
definition: Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).
has_alternative_id: BS:00228
has_exact_synonym: schellmann loop seven
has_exact_synonym: seven-residue schellmann loop
has_obo_namespace: sequence
id: SO:0001124
in_subset: biosapiens

Axiom
annotated source: schellmann_loop_seven
annotated property: definition
annotated target: Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

schellmann_loop_six
type: Class
subclass of: schellmann_loop
definition: Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).
has_alternative_id: BS:00227
has_exact_synonym: schellmann loop six
has_exact_synonym: six-residue schellmann loop
has_obo_namespace: sequence
id: SO:0001125
in_subset: biosapiens

Axiom
annotated source: schellmann_loop_six
annotated property: definition
annotated target: Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

serine_threonine_motif
type: Class
subclass of: polypeptide_secondary_structure
definition: A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
has_alternative_id: BS:00229
has_exact_synonym: serine/threonine motif
has_exact_synonym: st motif
has_exact_synonym: st_motif
has_obo_namespace: sequence
id: SO:0001126
in_subset: biosapiens

Axiom
annotated source: serine_threonine_motif
annotated property: definition
annotated target: A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

serine_threonine_staple_motif
type: Class
subclass of: polypeptide_secondary_structure
definition: A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.
has_alternative_id: BS:00230
has_exact_synonym: serine threonine staple motif
has_exact_synonym: st_staple
has_obo_namespace: sequence
id: SO:0001127
in_subset: biosapiens

Axiom
annotated source: serine_threonine_staple_motif
annotated property: definition
annotated target: A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

polypeptide_turn_motif
type: Class
subclass of: polypeptide_secondary_structure
definition: A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.
has_alternative_id: BS:00148
has_obo_namespace: sequence
has_related_synonym: turn
id: SO:0001128
in_subset: biosapiens
comment: Range.

Axiom
annotated source: polypeptide_turn_motif
annotated property: definition
annotated target: A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.
database_cross_reference: EBIBS:GAR
database_cross_reference: uniprot:feature_type

Axiom
annotated source: polypeptide_turn_motif
annotated property: has_related_synonym
annotated target: turn
has_synonym_type: biosapiens

asx_turn_left_handed_type_one
type: Class
subclass of: asx_turn
definition: Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
has_alternative_id: BS:00206
has_exact_synonym: asx turn left handed type one
has_obo_namespace: sequence
has_related_synonym: asx_turn_il
id: SO:0001129
in_subset: biosapiens

Axiom
annotated source: asx_turn_left_handed_type_one
annotated property: definition
annotated target: Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

asx_turn_left_handed_type_two
type: Class
subclass of: asx_turn
definition: Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
has_alternative_id: BS:00204
has_exact_synonym: asx turn left handed type two
has_exact_synonym: asx_turn_iil
has_obo_namespace: sequence
id: SO:0001130
in_subset: biosapiens

Axiom
annotated source: asx_turn_left_handed_type_two
annotated property: definition
annotated target: Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

asx_turn_right_handed_type_two
type: Class
subclass of: asx_turn
definition: Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
has_alternative_id: BS:00205
has_exact_synonym: asx turn right handed type two
has_exact_synonym: asx_turn_iir
has_obo_namespace: sequence
id: SO:0001131
in_subset: biosapiens

Axiom
annotated source: asx_turn_right_handed_type_two
annotated property: definition
annotated target: Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

asx_turn_right_handed_type_one
type: Class
subclass of: asx_turn
definition: Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
has_alternative_id: BS:00207
has_exact_synonym: asx turn type right handed type one
has_exact_synonym: asx_turn_ir
has_obo_namespace: sequence
id: SO:0001132
in_subset: biosapiens

Axiom
annotated source: asx_turn_right_handed_type_one
annotated property: definition
annotated target: Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

beta_turn
type: Class
subclass of: polypeptide_turn_motif
definition: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.
has_alternative_id: BS:00212
has_exact_synonym: beta turn
has_obo_namespace: sequence
id: SO:0001133
in_subset: biosapiens

Axiom
annotated source: beta_turn
annotated property: definition
annotated target: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

beta_turn_left_handed_type_one
type: Class
subclass of: beta_turn
definition: Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.
has_alternative_id: BS:00215
has_exact_synonym: beta turn left handed type one
has_exact_synonym: beta_turn_il
has_exact_synonym: type I' beta turn
has_exact_synonym: type I' turn
has_obo_namespace: sequence
id: SO:0001134
in_subset: biosapiens

Axiom
annotated source: beta_turn_left_handed_type_one
annotated property: definition
annotated target: Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

beta_turn_left_handed_type_two
type: Class
subclass of: beta_turn
definition: Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.
has_alternative_id: BS:00213
has_exact_synonym: beta turn left handed type two
has_exact_synonym: beta_turn_iil
has_exact_synonym: type II' beta turn
has_exact_synonym: type II' turn
has_obo_namespace: sequence
id: SO:0001135
in_subset: biosapiens

Axiom
annotated source: beta_turn_left_handed_type_two
annotated property: definition
annotated target: Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

beta_turn_right_handed_type_one
type: Class
subclass of: beta_turn
definition: Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
has_alternative_id: BS:00216
has_exact_synonym: beta turn right handed type one
has_exact_synonym: beta_turn_ir
has_exact_synonym: type I beta turn
has_exact_synonym: type I turn
has_obo_namespace: sequence
id: SO:0001136
in_subset: biosapiens

Axiom
annotated source: beta_turn_right_handed_type_one
annotated property: definition
annotated target: Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

beta_turn_right_handed_type_two
type: Class
subclass of: beta_turn
definition: Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
has_alternative_id: BS:00214
has_exact_synonym: beta turn right handed type two
has_exact_synonym: beta_turn_iir
has_exact_synonym: type II beta turn
has_exact_synonym: type II turn
has_obo_namespace: sequence
id: SO:0001137
in_subset: biosapiens

Axiom
annotated source: beta_turn_right_handed_type_two
annotated property: definition
annotated target: Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

gamma_turn
type: Class
subclass of: polypeptide_turn_motif
definition: Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
has_alternative_id: BS:00219
has_exact_synonym: gamma turn
has_obo_namespace: sequence
id: SO:0001138
in_subset: biosapiens

Axiom
annotated source: gamma_turn
annotated property: definition
annotated target: Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

gamma_turn_classic
type: Class
subclass of: gamma_turn
definition: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.
has_alternative_id: BS:00220
has_exact_synonym: classic gamma turn
has_exact_synonym: gamma turn classic
has_obo_namespace: sequence
id: SO:0001139
in_subset: biosapiens

Axiom
annotated source: gamma_turn_classic
annotated property: definition
annotated target: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

gamma_turn_inverse
type: Class
subclass of: gamma_turn
definition: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.
has_alternative_id: BS:00221
has_exact_synonym: gamma turn inverse
has_obo_namespace: sequence
id: SO:0001140
in_subset: biosapiens

Axiom
annotated source: gamma_turn_inverse
annotated property: definition
annotated target: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

serine_threonine_turn
type: Class
subclass of: polypeptide_turn_motif
definition: A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
has_alternative_id: BS:00231
has_exact_synonym: serine/threonine turn
has_exact_synonym: st_turn
has_obo_namespace: sequence
id: SO:0001141
in_subset: biosapiens

Axiom
annotated source: serine_threonine_turn
annotated property: definition
annotated target: A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

st_turn_left_handed_type_one
type: Class
subclass of: serine_threonine_turn
definition: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
has_alternative_id: BS:00234
has_exact_synonym: st turn left handed type one
has_exact_synonym: st_turn_il
has_obo_namespace: sequence
id: SO:0001142
in_subset: biosapiens

Axiom
annotated source: st_turn_left_handed_type_one
annotated property: definition
annotated target: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

st_turn_left_handed_type_two
type: Class
subclass of: serine_threonine_turn
definition: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
has_alternative_id: BS:00232
has_exact_synonym: st turn left handed type two
has_exact_synonym: st_turn_iil
has_obo_namespace: sequence
id: SO:0001143
in_subset: biosapiens

Axiom
annotated source: st_turn_left_handed_type_two
annotated property: definition
annotated target: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

st_turn_right_handed_type_one
type: Class
subclass of: serine_threonine_turn
definition: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
has_alternative_id: BS:00235
has_exact_synonym: st turn right handed type one
has_exact_synonym: st_turn_ir
has_obo_namespace: sequence
id: SO:0001144
in_subset: biosapiens

Axiom
annotated source: st_turn_right_handed_type_one
annotated property: definition
annotated target: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

st_turn_right_handed_type_two
type: Class
subclass of: serine_threonine_turn
definition: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
has_alternative_id: BS:00233
has_exact_synonym: st turn right handed type two
has_exact_synonym: st_turn_iir
has_obo_namespace: sequence
id: SO:0001145
in_subset: biosapiens

Axiom
annotated source: st_turn_right_handed_type_two
annotated property: definition
annotated target: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
database_cross_reference: EBIBS:GAR
database_cross_reference: http://www.ebi.ac.uk/msd-srv/msdmotif/

polypeptide_variation_site
type: Class
subclass of: polypeptide_region
definition: A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis.
has_alternative_id: BS:00336
has_exact_synonym: sequence_variations
has_obo_namespace: sequence
id: SO:0001146
in_subset: biosapiens
comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.

Axiom
annotated source: polypeptide_variation_site
annotated property: definition
annotated target: A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis.
database_cross_reference: EBIBS:GAR
database_cross_reference: SO:ke

natural_variant_site
type: Class
subclass of: polypeptide_variation_site
definition: Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.
has_alternative_id: BS:00071
has_broad_synonym: natural_variant
has_broad_synonym: sequence variation
has_broad_synonym: variant
has_obo_namespace: sequence
id: SO:0001147
in_subset: biosapiens
comment: Discrete.

Axiom
annotated source: natural_variant_site
annotated property: definition
annotated target: Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: natural_variant_site
annotated property: has_broad_synonym
annotated target: variant
database_cross_reference: uniprot:feature_type

mutated_variant_site
type: Class
subclass of: polypeptide_variation_site
definition: Site which has been experimentally altered.
has_alternative_id: BS:00036
has_exact_synonym: mutagen
has_exact_synonym: mutagenesis
has_exact_synonym: mutated_site
has_obo_namespace: sequence
id: SO:0001148
in_subset: biosapiens
comment: Discrete.

Axiom
annotated source: mutated_variant_site
annotated property: definition
annotated target: Site which has been experimentally altered.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: mutated_variant_site
annotated property: has_exact_synonym
annotated target: mutagen
database_cross_reference: uniprot:feature_type
has_synonym_type: biosapiens

alternate_sequence_site
type: Class
subclass of: polypeptide_variation_site
definition: Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
has_alternative_id: BS:00073
has_alternative_id: SO:0001065
has_exact_synonym: alternative_sequence
has_exact_synonym: var_seq
has_narrow_synonym: isoform
has_narrow_synonym: sequence variation
has_narrow_synonym: varsplic
has_obo_namespace: sequence
id: SO:0001149
in_subset: biosapiens
comment: Discrete.

Axiom
annotated source: alternate_sequence_site
annotated property: definition
annotated target: Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
database_cross_reference: EBIBS:GAR
database_cross_reference: UniProt:curation_manual

Axiom
annotated source: alternate_sequence_site
annotated property: has_exact_synonym
annotated target: var_seq
database_cross_reference: uniprot:feature_type

beta_turn_type_six
type: Class
subclass of: beta_turn
definition: A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.
has_exact_synonym: beta turn type six
has_exact_synonym: cis-proline loop
has_exact_synonym: type VI beta turn
has_exact_synonym: type VI turn
has_obo_namespace: sequence
id: SO:0001150
in_subset: biosapiens

Axiom
annotated source: beta_turn_type_six
annotated property: definition
annotated target: A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.
database_cross_reference: SO:cb

beta_turn_type_six_a
type: Class
subclass of: beta_turn_type_six
definition: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.
has_exact_synonym: beta turn type six a
has_exact_synonym: type VIa beta turn
has_exact_synonym: type VIa turn
has_obo_namespace: sequence
id: SO:0001151
in_subset: biosapiens

Axiom
annotated source: beta_turn_type_six_a
annotated property: definition
annotated target: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.
database_cross_reference: PMID:2371257
database_cross_reference: SO:cb

beta_turn_type_six_a_one
type: Class
subclass of: beta_turn_type_six_a
definition: A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees.
has_exact_synonym: beta turn type six a one
has_exact_synonym: type VIa1 beta turn
has_exact_synonym: type VIa1 turn
has_obo_namespace: sequence
id: SO:0001152
in_subset: biosapiens

Axiom
annotated source: beta_turn_type_six_a_one
annotated property: definition
annotated target: A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees.
database_cross_reference: PMID:27428516

beta_turn_type_six_a_two
type: Class
subclass of: beta_turn_type_six_a
definition: A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees.
has_exact_synonym: beta turn type six a two
has_exact_synonym: type VIa2 beta turn
has_exact_synonym: type VIa2 turn
has_obo_namespace: sequence
id: SO:0001153
in_subset: biosapiens

Axiom
annotated source: beta_turn_type_six_a_two
annotated property: definition
annotated target: A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees.
database_cross_reference: PMID:27428516

beta_turn_type_six_b
type: Class
subclass of: beta_turn_type_six
definition: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.
has_exact_synonym: beta turn type six b
has_exact_synonym: type VIb beta turn
has_exact_synonym: type VIb turn
has_obo_namespace: sequence
id: SO:0001154
in_subset: biosapiens

Axiom
annotated source: beta_turn_type_six_b
annotated property: definition
annotated target: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.
database_cross_reference: PMID:2371257
database_cross_reference: SO:cb

beta_turn_type_eight
type: Class
subclass of: beta_turn
definition: A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.
has_exact_synonym: beta turn type eight
has_exact_synonym: type VIII beta turn
has_exact_synonym: type VIII turn
has_obo_namespace: sequence
id: SO:0001155
in_subset: biosapiens

Axiom
annotated source: beta_turn_type_eight
annotated property: definition
annotated target: A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.
database_cross_reference: PMID:2371257
database_cross_reference: SO:cb

DRE_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.
has_exact_synonym: DRE motif
has_exact_synonym: NDM4
has_exact_synonym: WATCGATW_motif
has_obo_namespace: sequence
id: SO:0001156
comment: This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.

Axiom
annotated source: DRE_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.
database_cross_reference: PMID:12537576

DMv4_motif
type: Class
subclass of: promoter_element
definition: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).
has_exact_synonym: DMv4
has_exact_synonym: DMv4 motif
has_exact_synonym: directional motif v4
has_exact_synonym: motif 1 element
has_exact_synonym: promoter motif 1
has_narrow_synonym: YGGTCACATR
has_obo_namespace: sequence
id: SO:0001157

Axiom
annotated source: DMv4_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).
database_cross_reference: PMID:16827941:12537576

E_box_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).
has_exact_synonym: E box motif
has_exact_synonym: generic E box motif
has_narrow_synonym: AWCAGCTGWT
has_obo_namespace: sequence
has_related_synonym: NDM5
id: SO:0001158

Axiom
annotated source: E_box_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).
database_cross_reference: PMID:12537576:16827941

DMv5_motif
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
has_exact_synonym: DMv5
has_exact_synonym: DMv5 motif
has_exact_synonym: directional motif v5
has_narrow_synonym: KTYRGTATWTTT
has_obo_namespace: sequence
has_related_synonym: promoter motif 6
id: SO:0001159

Axiom
annotated source: DMv5_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
database_cross_reference: PMID:12537576:16827941

DMv3_motif
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).
has_exact_synonym: DMv3
has_exact_synonym: DMv3 motif
has_exact_synonym: directional motif v3
has_exact_synonym: promoter motif 7
has_narrow_synonym: KNNCAKCNCTRNY
has_obo_namespace: sequence
id: SO:0001160

Axiom
annotated source: DMv3_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).
database_cross_reference: PMID:12537576:16827941

DMv2_motif
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
has_exact_synonym: DMv2
has_exact_synonym: DMv2 motif
has_exact_synonym: directional motif v2
has_exact_synonym: promoter motif 8
has_narrow_synonym: MKSYGGCARCGSYSS
has_obo_namespace: sequence
id: SO:0001161

Axiom
annotated source: DMv2_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
database_cross_reference: PMID:12537576:16827941

MTE
type: Class
subclass of: core_eukaryotic_promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_core_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).
has_exact_synonym: motif ten element
has_exact_synonym: motif_ten_element
has_narrow_synonym: CSARCSSAACGS
has_obo_namespace: sequence
id: SO:0001162

Axiom
annotated source: MTE
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).
database_cross_reference: PMID:12537576:15231738
database_cross_reference: PMID:16858867

INR1_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A promoter motif with consensus sequence TCATTCG.
has_exact_synonym: DMp3
has_exact_synonym: INR1 motif
has_exact_synonym: directional motif p3
has_exact_synonym: directional promoter motif 3
has_obo_namespace: sequence
id: SO:0001163

Axiom
annotated source: INR1_motif
annotated property: definition
annotated target: A promoter motif with consensus sequence TCATTCG.
database_cross_reference: PMID:16827941

DPE1_motif
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A promoter motif with consensus sequence CGGACGT.
has_exact_synonym: DMp5
has_exact_synonym: DPE1 motif
has_exact_synonym: directional motif 5
has_obo_namespace: sequence
has_related_synonym: directional promoter motif 5
id: SO:0001164

Axiom
annotated source: DPE1_motif
annotated property: definition
annotated target: A promoter motif with consensus sequence CGGACGT.
database_cross_reference: PMID:16827941

DMv1_motif
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A promoter motif with consensus sequence CARCCCT.
has_exact_synonym: DMv1 motif
has_obo_namespace: sequence
has_related_synonym: DMv1
has_related_synonym: directional promoter motif v1
id: SO:0001165

Axiom
annotated source: DMv1_motif
annotated property: definition
annotated target: A promoter motif with consensus sequence CARCCCT.
database_cross_reference: PMID:16827941

GAGA_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A non directional promoter motif with consensus sequence GAGAGCG.
has_exact_synonym: GAGA
has_exact_synonym: GAGA motif
has_exact_synonym: NDM1
has_obo_namespace: sequence
id: SO:0001166

Axiom
annotated source: GAGA_motif
annotated property: definition
annotated target: A non directional promoter motif with consensus sequence GAGAGCG.
database_cross_reference: PMID:16827941

NDM2_motif
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A non directional promoter motif with consensus CGMYGYCR.
has_exact_synonym: NDM2
has_exact_synonym: NDM2 motif
has_exact_synonym: non directional promoter motif 2
has_obo_namespace: sequence
id: SO:0001167

Axiom
annotated source: NDM2_motif
annotated property: definition
annotated target: A non directional promoter motif with consensus CGMYGYCR.
database_cross_reference: PMID:16827941

NDM3_motif
type: Class
subclass of: promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A non directional promoter motif with consensus sequence GAAAGCT.
has_exact_synonym: NDM3
has_exact_synonym: NDM3 motif
has_exact_synonym: non directional motif 3
has_obo_namespace: sequence
id: SO:0001168

Axiom
annotated source: NDM3_motif
annotated property: definition
annotated target: A non directional promoter motif with consensus sequence GAAAGCT.
database_cross_reference: PMID:16827941

ds_RNA_viral_sequence
type: Class
subclass of: viral_sequence
definition: A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.
has_exact_synonym: double stranded RNA virus sequence
has_exact_synonym: ds RNA viral sequence
has_obo_namespace: sequence
id: SO:0001169

Axiom
annotated source: ds_RNA_viral_sequence
annotated property: definition
annotated target: A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.
database_cross_reference: SO:ke

polinton
type: Class
subclass of: terminal_inverted_repeat_element
definition: A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.
has_obo_namespace: sequence
has_related_synonym: maverick element
id: SO:0001170

Axiom
annotated source: polinton
annotated property: definition
annotated target: A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.
database_cross_reference: PMID:16537396

rRNA_21S
type: Class
definition: A component of the large ribosomal subunit in mitochondrial rRNA.
term replaced by: SO_0002345
has_exact_synonym: 21S LSU rRNA
has_exact_synonym: 21S rRNA
has_exact_synonym: 21S ribosomal RNA
has_exact_synonym: rRNA 21S
has_obo_namespace: sequence
id: SO:0001171
comment: This term has been merged into mt_LSU_rRNA (SO:0002345) as part of reorganization of rRNA child terms 10 June 2021. Requested by EBI. See GitHub Issue #493.
deprecated: true

Axiom
annotated source: rRNA_21S
annotated property: definition
annotated target: A component of the large ribosomal subunit in mitochondrial rRNA.
database_cross_reference: RSC:cb

tRNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: tRNA
definition: A region of a tRNA.
has_exact_synonym: tRNA region
has_obo_namespace: sequence
id: SO:0001172

Axiom
annotated source: tRNA_region
annotated property: definition
annotated target: A region of a tRNA.
database_cross_reference: RSC:cb

anticodon_loop
type: Class
subclass of: tRNA_region
definition: A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.
has_exact_synonym: anti-codon loop
has_exact_synonym: anticodon loop
has_obo_namespace: sequence
id: SO:0001173

Axiom
annotated source: anticodon_loop
annotated property: definition
annotated target: A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.
database_cross_reference: ISBN:0716719207

anticodon
type: Class
subclass of: tRNA_region
subclass of: Restriction
  on property: part_of
  some values from: anticodon_loop
definition: A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
database_cross_reference: http://en.wikipedia.org/wiki/Anticodon
has_exact_synonym: anti-codon
has_obo_namespace: sequence
id: SO:0001174

Axiom
annotated source: anticodon
annotated property: definition
annotated target: A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: anticodon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Anticodon

CCA_tail
type: Class
subclass of: tRNA_region
definition: Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.
has_exact_synonym: CCA sequence
has_exact_synonym: CCA tail
has_obo_namespace: sequence
id: SO:0001175

Axiom
annotated source: CCA_tail
annotated property: definition
annotated target: Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.
database_cross_reference: ISBN:0716719207

DHU_loop
type: Class
subclass of: tRNA_region
definition: Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
has_exact_synonym: DHU loop
has_obo_namespace: sequence
has_related_synonym: D loop
id: SO:0001176

Axiom
annotated source: DHU_loop
annotated property: definition
annotated target: Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
database_cross_reference: ISBN:071671920

T_loop
type: Class
subclass of: tRNA_region
definition: Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
has_exact_synonym: T loop
has_exact_synonym: TpsiC loop
has_obo_namespace: sequence
id: SO:0001177

Axiom
annotated source: T_loop
annotated property: definition
annotated target: Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
database_cross_reference: ISBN:0716719207

pyrrolysine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
definition: A primary transcript encoding pyrrolysyl tRNA (SO:0000766).
has_exact_synonym: pyrrolysine tRNA primary transcript
has_obo_namespace: sequence
id: SO:0001178

Axiom
annotated source: pyrrolysine_tRNA_primary_transcript
annotated property: definition
annotated target: A primary transcript encoding pyrrolysyl tRNA (SO:0000766).
database_cross_reference: RSC:cb

U3_snoRNA
type: Class
subclass of: C_D_box_snoRNA
definition: U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.
database_cross_reference: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3
has_exact_synonym: U3 small nucleolar RNA
has_exact_synonym: U3 snoRNA
has_exact_synonym: small nucleolar RNA U3
has_exact_synonym: snoRNA U3
has_obo_namespace: sequence
id: SO:0001179
comment: The definition is most of the old definition for snoRNA (SO:0000275).

Axiom
annotated source: U3_snoRNA
annotated property: definition
annotated target: U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.
database_cross_reference: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc

wiki
type: Axiom
annotated source: U3_snoRNA
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3

AU_rich_element
type: Class
subclass of: UTR_region
subclass of: Restriction
  on property: part_of
  some values from: three_prime_UTR
definition: A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.
database_cross_reference: http://en.wikipedia.org/wiki/AU-rich_element
has_exact_synonym: AU rich element
has_exact_synonym: AU-rich element
has_obo_namespace: sequence
has_related_synonym: ARE
id: SO:0001180

Axiom
annotated source: AU_rich_element
annotated property: definition
annotated target: A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.
database_cross_reference: PMID:7892223

wiki
type: Axiom
annotated source: AU_rich_element
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/AU-rich_element

Bruno_response_element
type: Class
subclass of: UTR_region
subclass of: Restriction
  on property: part_of
  some values from: three_prime_UTR
definition: A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
has_exact_synonym: Bruno response element
has_obo_namespace: sequence
has_related_synonym: BRE
id: SO:0001181
comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.

Axiom
annotated source: Bruno_response_element
annotated property: definition
annotated target: A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
database_cross_reference: PMID:10893231

iron_responsive_element
type: Class
subclass of: UTR_region
subclass of: Restriction
  on property: part_of
  some values from: UTR
definition: A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.
database_cross_reference: http://en.wikipedia.org/wiki/Iron_responsive_element
has_exact_synonym: IRE
has_exact_synonym: iron responsive element
has_obo_namespace: sequence
id: SO:0001182

Axiom
annotated source: iron_responsive_element
annotated property: definition
annotated target: A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.
database_cross_reference: PMID:3198610
database_cross_reference: PMID:8710843

wiki
type: Axiom
annotated source: iron_responsive_element
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Iron_responsive_element

morpholino_backbone
type: Class
subclass of: nucleic_acid
definition: An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.
database_cross_reference: http://en.wikipedia.org/wiki/Morpholino
has_exact_synonym: morpholino backbone
has_obo_namespace: sequence
id: SO:0001183
comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.

Axiom
annotated source: morpholino_backbone
annotated property: definition
annotated target: An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: morpholino_backbone
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Morpholino

PNA
type: Class
subclass of: nucleic_acid
definition: An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
has_obo_namespace: sequence
has_related_synonym: peptide nucleic acid
id: SO:0001184
comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.

Axiom
annotated source: PNA
annotated property: definition
annotated target: An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
database_cross_reference: RSC:cb

enzymatic
type: Class
subclass of: feature_attribute
definition: An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.
has_obo_namespace: sequence
id: SO:0001185
comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.

Axiom
annotated source: enzymatic
annotated property: definition
annotated target: An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.
database_cross_reference: RSC:cb

ribozymic
type: Class
subclass of: enzymatic
definition: An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.
has_obo_namespace: sequence
id: SO:0001186
comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.

Axiom
annotated source: ribozymic
annotated property: definition
annotated target: An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.
database_cross_reference: RSC:cb

pseudouridylation_guide_snoRNA
type: Class
subclass of: H_ACA_box_snoRNA
definition: A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
has_exact_synonym: pseudouridylation guide snoRNA
has_obo_namespace: sequence
id: SO:0001187
comment: Has RNA pseudouridylation guide activity (GO:0030558).

Axiom
annotated source: pseudouridylation_guide_snoRNA
annotated property: definition
annotated target: A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
database_cross_reference: GOC:mah
database_cross_reference: PMID:12457565

LNA
type: Class
subclass of: nucleic_acid
definition: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.
has_obo_namespace: sequence
id: SO:0001188
comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.

Axiom
annotated source: LNA
annotated property: definition
annotated target: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.
database_cross_reference: CHEBI:48010

LNA_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: LNA
subclass of: synthetic_oligo
subclass of: Restriction
  on property: has_quality
  some values from: LNA
definition: An oligo composed of LNA residues.
database_cross_reference: http://en.wikipedia.org/wiki/Locked_nucleic_acid
has_exact_synonym: LNA oligo
has_exact_synonym: locked nucleic acid
has_obo_namespace: sequence
id: SO:0001189

Axiom
annotated source: LNA_oligo
annotated property: definition
annotated target: An oligo composed of LNA residues.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: LNA_oligo
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Locked_nucleic_acid

TNA
type: Class
subclass of: nucleic_acid
definition: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.
has_obo_namespace: sequence
id: SO:0001190
comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.

Axiom
annotated source: TNA
annotated property: definition
annotated target: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.
database_cross_reference: CHEBI:48019

TNA_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: TNA
subclass of: synthetic_oligo
subclass of: Restriction
  on property: has_quality
  some values from: TNA
definition: An oligo composed of TNA residues.
database_cross_reference: http://en.wikipedia.org/wiki/Threose_nucleic_acid
has_exact_synonym: TNA oligo
has_exact_synonym: threose nucleic acid
has_obo_namespace: sequence
id: SO:0001191

Axiom
annotated source: TNA_oligo
annotated property: definition
annotated target: An oligo composed of TNA residues.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: TNA_oligo
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Threose_nucleic_acid

GNA
type: Class
subclass of: nucleic_acid
definition: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.
has_obo_namespace: sequence
id: SO:0001192
comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.

Axiom
annotated source: GNA
annotated property: definition
annotated target: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.
database_cross_reference: CHEBI:48015

GNA_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: GNA
subclass of: synthetic_oligo
subclass of: Restriction
  on property: has_quality
  some values from: GNA
definition: An oligo composed of GNA residues.
database_cross_reference: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid
has_exact_synonym: GNA oligo
has_exact_synonym: glycerol nucleic acid
has_exact_synonym: glycol nucleic acid
has_obo_namespace: sequence
id: SO:0001193

Axiom
annotated source: GNA_oligo
annotated property: definition
annotated target: An oligo composed of GNA residues.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: GNA_oligo
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid

R_GNA
type: Class
subclass of: GNA
definition: An attribute describing a GNA sequence in the (R)-GNA enantiomer.
has_exact_synonym: R GNA
has_obo_namespace: sequence
id: SO:0001194
comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.

Axiom
annotated source: R_GNA
annotated property: definition
annotated target: An attribute describing a GNA sequence in the (R)-GNA enantiomer.
database_cross_reference: CHEBI:48016

R_GNA_oligo
type: Class
equivalent class: Class
  intersection of: GNA_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: R_GNA
subclass of: GNA_oligo
subclass of: Restriction
  on property: has_quality
  some values from: R_GNA
definition: An oligo composed of (R)-GNA residues.
has_exact_synonym: (R)-glycerol nucleic acid
has_exact_synonym: (R)-glycol nucleic acid
has_exact_synonym: R GNA oligo
has_obo_namespace: sequence
id: SO:0001195

Axiom
annotated source: R_GNA_oligo
annotated property: definition
annotated target: An oligo composed of (R)-GNA residues.
database_cross_reference: RSC:cb

S_GNA
type: Class
subclass of: GNA
definition: An attribute describing a GNA sequence in the (S)-GNA enantiomer.
has_exact_synonym: S GNA
has_obo_namespace: sequence
id: SO:0001196
comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.

Axiom
annotated source: S_GNA
annotated property: definition
annotated target: An attribute describing a GNA sequence in the (S)-GNA enantiomer.
database_cross_reference: CHEBI:48017

S_GNA_oligo
type: Class
equivalent class: Class
  intersection of: GNA_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: S_GNA
subclass of: GNA_oligo
subclass of: Restriction
  on property: has_quality
  some values from: S_GNA
definition: An oligo composed of (S)-GNA residues.
has_exact_synonym: (S)-glycerol nucleic acid
has_exact_synonym: (S)-glycol nucleic acid
has_exact_synonym: S GNA oligo
has_obo_namespace: sequence
id: SO:0001197

Axiom
annotated source: S_GNA_oligo
annotated property: definition
annotated target: An oligo composed of (S)-GNA residues.
database_cross_reference: RSC:cb

ds_DNA_viral_sequence
type: Class
subclass of: viral_sequence
definition: A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.
has_exact_synonym: double stranded DNA virus
has_exact_synonym: ds DNA viral sequence
has_obo_namespace: sequence
id: SO:0001198

Axiom
annotated source: ds_DNA_viral_sequence
annotated property: definition
annotated target: A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.
database_cross_reference: SO:ke

ss_RNA_viral_sequence
type: Class
subclass of: viral_sequence
definition: A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.
has_exact_synonym: single strand RNA virus
has_exact_synonym: ss RNA viral sequence
has_obo_namespace: sequence
id: SO:0001199

Axiom
annotated source: ss_RNA_viral_sequence
annotated property: definition
annotated target: A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.
database_cross_reference: SO:ke

negative_sense_ssRNA_viral_sequence
type: Class
subclass of: ss_RNA_viral_sequence
definition: A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.
has_exact_synonym: negative sense ssRNA viral sequence
has_obo_namespace: sequence
has_related_synonym: negative sense single stranded RNA virus
id: SO:0001200

Axiom
annotated source: negative_sense_ssRNA_viral_sequence
annotated property: definition
annotated target: A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.
database_cross_reference: SO:ke

positive_sense_ssRNA_viral_sequence
type: Class
subclass of: ss_RNA_viral_sequence
definition: A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.
has_exact_synonym: positive sense ssRNA viral sequence
has_obo_namespace: sequence
has_related_synonym: positive sense single stranded RNA virus
id: SO:0001201

Axiom
annotated source: positive_sense_ssRNA_viral_sequence
annotated property: definition
annotated target: A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.
database_cross_reference: SO:ke

ambisense_ssRNA_viral_sequence
type: Class
subclass of: ss_RNA_viral_sequence
definition: A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.
has_exact_synonym: ambisense single stranded RNA virus
has_exact_synonym: ambisense ssRNA viral sequence
has_obo_namespace: sequence
id: SO:0001202

Axiom
annotated source: ambisense_ssRNA_viral_sequence
annotated property: definition
annotated target: A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.
database_cross_reference: SO:ke

RNA_polymerase_promoter
type: Class
definition: A region (DNA) to which RNA polymerase binds, to begin transcription.
term replaced by: promoter
has_exact_synonym: RNA polymerase promoter
has_obo_namespace: sequence
id: SO:0001203
comment: Term merged with promoter SO:0000167 in August 2020 as part of GREEKC initiative. See GitHub Issue 492 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/492)
deprecated: true

Axiom
annotated source: RNA_polymerase_promoter
annotated property: definition
annotated target: A region (DNA) to which RNA polymerase binds, to begin transcription.
database_cross_reference: xenbase:jb

Phage_RNA_Polymerase_Promoter
type: Class
subclass of: SO_0002311
definition: A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
has_exact_synonym: Phage RNA Polymerase Promoter
has_obo_namespace: sequence
id: SO:0001204
comment: former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.

Axiom
annotated source: Phage_RNA_Polymerase_Promoter
annotated property: definition
annotated target: A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
database_cross_reference: xenbase:jb

SP6_RNA_Polymerase_Promoter
type: Class
subclass of: Phage_RNA_Polymerase_Promoter
definition: A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
has_exact_synonym: SP6 RNA Polymerase Promoter
has_obo_namespace: sequence
id: SO:0001205

Axiom
annotated source: SP6_RNA_Polymerase_Promoter
annotated property: definition
annotated target: A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
database_cross_reference: xenbase:jb

T3_RNA_Polymerase_Promoter
type: Class
subclass of: Phage_RNA_Polymerase_Promoter
definition: A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
has_exact_synonym: T3 RNA Polymerase Promoter
has_obo_namespace: sequence
id: SO:0001206

Axiom
annotated source: T3_RNA_Polymerase_Promoter
annotated property: definition
annotated target: A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
database_cross_reference: xenbase:jb

T7_RNA_Polymerase_Promoter
type: Class
subclass of: Phage_RNA_Polymerase_Promoter
definition: A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
has_exact_synonym: T7 RNA Polymerase Promoter
has_obo_namespace: sequence
id: SO:0001207

Axiom
annotated source: T7_RNA_Polymerase_Promoter
annotated property: definition
annotated target: A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
database_cross_reference: xenbase:jb

five_prime_EST
type: Class
subclass of: EST
definition: An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.
has_exact_synonym: 5' EST
has_exact_synonym: five prime EST
has_obo_namespace: sequence
id: SO:0001208

Axiom
annotated source: five_prime_EST
annotated property: definition
annotated target: An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.
database_cross_reference: http://www.ncbi.nlm.nih.gov/About/primer/est.html

three_prime_EST
type: Class
subclass of: EST
definition: An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).
has_exact_synonym: 3' EST
has_exact_synonym: three prime EST
has_obo_namespace: sequence
id: SO:0001209

Axiom
annotated source: three_prime_EST
annotated property: definition
annotated target: An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).
database_cross_reference: http://www.ncbi.nlm.nih.gov/About/primer/est.html

translational_frameshift
type: Class
subclass of: mRNA_region
definition: The region of mRNA (not divisible by 3 bases) that is skipped or added during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
database_cross_reference: http://en.wikipedia.org/wiki/Translational_frameshift
has_exact_synonym: INSDC_qualifier:ribosomal_slippage
has_exact_synonym: ribosomal frameshift
has_exact_synonym: ribosomal slippage
has_exact_synonym: translational frameshift
has_obo_namespace: sequence
id: SO:0001210
comment: Added synonym 'ribosomal_slippage' on Feb 1, 2021, a term in INSDC and GenBank. See GitHub Issue #522.

Axiom
annotated source: translational_frameshift
annotated property: definition
annotated target: The region of mRNA (not divisible by 3 bases) that is skipped or added during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
database_cross_reference: SO:ke
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: translational_frameshift
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Translational_frameshift

plus_1_translational_frameshift
type: Class
subclass of: translational_frameshift
definition: The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
has_exact_synonym: plus 1 ribosomal frameshift
has_exact_synonym: plus 1 translational frameshift
has_obo_namespace: sequence
id: SO:0001211

Axiom
annotated source: plus_1_translational_frameshift
annotated property: definition
annotated target: The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
database_cross_reference: SO:ke

plus_2_translational_frameshift
type: Class
subclass of: translational_frameshift
definition: The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
has_exact_synonym: plus 2 ribosomal frameshift
has_exact_synonym: plus 2 translational frameshift
has_obo_namespace: sequence
id: SO:0001212

Axiom
annotated source: plus_2_translational_frameshift
annotated property: definition
annotated target: The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
database_cross_reference: SO:ke

group_III_intron
type: Class
subclass of: autocatalytically_spliced_intron
definition: Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.
database_cross_reference: http://en.wikipedia.org/wiki/Group_III_intron
has_exact_synonym: group III intron
has_obo_namespace: sequence
id: SO:0001213
comment: GO:0000374.

Axiom
annotated source: group_III_intron
annotated property: definition
annotated target: Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.
database_cross_reference: PMID:11377794

wiki
type: Axiom
annotated source: group_III_intron
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Group_III_intron

noncoding_region_of_exon
type: Class
subclass of: exon_region
definition: The maximal intersection of exon and UTR.
has_exact_synonym: noncoding region of exon
has_obo_namespace: sequence
id: SO:0001214
in_subset: SOFA
comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.

Axiom
annotated source: noncoding_region_of_exon
annotated property: definition
annotated target: The maximal intersection of exon and UTR.
database_cross_reference: SO:ke

coding_region_of_exon
type: Class
subclass of: exon_region
definition: The region of an exon that encodes for protein sequence.
has_exact_synonym: coding region of exon
has_obo_namespace: sequence
id: SO:0001215
in_subset: SOFA
comment: An exon containing either a start or stop codon will be partially coding and partially non coding.

Axiom
annotated source: coding_region_of_exon
annotated property: definition
annotated target: The region of an exon that encodes for protein sequence.
database_cross_reference: SO:ke

endonuclease_spliced_intron
type: Class
subclass of: intron
definition: An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
has_exact_synonym: endonuclease spliced intron
has_obo_namespace: sequence
id: SO:0001216

Axiom
annotated source: endonuclease_spliced_intron
annotated property: definition
annotated target: An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
database_cross_reference: SO:ke

protein_coding_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: protein_coding
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: protein_coding
definition: A gene that codes for an RNA that can be translated into a protein.
has_exact_synonym: protein coding gene
has_obo_namespace: sequence
id: SO:0001217
in_subset: Alliance of Genome Resources

transgenic_insertion
type: Class
equivalent class: Class
  intersection of: insertion
  intersection of: Restriction
    on property: has_quality
    some values from: transgenic
subclass of: insertion
subclass of: Restriction
  on property: has_quality
  some values from: transgenic
definition: An insertion that derives from another organism, via the use of recombinant DNA technology.
has_exact_synonym: transgenic insertion
has_obo_namespace: sequence
id: SO:0001218

Axiom
annotated source: transgenic_insertion
annotated property: definition
annotated target: An insertion that derives from another organism, via the use of recombinant DNA technology.
database_cross_reference: SO:bm

retrogene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: retrotransposed
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: retrotransposed
definition: A gene that has been produced as the product of a reverse transcriptase mediated event.
has_obo_namespace: sequence
id: SO:0001219

silenced_by_RNA_interference
type: Class
subclass of: silenced
definition: An attribute describing an epigenetic process where a gene is inactivated by RNA interference.
has_exact_synonym: silenced by RNA interference
has_obo_namespace: sequence
id: SO:0001220
comment: RNA interference is GO:0016246.

Axiom
annotated source: silenced_by_RNA_interference
annotated property: definition
annotated target: An attribute describing an epigenetic process where a gene is inactivated by RNA interference.
database_cross_reference: RSC:cb

silenced_by_histone_modification
type: Class
subclass of: silenced
definition: An attribute describing an epigenetic process where a gene is inactivated by histone modification.
has_exact_synonym: silenced by histone modification
has_obo_namespace: sequence
id: SO:0001221
comment: Histone modification is GO:0016570.

Axiom
annotated source: silenced_by_histone_modification
annotated property: definition
annotated target: An attribute describing an epigenetic process where a gene is inactivated by histone modification.
database_cross_reference: RSC:cb

silenced_by_histone_methylation
type: Class
subclass of: silenced_by_histone_modification
definition: An attribute describing an epigenetic process where a gene is inactivated by histone methylation.
has_exact_synonym: silenced by histone methylation
has_obo_namespace: sequence
id: SO:0001222
comment: Histone methylation is GO:0016571.

Axiom
annotated source: silenced_by_histone_methylation
annotated property: definition
annotated target: An attribute describing an epigenetic process where a gene is inactivated by histone methylation.
database_cross_reference: RSC:cb

silenced_by_histone_deacetylation
type: Class
subclass of: silenced_by_histone_modification
definition: An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.
has_exact_synonym: silenced by histone deacetylation
has_obo_namespace: sequence
id: SO:0001223
comment: Histone deacetylation is GO:0016573.

Axiom
annotated source: silenced_by_histone_deacetylation
annotated property: definition
annotated target: An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.
database_cross_reference: RSC:cb

gene_silenced_by_RNA_interference
type: Class
equivalent class: Class
  intersection of: silenced_gene
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_RNA_interference
subclass of: silenced_gene
subclass of: Restriction
  on property: has_quality
  some values from: silenced_by_RNA_interference
definition: A gene that is silenced by RNA interference.
has_exact_synonym: RNA interference silenced gene
has_exact_synonym: RNAi silenced gene
has_exact_synonym: gene silenced by RNA interference
has_obo_namespace: sequence
id: SO:0001224

Axiom
annotated source: gene_silenced_by_RNA_interference
annotated property: definition
annotated target: A gene that is silenced by RNA interference.
database_cross_reference: SO:xp

gene_silenced_by_histone_modification
type: Class
equivalent class: Class
  intersection of: silenced_gene
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_histone_modification
subclass of: silenced_gene
subclass of: Restriction
  on property: has_quality
  some values from: silenced_by_histone_modification
definition: A gene that is silenced by histone modification.
has_exact_synonym: gene silenced by histone modification
has_obo_namespace: sequence
id: SO:0001225

Axiom
annotated source: gene_silenced_by_histone_modification
annotated property: definition
annotated target: A gene that is silenced by histone modification.
database_cross_reference: SO:xp

gene_silenced_by_histone_methylation
type: Class
equivalent class: Class
  intersection of: gene_silenced_by_histone_modification
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_histone_methylation
subclass of: gene_silenced_by_histone_modification
subclass of: Restriction
  on property: has_quality
  some values from: silenced_by_histone_methylation
definition: A gene that is silenced by histone methylation.
has_exact_synonym: gene silenced by histone methylation
has_obo_namespace: sequence
id: SO:0001226

Axiom
annotated source: gene_silenced_by_histone_methylation
annotated property: definition
annotated target: A gene that is silenced by histone methylation.
database_cross_reference: SO:xp

gene_silenced_by_histone_deacetylation
type: Class
equivalent class: Class
  intersection of: gene_silenced_by_histone_modification
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_histone_deacetylation
subclass of: gene_silenced_by_histone_modification
subclass of: Restriction
  on property: has_quality
  some values from: silenced_by_histone_deacetylation
definition: A gene that is silenced by histone deacetylation.
has_exact_synonym: gene silenced by histone deacetylation
has_obo_namespace: sequence
id: SO:0001227

Axiom
annotated source: gene_silenced_by_histone_deacetylation
annotated property: definition
annotated target: A gene that is silenced by histone deacetylation.
database_cross_reference: SO:xp

dihydrouridine
type: Class
subclass of: modified_uridine
definition: A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.
database_cross_reference: RNAMOD:051
database_cross_reference: http://en.wikipedia.org/wiki/Dihydrouridine
has_exact_synonym: D
has_obo_namespace: sequence
id: SO:0001228

Axiom
annotated source: dihydrouridine
annotated property: definition
annotated target: A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: dihydrouridine
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Dihydrouridine

Axiom
annotated source: dihydrouridine
annotated property: has_exact_synonym
annotated target: D
has_synonym_type: RNA modification

pseudouridine
type: Class
subclass of: modified_uridine
definition: A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.
database_cross_reference: RNAMOD:050
database_cross_reference: http://en.wikipedia.org/wiki/Pseudouridine
has_exact_synonym: Y
has_obo_namespace: sequence
id: SO:0001229
comment: The free molecule is CHEBI:17802.

Axiom
annotated source: pseudouridine
annotated property: definition
annotated target: A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: pseudouridine
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Pseudouridine

Axiom
annotated source: pseudouridine
annotated property: has_exact_synonym
annotated target: Y
has_synonym_type: RNA modification

inosine
type: Class
subclass of: modified_RNA_base_feature
definition: A modified RNA base in which hypoxanthine is bound to the ribose ring.
database_cross_reference: http://en.wikipedia.org/wiki/Inosine
has_obo_namespace: sequence
has_related_synonym: I
has_related_synonym: RNAMOD:017
id: SO:0001230
comment: The free molecule is CHEBI:17596.

Axiom
annotated source: inosine
annotated property: definition
annotated target: A modified RNA base in which hypoxanthine is bound to the ribose ring.
database_cross_reference: RSC:cb
database_cross_reference: http://library.med.utah.edu/RNAmods/

wiki
type: Axiom
annotated source: inosine
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Inosine

seven_methylguanine
type: Class
subclass of: modified_RNA_base_feature
definition: A modified RNA base in which guanine is methylated at the 7- position.
has_exact_synonym: 7-methylguanine
has_exact_synonym: seven methylguanine
has_obo_namespace: sequence
id: SO:0001231
comment: The free molecule is CHEBI:2274.

Axiom
annotated source: seven_methylguanine
annotated property: definition
annotated target: A modified RNA base in which guanine is methylated at the 7- position.
database_cross_reference: RSC:cb

ribothymidine
type: Class
subclass of: modified_RNA_base_feature
definition: A modified RNA base in which thymine is bound to the ribose ring.
has_obo_namespace: sequence
id: SO:0001232
comment: The free molecule is CHEBI:30832.

Axiom
annotated source: ribothymidine
annotated property: definition
annotated target: A modified RNA base in which thymine is bound to the ribose ring.
database_cross_reference: RSC:cb

methylinosine
type: Class
subclass of: modified_inosine
definition: A modified RNA base in which methylhypoxanthine is bound to the ribose ring.
has_obo_namespace: sequence
id: SO:0001233

Axiom
annotated source: methylinosine
annotated property: definition
annotated target: A modified RNA base in which methylhypoxanthine is bound to the ribose ring.
database_cross_reference: RSC:cb

mobile
type: Class
subclass of: feature_attribute
definition: An attribute describing a feature that has either intra-genome or intracellular mobility.
database_cross_reference: http://en.wikipedia.org/wiki/Mobile
has_obo_namespace: sequence
id: SO:0001234

Axiom
annotated source: mobile
annotated property: definition
annotated target: An attribute describing a feature that has either intra-genome or intracellular mobility.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: mobile
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Mobile

replicon
type: Class
subclass of: biological_region
definition: A region containing at least one unique origin of replication and a unique termination site.
database_cross_reference: http://en.wikipedia.org/wiki/Replicon_(genetics)
has_obo_namespace: sequence
id: SO:0001235
in_subset: SOFA

Axiom
annotated source: replicon
annotated property: definition
annotated target: A region containing at least one unique origin of replication and a unique termination site.
database_cross_reference: ISBN:0716719207

wiki
type: Axiom
annotated source: replicon
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Replicon_(genetics)

base
type: Class
subclass of: biological_region
definition: A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
database_cross_reference: http://en.wikipedia.org/wiki/Nucleobase
has_obo_namespace: sequence
id: SO:0001236
in_subset: SOFA

Axiom
annotated source: base
annotated property: definition
annotated target: A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: base
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Nucleobase

amino_acid
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: part_of
  some values from: polypeptide
definition: A sequence feature that corresponds to a single amino acid residue in a polypeptide.
database_cross_reference: http://en.wikipedia.org/wiki/Amino_acid
has_exact_synonym: amino acid
has_obo_namespace: sequence
id: SO:0001237
comment: Probably in the future this will cross reference to Chebi.

Axiom
annotated source: amino_acid
annotated property: definition
annotated target: A sequence feature that corresponds to a single amino acid residue in a polypeptide.
database_cross_reference: RSC:cb

wiki
type: Axiom
annotated source: amino_acid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Amino_acid

major_TSS
type: Class
subclass of: TSS
definition: The tanscription start site that is most frequently used for transcription of a gene.
has_exact_synonym: major TSS
has_exact_synonym: major transcription start site
has_obo_namespace: sequence
id: SO:0001238

minor_TSS
type: Class
subclass of: TSS
definition: A tanscription start site that is not the most frequently used for transcription of a gene.
has_exact_synonym: minor TSS
has_obo_namespace: sequence
id: SO:0001239

TSS_region
type: Class
definition: The region of a gene from the 5' most TSS to the 3' TSS.
term replaced by: promoter
has_exact_synonym: TSS region
has_obo_namespace: sequence
id: SO:0001240
comment: Merged into promoter (SO:0000167) on 11 Feb 2021 by Dave Sant. GREEKC had asked us to merge these terms to reduce redundancy. See GitHub Issue #528
deprecated: true

Axiom
annotated source: TSS_region
annotated property: definition
annotated target: The region of a gene from the 5' most TSS to the 3' TSS.
database_cross_reference: BBOP:nw

encodes_alternate_transcription_start_sites
type: Class
subclass of: gene_attribute
definition: A gene that has multiple possible transcription start sites.
has_exact_synonym: encodes alternate transcription start sites
has_obo_namespace: sequence
id: SO:0001241

SO_0001242
type: Class
IAO_0000231: IAO_0000227
term replaced by: chromosome_breakpoint
deprecated: true

miRNA_primary_transcript_region
type: Class
subclass of: primary_transcript_region
definition: A part of an miRNA primary_transcript.
has_exact_synonym: miRNA primary transcript region
has_obo_namespace: sequence
id: SO:0001243

Axiom
annotated source: miRNA_primary_transcript_region
annotated property: definition
annotated target: A part of an miRNA primary_transcript.
database_cross_reference: SO:ke

pre_miRNA
type: Class
subclass of: miRNA_primary_transcript_region
definition: The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
has_exact_synonym: pre-miRNA
has_obo_namespace: sequence
id: SO:0001244

Axiom
annotated source: pre_miRNA
annotated property: definition
annotated target: The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
database_cross_reference: SO:ke

miRNA_stem
type: Class
subclass of: miRNA_primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: pre_miRNA
definition: The stem of the hairpin loop formed by folding of the pre-miRNA.
has_exact_synonym: miRNA stem
has_obo_namespace: sequence
id: SO:0001245

Axiom
annotated source: miRNA_stem
annotated property: definition
annotated target: The stem of the hairpin loop formed by folding of the pre-miRNA.
database_cross_reference: SO:ke

miRNA_loop
type: Class
subclass of: miRNA_primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: pre_miRNA
definition: The loop of the hairpin loop formed by folding of the pre-miRNA.
has_exact_synonym: miRNA loop
has_obo_namespace: sequence
id: SO:0001246

Axiom
annotated source: miRNA_loop
annotated property: definition
annotated target: The loop of the hairpin loop formed by folding of the pre-miRNA.
database_cross_reference: SO:ke

synthetic_oligo
type: Class
subclass of: oligo
definition: An oligo composed of synthetic nucleotides.
has_exact_synonym: synthetic oligo
has_obo_namespace: sequence
id: SO:0001247

Axiom
annotated source: synthetic_oligo
annotated property: definition
annotated target: An oligo composed of synthetic nucleotides.
database_cross_reference: SO:ke

assembly
type: Class
subclass of: experimental_feature
definition: A region of the genome of known length that is composed by ordering and aligning two or more different regions.
database_cross_reference: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly
has_obo_namespace: sequence
id: SO:0001248
in_subset: SOFA

Axiom
annotated source: assembly
annotated property: definition
annotated target: A region of the genome of known length that is composed by ordering and aligning two or more different regions.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: assembly
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly

fragment_assembly
type: Class
subclass of: assembly
definition: A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.
has_exact_synonym: fragment assembly
has_exact_synonym: physical map
has_obo_namespace: sequence
id: SO:0001249

Axiom
annotated source: fragment_assembly
annotated property: definition
annotated target: A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.
database_cross_reference: SO:ke

fingerprint_map
type: Class
subclass of: fragment_assembly
subclass of: Restriction
  on property: has_part
  some values from: restriction_fragment
definition: A fingerprint_map is a physical map composed of restriction fragments.
has_exact_synonym: BACmap
has_exact_synonym: FPC
has_exact_synonym: FPCmap
has_exact_synonym: fingerprint map
has_exact_synonym: restriction map
has_obo_namespace: sequence
id: SO:0001250

Axiom
annotated source: fingerprint_map
annotated property: definition
annotated target: A fingerprint_map is a physical map composed of restriction fragments.
database_cross_reference: SO:ke

STS_map
type: Class
subclass of: fragment_assembly
subclass of: Restriction
  on property: has_part
  some values from: STS
definition: An STS map is a physical map organized by the unique STS landmarks.
has_exact_synonym: STS map
has_obo_namespace: sequence
id: SO:0001251

Axiom
annotated source: STS_map
annotated property: definition
annotated target: An STS map is a physical map organized by the unique STS landmarks.
database_cross_reference: SO:ke

RH_map
type: Class
subclass of: fragment_assembly
subclass of: Restriction
  on property: has_part
  some values from: STS
definition: A radiation hybrid map is a physical map.
has_exact_synonym: RH map
has_exact_synonym: radiation hybrid map
has_obo_namespace: sequence
id: SO:0001252

Axiom
annotated source: RH_map
annotated property: definition
annotated target: A radiation hybrid map is a physical map.
database_cross_reference: SO:ke

sonicate_fragment
type: Class
subclass of: assembly_component
definition: A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.
has_exact_synonym: sonicate fragment
has_obo_namespace: sequence
id: SO:0001253

Axiom
annotated source: sonicate_fragment
annotated property: definition
annotated target: A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.
database_cross_reference: SO:ke

polyploid
type: Class
subclass of: SO_1000182
definition: A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.
database_cross_reference: http://en.wikipedia.org/wiki/Polyploid
has_obo_namespace: sequence
id: SO:0001254

Axiom
annotated source: polyploid
annotated property: definition
annotated target: A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: polyploid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Polyploid

autopolyploid
type: Class
subclass of: polyploid
definition: A polyploid where the multiple chromosome set was derived from the same organism.
database_cross_reference: http://en.wikipedia.org/wiki/Autopolyploid
has_obo_namespace: sequence
id: SO:0001255

Axiom
annotated source: autopolyploid
annotated property: definition
annotated target: A polyploid where the multiple chromosome set was derived from the same organism.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: autopolyploid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Autopolyploid

allopolyploid
type: Class
subclass of: polyploid
definition: A polyploid where the multiple chromosome set was derived from a different organism.
database_cross_reference: http://en.wikipedia.org/wiki/Allopolyploid
has_obo_namespace: sequence
id: SO:0001256

Axiom
annotated source: allopolyploid
annotated property: definition
annotated target: A polyploid where the multiple chromosome set was derived from a different organism.
database_cross_reference: SO:ke

wiki
type: Axiom
annotated source: allopolyploid
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Allopolyploid

homing_endonuclease_binding_site
type: Class
subclass of: nuclease_binding_site
definition: The binding site (recognition site) of a homing endonuclease. The binding site is typically large.
has_exact_synonym: homing endonuclease binding site
has_obo_namespace: sequence
id: SO:0001257

Axiom
annotated source: homing_endonuclease_binding_site
annotated property: definition
annotated target: The binding site (recognition site) of a homing endonuclease. The binding site is typically large.
database_cross_reference: SO:ke

octamer_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
definition: A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.
has_exact_synonym: octamer motif
has_obo_namespace: sequence
id: SO:0001258
comment: Nature. 1986 Oct 16-22;323(6089):640-3.

Axiom
annotated source: octamer_motif
annotated property: definition
annotated target: A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.
database_cross_reference: GOC:dh
database_cross_reference: PMID:3095662

apicoplast_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: apicoplast_sequence
subclass of: chromosome
subclass of: Restriction
  on property: has_origin
  some values from: apicoplast_sequence
definition: A chromosome originating in an apicoplast.
has_exact_synonym: apicoplast chromosome
has_obo_namespace: sequence
id: SO:0001259

Axiom
annotated source: apicoplast_chromosome
annotated property: definition
annotated target: A chromosome originating in an apicoplast.
database_cross_reference: SO:xp

sequence_collection
type: Class
definition: A collection of discontinuous sequences.
has_exact_synonym: sequence collection
has_obo_namespace: sequence
id: SO:0001260

Axiom
annotated source: sequence_collection
annotated property: definition
annotated target: A collection of discontinuous sequences.
database_cross_reference: SO:ke

overlapping_feature_set
type: Class
subclass of: experimental_result_region
definition: A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.
has_exact_synonym: overlapping feature set
has_obo_namespace: sequence
id: SO:0001261
comment: This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA.

Axiom
annotated source: overlapping_feature_set
annotated property: definition
annotated target: A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.
database_cross_reference: SO:ke

overlapping_EST_set
type: Class
subclass of: overlapping_feature_set
subclass of: Restriction
  on property: has_part
  some values from: EST
definition: A continous experimental result region extending the length of multiple overlapping EST's.
has_exact_synonym: overlapping EST set
has_obo_namespace: sequence
id: SO:0001262

Axiom
annotated source: overlapping_EST_set
annotated property: definition
annotated target: A continous experimental result region extending the length of multiple overlapping EST's.
database_cross_reference: SO:ke

ncRNA_gene
type: Class
subclass of: gene
definition: A gene that encodes a non-coding RNA.
has_exact_synonym: ncRNA gene
has_exact_synonym: non-coding RNA gene
has_obo_namespace: sequence
id: SO:0001263
in_subset: Alliance of Genome Resources

gRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: gRNA_encoding
subclass of: ncRNA_gene
subclass of: Restriction
  on property: has_quality
  some values from: gRNA_encoding
definition: A noncoding RNA that guides the insertion or deletion of uridine residues in mitochondrial mRNAs. This may also refer to synthetic RNAs used to guide DNA editing using the CRIPSR/Cas9 system.
has_exact_synonym: gRNA gene
has_obo_namespace: sequence
id: SO:0001264

miRNA_gene
type: Class
equivalent class: Class
  intersection of: SO_0002342
  intersection of: Restriction
    on property: has_quality
    some values from: miRNA_encoding
  intersection of: Restriction
    on property: has_quality
    some values from: stRNA_encoding
subclass of: SO_0002342
subclass of: Restriction
  on property: has_quality
  some values from: miRNA_encoding
subclass of: Restriction
  on property: has_quality
  some values from: stRNA_encoding
definition: A small noncoding RNA of approximately 22 nucleotides in length which may be involved in regulation of gene expression.
has_alternative_id: SO:0001270
has_exact_synonym: miRNA gene
has_exact_synonym: stRNA gene
has_exact_synonym: stRNA_gene
has_obo_namespace: sequence
id: SO:0001265
comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.

scRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: scRNA_encoding
subclass of: ncRNA_gene
subclass of: Restriction
  on property: has_quality
  some values from: scRNA_encoding
definition: A gene encoding a small noncoding RNA that is generally found only in the cytoplasm.
has_exact_synonym: scRNA gene
has_obo_namespace: sequence
id: SO:0001266

snoRNA_gene
type: Class
equivalent class: Class
  intersection of: SO_0002342
  intersection of: Restriction
    on property: has_quality
    some values from: snoRNA_encoding
subclass of: SO_0002342
subclass of: Restriction
  on property: has_quality
  some values from: snoRNA_encoding
definition: A gene encoding a small noncoding RNA that participates in the processing or chemical modifications of many RNAs, including ribosomal RNAs and spliceosomal RNAs.
has_exact_synonym: snoRNA gene
has_obo_namespace: sequence
id: SO:0001267
comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. Added additional children of snoRNA on 18 Nov 2021 at the request of Steven Marygold. See GitHub Issue #519.

snRNA_gene
type: Class
subclass of: SO_0002342
definition: A gene that encodes a small nuclear RNA.
has_exact_synonym: small nuclear RNA gene
has_exact_synonym: snRNA gene
has_obo_namespace: sequence
id: SO:0001268
comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.

Axiom
annotated source: snRNA_gene
annotated property: definition
annotated target: A gene that encodes a small nuclear RNA.
database_cross_reference: http://en.wikipedia.org/wiki/Small_nuclear_RNA

SRP_RNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: SRP_RNA_encoding
subclass of: ncRNA_gene
subclass of: Restriction
  on property: has_quality
  some values from: SRP_RNA_encoding
definition: A gene that encodes a signal recognition particle (SRP) RNA.
has_exact_synonym: SRP RNA gene
has_obo_namespace: sequence
id: SO:0001269

SO_0001270
type: Class
IAO_0000231: IAO_0000227
term replaced by: miRNA_gene
deprecated: true

tmRNA_gene
type: Class
equivalent class: Class
  intersection of: SO_0002342
  intersection of: Restriction
    on property: has_quality
    some values from: tmRNA_encoding
subclass of: SO_0002342
subclass of: Restriction
  on property: has_quality
  some values from: tmRNA_encoding
definition: A bacterial RNA with both tRNA and mRNA like properties.
has_exact_synonym: tmRNA gene
has_obo_namespace: sequence
id: SO:0001271
comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.

tRNA_gene
type: Class
equivalent class: Class
  intersection of: SO_0002342
  intersection of: Restriction
    on property: has_quality
    some values from: tRNA_encoding
subclass of: SO_0002342
subclass of: Restriction
  on property: has_quality
  some values from: tRNA_encoding
definition: A noncoding RNA that binds to a specific amino acid to allow that amino acid to be used by the ribosome during translation of RNA.
has_exact_synonym: tRNA gene
has_obo_namespace: sequence
id: SO:0001272
comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.

modified_adenosine
type: Class
subclass of: modified_RNA_base_feature
definition: A modified adenine is an adenine base feature that has been altered.
has_exact_synonym: modified adenosine
has_obo_namespace: sequence
id: SO:0001273

Axiom
annotated source: modified_adenosine
annotated property: definition
annotated target: A modified adenine is an adenine base feature that has been altered.
database_cross_reference: SO:ke

modified_inosine
type: Class
subclass of: inosine
definition: A modified inosine is an inosine base feature that has been altered.
has_exact_synonym: modified inosine
has_obo_namespace: sequence
id: SO:0001274

Axiom
annotated source: modified_inosine
annotated property: definition
annotated target: A modified inosine is an inosine base feature that has been altered.
database_cross_reference: SO:ke

modified_cytidine
type: Class
subclass of: modified_RNA_base_feature
definition: A modified cytidine is a cytidine base feature which has been altered.
has_exact_synonym: modified cytidine
has_obo_namespace: sequence
id: SO:0001275

Axiom
annotated source: modified_cytidine
annotated property: definition
annotated target: A modified cytidine is a cytidine base feature which has been altered.
database_cross_reference: SO:ke

modified_guanosine
type: Class
subclass of: modified_RNA_base_feature
definition: A guanosine base that has been modified.
has_exact_synonym: modified guanosine
has_obo_namespace: sequence
id: SO:0001276

modified_uridine
type: Class
subclass of: modified_RNA_base_feature
definition: A uridine base that has been modified.
has_exact_synonym: modified uridine
has_obo_namespace: sequence
id: SO:0001277

one_methylinosine
type: Class
subclass of: modified_inosine
definition: 1-methylinosine is a modified inosine.
database_cross_reference: RNAMOD:018
has_exact_synonym: 1-methylinosine
has_exact_synonym: m1I
has_exact_synonym: one methylinosine
has_obo_namespace: sequence
id: SO:0001278

Axiom
annotated source: one_methylinosine
annotated property: definition
annotated target: 1-methylinosine is a modified inosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: one_methylinosine
annotated property: has_exact_synonym
annotated target: m1I
has_synonym_type: RNA modification

one_two_prime_O_dimethylinosine
type: Class
subclass of: modified_inosine
definition: 1,2'-O-dimethylinosine is a modified inosine.
database_cross_reference: RNAMOD:019
has_exact_synonym: 1,2'-O-dimethylinosine
has_exact_synonym: m'Im
has_exact_synonym: one two prime O dimethylinosine
has_obo_namespace: sequence
id: SO:0001279

Axiom
annotated source: one_two_prime_O_dimethylinosine
annotated property: definition
annotated target: 1,2'-O-dimethylinosine is a modified inosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: one_two_prime_O_dimethylinosine
annotated property: has_exact_synonym
annotated target: m'Im
has_synonym_type: RNA modification

two_prime_O_methylinosine
type: Class
subclass of: modified_inosine
definition: 2'-O-methylinosine is a modified inosine.
database_cross_reference: RNAMOD:081
has_exact_synonym: 2'-O-methylinosine
has_exact_synonym: Im
has_exact_synonym: two prime O methylinosine
has_obo_namespace: sequence
id: SO:0001280

Axiom
annotated source: two_prime_O_methylinosine
annotated property: definition
annotated target: 2'-O-methylinosine is a modified inosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_prime_O_methylinosine
annotated property: has_exact_synonym
annotated target: Im
has_synonym_type: RNA modification

three_methylcytidine
type: Class
subclass of: modified_cytidine
definition: 3-methylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:020
has_exact_synonym: 3-methylcytidine
has_exact_synonym: m3C
has_exact_synonym: three methylcytidine
has_obo_namespace: sequence
id: SO:0001281

Axiom
annotated source: three_methylcytidine
annotated property: definition
annotated target: 3-methylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: three_methylcytidine
annotated property: has_exact_synonym
annotated target: m3C
has_synonym_type: RNA modification

five_methylcytidine
type: Class
subclass of: modified_cytidine
definition: 5-methylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:021
has_exact_synonym: 5-methylcytidine
has_exact_synonym: five methylcytidine
has_exact_synonym: m5C
has_obo_namespace: sequence
id: SO:0001282

Axiom
annotated source: five_methylcytidine
annotated property: definition
annotated target: 5-methylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methylcytidine
annotated property: has_exact_synonym
annotated target: m5C
has_synonym_type: RNA modification

two_prime_O_methylcytidine
type: Class
subclass of: modified_cytidine
definition: 2'-O-methylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:022
has_exact_synonym: 2'-O-methylcytidine
has_exact_synonym: Cm
has_exact_synonym: two prime O methylcytidine
has_obo_namespace: sequence
id: SO:0001283

Axiom
annotated source: two_prime_O_methylcytidine
annotated property: definition
annotated target: 2'-O-methylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_prime_O_methylcytidine
annotated property: has_exact_synonym
annotated target: Cm
has_synonym_type: RNA modification

two_thiocytidine
type: Class
subclass of: modified_cytidine
definition: 2-thiocytidine is a modified cytidine.
database_cross_reference: RNAMOD:023
has_exact_synonym: 2-thiocytidine
has_exact_synonym: s2C
has_exact_synonym: two thiocytidine
has_obo_namespace: sequence
id: SO:0001284

Axiom
annotated source: two_thiocytidine
annotated property: definition
annotated target: 2-thiocytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_thiocytidine
annotated property: has_exact_synonym
annotated target: s2C
has_synonym_type: RNA modification

N4_acetylcytidine
type: Class
subclass of: modified_cytidine
definition: N4-acetylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:024
has_exact_synonym: N4 acetylcytidine
has_exact_synonym: N4-acetylcytidine
has_exact_synonym: ac4C
has_obo_namespace: sequence
id: SO:0001285

Axiom
annotated source: N4_acetylcytidine
annotated property: definition
annotated target: N4-acetylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N4_acetylcytidine
annotated property: has_exact_synonym
annotated target: ac4C
has_synonym_type: RNA modification

five_formylcytidine
type: Class
subclass of: modified_cytidine
definition: 5-formylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:025
has_exact_synonym: 5-formylcytidine
has_exact_synonym: f5C
has_exact_synonym: five formylcytidine
has_obo_namespace: sequence
id: SO:0001286

Axiom
annotated source: five_formylcytidine
annotated property: definition
annotated target: 5-formylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_formylcytidine
annotated property: has_exact_synonym
annotated target: f5C
has_synonym_type: RNA modification

five_two_prime_O_dimethylcytidine
type: Class
subclass of: modified_cytidine
definition: 5,2'-O-dimethylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:026
has_exact_synonym: 5,2'-O-dimethylcytidine
has_exact_synonym: five two prime O dimethylcytidine
has_exact_synonym: m5Cm
has_obo_namespace: sequence
id: SO:0001287

Axiom
annotated source: five_two_prime_O_dimethylcytidine
annotated property: definition
annotated target: 5,2'-O-dimethylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_two_prime_O_dimethylcytidine
annotated property: has_exact_synonym
annotated target: m5Cm
has_synonym_type: RNA modification

N4_acetyl_2_prime_O_methylcytidine
type: Class
subclass of: modified_cytidine
definition: N4-acetyl-2'-O-methylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:027
has_exact_synonym: N4 acetyl 2 prime O methylcytidine
has_exact_synonym: N4-acetyl-2'-O-methylcytidine
has_exact_synonym: ac4Cm
has_obo_namespace: sequence
id: SO:0001288

Axiom
annotated source: N4_acetyl_2_prime_O_methylcytidine
annotated property: definition
annotated target: N4-acetyl-2'-O-methylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N4_acetyl_2_prime_O_methylcytidine
annotated property: has_exact_synonym
annotated target: ac4Cm
has_synonym_type: RNA modification

lysidine
type: Class
subclass of: modified_cytidine
definition: Lysidine is a modified cytidine.
database_cross_reference: RNAMOD:028
database_cross_reference: http://en.wikipedia.org/wiki/Lysidine
has_exact_synonym: k2C
has_obo_namespace: sequence
id: SO:0001289

Axiom
annotated source: lysidine
annotated property: definition
annotated target: Lysidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

wiki
type: Axiom
annotated source: lysidine
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Lysidine

Axiom
annotated source: lysidine
annotated property: has_exact_synonym
annotated target: k2C
has_synonym_type: RNA modification

N4_methylcytidine
type: Class
subclass of: modified_cytidine
definition: N4-methylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:082
has_exact_synonym: N4 methylcytidine
has_exact_synonym: N4-methylcytidine
has_exact_synonym: m4C
has_obo_namespace: sequence
id: SO:0001290

Axiom
annotated source: N4_methylcytidine
annotated property: definition
annotated target: N4-methylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N4_methylcytidine
annotated property: has_exact_synonym
annotated target: m4C
has_synonym_type: RNA modification

N4_2_prime_O_dimethylcytidine
type: Class
subclass of: modified_cytidine
definition: N4,2'-O-dimethylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:083
has_exact_synonym: N4 2 prime O dimethylcytidine
has_exact_synonym: N4,2'-O-dimethylcytidine
has_exact_synonym: m4Cm
has_obo_namespace: sequence
id: SO:0001291

Axiom
annotated source: N4_2_prime_O_dimethylcytidine
annotated property: definition
annotated target: N4,2'-O-dimethylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N4_2_prime_O_dimethylcytidine
annotated property: has_exact_synonym
annotated target: m4Cm
has_synonym_type: RNA modification

five_hydroxymethylcytidine
type: Class
subclass of: modified_cytidine
definition: 5-hydroxymethylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:084
has_exact_synonym: 5-hydroxymethylcytidine
has_exact_synonym: five hydroxymethylcytidine
has_exact_synonym: hm5C
has_obo_namespace: sequence
id: SO:0001292

Axiom
annotated source: five_hydroxymethylcytidine
annotated property: definition
annotated target: 5-hydroxymethylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_hydroxymethylcytidine
annotated property: has_exact_synonym
annotated target: hm5C
has_synonym_type: RNA modification

five_formyl_two_prime_O_methylcytidine
type: Class
subclass of: modified_cytidine
definition: 5-formyl-2'-O-methylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:095
has_exact_synonym: 5-formyl-2'-O-methylcytidine
has_exact_synonym: f5Cm
has_exact_synonym: five formyl two prime O methylcytidine
has_obo_namespace: sequence
id: SO:0001293

Axiom
annotated source: five_formyl_two_prime_O_methylcytidine
annotated property: definition
annotated target: 5-formyl-2'-O-methylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_formyl_two_prime_O_methylcytidine
annotated property: has_exact_synonym
annotated target: f5Cm
has_synonym_type: RNA modification

N4_N4_2_prime_O_trimethylcytidine
type: Class
subclass of: modified_cytidine
definition: N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.
database_cross_reference: RNAMOD:107
has_exact_synonym: N4,N4,2'-O-trimethylcytidine
has_exact_synonym: m42Cm
has_obo_namespace: sequence
id: SO:0001294

Axiom
annotated source: N4_N4_2_prime_O_trimethylcytidine
annotated property: definition
annotated target: N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N4_N4_2_prime_O_trimethylcytidine
annotated property: has_exact_synonym
annotated target: m42Cm
has_synonym_type: RNA modification

one_methyladenosine
type: Class
subclass of: modified_adenosine
definition: 1_methyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:001
has_exact_synonym: 1-methyladenosine
has_exact_synonym: m1A
has_exact_synonym: one methyladenosine
has_obo_namespace: sequence
id: SO:0001295

Axiom
annotated source: one_methyladenosine
annotated property: definition
annotated target: 1_methyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: one_methyladenosine
annotated property: has_exact_synonym
annotated target: m1A
has_synonym_type: RNA modification

two_methyladenosine
type: Class
subclass of: modified_adenosine
definition: 2_methyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:002
has_exact_synonym: 2-methyladenosine
has_exact_synonym: m2A
has_exact_synonym: two methyladenosine
has_obo_namespace: sequence
id: SO:0001296

Axiom
annotated source: two_methyladenosine
annotated property: definition
annotated target: 2_methyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_methyladenosine
annotated property: has_exact_synonym
annotated target: m2A
has_synonym_type: RNA modification

N6_methyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_methyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:003
has_exact_synonym: N6 methyladenosine
has_exact_synonym: N6-methyladenosine
has_exact_synonym: m6A
has_obo_namespace: sequence
id: SO:0001297

Axiom
annotated source: N6_methyladenosine
annotated property: definition
annotated target: N6_methyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_methyladenosine
annotated property: has_exact_synonym
annotated target: m6A
has_synonym_type: RNA modification

two_prime_O_methyladenosine
type: Class
subclass of: modified_adenosine
definition: 2prime_O_methyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:004
has_exact_synonym: 2'-O-methyladenosine
has_exact_synonym: Am
has_exact_synonym: two prime O methyladenosine
has_obo_namespace: sequence
id: SO:0001298

Axiom
annotated source: two_prime_O_methyladenosine
annotated property: definition
annotated target: 2prime_O_methyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_prime_O_methyladenosine
annotated property: has_exact_synonym
annotated target: Am
has_synonym_type: RNA modification

two_methylthio_N6_methyladenosine
type: Class
subclass of: modified_adenosine
definition: 2_methylthio_N6_methyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:005
has_exact_synonym: 2-methylthio-N6-methyladenosine
has_exact_synonym: ms2m6A
has_exact_synonym: two methylthio N6 methyladenosine
has_obo_namespace: sequence
id: SO:0001299

Axiom
annotated source: two_methylthio_N6_methyladenosine
annotated property: definition
annotated target: 2_methylthio_N6_methyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_methylthio_N6_methyladenosine
annotated property: has_exact_synonym
annotated target: ms2m6A
has_synonym_type: RNA modification

N6_isopentenyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_isopentenyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:006
has_exact_synonym: N6 isopentenyladenosine
has_exact_synonym: N6-isopentenyladenosine
has_exact_synonym: i6A
has_obo_namespace: sequence
id: SO:0001300

Axiom
annotated source: N6_isopentenyladenosine
annotated property: definition
annotated target: N6_isopentenyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_isopentenyladenosine
annotated property: has_exact_synonym
annotated target: i6A
has_synonym_type: RNA modification

two_methylthio_N6_isopentenyladenosine
type: Class
subclass of: modified_adenosine
definition: 2_methylthio_N6_isopentenyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:007
has_exact_synonym: 2-methylthio-N6-isopentenyladenosine
has_exact_synonym: ms2i6A
has_exact_synonym: two methylthio N6 isopentenyladenosine
has_obo_namespace: sequence
id: SO:0001301

Axiom
annotated source: two_methylthio_N6_isopentenyladenosine
annotated property: definition
annotated target: 2_methylthio_N6_isopentenyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_methylthio_N6_isopentenyladenosine
annotated property: has_exact_synonym
annotated target: ms2i6A
has_synonym_type: RNA modification

N6_cis_hydroxyisopentenyl_adenosine
type: Class
subclass of: modified_adenosine
definition: N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
database_cross_reference: RNAMOD:008
has_exact_synonym: N6 cis hydroxyisopentenyl adenosine
has_exact_synonym: N6-(cis-hydroxyisopentenyl)adenosine
has_exact_synonym: io6A
has_obo_namespace: sequence
id: SO:0001302

Axiom
annotated source: N6_cis_hydroxyisopentenyl_adenosine
annotated property: definition
annotated target: N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_cis_hydroxyisopentenyl_adenosine
annotated property: has_exact_synonym
annotated target: io6A
has_synonym_type: RNA modification

two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
type: Class
subclass of: modified_adenosine
definition: 2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
database_cross_reference: RNAMOD:009
has_exact_synonym: 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine
has_exact_synonym: ms2io6A
has_exact_synonym: two methylthio N6 cis hydroxyisopentenyl adenosine
has_obo_namespace: sequence
id: SO:0001303

Axiom
annotated source: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
annotated property: definition
annotated target: 2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
annotated property: has_exact_synonym
annotated target: ms2io6A
has_synonym_type: RNA modification

N6_glycinylcarbamoyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_glycinylcarbamoyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:010
has_exact_synonym: N6 glycinylcarbamoyladenosine
has_exact_synonym: N6-glycinylcarbamoyladenosine
has_exact_synonym: g6A
has_obo_namespace: sequence
id: SO:0001304

Axiom
annotated source: N6_glycinylcarbamoyladenosine
annotated property: definition
annotated target: N6_glycinylcarbamoyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_glycinylcarbamoyladenosine
annotated property: has_exact_synonym
annotated target: g6A
has_synonym_type: RNA modification

N6_threonylcarbamoyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_threonylcarbamoyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:011
has_exact_synonym: N6 threonylcarbamoyladenosine
has_exact_synonym: N6-threonylcarbamoyladenosine
has_exact_synonym: t6A
has_obo_namespace: sequence
id: SO:0001305

Axiom
annotated source: N6_threonylcarbamoyladenosine
annotated property: definition
annotated target: N6_threonylcarbamoyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_threonylcarbamoyladenosine
annotated property: has_exact_synonym
annotated target: t6A
has_synonym_type: RNA modification

two_methylthio_N6_threonyl_carbamoyladenosine
type: Class
subclass of: modified_adenosine
definition: 2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:012
has_exact_synonym: 2-methylthio-N6-threonyl carbamoyladenosine
has_exact_synonym: ms2t6A
has_exact_synonym: two methylthio N6 threonyl carbamoyladenosine
has_obo_namespace: sequence
id: SO:0001306

Axiom
annotated source: two_methylthio_N6_threonyl_carbamoyladenosine
annotated property: definition
annotated target: 2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_methylthio_N6_threonyl_carbamoyladenosine
annotated property: has_exact_synonym
annotated target: ms2t6A
has_synonym_type: RNA modification

N6_methyl_N6_threonylcarbamoyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:013
has_exact_synonym: N6 methyl N6 threonylcarbamoyladenosine
has_exact_synonym: N6-methyl-N6-threonylcarbamoyladenosine
has_exact_synonym: m6t6A
has_obo_namespace: sequence
id: SO:0001307

Axiom
annotated source: N6_methyl_N6_threonylcarbamoyladenosine
annotated property: definition
annotated target: N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_methyl_N6_threonylcarbamoyladenosine
annotated property: has_exact_synonym
annotated target: m6t6A
has_synonym_type: RNA modification

N6_hydroxynorvalylcarbamoyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:014
has_exact_synonym: N6 hydroxynorvalylcarbamoyladenosine
has_exact_synonym: N6-hydroxynorvalylcarbamoyladenosine
has_exact_synonym: hn6A
has_obo_namespace: sequence
id: SO:0001308

Axiom
annotated source: N6_hydroxynorvalylcarbamoyladenosine
annotated property: definition
annotated target: N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_hydroxynorvalylcarbamoyladenosine
annotated property: has_exact_synonym
annotated target: hn6A
has_synonym_type: RNA modification

two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
type: Class
subclass of: modified_adenosine
definition: 2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:015
has_exact_synonym: 2-methylthio-N6-hydroxynorvalyl carbamoyladenosine
has_exact_synonym: ms2hn6A
has_exact_synonym: two methylthio N6 hydroxynorvalyl carbamoyladenosine
has_obo_namespace: sequence
id: SO:0001309

Axiom
annotated source: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
annotated property: definition
annotated target: 2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
annotated property: has_exact_synonym
annotated target: ms2hn6A
has_synonym_type: RNA modification

two_prime_O_ribosyladenosine_phosphate
type: Class
subclass of: modified_adenosine
definition: 2prime_O_ribosyladenosine_phosphate is a modified adenosine.
database_cross_reference: RNAMOD:016
has_exact_synonym: 2'-O-ribosyladenosine (phosphate)
has_exact_synonym: Ar(p)
has_exact_synonym: two prime O ribosyladenosine phosphate
has_obo_namespace: sequence
id: SO:0001310

Axiom
annotated source: two_prime_O_ribosyladenosine_phosphate
annotated property: definition
annotated target: 2prime_O_ribosyladenosine_phosphate is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_prime_O_ribosyladenosine_phosphate
annotated property: has_exact_synonym
annotated target: Ar(p)
has_synonym_type: RNA modification

N6_N6_dimethyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_N6_dimethyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:080
has_exact_synonym: N6,N6-dimethyladenosine
has_exact_synonym: m62A
has_obo_namespace: sequence
id: SO:0001311

Axiom
annotated source: N6_N6_dimethyladenosine
annotated property: definition
annotated target: N6_N6_dimethyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_N6_dimethyladenosine
annotated property: has_exact_synonym
annotated target: m62A
has_synonym_type: RNA modification

N6_2_prime_O_dimethyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_2prime_O_dimethyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:088
has_exact_synonym: N6 2 prime O dimethyladenosine
has_exact_synonym: N6,2'-O-dimethyladenosine
has_exact_synonym: m6Am
has_obo_namespace: sequence
id: SO:0001312

Axiom
annotated source: N6_2_prime_O_dimethyladenosine
annotated property: definition
annotated target: N6_2prime_O_dimethyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_2_prime_O_dimethyladenosine
annotated property: has_exact_synonym
annotated target: m6Am
has_synonym_type: RNA modification

N6_N6_2_prime_O_trimethyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_N6_2prime_O_trimethyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:089
has_exact_synonym: N6,N6,2'-O-trimethyladenosine
has_exact_synonym: m62Am
has_obo_namespace: sequence
id: SO:0001313

Axiom
annotated source: N6_N6_2_prime_O_trimethyladenosine
annotated property: definition
annotated target: N6_N6_2prime_O_trimethyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_N6_2_prime_O_trimethyladenosine
annotated property: has_exact_synonym
annotated target: m62Am
has_synonym_type: RNA modification

one_two_prime_O_dimethyladenosine
type: Class
subclass of: modified_adenosine
definition: 1,2'-O-dimethyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:097
has_exact_synonym: 1,2'-O-dimethyladenosine
has_exact_synonym: m1Am
has_exact_synonym: one two prime O dimethyladenosine
has_obo_namespace: sequence
id: SO:0001314

Axiom
annotated source: one_two_prime_O_dimethyladenosine
annotated property: definition
annotated target: 1,2'-O-dimethyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: one_two_prime_O_dimethyladenosine
annotated property: has_exact_synonym
annotated target: m1Am
has_synonym_type: RNA modification

N6_acetyladenosine
type: Class
subclass of: modified_adenosine
definition: N6_acetyladenosine is a modified adenosine.
database_cross_reference: RNAMOD:102
has_exact_synonym: N6 acetyladenosine
has_exact_synonym: N6-acetyladenosine
has_exact_synonym: ac6A
has_obo_namespace: sequence
id: SO:0001315

Axiom
annotated source: N6_acetyladenosine
annotated property: definition
annotated target: N6_acetyladenosine is a modified adenosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N6_acetyladenosine
annotated property: has_exact_synonym
annotated target: ac6A
has_synonym_type: RNA modification

seven_deazaguanosine
type: Class
subclass of: modified_guanosine
definition: 7-deazaguanosine is a modified guanosine.
has_exact_synonym: seven deazaguanosine
has_obo_namespace: sequence
has_related_synonym: 7-deazaguanosine
id: SO:0001316

Axiom
annotated source: seven_deazaguanosine
annotated property: definition
annotated target: 7-deazaguanosine is a modified guanosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

queuosine
type: Class
subclass of: seven_deazaguanosine
definition: Queuosine is a modified 7-deazoguanosine.
database_cross_reference: RNAMOD:043
database_cross_reference: http://en.wikipedia.org/wiki/Queuosine
has_exact_synonym: Q
has_obo_namespace: sequence
id: SO:0001317

Axiom
annotated source: queuosine
annotated property: definition
annotated target: Queuosine is a modified 7-deazoguanosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

wiki
type: Axiom
annotated source: queuosine
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Queuosine

Axiom
annotated source: queuosine
annotated property: has_exact_synonym
annotated target: Q
has_synonym_type: RNA modification

epoxyqueuosine
type: Class
subclass of: seven_deazaguanosine
definition: Epoxyqueuosine is a modified 7-deazoguanosine.
database_cross_reference: RNAMOD:044
has_exact_synonym: eQ
has_obo_namespace: sequence
id: SO:0001318

Axiom
annotated source: epoxyqueuosine
annotated property: definition
annotated target: Epoxyqueuosine is a modified 7-deazoguanosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: epoxyqueuosine
annotated property: has_exact_synonym
annotated target: eQ
has_synonym_type: RNA modification

galactosyl_queuosine
type: Class
subclass of: seven_deazaguanosine
definition: Galactosyl_queuosine is a modified 7-deazoguanosine.
database_cross_reference: RNAMOD:045
has_exact_synonym: galQ
has_exact_synonym: galactosyl queuosine
has_exact_synonym: galactosyl-queuosine
has_obo_namespace: sequence
id: SO:0001319

Axiom
annotated source: galactosyl_queuosine
annotated property: definition
annotated target: Galactosyl_queuosine is a modified 7-deazoguanosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: galactosyl_queuosine
annotated property: has_exact_synonym
annotated target: galQ
has_synonym_type: RNA modification

mannosyl_queuosine
type: Class
subclass of: seven_deazaguanosine
definition: Mannosyl_queuosine is a modified 7-deazoguanosine.
database_cross_reference: RNAMOD:046
has_exact_synonym: manQ
has_exact_synonym: mannosyl queuosine
has_exact_synonym: mannosyl-queuosine
has_obo_namespace: sequence
id: SO:0001320

Axiom
annotated source: mannosyl_queuosine
annotated property: definition
annotated target: Mannosyl_queuosine is a modified 7-deazoguanosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: mannosyl_queuosine
annotated property: has_exact_synonym
annotated target: manQ
has_synonym_type: RNA modification

seven_cyano_seven_deazaguanosine
type: Class
subclass of: seven_deazaguanosine
definition: 7_cyano_7_deazaguanosine is a modified 7-deazoguanosine.
database_cross_reference: RNAMOD:047
has_exact_synonym: 7-cyano-7-deazaguanosine
has_exact_synonym: preQ0
has_exact_synonym: seven cyano seven deazaguanosine
has_obo_namespace: sequence
id: SO:0001321

Axiom
annotated source: seven_cyano_seven_deazaguanosine
annotated property: definition
annotated target: 7_cyano_7_deazaguanosine is a modified 7-deazoguanosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: seven_cyano_seven_deazaguanosine
annotated property: has_exact_synonym
annotated target: preQ0
has_synonym_type: RNA modification

seven_aminomethyl_seven_deazaguanosine
type: Class
subclass of: seven_deazaguanosine
definition: 7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine.
database_cross_reference: RNAMOD:048
has_exact_synonym: 7-aminomethyl-7-deazaguanosine
has_exact_synonym: preQ1
has_exact_synonym: seven aminomethyl seven deazaguanosine
has_obo_namespace: sequence
id: SO:0001322

Axiom
annotated source: seven_aminomethyl_seven_deazaguanosine
annotated property: definition
annotated target: 7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: seven_aminomethyl_seven_deazaguanosine
annotated property: has_exact_synonym
annotated target: preQ1
has_synonym_type: RNA modification

archaeosine
type: Class
subclass of: seven_deazaguanosine
definition: Archaeosine is a modified 7-deazoguanosine.
database_cross_reference: RNAMOD:049
has_exact_synonym: G+
has_obo_namespace: sequence
id: SO:0001323

Axiom
annotated source: archaeosine
annotated property: definition
annotated target: Archaeosine is a modified 7-deazoguanosine.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: archaeosine
annotated property: has_exact_synonym
annotated target: G+
has_synonym_type: RNA modification

one_methylguanosine
type: Class
subclass of: modified_guanosine
definition: 1_methylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:029
has_exact_synonym: 1-methylguanosine
has_exact_synonym: m1G
has_exact_synonym: one methylguanosine
has_obo_namespace: sequence
id: SO:0001324

Axiom
annotated source: one_methylguanosine
annotated property: definition
annotated target: 1_methylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: one_methylguanosine
annotated property: has_exact_synonym
annotated target: m1G
has_synonym_type: RNA modification

N2_methylguanosine
type: Class
subclass of: modified_guanosine
definition: N2_methylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:030
has_exact_synonym: N2 methylguanosine
has_exact_synonym: N2-methylguanosine
has_exact_synonym: m2G
has_obo_namespace: sequence
id: SO:0001325

Axiom
annotated source: N2_methylguanosine
annotated property: definition
annotated target: N2_methylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N2_methylguanosine
annotated property: has_exact_synonym
annotated target: m2G
has_synonym_type: RNA modification

seven_methylguanosine
type: Class
subclass of: modified_guanosine
definition: 7_methylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:031
has_exact_synonym: 7-methylguanosine
has_exact_synonym: m7G
has_exact_synonym: seven methylguanosine
has_obo_namespace: sequence
id: SO:0001326

Axiom
annotated source: seven_methylguanosine
annotated property: definition
annotated target: 7_methylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: seven_methylguanosine
annotated property: has_exact_synonym
annotated target: m7G
has_synonym_type: RNA modification

two_prime_O_methylguanosine
type: Class
subclass of: modified_guanosine
definition: 2prime_O_methylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:032
has_exact_synonym: 2'-O-methylguanosine
has_exact_synonym: Gm
has_exact_synonym: two prime O methylguanosine
has_obo_namespace: sequence
id: SO:0001327

Axiom
annotated source: two_prime_O_methylguanosine
annotated property: definition
annotated target: 2prime_O_methylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_prime_O_methylguanosine
annotated property: has_exact_synonym
annotated target: Gm
has_synonym_type: RNA modification

N2_N2_dimethylguanosine
type: Class
subclass of: modified_guanosine
definition: N2_N2_dimethylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:033
has_exact_synonym: N2,N2-dimethylguanosine
has_exact_synonym: m22G
has_obo_namespace: sequence
id: SO:0001328

Axiom
annotated source: N2_N2_dimethylguanosine
annotated property: definition
annotated target: N2_N2_dimethylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N2_N2_dimethylguanosine
annotated property: has_exact_synonym
annotated target: m22G
has_synonym_type: RNA modification

N2_2_prime_O_dimethylguanosine
type: Class
subclass of: modified_guanosine
definition: N2_2prime_O_dimethylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:034
has_exact_synonym: N2 2 prime O dimethylguanosine
has_exact_synonym: N2,2'-O-dimethylguanosine
has_exact_synonym: m2Gm
has_obo_namespace: sequence
id: SO:0001329

Axiom
annotated source: N2_2_prime_O_dimethylguanosine
annotated property: definition
annotated target: N2_2prime_O_dimethylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N2_2_prime_O_dimethylguanosine
annotated property: has_exact_synonym
annotated target: m2Gm
has_synonym_type: RNA modification

N2_N2_2_prime_O_trimethylguanosine
type: Class
subclass of: modified_guanosine
definition: N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:035
has_exact_synonym: N2,N2,2'-O-trimethylguanosine
has_exact_synonym: m22Gmv
has_obo_namespace: sequence
id: SO:0001330

Axiom
annotated source: N2_N2_2_prime_O_trimethylguanosine
annotated property: definition
annotated target: N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N2_N2_2_prime_O_trimethylguanosine
annotated property: has_exact_synonym
annotated target: m22Gmv
has_synonym_type: RNA modification

two_prime_O_ribosylguanosine_phosphate
type: Class
subclass of: modified_guanosine
definition: 2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature.
database_cross_reference: RNAMOD:036
has_exact_synonym: 2'-O-ribosylguanosine (phosphate)
has_exact_synonym: Gr(p)
has_exact_synonym: two prime O ribosylguanosine phosphate
has_obo_namespace: sequence
id: SO:0001331

Axiom
annotated source: two_prime_O_ribosylguanosine_phosphate
annotated property: definition
annotated target: 2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_prime_O_ribosylguanosine_phosphate
annotated property: has_exact_synonym
annotated target: Gr(p)
has_synonym_type: RNA modification

wybutosine
type: Class
subclass of: modified_guanosine
definition: Wybutosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:037
has_exact_synonym: yW
has_obo_namespace: sequence
id: SO:0001332

Axiom
annotated source: wybutosine
annotated property: definition
annotated target: Wybutosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: wybutosine
annotated property: has_exact_synonym
annotated target: yW
has_synonym_type: RNA modification

peroxywybutosine
type: Class
subclass of: modified_guanosine
definition: Peroxywybutosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:038
has_exact_synonym: o2yW
has_obo_namespace: sequence
id: SO:0001333

Axiom
annotated source: peroxywybutosine
annotated property: definition
annotated target: Peroxywybutosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: peroxywybutosine
annotated property: has_exact_synonym
annotated target: o2yW
has_synonym_type: RNA modification

hydroxywybutosine
type: Class
subclass of: modified_guanosine
definition: Hydroxywybutosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:039
has_exact_synonym: OHyW
has_obo_namespace: sequence
id: SO:0001334

Axiom
annotated source: hydroxywybutosine
annotated property: definition
annotated target: Hydroxywybutosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: hydroxywybutosine
annotated property: has_exact_synonym
annotated target: OHyW
has_synonym_type: RNA modification

undermodified_hydroxywybutosine
type: Class
subclass of: modified_guanosine
definition: Undermodified_hydroxywybutosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:040
has_exact_synonym: OHyW*
has_exact_synonym: undermodified hydroxywybutosine
has_obo_namespace: sequence
id: SO:0001335

Axiom
annotated source: undermodified_hydroxywybutosine
annotated property: definition
annotated target: Undermodified_hydroxywybutosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: undermodified_hydroxywybutosine
annotated property: has_exact_synonym
annotated target: OHyW*
has_synonym_type: RNA modification

wyosine
type: Class
subclass of: modified_guanosine
definition: Wyosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:041
has_exact_synonym: IMG
has_obo_namespace: sequence
id: SO:0001336

Axiom
annotated source: wyosine
annotated property: definition
annotated target: Wyosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: wyosine
annotated property: has_exact_synonym
annotated target: IMG
has_synonym_type: RNA modification

methylwyosine
type: Class
subclass of: modified_guanosine
definition: Methylwyosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:042
has_exact_synonym: mimG
has_obo_namespace: sequence
id: SO:0001337

Axiom
annotated source: methylwyosine
annotated property: definition
annotated target: Methylwyosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: methylwyosine
annotated property: has_exact_synonym
annotated target: mimG
has_synonym_type: RNA modification

N2_7_dimethylguanosine
type: Class
subclass of: modified_guanosine
definition: N2_7_dimethylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:090
has_exact_synonym: N2 7 dimethylguanosine
has_exact_synonym: N2,7-dimethylguanosine
has_exact_synonym: m2,7G
has_obo_namespace: sequence
id: SO:0001338

Axiom
annotated source: N2_7_dimethylguanosine
annotated property: definition
annotated target: N2_7_dimethylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N2_7_dimethylguanosine
annotated property: has_exact_synonym
annotated target: m2,7G
has_synonym_type: RNA modification

N2_N2_7_trimethylguanosine
type: Class
subclass of: modified_guanosine
definition: N2_N2_7_trimethylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:091
has_exact_synonym: N2,N2,7-trimethylguanosine
has_exact_synonym: m2,2,7G
has_obo_namespace: sequence
id: SO:0001339

Axiom
annotated source: N2_N2_7_trimethylguanosine
annotated property: definition
annotated target: N2_N2_7_trimethylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N2_N2_7_trimethylguanosine
annotated property: has_exact_synonym
annotated target: m2,2,7G
has_synonym_type: RNA modification

one_two_prime_O_dimethylguanosine
type: Class
subclass of: modified_guanosine
definition: 1_2prime_O_dimethylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:096
has_exact_synonym: 1,2'-O-dimethylguanosine
has_exact_synonym: m1Gm
has_exact_synonym: one two prime O dimethylguanosine
has_obo_namespace: sequence
id: SO:0001340

Axiom
annotated source: one_two_prime_O_dimethylguanosine
annotated property: definition
annotated target: 1_2prime_O_dimethylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: one_two_prime_O_dimethylguanosine
annotated property: has_exact_synonym
annotated target: m1Gm
has_synonym_type: RNA modification

four_demethylwyosine
type: Class
subclass of: modified_guanosine
definition: 4_demethylwyosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:100
has_exact_synonym: 4-demethylwyosine
has_exact_synonym: four demethylwyosine
has_exact_synonym: imG-14
has_obo_namespace: sequence
id: SO:0001341

Axiom
annotated source: four_demethylwyosine
annotated property: definition
annotated target: 4_demethylwyosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: four_demethylwyosine
annotated property: has_exact_synonym
annotated target: imG-14
has_synonym_type: RNA modification

isowyosine
type: Class
subclass of: modified_guanosine
definition: Isowyosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:101
has_exact_synonym: imG2
has_obo_namespace: sequence
id: SO:0001342

Axiom
annotated source: isowyosine
annotated property: definition
annotated target: Isowyosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: isowyosine
annotated property: has_exact_synonym
annotated target: imG2
has_synonym_type: RNA modification

N2_7_2prirme_O_trimethylguanosine
type: Class
subclass of: modified_guanosine
definition: N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature.
database_cross_reference: RNAMOD:106
has_exact_synonym: N2 7 2prirme O trimethylguanosine
has_exact_synonym: N2,7,2'-O-trimethylguanosine
has_exact_synonym: m2,7Gm
has_obo_namespace: sequence
id: SO:0001343

Axiom
annotated source: N2_7_2prirme_O_trimethylguanosine
annotated property: definition
annotated target: N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: N2_7_2prirme_O_trimethylguanosine
annotated property: has_exact_synonym
annotated target: m2,7Gm
has_synonym_type: RNA modification

five_methyluridine
type: Class
subclass of: modified_uridine
definition: 5_methyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:052
database_cross_reference: http://en.wikipedia.org/wiki/5-methyluridine
has_exact_synonym: 5-methyluridine
has_exact_synonym: five methyluridine
has_exact_synonym: m5U
has_obo_namespace: sequence
id: SO:0001344

Axiom
annotated source: five_methyluridine
annotated property: definition
annotated target: 5_methyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

wiki
type: Axiom
annotated source: five_methyluridine
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/5-methyluridine

Axiom
annotated source: five_methyluridine
annotated property: has_exact_synonym
annotated target: m5U
has_synonym_type: RNA modification

two_prime_O_methyluridine
type: Class
subclass of: modified_uridine
definition: 2prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:053
has_exact_synonym: 2'-O-methyluridine
has_exact_synonym: Um
has_exact_synonym: two prime O methyluridine
has_obo_namespace: sequence
id: SO:0001345

Axiom
annotated source: two_prime_O_methyluridine
annotated property: definition
annotated target: 2prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_prime_O_methyluridine
annotated property: has_exact_synonym
annotated target: Um
has_synonym_type: RNA modification

five_two_prime_O_dimethyluridine
type: Class
subclass of: modified_uridine
definition: 5_2_prime_O_dimethyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:054
has_exact_synonym: 5,2'-O-dimethyluridine
has_exact_synonym: five two prime O dimethyluridine
has_exact_synonym: m5Um
has_obo_namespace: sequence
id: SO:0001346

Axiom
annotated source: five_two_prime_O_dimethyluridine
annotated property: definition
annotated target: 5_2_prime_O_dimethyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_two_prime_O_dimethyluridine
annotated property: has_exact_synonym
annotated target: m5Um
has_synonym_type: RNA modification

one_methylpseudouridine
type: Class
subclass of: modified_uridine
definition: 1_methylpseudouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:055
has_exact_synonym: 1-methylpseudouridine
has_exact_synonym: m1Y
has_exact_synonym: one methylpseudouridine
has_obo_namespace: sequence
id: SO:0001347

Axiom
annotated source: one_methylpseudouridine
annotated property: definition
annotated target: 1_methylpseudouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: one_methylpseudouridine
annotated property: has_exact_synonym
annotated target: m1Y
has_synonym_type: RNA modification

two_prime_O_methylpseudouridine
type: Class
subclass of: modified_uridine
definition: 2prime_O_methylpseudouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:056
has_exact_synonym: 2'-O-methylpseudouridine
has_exact_synonym: Ym
has_exact_synonym: two prime O methylpseudouridine
has_obo_namespace: sequence
id: SO:0001348

Axiom
annotated source: two_prime_O_methylpseudouridine
annotated property: definition
annotated target: 2prime_O_methylpseudouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_prime_O_methylpseudouridine
annotated property: has_exact_synonym
annotated target: Ym
has_synonym_type: RNA modification

two_thiouridine
type: Class
subclass of: modified_uridine
definition: 2_thiouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:057
has_exact_synonym: 2-thiouridine
has_exact_synonym: s2U
has_exact_synonym: two thiouridine
has_obo_namespace: sequence
id: SO:0001349

Axiom
annotated source: two_thiouridine
annotated property: definition
annotated target: 2_thiouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_thiouridine
annotated property: has_exact_synonym
annotated target: s2U
has_synonym_type: RNA modification

four_thiouridine
type: Class
subclass of: modified_uridine
definition: 4_thiouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:058
has_exact_synonym: 4-thiouridine
has_exact_synonym: four thiouridine
has_exact_synonym: s4U
has_obo_namespace: sequence
id: SO:0001350

Axiom
annotated source: four_thiouridine
annotated property: definition
annotated target: 4_thiouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: four_thiouridine
annotated property: has_exact_synonym
annotated target: s4U
has_synonym_type: RNA modification

five_methyl_2_thiouridine
type: Class
subclass of: modified_uridine
definition: 5_methyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:059
has_exact_synonym: 5-methyl-2-thiouridine
has_exact_synonym: five methyl 2 thiouridine
has_exact_synonym: m5s2U
has_obo_namespace: sequence
id: SO:0001351

Axiom
annotated source: five_methyl_2_thiouridine
annotated property: definition
annotated target: 5_methyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methyl_2_thiouridine
annotated property: has_exact_synonym
annotated target: m5s2U
has_synonym_type: RNA modification

two_thio_two_prime_O_methyluridine
type: Class
subclass of: modified_uridine
definition: 2_thio_2prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:060
has_exact_synonym: 2-thio-2'-O-methyluridine
has_exact_synonym: s2Um
has_exact_synonym: two thio two prime O methyluridine
has_obo_namespace: sequence
id: SO:0001352

Axiom
annotated source: two_thio_two_prime_O_methyluridine
annotated property: definition
annotated target: 2_thio_2prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: two_thio_two_prime_O_methyluridine
annotated property: has_exact_synonym
annotated target: s2Um
has_synonym_type: RNA modification

three_three_amino_three_carboxypropyl_uridine
type: Class
subclass of: modified_uridine
definition: 3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature.
database_cross_reference: RNAMOD:061
has_exact_synonym: 3-(3-amino-3-carboxypropyl)uridine
has_exact_synonym: acp3U
has_obo_namespace: sequence
id: SO:0001353

Axiom
annotated source: three_three_amino_three_carboxypropyl_uridine
annotated property: definition
annotated target: 3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: three_three_amino_three_carboxypropyl_uridine
annotated property: has_exact_synonym
annotated target: acp3U
has_synonym_type: RNA modification

five_hydroxyuridine
type: Class
subclass of: modified_uridine
definition: 5_hydroxyuridine is a modified uridine base feature.
database_cross_reference: RNAMOD:060
has_exact_synonym: 5-hydroxyuridine
has_exact_synonym: five hydroxyuridine
has_exact_synonym: ho5U
has_obo_namespace: sequence
id: SO:0001354

Axiom
annotated source: five_hydroxyuridine
annotated property: definition
annotated target: 5_hydroxyuridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_hydroxyuridine
annotated property: has_exact_synonym
annotated target: ho5U
has_synonym_type: RNA modification

five_methoxyuridine
type: Class
subclass of: modified_uridine
definition: 5_methoxyuridine is a modified uridine base feature.
database_cross_reference: RNAMOD:063
has_exact_synonym: 5-methoxyuridine
has_exact_synonym: five methoxyuridine
has_exact_synonym: mo5U
has_obo_namespace: sequence
id: SO:0001355

Axiom
annotated source: five_methoxyuridine
annotated property: definition
annotated target: 5_methoxyuridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methoxyuridine
annotated property: has_exact_synonym
annotated target: mo5U
has_synonym_type: RNA modification

uridine_five_oxyacetic_acid
type: Class
subclass of: modified_uridine
definition: Uridine_5_oxyacetic_acid is a modified uridine base feature.
database_cross_reference: RNAMOD:064
has_exact_synonym: cmo5U
has_exact_synonym: uridine 5-oxyacetic acid
has_exact_synonym: uridine five oxyacetic acid
has_obo_namespace: sequence
id: SO:0001356

Axiom
annotated source: uridine_five_oxyacetic_acid
annotated property: definition
annotated target: Uridine_5_oxyacetic_acid is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: uridine_five_oxyacetic_acid
annotated property: has_exact_synonym
annotated target: cmo5U
has_synonym_type: RNA modification

uridine_five_oxyacetic_acid_methyl_ester
type: Class
subclass of: modified_uridine
definition: Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature.
database_cross_reference: RNAMOD:065
has_exact_synonym: mcmo5U
has_exact_synonym: uridine 5-oxyacetic acid methyl ester
has_exact_synonym: uridine five oxyacetic acid methyl ester
has_obo_namespace: sequence
id: SO:0001357

Axiom
annotated source: uridine_five_oxyacetic_acid_methyl_ester
annotated property: definition
annotated target: Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: uridine_five_oxyacetic_acid_methyl_ester
annotated property: has_exact_synonym
annotated target: mcmo5U
has_synonym_type: RNA modification

five_carboxyhydroxymethyl_uridine
type: Class
subclass of: modified_uridine
definition: 5_carboxyhydroxymethyl_uridine is a modified uridine base feature.
database_cross_reference: RNAMOD:066
has_exact_synonym: 5-(carboxyhydroxymethyl)uridine
has_exact_synonym: chm5U
has_exact_synonym: five carboxyhydroxymethyl uridine
has_obo_namespace: sequence
id: SO:0001358

Axiom
annotated source: five_carboxyhydroxymethyl_uridine
annotated property: definition
annotated target: 5_carboxyhydroxymethyl_uridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_carboxyhydroxymethyl_uridine
annotated property: has_exact_synonym
annotated target: chm5U
has_synonym_type: RNA modification

five_carboxyhydroxymethyl_uridine_methyl_ester
type: Class
subclass of: modified_uridine
definition: 5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature.
database_cross_reference: RNAMOD:067
has_exact_synonym: 5-(carboxyhydroxymethyl)uridine methyl ester
has_exact_synonym: five carboxyhydroxymethyl uridine methyl ester
has_exact_synonym: mchm5U
has_obo_namespace: sequence
id: SO:0001359

Axiom
annotated source: five_carboxyhydroxymethyl_uridine_methyl_ester
annotated property: definition
annotated target: 5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_carboxyhydroxymethyl_uridine_methyl_ester
annotated property: has_exact_synonym
annotated target: mchm5U
has_synonym_type: RNA modification

five_methoxycarbonylmethyluridine
type: Class
subclass of: modified_uridine
definition: Five_methoxycarbonylmethyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:068
has_exact_synonym: 5-methoxycarbonylmethyluridine
has_exact_synonym: five methoxycarbonylmethyluridine
has_exact_synonym: mcm5U
has_obo_namespace: sequence
id: SO:0001360

Axiom
annotated source: five_methoxycarbonylmethyluridine
annotated property: definition
annotated target: Five_methoxycarbonylmethyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methoxycarbonylmethyluridine
annotated property: has_exact_synonym
annotated target: mcm5U
has_synonym_type: RNA modification

five_methoxycarbonylmethyl_two_prime_O_methyluridine
type: Class
subclass of: modified_uridine
definition: Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:069
has_exact_synonym: 5-methoxycarbonylmethyl-2'-O-methyluridine
has_exact_synonym: five methoxycarbonylmethyl two prime O methyluridine
has_exact_synonym: mcm5Um
has_obo_namespace: sequence
id: SO:0001361

Axiom
annotated source: five_methoxycarbonylmethyl_two_prime_O_methyluridine
annotated property: definition
annotated target: Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methoxycarbonylmethyl_two_prime_O_methyluridine
annotated property: has_exact_synonym
annotated target: mcm5Um
has_synonym_type: RNA modification

five_methoxycarbonylmethyl_two_thiouridine
type: Class
subclass of: modified_uridine
definition: 5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:070
has_exact_synonym: 5-methoxycarbonylmethyl-2-thiouridine
has_exact_synonym: five methoxycarbonylmethyl two thiouridine
has_exact_synonym: mcm5s2U
has_obo_namespace: sequence
id: SO:0001362

Axiom
annotated source: five_methoxycarbonylmethyl_two_thiouridine
annotated property: definition
annotated target: 5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methoxycarbonylmethyl_two_thiouridine
annotated property: has_exact_synonym
annotated target: mcm5s2U
has_synonym_type: RNA modification

five_aminomethyl_two_thiouridine
type: Class
subclass of: modified_uridine
definition: 5_aminomethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:071
has_exact_synonym: 5-aminomethyl-2-thiouridine
has_exact_synonym: five aminomethyl two thiouridine
has_exact_synonym: nm5s2U
has_obo_namespace: sequence
id: SO:0001363

Axiom
annotated source: five_aminomethyl_two_thiouridine
annotated property: definition
annotated target: 5_aminomethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_aminomethyl_two_thiouridine
annotated property: has_exact_synonym
annotated target: nm5s2U
has_synonym_type: RNA modification

five_methylaminomethyluridine
type: Class
subclass of: modified_uridine
definition: 5_methylaminomethyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:072
has_exact_synonym: 5-methylaminomethyluridine
has_exact_synonym: five methylaminomethyluridine
has_exact_synonym: mnm5U
has_obo_namespace: sequence
id: SO:0001364

Axiom
annotated source: five_methylaminomethyluridine
annotated property: definition
annotated target: 5_methylaminomethyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methylaminomethyluridine
annotated property: has_exact_synonym
annotated target: mnm5U
has_synonym_type: RNA modification

five_methylaminomethyl_two_thiouridine
type: Class
subclass of: modified_uridine
definition: 5_methylaminomethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:073
has_exact_synonym: 5-methylaminomethyl-2-thiouridine
has_exact_synonym: five methylaminomethyl two thiouridine
has_exact_synonym: mnm5s2U
has_obo_namespace: sequence
id: SO:0001365

Axiom
annotated source: five_methylaminomethyl_two_thiouridine
annotated property: definition
annotated target: 5_methylaminomethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methylaminomethyl_two_thiouridine
annotated property: has_exact_synonym
annotated target: mnm5s2U
has_synonym_type: RNA modification

five_methylaminomethyl_two_selenouridine
type: Class
subclass of: modified_uridine
definition: 5_methylaminomethyl_2_selenouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:074
has_exact_synonym: 5-methylaminomethyl-2-selenouridine
has_exact_synonym: five methylaminomethyl two selenouridine
has_exact_synonym: mnm5se2U
has_obo_namespace: sequence
id: SO:0001366

Axiom
annotated source: five_methylaminomethyl_two_selenouridine
annotated property: definition
annotated target: 5_methylaminomethyl_2_selenouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methylaminomethyl_two_selenouridine
annotated property: has_exact_synonym
annotated target: mnm5se2U
has_synonym_type: RNA modification

five_carbamoylmethyluridine
type: Class
subclass of: modified_uridine
definition: 5_carbamoylmethyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:075
has_exact_synonym: 5-carbamoylmethyluridine
has_exact_synonym: five carbamoylmethyluridine
has_exact_synonym: ncm5U
has_obo_namespace: sequence
id: SO:0001367

Axiom
annotated source: five_carbamoylmethyluridine
annotated property: definition
annotated target: 5_carbamoylmethyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_carbamoylmethyluridine
annotated property: has_exact_synonym
annotated target: ncm5U
has_synonym_type: RNA modification

five_carbamoylmethyl_two_prime_O_methyluridine
type: Class
subclass of: modified_uridine
definition: 5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:076
has_exact_synonym: 5-carbamoylmethyl-2'-O-methyluridine
has_exact_synonym: five carbamoylmethyl two prime O methyluridine
has_exact_synonym: ncm5Um
has_obo_namespace: sequence
id: SO:0001368

Axiom
annotated source: five_carbamoylmethyl_two_prime_O_methyluridine
annotated property: definition
annotated target: 5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_carbamoylmethyl_two_prime_O_methyluridine
annotated property: has_exact_synonym
annotated target: ncm5Um
has_synonym_type: RNA modification

five_carboxymethylaminomethyluridine
type: Class
subclass of: modified_uridine
definition: 5_carboxymethylaminomethyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:077
has_exact_synonym: 5-carboxymethylaminomethyluridine
has_exact_synonym: cmnm5U
has_exact_synonym: five carboxymethylaminomethyluridine
has_obo_namespace: sequence
id: SO:0001369

Axiom
annotated source: five_carboxymethylaminomethyluridine
annotated property: definition
annotated target: 5_carboxymethylaminomethyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_carboxymethylaminomethyluridine
annotated property: has_exact_synonym
annotated target: cmnm5U
has_synonym_type: RNA modification

five_carboxymethylaminomethyl_two_prime_O_methyluridine
type: Class
subclass of: modified_uridine
definition: 5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:078
has_exact_synonym: 5-carboxymethylaminomethyl- 2'-O-methyluridine
has_exact_synonym: cmnm5Um
has_exact_synonym: five carboxymethylaminomethyl two prime O methyluridine
has_obo_namespace: sequence
id: SO:0001370

Axiom
annotated source: five_carboxymethylaminomethyl_two_prime_O_methyluridine
annotated property: definition
annotated target: 5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_carboxymethylaminomethyl_two_prime_O_methyluridine
annotated property: has_exact_synonym
annotated target: cmnm5Um
has_synonym_type: RNA modification

five_carboxymethylaminomethyl_two_thiouridine
type: Class
subclass of: modified_uridine
definition: 5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:079
has_exact_synonym: 5-carboxymethylaminomethyl-2-thiouridine
has_exact_synonym: cmnm5s2U
has_exact_synonym: five carboxymethylaminomethyl two thiouridine
has_obo_namespace: sequence
id: SO:0001371

Axiom
annotated source: five_carboxymethylaminomethyl_two_thiouridine
annotated property: definition
annotated target: 5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_carboxymethylaminomethyl_two_thiouridine
annotated property: has_exact_synonym
annotated target: cmnm5s2U
has_synonym_type: RNA modification

three_methyluridine
type: Class
subclass of: modified_uridine
definition: 3_methyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:085
has_exact_synonym: 3-methyluridine
has_exact_synonym: m3U
has_exact_synonym: three methyluridine
has_obo_namespace: sequence
id: SO:0001372

Axiom
annotated source: three_methyluridine
annotated property: definition
annotated target: 3_methyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: three_methyluridine
annotated property: has_exact_synonym
annotated target: m3U
has_synonym_type: RNA modification

one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
type: Class
subclass of: modified_uridine
definition: 1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:086
has_exact_synonym: 1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine
has_exact_synonym: m1acp3Y
has_obo_namespace: sequence
id: SO:0001373

Axiom
annotated source: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
annotated property: definition
annotated target: 1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
annotated property: has_exact_synonym
annotated target: m1acp3Y
has_synonym_type: RNA modification

five_carboxymethyluridine
type: Class
subclass of: modified_uridine
definition: 5_carboxymethyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:087
has_exact_synonym: 5-carboxymethyluridine
has_exact_synonym: cm5U
has_exact_synonym: five carboxymethyluridine
has_obo_namespace: sequence
id: SO:0001374

Axiom
annotated source: five_carboxymethyluridine
annotated property: definition
annotated target: 5_carboxymethyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_carboxymethyluridine
annotated property: has_exact_synonym
annotated target: cm5U
has_synonym_type: RNA modification

three_two_prime_O_dimethyluridine
type: Class
subclass of: modified_uridine
definition: 3_2prime_O_dimethyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:092
has_exact_synonym: 3,2'-O-dimethyluridine
has_exact_synonym: m3Um
has_exact_synonym: three two prime O dimethyluridine
has_obo_namespace: sequence
id: SO:0001375

Axiom
annotated source: three_two_prime_O_dimethyluridine
annotated property: definition
annotated target: 3_2prime_O_dimethyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: three_two_prime_O_dimethyluridine
annotated property: has_exact_synonym
annotated target: m3Um
has_synonym_type: RNA modification

five_methyldihydrouridine
type: Class
subclass of: modified_uridine
definition: 5_methyldihydrouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:093
has_exact_synonym: 5-methyldihydrouridine
has_exact_synonym: five methyldihydrouridine
has_exact_synonym: m5D
has_obo_namespace: sequence
id: SO:0001376

Axiom
annotated source: five_methyldihydrouridine
annotated property: definition
annotated target: 5_methyldihydrouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_methyldihydrouridine
annotated property: has_exact_synonym
annotated target: m5D
has_synonym_type: RNA modification

three_methylpseudouridine
type: Class
subclass of: modified_uridine
definition: 3_methylpseudouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:094
has_exact_synonym: 3-methylpseudouridine
has_exact_synonym: m3Y
has_exact_synonym: three methylpseudouridine
has_obo_namespace: sequence
id: SO:0001377

Axiom
annotated source: three_methylpseudouridine
annotated property: definition
annotated target: 3_methylpseudouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: three_methylpseudouridine
annotated property: has_exact_synonym
annotated target: m3Y
has_synonym_type: RNA modification

five_taurinomethyluridine
type: Class
subclass of: modified_uridine
definition: 5_taurinomethyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:098
has_exact_synonym: 5-taurinomethyluridine
has_exact_synonym: five taurinomethyluridine
has_exact_synonym: tm5U
has_obo_namespace: sequence
id: SO:0001378

Axiom
annotated source: five_taurinomethyluridine
annotated property: definition
annotated target: 5_taurinomethyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_taurinomethyluridine
annotated property: has_exact_synonym
annotated target: tm5U
has_synonym_type: RNA modification

five_taurinomethyl_two_thiouridine
type: Class
subclass of: modified_uridine
definition: 5_taurinomethyl_2_thiouridineis a modified uridine base feature.
database_cross_reference: RNAMOD:099
has_exact_synonym: 5-taurinomethyl-2-thiouridine
has_exact_synonym: five taurinomethyl two thiouridine
has_exact_synonym: tm5s2U
has_obo_namespace: sequence
id: SO:0001379

Axiom
annotated source: five_taurinomethyl_two_thiouridine
annotated property: definition
annotated target: 5_taurinomethyl_2_thiouridineis a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_taurinomethyl_two_thiouridine
annotated property: has_exact_synonym
annotated target: tm5s2U
has_synonym_type: RNA modification

five_isopentenylaminomethyl_uridine
type: Class
subclass of: modified_uridine
definition: 5_isopentenylaminomethyl_uridine is a modified uridine base feature.
database_cross_reference: RNAMOD:103
has_exact_synonym: 5-(isopentenylaminomethyl)uridine
has_exact_synonym: five isopentenylaminomethyl uridine
has_exact_synonym: inm5U
has_obo_namespace: sequence
id: SO:0001380

Axiom
annotated source: five_isopentenylaminomethyl_uridine
annotated property: definition
annotated target: 5_isopentenylaminomethyl_uridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_isopentenylaminomethyl_uridine
annotated property: has_exact_synonym
annotated target: inm5U
has_synonym_type: RNA modification

five_isopentenylaminomethyl_two_thiouridine
type: Class
subclass of: modified_uridine
definition: 5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: RNAMOD:104
has_exact_synonym: 5-(isopentenylaminomethyl)- 2-thiouridine
has_exact_synonym: five isopentenylaminomethyl two thiouridine
has_exact_synonym: inm5s2U
has_obo_namespace: sequence
id: SO:0001381

Axiom
annotated source: five_isopentenylaminomethyl_two_thiouridine
annotated property: definition
annotated target: 5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_isopentenylaminomethyl_two_thiouridine
annotated property: has_exact_synonym
annotated target: inm5s2U
has_synonym_type: RNA modification

five_isopentenylaminomethyl_two_prime_O_methyluridine
type: Class
subclass of: modified_uridine
definition: 5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: RNAMOD:105
has_exact_synonym: 5-(isopentenylaminomethyl)- 2'-O-methyluridine
has_exact_synonym: five isopentenylaminomethyl two prime O methyluridine
has_exact_synonym: inm5Um
has_obo_namespace: sequence
id: SO:0001382

Axiom
annotated source: five_isopentenylaminomethyl_two_prime_O_methyluridine
annotated property: definition
annotated target: 5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature.
database_cross_reference: http://library.med.utah.edu/RNAmods/

Axiom
annotated source: five_isopentenylaminomethyl_two_prime_O_methyluridine
annotated property: has_exact_synonym
annotated target: inm5Um
has_synonym_type: RNA modification

histone_binding_site
type: Class
subclass of: nucleotide_to_protein_binding_site
definition: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone.
has_exact_synonym: histone binding site
has_obo_namespace: sequence
id: SO:0001383

Axiom
annotated source: histone_binding_site
annotated property: definition
annotated target: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone.
database_cross_reference: SO:ke

CDS_fragment
type: Class
equivalent class: Class
  intersection of: CDS
  intersection of: Restriction
    on property: has_quality
    some values from: fragmentary
subclass of: CDS
subclass of: Restriction
  on property: has_quality
  some values from: fragmentary
definition: A portion of a CDS that is not the complete CDS.
has_exact_synonym: CDS fragment
has_exact_synonym: incomplete CDS
has_obo_namespace: sequence
id: SO:0001384

modified_amino_acid_feature
type: Class
subclass of: amino_acid
definition: A post translationally modified amino acid feature.
has_exact_synonym: modified amino acid feature
has_obo_namespace: sequence
id: SO:0001385

Axiom
annotated source: modified_amino_acid_feature
annotated property: definition
annotated target: A post translationally modified amino acid feature.
database_cross_reference: SO:ke

modified_glycine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified glycine amino acid feature.
database_cross_reference: MOD:00908
has_exact_synonym: ModGly
has_exact_synonym: modified glycine
has_obo_namespace: sequence
id: SO:0001386

Axiom
annotated source: modified_glycine
annotated property: definition
annotated target: A post translationally modified glycine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_glycine
annotated property: has_exact_synonym
annotated target: ModGly
has_synonym_type: amino acid modification

modified_L_alanine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified alanine amino acid feature.
database_cross_reference: MOD:00901
has_exact_synonym: ModAla
has_exact_synonym: modified L alanine
has_exact_synonym: modified L-alanine
has_obo_namespace: sequence
id: SO:0001387

Axiom
annotated source: modified_L_alanine
annotated property: definition
annotated target: A post translationally modified alanine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_alanine
annotated property: has_exact_synonym
annotated target: ModAla
has_synonym_type: amino acid modification

modified_L_asparagine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified asparagine amino acid feature.
database_cross_reference: MOD:00903
has_exact_synonym: ModAsn
has_exact_synonym: modified L asparagine
has_exact_synonym: modified L-asparagine
has_obo_namespace: sequence
id: SO:0001388

Axiom
annotated source: modified_L_asparagine
annotated property: definition
annotated target: A post translationally modified asparagine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_asparagine
annotated property: has_exact_synonym
annotated target: ModAsn
has_synonym_type: amino acid modification

modified_L_aspartic_acid
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified aspartic acid amino acid feature.
database_cross_reference: MOD:00904
has_exact_synonym: ModAsp
has_exact_synonym: modified L aspartic acid
has_exact_synonym: modified L-aspartic acid
has_obo_namespace: sequence
id: SO:0001389

Axiom
annotated source: modified_L_aspartic_acid
annotated property: definition
annotated target: A post translationally modified aspartic acid amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_aspartic_acid
annotated property: has_exact_synonym
annotated target: ModAsp
has_synonym_type: amino acid modification

modified_L_cysteine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified cysteine amino acid feature.
database_cross_reference: MOD:00905
has_exact_synonym: ModCys
has_exact_synonym: modified L cysteine
has_exact_synonym: modified L-cysteine
has_obo_namespace: sequence
id: SO:0001390

Axiom
annotated source: modified_L_cysteine
annotated property: definition
annotated target: A post translationally modified cysteine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_cysteine
annotated property: has_exact_synonym
annotated target: ModCys
has_synonym_type: amino acid modification

modified_L_glutamic_acid
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified glutamic acid.
database_cross_reference: MOD:00906
has_exact_synonym: ModGlu
has_exact_synonym: modified L glutamic acid
has_exact_synonym: modified L-glutamic acid
has_obo_namespace: sequence
id: SO:0001391

Axiom
annotated source: modified_L_glutamic_acid
annotated property: has_exact_synonym
annotated target: ModGlu
has_synonym_type: amino acid modification

modified_L_threonine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified threonine amino acid feature.
database_cross_reference: MOD:00917
has_exact_synonym: ModThr
has_exact_synonym: modified L threonine
has_exact_synonym: modified L-threonine
has_obo_namespace: sequence
id: SO:0001392

Axiom
annotated source: modified_L_threonine
annotated property: definition
annotated target: A post translationally modified threonine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_threonine
annotated property: has_exact_synonym
annotated target: ModThr
has_synonym_type: amino acid modification

modified_L_tryptophan
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified tryptophan amino acid feature.
database_cross_reference: MOD:00918
has_exact_synonym: ModTrp
has_exact_synonym: modified L tryptophan
has_exact_synonym: modified L-tryptophan
has_obo_namespace: sequence
id: SO:0001393

Axiom
annotated source: modified_L_tryptophan
annotated property: definition
annotated target: A post translationally modified tryptophan amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_tryptophan
annotated property: has_exact_synonym
annotated target: ModTrp
has_synonym_type: amino acid modification

modified_L_glutamine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified glutamine amino acid feature.
database_cross_reference: MOD:00907
has_exact_synonym: ModGln
has_exact_synonym: modified L glutamine
has_exact_synonym: modified L-glutamine
has_obo_namespace: sequence
id: SO:0001394

Axiom
annotated source: modified_L_glutamine
annotated property: definition
annotated target: A post translationally modified glutamine amino acid feature.
database_cross_reference: SO:ke

modified_L_methionine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified methionine amino acid feature.
database_cross_reference: MOD:00913
has_exact_synonym: ModMet
has_exact_synonym: modified L methionine
has_exact_synonym: modified L-methionine
has_obo_namespace: sequence
id: SO:0001395

Axiom
annotated source: modified_L_methionine
annotated property: definition
annotated target: A post translationally modified methionine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_methionine
annotated property: has_exact_synonym
annotated target: ModMet
has_synonym_type: amino acid modification

modified_L_isoleucine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified isoleucine amino acid feature.
database_cross_reference: MOD:00910
has_exact_synonym: ModIle
has_exact_synonym: modified L isoleucine
has_exact_synonym: modified L-isoleucine
has_obo_namespace: sequence
id: SO:0001396

Axiom
annotated source: modified_L_isoleucine
annotated property: definition
annotated target: A post translationally modified isoleucine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_isoleucine
annotated property: has_exact_synonym
annotated target: ModIle
has_synonym_type: amino acid modification

modified_L_phenylalanine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified phenylalanine amino acid feature.
database_cross_reference: MOD:00914
has_exact_synonym: ModPhe
has_exact_synonym: modified L phenylalanine
has_exact_synonym: modified L-phenylalanine
has_obo_namespace: sequence
id: SO:0001397

Axiom
annotated source: modified_L_phenylalanine
annotated property: definition
annotated target: A post translationally modified phenylalanine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_phenylalanine
annotated property: has_exact_synonym
annotated target: ModPhe
has_synonym_type: amino acid modification

modified_L_histidine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified histidine amino acid feature.
database_cross_reference: MOD:00909
has_exact_synonym: ModHis
has_exact_synonym: modified L histidine
has_exact_synonym: modified L-histidine
has_obo_namespace: sequence
id: SO:0001398

Axiom
annotated source: modified_L_histidine
annotated property: definition
annotated target: A post translationally modified histidine amino acid feature.
database_cross_reference: SO:ke

modified_L_serine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified serine amino acid feature.
database_cross_reference: MOD:00916
has_exact_synonym: MosSer
has_exact_synonym: modified L serine
has_exact_synonym: modified L-serine
has_obo_namespace: sequence
id: SO:0001399

Axiom
annotated source: modified_L_serine
annotated property: definition
annotated target: A post translationally modified serine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_serine
annotated property: database_cross_reference
annotated target: MOD:00916
label: http://www.psidev.info/index.php

Axiom
annotated source: modified_L_serine
annotated property: has_exact_synonym
annotated target: MosSer
has_synonym_type: amino acid modification

modified_L_lysine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified lysine amino acid feature.
database_cross_reference: MOD:00912
has_exact_synonym: ModLys
has_exact_synonym: modified L lysine
has_exact_synonym: modified L-lysine
has_obo_namespace: sequence
id: SO:0001400

Axiom
annotated source: modified_L_lysine
annotated property: definition
annotated target: A post translationally modified lysine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_lysine
annotated property: has_exact_synonym
annotated target: ModLys
has_synonym_type: amino acid modification

modified_L_leucine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified leucine amino acid feature.
database_cross_reference: MOD:00911
has_exact_synonym: ModLeu
has_exact_synonym: modified L leucine
has_exact_synonym: modified L-leucine
has_obo_namespace: sequence
id: SO:0001401

Axiom
annotated source: modified_L_leucine
annotated property: definition
annotated target: A post translationally modified leucine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_leucine
annotated property: has_exact_synonym
annotated target: ModLeu
has_synonym_type: amino acid modification

modified_L_selenocysteine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified selenocysteine amino acid feature.
database_cross_reference: MOD:01158
has_exact_synonym: modified L selenocysteine
has_exact_synonym: modified L-selenocysteine
has_obo_namespace: sequence
id: SO:0001402

Axiom
annotated source: modified_L_selenocysteine
annotated property: definition
annotated target: A post translationally modified selenocysteine amino acid feature.
database_cross_reference: SO:ke

modified_L_valine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified valine amino acid feature.
database_cross_reference: MOD:00920
has_exact_synonym: ModVal
has_exact_synonym: modified L valine
has_exact_synonym: modified L-valine
has_obo_namespace: sequence
id: SO:0001403

Axiom
annotated source: modified_L_valine
annotated property: definition
annotated target: A post translationally modified valine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_valine
annotated property: has_exact_synonym
annotated target: ModVal
has_synonym_type: amino acid modification

modified_L_proline
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified proline amino acid feature.
database_cross_reference: MOD:00915
has_exact_synonym: ModPro
has_exact_synonym: modified L proline
has_exact_synonym: modified L-proline
has_obo_namespace: sequence
id: SO:0001404

Axiom
annotated source: modified_L_proline
annotated property: definition
annotated target: A post translationally modified proline amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_proline
annotated property: has_exact_synonym
annotated target: ModPro
has_synonym_type: amino acid modification

modified_L_tyrosine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified tyrosine amino acid feature.
database_cross_reference: MOD:00919
has_exact_synonym: ModTry
has_exact_synonym: modified L tyrosine
has_exact_synonym: modified L-tyrosine
has_obo_namespace: sequence
id: SO:0001405

Axiom
annotated source: modified_L_tyrosine
annotated property: definition
annotated target: A post translationally modified tyrosine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_tyrosine
annotated property: has_exact_synonym
annotated target: ModTry
has_synonym_type: amino acid modification

modified_L_arginine
type: Class
subclass of: modified_amino_acid_feature
definition: A post translationally modified arginine amino acid feature.
database_cross_reference: MOD:00902
has_exact_synonym: ModArg
has_exact_synonym: modified L arginine
has_exact_synonym: modified L-arginine
has_obo_namespace: sequence
id: SO:0001406

Axiom
annotated source: modified_L_arginine
annotated property: definition
annotated target: A post translationally modified arginine amino acid feature.
database_cross_reference: SO:ke

Axiom
annotated source: modified_L_arginine
annotated property: has_exact_synonym
annotated target: ModArg
has_synonym_type: amino acid modification

peptidyl
type: Class
subclass of: polymer_attribute
definition: An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds.
has_obo_namespace: sequence
id: SO:0001407

Axiom
annotated source: peptidyl
annotated property: definition
annotated target: An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds.
database_cross_reference: SO:ke

cleaved_for_gpi_anchor_region
type: Class
subclass of: SO_0100011
definition: The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor.
has_exact_synonym: cleaved for gpi anchor region
has_obo_namespace: sequence
id: SO:0001408

Axiom
annotated source: cleaved_for_gpi_anchor_region
annotated property: definition
annotated target: The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor.
database_cross_reference: EBI:rh

biomaterial_region
type: Class
subclass of: region
definition: A region which is intended for use in an experiment.
has_exact_synonym: biomaterial region
has_obo_namespace: sequence
id: SO:0001409
in_subset: SOFA

Axiom
annotated source: biomaterial_region
annotated property: definition
annotated target: A region which is intended for use in an experiment.
database_cross_reference: SO:cb

experimental_feature
type: Class
subclass of: region
definition: A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
has_exact_synonym: experimental output artefact
has_exact_synonym: experimental_output_artefact
has_obo_namespace: sequence
has_related_synonym: analysis feature
id: SO:0001410
in_subset: SOFA

Axiom
annotated source: experimental_feature
annotated property: definition
annotated target: A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
database_cross_reference: SO:cb

biological_region
type: Class
subclass of: region
definition: A region defined by its disposition to be involved in a biological process.
has_broad_synonym: INSDC_misc_feature
has_exact_synonym: INSDC_note:biological_region
has_exact_synonym: biological region
has_obo_namespace: sequence
id: SO:0001411
in_subset: SOFA

Axiom
annotated source: biological_region
annotated property: definition
annotated target: A region defined by its disposition to be involved in a biological process.
database_cross_reference: SO:cb

topologically_defined_region
type: Class
subclass of: region
definition: A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping.
has_exact_synonym: topologically defined region
has_obo_namespace: sequence
id: SO:0001412
in_subset: SOFA

Axiom
annotated source: topologically_defined_region
annotated property: definition
annotated target: A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping.
database_cross_reference: PMID:32782014
database_cross_reference: SO:cb

translocation_breakpoint
type: Class
subclass of: chromosome_breakpoint
definition: The point within a chromosome where a translocation begins or ends.
has_exact_synonym: translocation breakpoint
has_obo_namespace: sequence
id: SO:0001413

Axiom
annotated source: translocation_breakpoint
annotated property: definition
annotated target: The point within a chromosome where a translocation begins or ends.
database_cross_reference: SO:cb

insertion_breakpoint
type: Class
subclass of: chromosome_breakpoint
definition: The point within a chromosome where a insertion begins or ends.
has_exact_synonym: insertion breakpoint
has_obo_namespace: sequence
id: SO:0001414

Axiom
annotated source: insertion_breakpoint
annotated property: definition
annotated target: The point within a chromosome where a insertion begins or ends.
database_cross_reference: SO:cb

deletion_breakpoint
type: Class
subclass of: chromosome_breakpoint
definition: The point within a chromosome where a deletion begins or ends.
has_exact_synonym: deletion breakpoint
has_obo_namespace: sequence
id: SO:0001415

Axiom
annotated source: deletion_breakpoint
annotated property: definition
annotated target: The point within a chromosome where a deletion begins or ends.
database_cross_reference: SO:cb

five_prime_flanking_region
type: Class
subclass of: flanking_region
definition: A flanking region located five prime of a specific region.
has_exact_synonym: five prime flanking region
has_obo_namespace: sequence
has_related_synonym: 5' flanking region
id: SO:0001416

Axiom
annotated source: five_prime_flanking_region
annotated property: definition
annotated target: A flanking region located five prime of a specific region.
database_cross_reference: SO:chado

three_prime_flanking_region
type: Class
subclass of: flanking_region
definition: A flanking region located three prime of a specific region.
has_exact_synonym: three prime flanking region
has_obo_namespace: sequence
has_related_synonym: 3' flanking region
id: SO:0001417

Axiom
annotated source: three_prime_flanking_region
annotated property: definition
annotated target: A flanking region located three prime of a specific region.
database_cross_reference: SO:chado

transcribed_fragment
type: Class
subclass of: experimental_feature
definition: An experimental region, defined by a tiling array experiment to be transcribed at some level.
has_exact_synonym: transcribed fragment
has_obo_namespace: sequence
has_related_synonym: transfrag
id: SO:0001418
comment: Term requested by the MODencode group.

Axiom
annotated source: transcribed_fragment
annotated property: definition
annotated target: An experimental region, defined by a tiling array experiment to be transcribed at some level.
database_cross_reference: SO:ke

cis_splice_site
type: Class
subclass of: splice_site
definition: Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
has_exact_synonym: cis splice site
has_obo_namespace: sequence
id: SO:0001419
in_subset: SOFA

Axiom
annotated source: cis_splice_site
annotated property: definition
annotated target: Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
database_cross_reference: SO:cjm
database_cross_reference: SO:ke

trans_splice_site
type: Class
subclass of: splice_site
definition: Primary transcript region bordering trans-splice junction.
has_exact_synonym: trans splice site
has_obo_namespace: sequence
id: SO:0001420
in_subset: SOFA

Axiom
annotated source: trans_splice_site
annotated property: definition
annotated target: Primary transcript region bordering trans-splice junction.
database_cross_reference: SO:ke

splice_junction
type: Class
subclass of: junction
definition: The boundary between an intron and an exon.
has_exact_synonym: splice boundary
has_exact_synonym: splice junction
has_obo_namespace: sequence
id: SO:0001421

Axiom
annotated source: splice_junction
annotated property: definition
annotated target: The boundary between an intron and an exon.
database_cross_reference: SO:ke

conformational_switch
type: Class
subclass of: SO_0100001
definition: A region of a polypeptide, involved in the transition from one conformational state to another.
has_exact_synonym: polypeptide conformational switch
has_obo_namespace: sequence
id: SO:0001422
comment: MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999.

Axiom
annotated source: conformational_switch
annotated property: definition
annotated target: A region of a polypeptide, involved in the transition from one conformational state to another.
database_cross_reference: SO:ke

dye_terminator_read
type: Class
subclass of: read
definition: A read produced by the dye terminator method of sequencing.
has_obo_namespace: sequence
has_related_synonym: dye terminator read
id: SO:0001423

Axiom
annotated source: dye_terminator_read
annotated property: definition
annotated target: A read produced by the dye terminator method of sequencing.
database_cross_reference: SO:ke

pyrosequenced_read
type: Class
subclass of: read
definition: A read produced by pyrosequencing technology.
has_obo_namespace: sequence
has_related_synonym: pyorsequenced read
id: SO:0001424
comment: An example is a read produced by Roche 454 technology.

Axiom
annotated source: pyrosequenced_read
annotated property: definition
annotated target: A read produced by pyrosequencing technology.
database_cross_reference: SO:ke

ligation_based_read
type: Class
subclass of: read
definition: A read produced by ligation based sequencing technologies.
has_obo_namespace: sequence
has_related_synonym: ligation based read
id: SO:0001425
comment: An example of this kind of read is one produced by ABI SOLiD.

Axiom
annotated source: ligation_based_read
annotated property: definition
annotated target: A read produced by ligation based sequencing technologies.
database_cross_reference: SO:ke

polymerase_synthesis_read
type: Class
subclass of: read
definition: A read produced by the polymerase based sequence by synthesis method.
has_obo_namespace: sequence
has_related_synonym: polymerase synthesis read
id: SO:0001426
comment: An example is a read produced by Illumina technology.

Axiom
annotated source: polymerase_synthesis_read
annotated property: definition
annotated target: A read produced by the polymerase based sequence by synthesis method.
database_cross_reference: SO:ke

cis_regulatory_frameshift_element
type: Class
subclass of: transcriptional_cis_regulatory_region
definition: A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.
has_exact_synonym: cis regulatory frameshift element
has_obo_namespace: sequence
id: SO:0001427
comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: cis_regulatory_frameshift_element
annotated property: definition
annotated target: A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.
database_cross_reference: RFAM:jd

expressed_sequence_assembly
type: Class
subclass of: sequence_assembly
definition: A sequence assembly derived from expressed sequences.
has_exact_synonym: expressed sequence assembly
has_obo_namespace: sequence
id: SO:0001428
comment: From tracker [ 2372385 ] expressed_sequence_assembly.

Axiom
annotated source: expressed_sequence_assembly
annotated property: definition
annotated target: A sequence assembly derived from expressed sequences.
database_cross_reference: SO:ke

DNA_binding_site
type: Class
subclass of: nucleotide_binding_site
definition: A binding site that, in the molecule, interacts selectively and non-covalently with DNA.
has_exact_synonym: DNA binding site
has_obo_namespace: sequence
id: SO:0001429

Axiom
annotated source: DNA_binding_site
annotated property: definition
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with DNA.
database_cross_reference: SO:ke

SO_0001430
type: Class
IAO_0000231: IAO_0000227
term replaced by: polyA_site
deprecated: true

cryptic_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: cryptic
subclass of: gene
subclass of: Restriction
  on property: has_quality
  some values from: cryptic
definition: A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.
has_exact_synonym: cryptic gene
has_obo_namespace: sequence
id: SO:0001431

Axiom
annotated source: cryptic_gene
annotated property: definition
annotated target: A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.
database_cross_reference: SO:ke

sequence_variant_affecting_polyadenylation
type: Class
term replaced by: polyadenylation_variant
has_exact_synonym: sequence variant affecting polyadenylation
has_obo_namespace: sequence
has_related_synonym: mutation affecting polyadenylation
id: SO:0001432
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
deprecated: true

three_prime_RACE_clone
type: Class
subclass of: cDNA_clone
definition: A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host.
has_obo_namespace: sequence
has_related_synonym: 3' RACE clone
id: SO:0001433

Axiom
annotated source: three_prime_RACE_clone
annotated property: definition
annotated target: A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host.
database_cross_reference: modENCODE:nlw

cassette_pseudogene
type: Class
subclass of: SO_0001760
definition: A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy.
has_exact_synonym: cassette pseudogene
has_obo_namespace: sequence
has_related_synonym: cassette type psedogene
id: SO:0001434
comment: Requested by the Trypanosome community.

Axiom
annotated source: cassette_pseudogene
annotated property: definition
annotated target: A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy.
database_cross_reference: SO:ke

alanine
type: Class
subclass of: amino_acid
definition: A non-polar, hydorophobic amino acid encoded by the codons GCN (GCT, GCC, GCA and GCG).
has_exact_synonym: A
has_exact_synonym: Ala
has_obo_namespace: sequence
id: SO:0001435
comment: A place holder for a cross product with chebi.

Axiom
annotated source: alanine
annotated property: has_exact_synonym
annotated target: A
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: alanine
annotated property: has_exact_synonym
annotated target: Ala
has_synonym_type: amino acid 3 letter code

valine
type: Class
subclass of: amino_acid
definition: A non-polar, hydorophobic amino acid encoded by the codons GTN (GTT, GTC, GTA and GTG).
has_exact_synonym: V
has_exact_synonym: Val
has_obo_namespace: sequence
id: SO:0001436
comment: A place holder for a cross product with chebi.

Axiom
annotated source: valine
annotated property: has_exact_synonym
annotated target: V
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: valine
annotated property: has_exact_synonym
annotated target: Val
has_synonym_type: amino acid 3 letter code

leucine
type: Class
subclass of: amino_acid
definition: A non-polar, hydorophobic amino acid encoded by the codons CTN (CTT, CTC, CTA and CTG), TTA and TTG.
has_exact_synonym: L
has_exact_synonym: Leu
has_obo_namespace: sequence
id: SO:0001437
comment: A place holder for a cross product with chebi.

Axiom
annotated source: leucine
annotated property: has_exact_synonym
annotated target: L
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: leucine
annotated property: has_exact_synonym
annotated target: Leu
has_synonym_type: amino acid 3 letter code

isoleucine
type: Class
subclass of: amino_acid
definition: A non-polar, hydorophobic amino acid encoded by the codons ATH (ATT, ATC and ATA).
has_exact_synonym: I
has_exact_synonym: Ile
has_obo_namespace: sequence
id: SO:0001438
comment: A place holder for a cross product with chebi.

Axiom
annotated source: isoleucine
annotated property: has_exact_synonym
annotated target: I
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: isoleucine
annotated property: has_exact_synonym
annotated target: Ile
has_synonym_type: amino acid 3 letter code

proline
type: Class
subclass of: amino_acid
definition: A non-polar, hydorophobic amino acid encoded by the codons CCN (CCT, CCC, CCA and CCG).
has_exact_synonym: P
has_exact_synonym: Pro
has_obo_namespace: sequence
id: SO:0001439
comment: A place holder for a cross product with chebi.

Axiom
annotated source: proline
annotated property: has_exact_synonym
annotated target: P
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: proline
annotated property: has_exact_synonym
annotated target: Pro
has_synonym_type: amino acid 3 letter code

tryptophan
type: Class
subclass of: amino_acid
definition: A non-polar, hydorophobic amino acid encoded by the codon TGG.
has_exact_synonym: Trp
has_exact_synonym: W
has_obo_namespace: sequence
id: SO:0001440
comment: A place holder for a cross product with chebi.

Axiom
annotated source: tryptophan
annotated property: has_exact_synonym
annotated target: Trp
has_synonym_type: amino acid 3 letter code

Axiom
annotated source: tryptophan
annotated property: has_exact_synonym
annotated target: W
has_synonym_type: amino acid 1 letter code

phenylalanine
type: Class
subclass of: amino_acid
definition: A non-polar, hydorophobic amino acid encoded by the codons TTT and TTC.
has_exact_synonym: F
has_exact_synonym: Phe
has_obo_namespace: sequence
id: SO:0001441
comment: A place holder for a cross product with chebi.

Axiom
annotated source: phenylalanine
annotated property: has_exact_synonym
annotated target: F
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: phenylalanine
annotated property: has_exact_synonym
annotated target: Phe
has_synonym_type: amino acid 3 letter code

methionine
type: Class
subclass of: amino_acid
definition: A non-polar, hydorophobic amino acid encoded by the codon ATG.
has_exact_synonym: M
has_exact_synonym: Met
has_obo_namespace: sequence
id: SO:0001442
comment: A place holder for a cross product with chebi.

Axiom
annotated source: methionine
annotated property: has_exact_synonym
annotated target: M
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: methionine
annotated property: has_exact_synonym
annotated target: Met
has_synonym_type: amino acid 3 letter code

glycine
type: Class
subclass of: amino_acid
definition: A non-polar, hydorophilic amino acid encoded by the codons GGN (GGT, GGC, GGA and GGG).
has_exact_synonym: G
has_exact_synonym: Gly
has_obo_namespace: sequence
id: SO:0001443
comment: A place holder for a cross product with chebi.

Axiom
annotated source: glycine
annotated property: has_exact_synonym
annotated target: G
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: glycine
annotated property: has_exact_synonym
annotated target: Gly
has_synonym_type: amino acid 3 letter code

serine
type: Class
subclass of: amino_acid
definition: A polar, hydorophilic amino acid encoded by the codons TCN (TCT, TCC, TCA, TCG), AGT and AGC.
has_exact_synonym: S
has_exact_synonym: Ser
has_obo_namespace: sequence
id: SO:0001444
comment: A place holder for a cross product with chebi.

Axiom
annotated source: serine
annotated property: has_exact_synonym
annotated target: S
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: serine
annotated property: has_exact_synonym
annotated target: Ser
has_synonym_type: amino acid 3 letter code

threonine
type: Class
subclass of: amino_acid
definition: A polar, hydorophilic amino acid encoded by the codons ACN (ACT, ACC, ACA and ACG).
has_exact_synonym: T
has_exact_synonym: Thr
has_obo_namespace: sequence
id: SO:0001445
comment: A place holder for a cross product with chebi.

Axiom
annotated source: threonine
annotated property: has_exact_synonym
annotated target: T
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: threonine
annotated property: has_exact_synonym
annotated target: Thr
has_synonym_type: amino acid 3 letter code

tyrosine
type: Class
subclass of: amino_acid
definition: A polar, hydorophilic amino acid encoded by the codons TAT and TAC.
has_exact_synonym: Tyr
has_exact_synonym: Y
has_obo_namespace: sequence
id: SO:0001446
comment: A place holder for a cross product with chebi.

Axiom
annotated source: tyrosine
annotated property: has_exact_synonym
annotated target: Tyr
has_synonym_type: amino acid 3 letter code

Axiom
annotated source: tyrosine
annotated property: has_exact_synonym
annotated target: Y
has_synonym_type: amino acid 1 letter code

cysteine
type: Class
subclass of: amino_acid
definition: A polar amino acid encoded by the codons TGT and TGC.
has_exact_synonym: C
has_exact_synonym: Cys
has_obo_namespace: sequence
id: SO:0001447
comment: A place holder for a cross product with chebi.

Axiom
annotated source: cysteine
annotated property: has_exact_synonym
annotated target: C
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: cysteine
annotated property: has_exact_synonym
annotated target: Cys
has_synonym_type: amino acid 3 letter code

glutamine
type: Class
subclass of: amino_acid
definition: A polar, hydorophilic amino acid encoded by the codons CAA and CAG.
has_exact_synonym: Gln
has_exact_synonym: Q
has_obo_namespace: sequence
id: SO:0001448
comment: A place holder for a cross product with chebi.

Axiom
annotated source: glutamine
annotated property: has_exact_synonym
annotated target: Gln
has_synonym_type: amino acid 3 letter code

Axiom
annotated source: glutamine
annotated property: has_exact_synonym
annotated target: Q
has_synonym_type: amino acid 1 letter code

asparagine
type: Class
subclass of: amino_acid
definition: A polar, hydorophilic amino acid encoded by the codons AAT and AAC.
has_exact_synonym: Asn
has_exact_synonym: N
has_obo_namespace: sequence
id: SO:0001449
comment: A place holder for a cross product with chebi.

Axiom
annotated source: asparagine
annotated property: has_exact_synonym
annotated target: Asn
has_synonym_type: amino acid 3 letter code

Axiom
annotated source: asparagine
annotated property: has_exact_synonym
annotated target: N
has_synonym_type: amino acid 1 letter code

lysine
type: Class
subclass of: amino_acid
definition: A positively charged, hydorophilic amino acid encoded by the codons AAA and AAG.
has_exact_synonym: K
has_exact_synonym: Lys
has_obo_namespace: sequence
id: SO:0001450
comment: A place holder for a cross product with chebi.

Axiom
annotated source: lysine
annotated property: has_exact_synonym
annotated target: K
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: lysine
annotated property: has_exact_synonym
annotated target: Lys
has_synonym_type: amino acid 3 letter code

arginine
type: Class
subclass of: amino_acid
definition: A positively charged, hydorophilic amino acid encoded by the codons CGN (CGT, CGC, CGA and CGG), AGA and AGG.
has_exact_synonym: Arg
has_exact_synonym: R
has_obo_namespace: sequence
id: SO:0001451
comment: A place holder for a cross product with chebi.

Axiom
annotated source: arginine
annotated property: has_exact_synonym
annotated target: Arg
has_synonym_type: amino acid 3 letter code

Axiom
annotated source: arginine
annotated property: has_exact_synonym
annotated target: R
has_synonym_type: amino acid 1 letter code

histidine
type: Class
subclass of: amino_acid
definition: A positively charged, hydorophilic amino acid encoded by the codons CAT and CAC.
has_exact_synonym: H
has_exact_synonym: His
has_obo_namespace: sequence
id: SO:0001452
comment: A place holder for a cross product with chebi.

Axiom
annotated source: histidine
annotated property: has_exact_synonym
annotated target: H
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: histidine
annotated property: has_exact_synonym
annotated target: His
has_synonym_type: amino acid 3 letter code

aspartic_acid
type: Class
subclass of: amino_acid
definition: A negatively charged, hydorophilic amino acid encoded by the codons GAT and GAC.
has_exact_synonym: Asp
has_exact_synonym: D
has_exact_synonym: aspartic acid
has_obo_namespace: sequence
id: SO:0001453
comment: A place holder for a cross product with chebi.

Axiom
annotated source: aspartic_acid
annotated property: has_exact_synonym
annotated target: Asp
has_synonym_type: amino acid 3 letter code

Axiom
annotated source: aspartic_acid
annotated property: has_exact_synonym
annotated target: D
has_synonym_type: amino acid 1 letter code

glutamic_acid
type: Class
subclass of: amino_acid
definition: A negatively charged, hydorophilic amino acid encoded by the codons GAA and GAG.
has_exact_synonym: E
has_exact_synonym: Glu
has_exact_synonym: glutamic acid
has_obo_namespace: sequence
id: SO:0001454
comment: A place holder for a cross product with chebi.

Axiom
annotated source: glutamic_acid
annotated property: has_exact_synonym
annotated target: E
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: glutamic_acid
annotated property: has_exact_synonym
annotated target: Glu
has_synonym_type: amino acid 3 letter code

selenocysteine
type: Class
subclass of: amino_acid
definition: A relatively rare amino acid encoded by the codon UGA in some contexts, whereas UGA is a termination codon in other contexts.
has_exact_synonym: Sec
has_exact_synonym: U
has_obo_namespace: sequence
id: SO:0001455
comment: A place holder for a cross product with chebi.

Axiom
annotated source: selenocysteine
annotated property: definition
annotated target: A relatively rare amino acid encoded by the codon UGA in some contexts, whereas UGA is a termination codon in other contexts.
database_cross_reference: PMID:23275319

Axiom
annotated source: selenocysteine
annotated property: has_exact_synonym
annotated target: Sec
has_synonym_type: amino acid 3 letter code

Axiom
annotated source: selenocysteine
annotated property: has_exact_synonym
annotated target: U
has_synonym_type: amino acid 1 letter code

pyrrolysine
type: Class
subclass of: amino_acid
definition: A relatively rare amino acid encoded by the codon UAG in some contexts, whereas UAG is a termination codon in other contexts.
has_exact_synonym: O
has_exact_synonym: Pyl
has_obo_namespace: sequence
id: SO:0001456
comment: A place holder for a cross product with chebi.

Axiom
annotated source: pyrrolysine
annotated property: definition
annotated target: A relatively rare amino acid encoded by the codon UAG in some contexts, whereas UAG is a termination codon in other contexts.
database_cross_reference: PMID:15788401

Axiom
annotated source: pyrrolysine
annotated property: has_exact_synonym
annotated target: O
has_synonym_type: amino acid 1 letter code

Axiom
annotated source: pyrrolysine
annotated property: has_exact_synonym
annotated target: Pyl
has_synonym_type: amino acid 3 letter code

transcribed_cluster
type: Class
subclass of: experimental_feature
subclass of: Restriction
  on property: has_part
  some values from: reagent
definition: A region defined by a set of transcribed sequences from the same gene or expressed pseudogene.
has_exact_synonym: transcribed cluster
has_obo_namespace: sequence
has_related_synonym: unigene cluster
id: SO:0001457
comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.

Axiom
annotated source: transcribed_cluster
annotated property: definition
annotated target: A region defined by a set of transcribed sequences from the same gene or expressed pseudogene.
database_cross_reference: SO:ke

unigene_cluster
type: Class
subclass of: transcribed_cluster
definition: A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene.
has_obo_namespace: sequence
has_related_synonym: unigene cluster
id: SO:0001458
comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.

Axiom
annotated source: unigene_cluster
annotated property: definition
annotated target: A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene.
database_cross_reference: SO:ke

CRISPR
type: Class
subclass of: direct_repeat
definition: Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences.
database_cross_reference: http:en.wikipedia.org/wiki/CRISPR
has_exact_synonym: CRISPR element
has_exact_synonym: Clustered_Regularly_Interspaced_Short_Palindromic_Repeat
has_obo_namespace: sequence
id: SO:0001459

Axiom
annotated source: CRISPR
annotated property: definition
annotated target: Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences.
database_cross_reference: RFAM:jd

insulator_binding_site
type: Class
subclass of: nucleotide_to_protein_binding_site
subclass of: Restriction
  on property: part_of
  some values from: insulator
definition: A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
has_obo_namespace: sequence
has_related_synonym: insulator binding site
id: SO:0001460
comment: See tracker ID 2060908.

Axiom
annotated source: insulator_binding_site
annotated property: definition
annotated target: A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
database_cross_reference: SO:ke

enhancer_binding_site
type: Class
subclass of: nucleotide_to_protein_binding_site
subclass of: Restriction
  on property: part_of
  some values from: enhancer
definition: A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
has_obo_namespace: sequence
has_related_synonym: enhancer binding site
id: SO:0001461

Axiom
annotated source: enhancer_binding_site
annotated property: definition
annotated target: A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
database_cross_reference: SO:ke

contig_collection
type: Class
equivalent class: Class
  intersection of: sequence_conflict
  intersection of: Restriction
    on property: has_part
    some values from: contig
subclass of: sequence_conflict
subclass of: sequence_collection
subclass of: Restriction
  on property: has_part
  some values from: contig
definition: A collection of contigs.
has_exact_synonym: contig collection
has_obo_namespace: sequence
id: SO:0001462
comment: See tracker ID: 2138359.

Axiom
annotated source: contig_collection
annotated property: definition
annotated target: A collection of contigs.
database_cross_reference: SO:ke

lincRNA
type: Class
subclass of: SO_0001877
definition: Long, intervening non-coding RNA. A transcript that does not overlap within the start or end genomic coordinates of a coding gene or pseudogene on either strand.
has_exact_synonym: large intervening non-coding RNA
has_exact_synonym: long intergenic non-coding RNA
has_exact_synonym: long intervening non-coding RNA
has_obo_namespace: sequence
id: SO:0001463

Axiom
annotated source: lincRNA
annotated property: definition
annotated target: Long, intervening non-coding RNA. A transcript that does not overlap within the start or end genomic coordinates of a coding gene or pseudogene on either strand.
database_cross_reference: PMID:19182780
database_cross_reference: PMID:23463798
database_cross_reference: SO:ke
database_cross_reference: http://www.gencodegenes.org/gencode_biotypes.html

UST
type: Class
subclass of: EST
definition: An EST spanning part or all of the untranslated regions of a protein-coding transcript.
has_exact_synonym: UTR sequence tag
has_obo_namespace: sequence
id: SO:0001464

Axiom
annotated source: UST
annotated property: definition
annotated target: An EST spanning part or all of the untranslated regions of a protein-coding transcript.
database_cross_reference: SO:nlw

three_prime_UST
type: Class
subclass of: UST
definition: A UST located in the 3'UTR of a protein-coding transcript.
has_obo_namespace: sequence
has_related_synonym: 3' UST
id: SO:0001465

Axiom
annotated source: three_prime_UST
annotated property: definition
annotated target: A UST located in the 3'UTR of a protein-coding transcript.
database_cross_reference: SO:nlw

five_prime_UST
type: Class
subclass of: UST
definition: An UST located in the 5'UTR of a protein-coding transcript.
has_obo_namespace: sequence
has_related_synonym: 5' UST
id: SO:0001466

Axiom
annotated source: five_prime_UST
annotated property: definition
annotated target: An UST located in the 5'UTR of a protein-coding transcript.
database_cross_reference: SO:nlw

RST
type: Class
subclass of: EST
definition: A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long.
has_exact_synonym: RACE sequence tag
has_obo_namespace: sequence
id: SO:0001467

Axiom
annotated source: RST
annotated property: definition
annotated target: A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long.
database_cross_reference: SO:nlw

three_prime_RST
type: Class
subclass of: RST
definition: A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long.
has_exact_synonym: 3' RST
has_obo_namespace: sequence
id: SO:0001468

Axiom
annotated source: three_prime_RST
annotated property: definition
annotated target: A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long.
database_cross_reference: SO:nlw

five_prime_RST
type: Class
subclass of: RST
definition: A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long.
has_obo_namespace: sequence
has_related_synonym: 5' RST
id: SO:0001469

Axiom
annotated source: five_prime_RST
annotated property: definition
annotated target: A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long.
database_cross_reference: SO:nlw

UST_match
type: Class
subclass of: expressed_sequence_match
definition: A match against an UST sequence.
has_exact_synonym: UST match
has_obo_namespace: sequence
id: SO:0001470

Axiom
annotated source: UST_match
annotated property: definition
annotated target: A match against an UST sequence.
database_cross_reference: SO:nlw

RST_match
type: Class
subclass of: expressed_sequence_match
definition: A match against an RST sequence.
has_exact_synonym: RST match
has_obo_namespace: sequence
id: SO:0001471

Axiom
annotated source: RST_match
annotated property: definition
annotated target: A match against an RST sequence.
database_cross_reference: SO:nlw

primer_match
type: Class
subclass of: nucleotide_match
definition: A nucleotide match to a primer sequence.
has_exact_synonym: primer match
has_obo_namespace: sequence
id: SO:0001472

Axiom
annotated source: primer_match
annotated property: definition
annotated target: A nucleotide match to a primer sequence.
database_cross_reference: SO:nlw

miRNA_antiguide
type: Class
subclass of: miRNA_primary_transcript_region
definition: A region of the pri miRNA that base pairs with the guide to form the hairpin.
created by: kareneilbeck
creation date: 2009-05-27T03:35:43Z
has_exact_synonym: miRNA antiguide
has_exact_synonym: miRNA passenger strand
has_exact_synonym: miRNA star
has_obo_namespace: sequence
id: SO:0001473

Axiom
annotated source: miRNA_antiguide
annotated property: definition
annotated target: A region of the pri miRNA that base pairs with the guide to form the hairpin.
database_cross_reference: SO:ke

trans_splice_junction
type: Class
subclass of: junction
definition: The boundary between the spliced leader and the first exon of the mRNA.
created by: kareneilbeck
creation date: 2009-07-13T04:50:49Z
has_exact_synonym: trans-splice junction
has_obo_namespace: sequence
id: SO:0001474

Axiom
annotated source: trans_splice_junction
annotated property: definition
annotated target: The boundary between the spliced leader and the first exon of the mRNA.
database_cross_reference: SO:ke

outron
type: Class
subclass of: primary_transcript_region
definition: A region of a primary transcript, that is removed via trans splicing.
created by: kareneilbeck
creation date: 2009-07-14T11:36:08Z
has_obo_namespace: sequence
id: SO:0001475

Axiom
annotated source: outron
annotated property: definition
annotated target: A region of a primary transcript, that is removed via trans splicing.
database_cross_reference: PMID:16401417
database_cross_reference: SO:ke

natural_plasmid
type: Class
equivalent class: Class
  intersection of: plasmid
  intersection of: Restriction
    on property: has_quality
    some values from: natural
subclass of: plasmid
subclass of: extrachromosomal_mobile_genetic_element
subclass of: Restriction
  on property: has_quality
  some values from: natural
definition: A plasmid that occurs naturally.
created by: kareneilbeck
creation date: 2009-09-01T03:43:06Z
has_exact_synonym: natural plasmid
has_obo_namespace: sequence
id: SO:0001476

Axiom
annotated source: natural_plasmid
annotated property: definition
annotated target: A plasmid that occurs naturally.
database_cross_reference: SO:xp

gene_trap_construct
type: Class
subclass of: engineered_plasmid
definition: A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.
created by: kareneilbeck
creation date: 2009-09-01T03:49:09Z
has_exact_synonym: gene trap construct
has_obo_namespace: sequence
id: SO:0001477

Axiom
annotated source: gene_trap_construct
annotated property: definition
annotated target: A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.
database_cross_reference: ZFIN:dh

promoter_trap_construct
type: Class
subclass of: engineered_plasmid
definition: A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.
created by: kareneilbeck
creation date: 2009-09-01T03:52:01Z
has_exact_synonym: promoter trap construct
has_obo_namespace: sequence
id: SO:0001478

Axiom
annotated source: promoter_trap_construct
annotated property: definition
annotated target: A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.
database_cross_reference: ZFIN:dh

enhancer_trap_construct
type: Class
subclass of: engineered_plasmid
definition: An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.
created by: kareneilbeck
creation date: 2009-09-01T03:53:26Z
has_exact_synonym: enhancer trap construct
has_obo_namespace: sequence
id: SO:0001479

Axiom
annotated source: enhancer_trap_construct
annotated property: definition
annotated target: An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.
database_cross_reference: ZFIN:dh

PAC_end
type: Class
subclass of: read
subclass of: Restriction
  on property: part_of
  some values from: PAC
definition: A region of sequence from the end of a PAC clone that may provide a highly specific marker.
created by: kareneilbeck
creation date: 2009-09-09T05:18:12Z
has_exact_synonym: PAC end
has_obo_namespace: sequence
id: SO:0001480

Axiom
annotated source: PAC_end
annotated property: definition
annotated target: A region of sequence from the end of a PAC clone that may provide a highly specific marker.
database_cross_reference: ZFIN:mh

RAPD
type: Class
subclass of: PCR_product
definition: RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers.
created by: kareneilbeck
creation date: 2009-09-09T05:26:10Z
has_exact_synonym: Random Amplification Polymorphic DNA
has_obo_namespace: sequence
id: SO:0001481

Axiom
annotated source: RAPD
annotated property: definition
annotated target: RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers.
database_cross_reference: ZFIN:mh

shadow_enhancer
type: Class
subclass of: enhancer
definition: An enhancer that drives the pattern of transcription and binds to the same TF as the primary enhancer, but is located in the intron of or on the far side of a neighboring gene.
created by: kareneilbeck
creation date: 2009-09-09T05:29:29Z
has_exact_synonym: shadow enhancer
has_obo_namespace: sequence
id: SO:0001482

Axiom
annotated source: shadow_enhancer
annotated property: definition
annotated target: An enhancer that drives the pattern of transcription and binds to the same TF as the primary enhancer, but is located in the intron of or on the far side of a neighboring gene.
database_cross_reference: PMID:22083793

SNV
type: Class
subclass of: SO_1000002
definition: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
created by: kareneilbeck
creation date: 2009-10-08T11:37:49Z
has_exact_synonym: single nucleotide variant
has_obo_namespace: sequence
id: SO:0001483
in_subset: SOFA

Axiom
annotated source: SNV
annotated property: definition
annotated target: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
database_cross_reference: SO:bm

X_element_combinatorial_repeat
type: Class
subclass of: repeat_region
subclass of: Restriction
  on property: part_of
  some values from: telomere
definition: An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element.
created by: kareneilbeck
creation date: 2009-11-10T11:03:37Z
has_broad_synonym: INSDC_feature:repeat_region
has_exact_synonym: INSDC_qualifier:x_element_combinatorial_repeat
has_exact_synonym: X element combinatorial repeat
has_obo_namespace: sequence
id: SO:0001484
comment: X element combinatorial repeats contain Tbf1p binding sites, and possible functions include a role in telomerase-independent telomere maintenance via recombination or as a barrier against transcriptional silencing. These are usually present as a combination of one or more of several types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.

Axiom
annotated source: X_element_combinatorial_repeat
annotated property: definition
annotated target: An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element.
database_cross_reference: http://www.yeastgenome.org/help/glossary.html

Y_prime_element
type: Class
subclass of: repeat_region
subclass of: Restriction
  on property: part_of
  some values from: telomere
definition: A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies.
created by: kareneilbeck
creation date: 2009-11-10T12:08:57Z
has_broad_synonym: INSDC_feature:repeat_region
has_exact_synonym: INSDC_qualifier:Y_prime_element
has_exact_synonym: Y prime element
has_exact_synonym: Y' element
has_obo_namespace: sequence
id: SO:0001485
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.

Axiom
annotated source: Y_prime_element
annotated property: definition
annotated target: A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies.
database_cross_reference: http:http://www.yeastgenome.org/help/glossary.html

standard_draft
type: Class
subclass of: whole_genome_sequence_status
definition: The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete.
created by: kareneilbeck
creation date: 2009-10-23T12:48:32Z
has_exact_synonym: standard draft
has_obo_namespace: sequence
id: SO:0001486

Axiom
annotated source: standard_draft
annotated property: definition
annotated target: The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete.
database_cross_reference: DOI:10.1126

high_quality_draft
type: Class
subclass of: whole_genome_sequence_status
definition: The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.
created by: kareneilbeck
creation date: 2009-10-23T12:52:36Z
has_exact_synonym: high quality draft
has_obo_namespace: sequence
id: SO:0001487

Axiom
annotated source: high_quality_draft
annotated property: definition
annotated target: The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.
database_cross_reference: DOI:10.1126

improved_high_quality_draft
type: Class
subclass of: whole_genome_sequence_status
definition: The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution.
created by: kareneilbeck
creation date: 2009-10-23T12:54:35Z
has_exact_synonym: improved high quality draft
has_obo_namespace: sequence
id: SO:0001488

Axiom
annotated source: improved_high_quality_draft
annotated property: definition
annotated target: The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution.
database_cross_reference: DOI:10.1126

annotation_directed_improved_draft
type: Class
subclass of: whole_genome_sequence_status
definition: The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.
created by: kareneilbeck
creation date: 2009-10-23T12:57:10Z
has_exact_synonym: annotation directed improvement
has_obo_namespace: sequence
id: SO:0001489

Axiom
annotated source: annotation_directed_improved_draft
annotated property: definition
annotated target: The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.
database_cross_reference: DOI:10.1126

noncontiguous_finished
type: Class
subclass of: whole_genome_sequence_status
definition: The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions.
created by: kareneilbeck
creation date: 2009-10-23T01:01:07Z
has_exact_synonym: non contiguous finished
has_obo_namespace: sequence
id: SO:0001490

Axiom
annotated source: noncontiguous_finished
annotated property: definition
annotated target: The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions.
database_cross_reference: DOI:10.1126

finished_genome
type: Class
subclass of: whole_genome_sequence_status
definition: The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.
created by: kareneilbeck
creation date: 2009-10-23T01:04:43Z
has_exact_synonym: finished
has_exact_synonym: finished genome
has_obo_namespace: sequence
id: SO:0001491

Axiom
annotated source: finished_genome
annotated property: definition
annotated target: The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.
database_cross_reference: DOI:10.1126

intronic_regulatory_region
type: Class
subclass of: transcriptional_cis_regulatory_region
subclass of: Restriction
  on property: part_of
  some values from: intron
definition: A regulatory region that is part of an intron.
created by: kareneilbeck
creation date: 2009-11-08T02:48:02Z
has_exact_synonym: intronic regulatory region
has_obo_namespace: sequence
id: SO:0001492
comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: intronic_regulatory_region
annotated property: definition
annotated target: A regulatory region that is part of an intron.
database_cross_reference: SO:ke

centromere_DNA_Element_I
type: Class
subclass of: conserved_region
subclass of: Restriction
  on property: part_of
  some values from: SO_0001794
definition: A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).
created by: kareneilbeck
creation date: 2009-11-09T05:47:23Z
has_exact_synonym: CDEI
has_exact_synonym: Centromere DNA Element I
has_obo_namespace: sequence
id: SO:0001493
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.

Axiom
annotated source: centromere_DNA_Element_I
annotated property: definition
annotated target: A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).
database_cross_reference: PMID:11222754

centromere_DNA_Element_II
type: Class
subclass of: conserved_region
subclass of: Restriction
  on property: part_of
  some values from: SO_0001794
definition: A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.
created by: kareneilbeck
creation date: 2009-11-09T05:51:26Z
has_exact_synonym: CDEII
has_exact_synonym: centromere DNA Element II
has_obo_namespace: sequence
id: SO:0001494
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.

Axiom
annotated source: centromere_DNA_Element_II
annotated property: definition
annotated target: A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.
database_cross_reference: PMID:11222754

centromere_DNA_Element_III
type: Class
subclass of: conserved_region
subclass of: Restriction
  on property: part_of
  some values from: SO_0001794
definition: A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.
created by: kareneilbeck
creation date: 2009-11-09T05:54:47Z
has_exact_synonym: CDEIII
has_exact_synonym: centromere DNA Element III
has_obo_namespace: sequence
id: SO:0001495
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.

Axiom
annotated source: centromere_DNA_Element_III
annotated property: definition
annotated target: A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.
database_cross_reference: PMID:11222754

telomeric_repeat
type: Class
subclass of: repeat_region
subclass of: Restriction
  on property: part_of
  some values from: telomere
definition: The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.
created by: kareneilbeck
creation date: 2009-11-09T06:00:42Z
has_broad_synonym: INSDC_feature:repeat_region
has_exact_synonym: INSDC_qualifier:telomeric_repeat
has_exact_synonym: telomeric repeat
has_obo_namespace: sequence
id: SO:0001496
comment: The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739.

Axiom
annotated source: telomeric_repeat
annotated property: definition
annotated target: The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.
database_cross_reference: PMID:8720065

X_element
type: Class
subclass of: conserved_region
subclass of: Restriction
  on property: part_of
  some values from: telomere
definition: The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.
created by: kareneilbeck
creation date: 2009-11-10T10:56:54Z
has_exact_synonym: X element core sequence
has_obo_namespace: sequence
has_related_synonym: X element
id: SO:0001497
comment: Possible functions include roles in chromosomal segregation, maintenance of chromosome stability, recombinational sequestering, or as a barrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. From Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1.

Axiom
annotated source: X_element
annotated property: definition
annotated target: The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.
database_cross_reference: PMID:7785338
database_cross_reference: PMID:8005434
database_cross_reference: http://www.yeastgenome.org/help/glossary.html#xelemcoresequence

YAC_end
type: Class
subclass of: read
subclass of: Restriction
  on property: part_of
  some values from: YAC
definition: A region of sequence from the end of a YAC clone that may provide a highly specific marker.
created by: kareneilbeck
creation date: 2009-11-19T11:07:18Z
has_exact_synonym: YAC end
has_obo_namespace: sequence
id: SO:0001498

Axiom
annotated source: YAC_end
annotated property: definition
annotated target: A region of sequence from the end of a YAC clone that may provide a highly specific marker.
database_cross_reference: SO:ke

whole_genome_sequence_status
type: Class
subclass of: status
definition: The status of whole genome sequence.
created by: kareneilbeck
creation date: 2009-10-23T12:47:47Z
has_exact_synonym: whole genome sequence status
has_obo_namespace: sequence
id: SO:0001499
comment: This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms.

Axiom
annotated source: whole_genome_sequence_status
annotated property: definition
annotated target: The status of whole genome sequence.
database_cross_reference: DOI:10.1126

heritable_phenotypic_marker
type: Class
subclass of: genetic_marker
definition: A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.
created by: kareneilbeck
creation date: 2009-12-07T01:50:55Z
has_exact_synonym: heritable phenotypic marker
has_exact_synonym: phenotypic marker
has_obo_namespace: sequence
id: SO:0001500

Axiom
annotated source: heritable_phenotypic_marker
annotated property: definition
annotated target: A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.
database_cross_reference: JAX:hdene

peptide_collection
type: Class
equivalent class: Class
  intersection of: sequence_collection
  intersection of: Restriction
    on property: has_part
    some values from: polypeptide
subclass of: sequence_collection
subclass of: Restriction
  on property: has_part
  some values from: polypeptide
definition: A collection of peptide sequences.
created by: kareneilbeck
creation date: 2009-12-11T10:58:58Z
has_exact_synonym: peptide collection
has_exact_synonym: peptide set
has_obo_namespace: sequence
id: SO:0001501
comment: Term requested via tracker ID: 2910829.

Axiom
annotated source: peptide_collection
annotated property: definition
annotated target: A collection of peptide sequences.
database_cross_reference: BBOP:nlw

high_identity_region
type: Class
subclass of: experimental_feature
definition: An experimental feature with high sequence identity to another sequence.
created by: kareneilbeck
creation date: 2009-12-11T11:06:05Z
has_exact_synonym: high identity region
has_obo_namespace: sequence
id: SO:0001502
comment: Requested by tracker ID: 2902685.

Axiom
annotated source: high_identity_region
annotated property: definition
annotated target: An experimental feature with high sequence identity to another sequence.
database_cross_reference: SO:ke

processed_transcript
type: Class
subclass of: transcript
definition: A transcript for which no open reading frame has been identified and for which no other function has been determined.
created by: kareneilbeck
creation date: 2009-12-21T05:37:14Z
has_exact_synonym: processed transcript
has_obo_namespace: sequence
id: SO:0001503
comment: Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.

Axiom
annotated source: processed_transcript
annotated property: definition
annotated target: A transcript for which no open reading frame has been identified and for which no other function has been determined.
database_cross_reference: MGI:hdeen

assortment_derived_variation
type: Class
subclass of: chromosome_variation
definition: A chromosome variation derived from an event during meiosis.
created by: kareneilbeck
creation date: 2010-03-02T05:03:18Z
has_obo_namespace: sequence
has_related_synonym: assortment derived variation
id: SO:0001504

Axiom
annotated source: assortment_derived_variation
annotated property: definition
annotated target: A chromosome variation derived from an event during meiosis.
database_cross_reference: SO:ke

reference_genome
type: Class
subclass of: genome
definition: A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.
created by: kareneilbeck
creation date: 2010-03-03T02:10:03Z
has_obo_namespace: sequence
has_related_synonym: reference genome
id: SO:0001505

Axiom
annotated source: reference_genome
annotated property: definition
annotated target: A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.
database_cross_reference: SO:ke

variant_genome
type: Class
subclass of: genome
definition: A collection of sequences (often chromosomes) of an individual.
created by: kareneilbeck
creation date: 2010-03-03T02:11:25Z
has_obo_namespace: sequence
has_related_synonym: variant genome
id: SO:0001506

Axiom
annotated source: variant_genome
annotated property: definition
annotated target: A collection of sequences (often chromosomes) of an individual.
database_cross_reference: SO:ke

variant_collection
type: Class
equivalent class: Class
  intersection of: sequence_collection
  intersection of: Restriction
    on property: has_part
    some values from: sequence_alteration
subclass of: sequence_collection
subclass of: Restriction
  on property: has_part
  some values from: sequence_alteration
definition: A collection of one or more sequences of an individual.
created by: kareneilbeck
creation date: 2010-03-03T02:13:28Z
has_obo_namespace: sequence
has_related_synonym: variant collection
id: SO:0001507

Axiom
annotated source: variant_collection
annotated property: definition
annotated target: A collection of one or more sequences of an individual.
database_cross_reference: SO:ke

alteration_attribute
type: Class
subclass of: feature_attribute
definition: An attribute of alteration of one or more chromosomes.
created by: kareneilbeck
creation date: 2010-03-04T02:53:23Z
has_exact_synonym: alteration attribute
has_obo_namespace: sequence
id: SO:0001508

chromosomal_variation_attribute
type: Class
subclass of: alteration_attribute
definition: An attribute of a change in the structure or number of a chromosomes.
created by: kareneilbeck
creation date: 2010-03-04T02:54:30Z
has_exact_synonym: chromosomal variation attribute
has_obo_namespace: sequence
id: SO:0001509

intrachromosomal
type: Class
subclass of: chromosomal_variation_attribute
definition: A change in chromosomes that occurs between two separate chromosomes.
created by: kareneilbeck
creation date: 2010-03-04T02:55:25Z
has_obo_namespace: sequence
id: SO:0001510

interchromosomal
type: Class
subclass of: chromosomal_variation_attribute
definition: A change in chromosomes that occurs between two sections of the same chromosome or between homologous chromosomes.
created by: kareneilbeck
creation date: 2010-03-04T02:55:43Z
has_obo_namespace: sequence
id: SO:0001511

insertion_attribute
type: Class
subclass of: alteration_attribute
definition: A quality of a chromosomal insertion,.
created by: kareneilbeck
creation date: 2010-03-04T02:55:56Z
has_exact_synonym: insertion attribute
has_obo_namespace: sequence
id: SO:0001512

Axiom
annotated source: insertion_attribute
annotated property: definition
annotated target: A quality of a chromosomal insertion,.
database_cross_reference: SO:ke

tandem
type: Class
subclass of: insertion_attribute
definition: An insertion of extension of a tandem repeat.
created by: kareneilbeck
creation date: 2010-03-04T02:56:37Z
has_obo_namespace: sequence
id: SO:0001513

direct
type: Class
subclass of: insertion_attribute
definition: A quality of an insertion where the insert is not in a cytologically inverted orientation.
created by: kareneilbeck
creation date: 2010-03-04T02:56:49Z
has_obo_namespace: sequence
id: SO:0001514

Axiom
annotated source: direct
annotated property: definition
annotated target: A quality of an insertion where the insert is not in a cytologically inverted orientation.
database_cross_reference: SO:ke

inverted
type: Class
subclass of: insertion_attribute
definition: A quality of an insertion where the insert is in a cytologically inverted orientation.
created by: kareneilbeck
creation date: 2010-03-04T02:57:40Z
has_obo_namespace: sequence
id: SO:0001515

Axiom
annotated source: inverted
annotated property: definition
annotated target: A quality of an insertion where the insert is in a cytologically inverted orientation.
database_cross_reference: SO:ke

free
type: Class
subclass of: duplication_attribute
definition: The quality of a duplication where the new region exists independently of the original.
created by: kareneilbeck
creation date: 2010-03-04T02:57:51Z
has_obo_namespace: sequence
id: SO:0001516

Axiom
annotated source: free
annotated property: definition
annotated target: The quality of a duplication where the new region exists independently of the original.
database_cross_reference: SO:ke

inversion_attribute
type: Class
subclass of: alteration_attribute
definition: When a region of a chromosome is changed to the reverse order without duplication or deletion.
created by: kareneilbeck
creation date: 2010-03-04T02:58:10Z
has_exact_synonym: inversion attribute
has_obo_namespace: sequence
id: SO:0001517

pericentric
type: Class
subclass of: inversion_attribute
definition: An inversion event that includes the centromere.
created by: kareneilbeck
creation date: 2010-03-04T02:58:24Z
has_obo_namespace: sequence
id: SO:0001518

paracentric
type: Class
subclass of: inversion_attribute
definition: An inversion event that does not include the centromere.
created by: kareneilbeck
creation date: 2010-03-04T02:58:35Z
has_obo_namespace: sequence
id: SO:0001519

translocaton_attribute
type: Class
subclass of: alteration_attribute
definition: An attribute of a translocation, which is then a region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions.
created by: kareneilbeck
creation date: 2010-03-04T02:58:47Z
has_exact_synonym: translocation attribute
has_obo_namespace: sequence
id: SO:0001520

reciprocal
type: Class
subclass of: translocaton_attribute
definition: When translocation occurs between nonhomologous chromosomes and involved an equal exchange of genetic materials.
created by: kareneilbeck
creation date: 2010-03-04T02:59:34Z
has_obo_namespace: sequence
id: SO:0001521

insertional
type: Class
subclass of: translocaton_attribute
definition: When a translocation is simply moving genetic material from one chromosome to another.
created by: kareneilbeck
creation date: 2010-03-04T02:59:51Z
has_obo_namespace: sequence
id: SO:0001522

duplication_attribute
type: Class
subclass of: alteration_attribute
definition: An attribute of a duplication, which is an insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome.
created by: kareneilbeck
creation date: 2010-03-05T01:56:33Z
has_obo_namespace: sequence
has_related_synonym: duplication attribute
id: SO:0001523

chromosomally_aberrant_genome
type: Class
subclass of: variant_genome
definition: When a genome contains an abnormal amount of chromosomes.
created by: kareneilbeck
creation date: 2010-03-05T02:21:00Z
has_obo_namespace: sequence
has_related_synonym: chromosomally aberrant genome
id: SO:0001524

assembly_error_correction
type: Class
subclass of: sequence_difference
definition: A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake.
created by: kareneilbeck
creation date: 2010-03-09T02:16:31Z
has_obo_namespace: sequence
has_related_synonym: assembly error correction
id: SO:0001525

Axiom
annotated source: assembly_error_correction
annotated property: definition
annotated target: A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake.
database_cross_reference: SO:ke

base_call_error_correction
type: Class
subclass of: sequence_difference
definition: A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake.
created by: kareneilbeck
creation date: 2010-03-09T02:18:07Z
has_obo_namespace: sequence
has_related_synonym: base call error correction
id: SO:0001526

Axiom
annotated source: base_call_error_correction
annotated property: definition
annotated target: A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake.
database_cross_reference: SO:ke

peptide_localization_signal
type: Class
subclass of: polypeptide_region
definition: A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
created by: kareneilbeck
creation date: 2010-03-11T02:15:05Z
has_exact_synonym: peptide localization signal
has_obo_namespace: sequence
has_related_synonym: localization signal
id: SO:0001527
in_subset: SOFA

Axiom
annotated source: peptide_localization_signal
annotated property: definition
annotated target: A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
database_cross_reference: SO:ke

nuclear_localization_signal
type: Class
subclass of: peptide_localization_signal
definition: A polypeptide region that targets a polypeptide to the nucleus.
created by: kareneilbeck
creation date: 2010-03-11T02:16:38Z
database_cross_reference: http://en.wikipedia.org/wiki/Nuclear_localization_signal
has_exact_synonym: NLS
has_obo_namespace: sequence
id: SO:0001528

Axiom
annotated source: nuclear_localization_signal
annotated property: definition
annotated target: A polypeptide region that targets a polypeptide to the nucleus.
database_cross_reference: SO:ke

wikipedia
type: Axiom
annotated source: nuclear_localization_signal
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Nuclear_localization_signal

endosomal_localization_signal
type: Class
subclass of: peptide_localization_signal
definition: A polypeptide region that targets a polypeptide to the endosome.
created by: kareneilbeck
creation date: 2010-03-11T02:20:58Z
has_exact_synonym: endosomal localization signal
has_obo_namespace: sequence
id: SO:0001529

Axiom
annotated source: endosomal_localization_signal
annotated property: definition
annotated target: A polypeptide region that targets a polypeptide to the endosome.
database_cross_reference: SO:ke

lysosomal_localization_signal
type: Class
subclass of: peptide_localization_signal
definition: A polypeptide region that targets a polypeptide to the lysosome.
created by: kareneilbeck
creation date: 2010-03-11T02:24:10Z
has_exact_synonym: lysosomal localization signal
has_obo_namespace: sequence
id: SO:0001530

Axiom
annotated source: lysosomal_localization_signal
annotated property: definition
annotated target: A polypeptide region that targets a polypeptide to the lysosome.
database_cross_reference: SO:ke

nuclear_export_signal
type: Class
subclass of: peptide_localization_signal
definition: A polypeptide region that targets a polypeptide to he cytoplasm.
created by: kareneilbeck
creation date: 2010-03-11T02:25:25Z
database_cross_reference: http://en.wikipedia.org/wiki/Nuclear_export_signal
has_exact_synonym: NES
has_exact_synonym: nuclear export signal
has_obo_namespace: sequence
id: SO:0001531

Axiom
annotated source: nuclear_export_signal
annotated property: definition
annotated target: A polypeptide region that targets a polypeptide to he cytoplasm.
database_cross_reference: SO:ke

recombination_signal_sequence
type: Class
subclass of: specific_recombination_site
definition: A region recognized by a recombinase.
created by: kareneilbeck
creation date: 2010-03-11T03:16:47Z
database_cross_reference: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences
has_obo_namespace: sequence
has_related_synonym: recombination signal sequence
id: SO:0001532

Axiom
annotated source: recombination_signal_sequence
annotated property: definition
annotated target: A region recognized by a recombinase.
database_cross_reference: SO:ke

wikipedia
type: Axiom
annotated source: recombination_signal_sequence
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences

cryptic_splice_site
type: Class
subclass of: splice_site
definition: A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.
created by: kareneilbeck
creation date: 2010-03-11T03:25:06Z
has_exact_synonym: cryptic splice site
has_obo_namespace: sequence
has_related_synonym: cryptic splice signal
id: SO:0001533

Axiom
annotated source: cryptic_splice_site
annotated property: definition
annotated target: A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.
database_cross_reference: SO:ke

nuclear_rim_localization_signal
type: Class
subclass of: peptide_localization_signal
definition: A polypeptide region that targets a polypeptide to the nuclear rim.
created by: kareneilbeck
creation date: 2010-03-11T03:31:30Z
database_cross_reference: PMID:16027110
has_obo_namespace: sequence
has_related_synonym: nuclear rim localization signal
id: SO:0001534

Axiom
annotated source: nuclear_rim_localization_signal
annotated property: definition
annotated target: A polypeptide region that targets a polypeptide to the nuclear rim.
database_cross_reference: SO:ke

P_TIR_transposon
type: Class
subclass of: terminal_inverted_repeat_element
definition: A P-element is a DNA transposon responsible for hybrid dysgenesis. P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain.
created by: kareneilbeck
creation date: 2010-03-12T03:40:33Z
has_exact_synonym: DTP transposon
has_exact_synonym: P TIR transposon
has_exact_synonym: P element
has_exact_synonym: P transposable element
has_exact_synonym: P-element
has_obo_namespace: sequence
id: SO:0001535
comment: Moved from under DNA_transposon (SO:0000182) by Dave Sant as per request from GitHub issue #488 on June 25, 2020

Axiom
annotated source: P_TIR_transposon
annotated property: definition
annotated target: A P-element is a DNA transposon responsible for hybrid dysgenesis. P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain.
database_cross_reference: PMID:6309410
database_cross_reference: SO:ke

functional_effect_variant
type: Class
subclass of: sequence_variant
definition: A variant whereby the effect is evaluated with respect to a reference.
created by: kareneilbeck
creation date: 2010-03-22T11:30:25Z
has_exact_synonym: functional effect variant
has_exact_synonym: functional variant
has_obo_namespace: sequence
id: SO:0001536
comment: Updated after request from Lea Starita, lea.starita@gmail.com from the NCBI.

Axiom
annotated source: functional_effect_variant
annotated property: definition
annotated target: A variant whereby the effect is evaluated with respect to a reference.
database_cross_reference: SO:ke

structural_variant
type: Class
subclass of: sequence_variant
definition: A sequence variant that changes one or more structural features.
created by: kareneilbeck
creation date: 2010-03-22T11:31:01Z
database_cross_reference: http://vat.gersteinlab.org/formats.php
has_exact_synonym: Jannovar:structural_variant
has_exact_synonym: VAT:svOverlap
has_obo_namespace: sequence
has_related_synonym: structural variant
id: SO:0001537

Axiom
annotated source: structural_variant
annotated property: definition
annotated target: A sequence variant that changes one or more structural features.
database_cross_reference: SO:ke

VAT
type: Axiom
annotated source: structural_variant
annotated property: database_cross_reference
annotated target: http://vat.gersteinlab.org/formats.php

Axiom
annotated source: structural_variant
annotated property: has_exact_synonym
annotated target: Jannovar:structural_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: structural_variant
annotated property: has_exact_synonym
annotated target: VAT:svOverlap
has_synonym_type: variant annotation term

transcript_function_variant
type: Class
subclass of: SO_0002218
definition: A sequence variant which alters the functioning of a transcript with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:32:58Z
has_exact_synonym: transcript function variant
has_obo_namespace: sequence
id: SO:0001538

Axiom
annotated source: transcript_function_variant
annotated property: definition
annotated target: A sequence variant which alters the functioning of a transcript with respect to a reference sequence.
database_cross_reference: SO:ke

translational_product_function_variant
type: Class
subclass of: SO_0002218
definition: A sequence variant that affects the functioning of a translational product with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:46:15Z
has_exact_synonym: translational product variant
has_obo_namespace: sequence
id: SO:0001539

Axiom
annotated source: translational_product_function_variant
annotated property: definition
annotated target: A sequence variant that affects the functioning of a translational product with respect to a reference sequence.
database_cross_reference: SO:ke

level_of_transcript_variant
type: Class
subclass of: transcript_function_variant
definition: A sequence variant which alters the level of a transcript.
created by: kareneilbeck
creation date: 2010-03-22T11:47:07Z
has_exact_synonym: level of transcript variant
has_obo_namespace: sequence
id: SO:0001540

Axiom
annotated source: level_of_transcript_variant
annotated property: definition
annotated target: A sequence variant which alters the level of a transcript.
database_cross_reference: SO:ke

decreased_transcript_level_variant
type: Class
subclass of: level_of_transcript_variant
definition: A sequence variant that decreases the level of mature, spliced and processed RNA with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:47:47Z
has_exact_synonym: decreased transcript level
has_obo_namespace: sequence
id: SO:0001541

Axiom
annotated source: decreased_transcript_level_variant
annotated property: definition
annotated target: A sequence variant that decreases the level of mature, spliced and processed RNA with respect to a reference sequence.
database_cross_reference: SO:ke

increased_transcript_level_variant
type: Class
subclass of: level_of_transcript_variant
definition: A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:48:17Z
has_exact_synonym: increased transcript level variant
has_obo_namespace: sequence
id: SO:0001542

Axiom
annotated source: increased_transcript_level_variant
annotated property: definition
annotated target: A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.
database_cross_reference: SO:ke

transcript_processing_variant
type: Class
subclass of: transcript_function_variant
definition: A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:48:48Z
has_exact_synonym: transcript processing variant
has_obo_namespace: sequence
id: SO:0001543

Axiom
annotated source: transcript_processing_variant
annotated property: definition
annotated target: A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence.
database_cross_reference: SO:ke

editing_variant
type: Class
subclass of: transcript_processing_variant
definition: A transcript processing variant whereby the process of editing is disrupted with respect to the reference.
created by: kareneilbeck
creation date: 2010-03-22T11:49:25Z
has_exact_synonym: editing variant
has_obo_namespace: sequence
id: SO:0001544

Axiom
annotated source: editing_variant
annotated property: definition
annotated target: A transcript processing variant whereby the process of editing is disrupted with respect to the reference.
database_cross_reference: SO:ke

polyadenylation_variant
type: Class
subclass of: transcript_processing_variant
definition: A sequence variant that changes polyadenylation with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:49:40Z
has_exact_synonym: polyadenylation variant
has_obo_namespace: sequence
id: SO:0001545

Axiom
annotated source: polyadenylation_variant
annotated property: definition
annotated target: A sequence variant that changes polyadenylation with respect to a reference sequence.
database_cross_reference: SO:ke

transcript_stability_variant
type: Class
subclass of: transcript_function_variant
definition: A variant that changes the stability of a transcript with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:50:01Z
has_exact_synonym: transcript stability variant
has_obo_namespace: sequence
id: SO:0001546

Axiom
annotated source: transcript_stability_variant
annotated property: definition
annotated target: A variant that changes the stability of a transcript with respect to a reference sequence.
database_cross_reference: SO:ke

decreased_transcript_stability_variant
type: Class
subclass of: transcript_stability_variant
definition: A sequence variant that decreases transcript stability with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:50:23Z
has_exact_synonym: decrease transcript stability variant
has_obo_namespace: sequence
id: SO:0001547

Axiom
annotated source: decreased_transcript_stability_variant
annotated property: definition
annotated target: A sequence variant that decreases transcript stability with respect to a reference sequence.
database_cross_reference: SO:ke

increased_transcript_stability_variant
type: Class
subclass of: transcript_stability_variant
definition: A sequence variant that increases transcript stability with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:50:39Z
has_exact_synonym: increased transcript stability variant
has_obo_namespace: sequence
id: SO:0001548

Axiom
annotated source: increased_transcript_stability_variant
annotated property: definition
annotated target: A sequence variant that increases transcript stability with respect to a reference sequence.
database_cross_reference: SO:ke

transcription_variant
type: Class
subclass of: transcript_function_variant
definition: A variant that changes alters the transcription of a transcript with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:51:26Z
has_exact_synonym: transcription variant
has_obo_namespace: sequence
id: SO:0001549

Axiom
annotated source: transcription_variant
annotated property: definition
annotated target: A variant that changes alters the transcription of a transcript with respect to a reference sequence.
database_cross_reference: SO:ke

rate_of_transcription_variant
type: Class
subclass of: transcription_variant
definition: A sequence variant that changes the rate of transcription with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:51:50Z
has_exact_synonym: rate of transcription variant
has_obo_namespace: sequence
id: SO:0001550

Axiom
annotated source: rate_of_transcription_variant
annotated property: definition
annotated target: A sequence variant that changes the rate of transcription with respect to a reference sequence.
database_cross_reference: SO:ke

increased_transcription_rate_variant
type: Class
subclass of: rate_of_transcription_variant
definition: A sequence variant that increases the rate of transcription with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:52:17Z
has_exact_synonym: increased transcription rate variant
has_obo_namespace: sequence
id: SO:0001551

Axiom
annotated source: increased_transcription_rate_variant
annotated property: definition
annotated target: A sequence variant that increases the rate of transcription with respect to a reference sequence.
database_cross_reference: SO:ke

decreased_transcription_rate_variant
type: Class
subclass of: rate_of_transcription_variant
definition: A sequence variant that decreases the rate of transcription with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:52:43Z
has_exact_synonym: decreased transcription rate variant
has_obo_namespace: sequence
id: SO:0001552

Axiom
annotated source: decreased_transcription_rate_variant
annotated property: definition
annotated target: A sequence variant that decreases the rate of transcription with respect to a reference sequence.
database_cross_reference: SO:ke

translational_product_level_variant
type: Class
subclass of: translational_product_function_variant
definition: A functional variant that changes the translational product level with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:53:32Z
has_exact_synonym: translational product level variant
has_obo_namespace: sequence
id: SO:0001553

Axiom
annotated source: translational_product_level_variant
annotated property: definition
annotated target: A functional variant that changes the translational product level with respect to a reference sequence.
database_cross_reference: SO:ke

polypeptide_function_variant
type: Class
subclass of: translational_product_function_variant
definition: A sequence variant which changes polypeptide functioning with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:53:54Z
has_exact_synonym: polypeptide function variant
has_obo_namespace: sequence
id: SO:0001554

Axiom
annotated source: polypeptide_function_variant
annotated property: definition
annotated target: A sequence variant which changes polypeptide functioning with respect to a reference sequence.
database_cross_reference: SO:ke

decreased_translational_product_level
type: Class
subclass of: translational_product_level_variant
definition: A sequence variant which decreases the translational product level with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:54:25Z
has_exact_synonym: decrease translational product level
has_obo_namespace: sequence
id: SO:0001555

Axiom
annotated source: decreased_translational_product_level
annotated property: definition
annotated target: A sequence variant which decreases the translational product level with respect to a reference sequence.
database_cross_reference: SO:ke

increased_translational_product_level
type: Class
subclass of: translational_product_level_variant
definition: A sequence variant which increases the translational product level with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:55:25Z
has_exact_synonym: increase translational product level
has_obo_namespace: sequence
id: SO:0001556

Axiom
annotated source: increased_translational_product_level
annotated property: definition
annotated target: A sequence variant which increases the translational product level with respect to a reference sequence.
database_cross_reference: SO:ke

polypeptide_gain_of_function_variant
type: Class
subclass of: polypeptide_function_variant
definition: A sequence variant which causes gain of polypeptide function with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:56:12Z
has_exact_synonym: polypeptide gain of function variant
has_obo_namespace: sequence
id: SO:0001557

Axiom
annotated source: polypeptide_gain_of_function_variant
annotated property: definition
annotated target: A sequence variant which causes gain of polypeptide function with respect to a reference sequence.
database_cross_reference: SO:ke

polypeptide_localization_variant
type: Class
subclass of: polypeptide_function_variant
definition: A sequence variant which changes the localization of a polypeptide with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:56:37Z
has_exact_synonym: polypeptide localization variant
has_obo_namespace: sequence
id: SO:0001558

Axiom
annotated source: polypeptide_localization_variant
annotated property: definition
annotated target: A sequence variant which changes the localization of a polypeptide with respect to a reference sequence.
database_cross_reference: SO:ke

polypeptide_loss_of_function_variant
type: Class
subclass of: polypeptide_function_variant
definition: A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:56:58Z
has_exact_synonym: polypeptide loss of function variant
has_obo_namespace: sequence
id: SO:0001559

Axiom
annotated source: polypeptide_loss_of_function_variant
annotated property: definition
annotated target: A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence.
database_cross_reference: SO:ke

inactive_ligand_binding_site
type: Class
subclass of: polypeptide_loss_of_function_variant
definition: A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:58:00Z
has_exact_synonym: inactive ligand binding site
has_obo_namespace: sequence
id: SO:0001560

Axiom
annotated source: inactive_ligand_binding_site
annotated property: definition
annotated target: A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence.
database_cross_reference: SO:ke

polypeptide_partial_loss_of_function
type: Class
subclass of: polypeptide_loss_of_function_variant
definition: A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:58:32Z
has_exact_synonym: polypeptide partial loss of function
has_obo_namespace: sequence
id: SO:0001561

Axiom
annotated source: polypeptide_partial_loss_of_function
annotated property: definition
annotated target: A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence.
database_cross_reference: SO:ke

polypeptide_post_translational_processing_variant
type: Class
subclass of: polypeptide_function_variant
definition: A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T11:59:06Z
has_exact_synonym: polypeptide post translational processing variant
has_obo_namespace: sequence
id: SO:0001562

Axiom
annotated source: polypeptide_post_translational_processing_variant
annotated property: definition
annotated target: A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence.
database_cross_reference: SO:ke

copy_number_change
type: Class
subclass of: SO_0002160
definition: A sequence variant where copies of a feature (CNV) are either increased or decreased.
created by: kareneilbeck
creation date: 2010-03-22T02:27:33Z
has_exact_synonym: copy number change
has_obo_namespace: sequence
id: SO:0001563

Axiom
annotated source: copy_number_change
annotated property: definition
annotated target: A sequence variant where copies of a feature (CNV) are either increased or decreased.
database_cross_reference: SO:ke

gene_variant
type: Class
subclass of: SO_0001878
definition: A sequence variant where the structure of the gene is changed.
created by: kareneilbeck
creation date: 2010-03-22T02:28:01Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
has_exact_synonym: Jannovar:gene_variant
has_exact_synonym: VAAST:gene_variant
has_exact_synonym: gene structure variant
has_exact_synonym: snpEff:GENE
has_obo_namespace: sequence
id: SO:0001564

Axiom
annotated source: gene_variant
annotated property: definition
annotated target: A sequence variant where the structure of the gene is changed.
database_cross_reference: SO:ke

Axiom
annotated source: gene_variant
annotated property: has_exact_synonym
annotated target: Jannovar:gene_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: gene_variant
annotated property: has_exact_synonym
annotated target: VAAST:gene_variant
has_synonym_type: variant annotation term

Axiom
annotated source: gene_variant
annotated property: has_exact_synonym
annotated target: snpEff:GENE
has_synonym_type: variant annotation term

gene_fusion
type: Class
subclass of: gene_variant
subclass of: SO_0001882
definition: A sequence variant whereby a two genes have become joined.
created by: kareneilbeck
creation date: 2010-03-22T02:28:28Z
has_exact_synonym: gene fusion
has_obo_namespace: sequence
id: SO:0001565

Axiom
annotated source: gene_fusion
annotated property: definition
annotated target: A sequence variant whereby a two genes have become joined.
database_cross_reference: SO:ke

regulatory_region_variant
type: Class
subclass of: SO_0001878
definition: A sequence variant located within a regulatory region.
created by: kareneilbeck
creation date: 2010-03-22T02:28:48Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:regulatory_region_variant
has_exact_synonym: VEP:regulatory_region_variant
has_exact_synonym: regulatory region variant
has_exact_synonym: regulatory_region_
has_exact_synonym: snpEff:REGULATION
has_obo_namespace: sequence
id: SO:0001566
comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.

Axiom
annotated source: regulatory_region_variant
annotated property: definition
annotated target: A sequence variant located within a regulatory region.
database_cross_reference: SO:ke

Axiom
annotated source: regulatory_region_variant
annotated property: has_exact_synonym
annotated target: Jannovar:regulatory_region_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: regulatory_region_variant
annotated property: has_exact_synonym
annotated target: VEP:regulatory_region_variant
has_synonym_type: variant annotation term

Axiom
annotated source: regulatory_region_variant
annotated property: has_exact_synonym
annotated target: regulatory_region_
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: regulatory_region_variant
annotated property: has_exact_synonym
annotated target: snpEff:REGULATION
has_synonym_type: variant annotation term

stop_retained_variant
type: Class
subclass of: terminator_codon_variant
subclass of: SO_0001819
definition: A sequence variant where at least one base in the terminator codon is changed, but the terminator remains.
created by: kareneilbeck
creation date: 2010-04-19T05:02:30Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:stop_retained_variant
has_exact_synonym: VAAST:stop_retained
has_exact_synonym: VAAST:stop_retained_variant
has_exact_synonym: VEP:stop_retained_variant
has_exact_synonym: snpEff:NON_SYNONYMOUS_STOP
has_exact_synonym: snpEff:SYNONYMOUS_STOP
has_exact_synonym: stop retained variant
has_obo_namespace: sequence
id: SO:0001567

Axiom
annotated source: stop_retained_variant
annotated property: definition
annotated target: A sequence variant where at least one base in the terminator codon is changed, but the terminator remains.
database_cross_reference: SO:ke

Axiom
annotated source: stop_retained_variant
annotated property: has_exact_synonym
annotated target: Jannovar:stop_retained_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: stop_retained_variant
annotated property: has_exact_synonym
annotated target: VAAST:stop_retained
has_synonym_type: variant annotation term

Axiom
annotated source: stop_retained_variant
annotated property: has_exact_synonym
annotated target: VAAST:stop_retained_variant
has_synonym_type: variant annotation term

Axiom
annotated source: stop_retained_variant
annotated property: has_exact_synonym
annotated target: VEP:stop_retained_variant
has_synonym_type: variant annotation term

Axiom
annotated source: stop_retained_variant
annotated property: has_exact_synonym
annotated target: snpEff:NON_SYNONYMOUS_STOP
has_synonym_type: variant annotation term

Axiom
annotated source: stop_retained_variant
annotated property: has_exact_synonym
annotated target: snpEff:SYNONYMOUS_STOP
has_synonym_type: variant annotation term

splicing_variant
type: Class
subclass of: transcript_variant
definition: A sequence variant that changes the process of splicing.
created by: kareneilbeck
creation date: 2010-03-22T02:29:22Z
has_exact_synonym: Jannovar:splicing_variant
has_exact_synonym: splicing variant
has_obo_namespace: sequence
id: SO:0001568

Axiom
annotated source: splicing_variant
annotated property: definition
annotated target: A sequence variant that changes the process of splicing.
database_cross_reference: SO:ke

Axiom
annotated source: splicing_variant
annotated property: has_exact_synonym
annotated target: Jannovar:splicing_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

cryptic_splice_site_variant
type: Class
subclass of: splicing_variant
definition: A sequence variant causing a new (functional) splice site.
created by: kareneilbeck
creation date: 2010-03-22T02:29:41Z
has_exact_synonym: cryptic splice site activation
has_obo_namespace: sequence
id: SO:0001569

Axiom
annotated source: cryptic_splice_site_variant
annotated property: definition
annotated target: A sequence variant causing a new (functional) splice site.
database_cross_reference: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html

cryptic_splice_acceptor
type: Class
subclass of: cryptic_splice_site_variant
definition: A sequence variant whereby a new splice site is created due to the activation of a new acceptor.
created by: kareneilbeck
creation date: 2010-03-22T02:30:11Z
has_exact_synonym: cryptic splice acceptor
has_obo_namespace: sequence
id: SO:0001570

Axiom
annotated source: cryptic_splice_acceptor
annotated property: definition
annotated target: A sequence variant whereby a new splice site is created due to the activation of a new acceptor.
database_cross_reference: SO:ke

cryptic_splice_donor
type: Class
subclass of: cryptic_splice_site_variant
definition: A sequence variant whereby a new splice site is created due to the activation of a new donor.
created by: kareneilbeck
creation date: 2010-03-22T02:30:35Z
has_exact_synonym: cryptic splice donor
has_obo_namespace: sequence
id: SO:0001571

Axiom
annotated source: cryptic_splice_donor
annotated property: definition
annotated target: A sequence variant whereby a new splice site is created due to the activation of a new donor.
database_cross_reference: SO:ke

exon_loss_variant
type: Class
subclass of: splicing_variant
definition: A sequence variant whereby an exon is lost from the transcript.
created by: kareneilbeck
creation date: 2010-03-22T02:31:09Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
has_exact_synonym: Jannovar:exon_loss_variant
has_exact_synonym: exon loss
has_exact_synonym: snpEff:EXON_DELETED
has_obo_namespace: sequence
id: SO:0001572

Axiom
annotated source: exon_loss_variant
annotated property: definition
annotated target: A sequence variant whereby an exon is lost from the transcript.
database_cross_reference: SO:ke

Axiom
annotated source: exon_loss_variant
annotated property: has_exact_synonym
annotated target: Jannovar:exon_loss_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: exon_loss_variant
annotated property: has_exact_synonym
annotated target: snpEff:EXON_DELETED
has_synonym_type: variant annotation term

intron_gain_variant
type: Class
subclass of: splicing_variant
definition: A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor.
created by: kareneilbeck
creation date: 2010-03-22T02:31:25Z
has_exact_synonym: intron gain
has_exact_synonym: intron gain variant
has_obo_namespace: sequence
id: SO:0001573

Axiom
annotated source: intron_gain_variant
annotated property: definition
annotated target: A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor.
database_cross_reference: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html

splice_acceptor_variant
type: Class
subclass of: splice_site_variant
definition: A splice variant that changes the 2 base region at the 3' end of an intron.
created by: kareneilbeck
creation date: 2010-03-22T02:31:52Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:splice_acceptor_variant
has_exact_synonym: Seattleseq:splice-acceptor
has_exact_synonym: VAAST:splice_acceptor_variant
has_exact_synonym: VEP:splice_acceptor_variant
has_exact_synonym: snpEff:SPLICE_SITE_ACCEPTOR
has_exact_synonym: splice acceptor variant
has_obo_namespace: sequence
id: SO:0001574

Axiom
annotated source: splice_acceptor_variant
annotated property: definition
annotated target: A splice variant that changes the 2 base region at the 3' end of an intron.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: splice_acceptor_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: splice_acceptor_variant
annotated property: has_exact_synonym
annotated target: Jannovar:splice_acceptor_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: splice_acceptor_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:splice-acceptor
has_synonym_type: variant annotation term

Axiom
annotated source: splice_acceptor_variant
annotated property: has_exact_synonym
annotated target: VAAST:splice_acceptor_variant
has_synonym_type: variant annotation term

Axiom
annotated source: splice_acceptor_variant
annotated property: has_exact_synonym
annotated target: VEP:splice_acceptor_variant
has_synonym_type: variant annotation term

Axiom
annotated source: splice_acceptor_variant
annotated property: has_exact_synonym
annotated target: snpEff:SPLICE_SITE_ACCEPTOR
has_synonym_type: variant annotation term

splice_donor_variant
type: Class
subclass of: splice_site_variant
definition: A splice variant that changes the 2 base pair region at the 5' end of an intron.
created by: kareneilbeck
creation date: 2010-03-22T02:32:10Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:splice_donor_variant
has_exact_synonym: Seattleseq:splice-donor
has_exact_synonym: VAAST:splice_donor_variant
has_exact_synonym: VEP:splice_donor_variant
has_exact_synonym: snpEff:SPLICE_SITE_DONOR
has_exact_synonym: splice donor variant
has_obo_namespace: sequence
id: SO:0001575

Axiom
annotated source: splice_donor_variant
annotated property: definition
annotated target: A splice variant that changes the 2 base pair region at the 5' end of an intron.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: splice_donor_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: splice_donor_variant
annotated property: has_exact_synonym
annotated target: Jannovar:splice_donor_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: splice_donor_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:splice-donor
has_synonym_type: variant annotation term

Axiom
annotated source: splice_donor_variant
annotated property: has_exact_synonym
annotated target: VAAST:splice_donor_variant
has_synonym_type: variant annotation term

Axiom
annotated source: splice_donor_variant
annotated property: has_exact_synonym
annotated target: VEP:splice_donor_variant
has_synonym_type: variant annotation term

Axiom
annotated source: splice_donor_variant
annotated property: has_exact_synonym
annotated target: snpEff:SPLICE_SITE_DONOR
has_synonym_type: variant annotation term

transcript_variant
type: Class
subclass of: gene_variant
definition: A sequence variant that changes the structure of the transcript.
created by: kareneilbeck
creation date: 2010-03-22T02:32:41Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
has_exact_synonym: Jannovar:transcript_variant
has_exact_synonym: VAAST:transcript_variant
has_exact_synonym: snpEff:TRANSCRIPT
has_exact_synonym: transcript variant
has_obo_namespace: sequence
id: SO:0001576

Axiom
annotated source: transcript_variant
annotated property: definition
annotated target: A sequence variant that changes the structure of the transcript.
database_cross_reference: SO:ke

Axiom
annotated source: transcript_variant
annotated property: has_exact_synonym
annotated target: Jannovar:transcript_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: transcript_variant
annotated property: has_exact_synonym
annotated target: VAAST:transcript_variant
has_synonym_type: variant annotation term

Axiom
annotated source: transcript_variant
annotated property: has_exact_synonym
annotated target: snpEff:TRANSCRIPT
has_synonym_type: variant annotation term

complex_transcript_variant
type: Class
subclass of: transcript_variant
definition: A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
created by: kareneilbeck
creation date: 2010-03-22T02:33:03Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
has_exact_synonym: complex change in transcript
has_exact_synonym: complex transcript variant
has_exact_synonym: complex_indel
has_obo_namespace: sequence
has_related_synonym: Seattleseq:codingComplex
has_related_synonym: Seattleseq:codingComplex-near-splice
id: SO:0001577
comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.

Axiom
annotated source: complex_transcript_variant
annotated property: definition
annotated target: A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
database_cross_reference: http://ensembl.org/info/docs/variation/index.html

Seattleseq
type: Axiom
annotated source: complex_transcript_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: complex_transcript_variant
annotated property: has_exact_synonym
annotated target: complex_indel
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: complex_transcript_variant
annotated property: has_related_synonym
annotated target: Seattleseq:codingComplex
has_synonym_type: variant annotation term

Axiom
annotated source: complex_transcript_variant
annotated property: has_related_synonym
annotated target: Seattleseq:codingComplex-near-splice
has_synonym_type: variant annotation term

stop_lost
type: Class
subclass of: terminator_codon_variant
subclass of: SO_0001907
subclass of: SO_0001992
definition: A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript.
created by: kareneilbeck
creation date: 2010-03-23T03:46:42Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http://vat.gersteinlab.org/formats.php
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: ANNOVAR:stoploss
has_exact_synonym: Jannovar:stop_lost
has_exact_synonym: Seattleseq:stop-lost
has_exact_synonym: VAAST:stop_lost
has_exact_synonym: VAT:removedStop
has_exact_synonym: VEP:stop_lost
has_exact_synonym: snpEff:STOP_LOST
has_exact_synonym: stop codon lost
has_exact_synonym: stop lost
has_obo_namespace: sequence
has_related_synonym: Seattleseq:stop-lost-near-splice
id: SO:0001578
comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.

Axiom
annotated source: stop_lost
annotated property: definition
annotated target: A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: stop_lost
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

VAT
type: Axiom
annotated source: stop_lost
annotated property: database_cross_reference
annotated target: http://vat.gersteinlab.org/formats.php

Axiom
annotated source: stop_lost
annotated property: has_exact_synonym
annotated target: ANNOVAR:stoploss
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

Axiom
annotated source: stop_lost
annotated property: has_exact_synonym
annotated target: Jannovar:stop_lost
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: stop_lost
annotated property: has_exact_synonym
annotated target: Seattleseq:stop-lost
has_synonym_type: variant annotation term

Axiom
annotated source: stop_lost
annotated property: has_exact_synonym
annotated target: VAAST:stop_lost
has_synonym_type: variant annotation term

Axiom
annotated source: stop_lost
annotated property: has_exact_synonym
annotated target: VAT:removedStop
has_synonym_type: variant annotation term

Axiom
annotated source: stop_lost
annotated property: has_exact_synonym
annotated target: VEP:stop_lost
has_synonym_type: variant annotation term

Axiom
annotated source: stop_lost
annotated property: has_exact_synonym
annotated target: snpEff:STOP_LOST
has_synonym_type: variant annotation term

Axiom
annotated source: stop_lost
annotated property: has_exact_synonym
annotated target: stop lost
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: stop_lost
annotated property: has_related_synonym
annotated target: Seattleseq:stop-lost-near-splice
has_synonym_type: variant annotation term

transcript_sequence_variant
type: Class
has_exact_synonym: transcript sequence variant
has_obo_namespace: sequence
id: SO:0001579
deprecated: true

coding_sequence_variant
type: Class
subclass of: SO_0001791
subclass of: SO_0001968
definition: A sequence variant that changes the coding sequence.
created by: kareneilbeck
creation date: 2010-03-22T02:34:36Z
has_alternative_id: SO:0001581
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:coding_sequence_variant
has_exact_synonym: Seattleseq:coding
has_exact_synonym: VAAST:coding_sequence_variant
has_exact_synonym: VEP:coding_sequence_variant
has_exact_synonym: coding sequence variant
has_exact_synonym: coding variant
has_exact_synonym: codon variant
has_exact_synonym: codon_variant
has_exact_synonym: snpEff:CDS
has_obo_namespace: sequence
has_related_synonym: snpEff:CODON_CHANGE
id: SO:0001580

Axiom
annotated source: coding_sequence_variant
annotated property: definition
annotated target: A sequence variant that changes the coding sequence.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: coding_sequence_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: coding_sequence_variant
annotated property: has_exact_synonym
annotated target: Jannovar:coding_sequence_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: coding_sequence_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:coding
has_synonym_type: variant annotation term

Axiom
annotated source: coding_sequence_variant
annotated property: has_exact_synonym
annotated target: VAAST:coding_sequence_variant
has_synonym_type: variant annotation term

Axiom
annotated source: coding_sequence_variant
annotated property: has_exact_synonym
annotated target: VEP:coding_sequence_variant
has_synonym_type: variant annotation term

Axiom
annotated source: coding_sequence_variant
annotated property: has_exact_synonym
annotated target: snpEff:CDS
has_synonym_type: variant annotation term

Axiom
annotated source: coding_sequence_variant
annotated property: has_related_synonym
annotated target: snpEff:CODON_CHANGE
has_synonym_type: variant annotation term

SO_0001581
type: Class
IAO_0000231: IAO_0000227
term replaced by: coding_sequence_variant
deprecated: true

initiator_codon_variant
type: Class
subclass of: coding_sequence_variant
definition: A codon variant that changes at least one base of the first codon of a transcript.
created by: kareneilbeck
creation date: 2010-03-22T02:35:18Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http://vat.gersteinlab.org/formats.php
database_cross_reference: loinc:LA6695-6
has_exact_synonym: Jannovar:initiator_codon_variant
has_exact_synonym: VAT:startOverlap
has_exact_synonym: initiatior codon variant
has_exact_synonym: initiator codon change
has_obo_namespace: sequence
has_related_synonym: snpEff:NON_SYNONYMOUS_START
id: SO:0001582
comment: This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called.

Axiom
annotated source: initiator_codon_variant
annotated property: definition
annotated target: A codon variant that changes at least one base of the first codon of a transcript.
database_cross_reference: SO:ke

VAT
type: Axiom
annotated source: initiator_codon_variant
annotated property: database_cross_reference
annotated target: http://vat.gersteinlab.org/formats.php

Initiating Methionine
type: Axiom
annotated source: initiator_codon_variant
annotated property: database_cross_reference
annotated target: loinc:LA6695-6

Axiom
annotated source: initiator_codon_variant
annotated property: has_exact_synonym
annotated target: Jannovar:initiator_codon_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: initiator_codon_variant
annotated property: has_exact_synonym
annotated target: VAT:startOverlap
has_synonym_type: variant annotation term

Axiom
annotated source: initiator_codon_variant
annotated property: has_related_synonym
annotated target: snpEff:NON_SYNONYMOUS_START
has_synonym_type: variant annotation term

missense_variant
type: Class
subclass of: SO_0001992
definition: A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.
created by: kareneilbeck
creation date: 2010-03-22T02:35:49Z
has_alternative_id: SO:0001584
has_alternative_id: SO:0001783
database_cross_reference: http://en.wikipedia.org/wiki/Missense_mutation
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http://vat.gersteinlab.org/formats.php
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
database_cross_reference: loinc:LA6698-0
has_exact_synonym: Jannovar:missense_variant
has_exact_synonym: Seattleseq:missense
has_exact_synonym: VAAST:missense_variant
has_exact_synonym: VAT:nonsynonymous
has_exact_synonym: VEP:missense_variant
has_exact_synonym: missense
has_exact_synonym: missense codon
has_exact_synonym: snpEff:NON_SYNONYMOUS_CODING
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:nonsynonymous SNV
has_related_synonym: Seattleseq:missense-near-splice
has_related_synonym: VAAST:non_synonymous_codon
id: SO:0001583
comment: EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.

Axiom
annotated source: missense_variant
annotated property: definition
annotated target: A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.
database_cross_reference: EBI:fc
database_cross_reference: EBI:gr
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: missense_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

VAT
type: Axiom
annotated source: missense_variant
annotated property: database_cross_reference
annotated target: http://vat.gersteinlab.org/formats.php

Missense
type: Axiom
annotated source: missense_variant
annotated property: database_cross_reference
annotated target: loinc:LA6698-0

Axiom
annotated source: missense_variant
annotated property: has_exact_synonym
annotated target: Jannovar:missense_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: missense_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:missense
has_synonym_type: variant annotation term

Axiom
annotated source: missense_variant
annotated property: has_exact_synonym
annotated target: VAAST:missense_variant
has_synonym_type: variant annotation term

Axiom
annotated source: missense_variant
annotated property: has_exact_synonym
annotated target: VAT:nonsynonymous
has_synonym_type: variant annotation term

Axiom
annotated source: missense_variant
annotated property: has_exact_synonym
annotated target: VEP:missense_variant
has_synonym_type: variant annotation term

Axiom
annotated source: missense_variant
annotated property: has_exact_synonym
annotated target: missense
database_cross_reference: ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd

Axiom
annotated source: missense_variant
annotated property: has_exact_synonym
annotated target: snpEff:NON_SYNONYMOUS_CODING
has_synonym_type: variant annotation term

Axiom
annotated source: missense_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:nonsynonymous SNV
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

Axiom
annotated source: missense_variant
annotated property: has_related_synonym
annotated target: Seattleseq:missense-near-splice
has_synonym_type: variant annotation term

Axiom
annotated source: missense_variant
annotated property: has_related_synonym
annotated target: VAAST:non_synonymous_codon
has_synonym_type: variant annotation term

SO_0001584
type: Class
IAO_0000231: IAO_0000227
term replaced by: missense_variant
deprecated: true

conservative_missense_variant
type: Class
subclass of: missense_variant
definition: A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious.
created by: kareneilbeck
creation date: 2010-03-22T02:36:40Z
has_exact_synonym: conservative missense codon
has_exact_synonym: conservative missense variant
has_obo_namespace: sequence
has_related_synonym: neutral missense codon
has_related_synonym: quiet missense codon
id: SO:0001585

Axiom
annotated source: conservative_missense_variant
annotated property: definition
annotated target: A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious.
database_cross_reference: SO:ke

non_conservative_missense_variant
type: Class
subclass of: missense_variant
definition: A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties.
created by: kareneilbeck
creation date: 2010-03-22T02:37:16Z
has_exact_synonym: non conservative missense codon
has_exact_synonym: non conservative missense variant
has_obo_namespace: sequence
id: SO:0001586

Axiom
annotated source: non_conservative_missense_variant
annotated property: definition
annotated target: A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties.
database_cross_reference: SO:ke

stop_gained
type: Class
subclass of: SO_0001906
subclass of: SO_0001992
definition: A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide.
created by: kareneilbeck
creation date: 2010-03-22T02:37:52Z
database_cross_reference: http://ensembl.org/info/genome/variation/prediction/predicted_data.html
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http://vat.gersteinlab.org/formats.php
database_cross_reference: loinc:LA6699-8
has_exact_synonym: ANNOVAR:stopgain
has_exact_synonym: Jannovar:stop_gained
has_exact_synonym: Seattleseq:stop-gained
has_exact_synonym: VAAST:stop_gained
has_exact_synonym: VAT:prematureStop
has_exact_synonym: VEP:stop_gained
has_exact_synonym: nonsense
has_exact_synonym: nonsense codon
has_exact_synonym: snpEff:STOP_GAINED
has_exact_synonym: stop gained
has_obo_namespace: sequence
has_related_synonym: Seattleseq:stop-gained-near-splice
has_related_synonym: stop codon gained
id: SO:0001587
comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).

Axiom
annotated source: stop_gained
annotated property: definition
annotated target: A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: stop_gained
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

VAT
type: Axiom
annotated source: stop_gained
annotated property: database_cross_reference
annotated target: http://vat.gersteinlab.org/formats.php

Nonsense
type: Axiom
annotated source: stop_gained
annotated property: database_cross_reference
annotated target: loinc:LA6699-8

Axiom
annotated source: stop_gained
annotated property: has_exact_synonym
annotated target: ANNOVAR:stopgain
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

Axiom
annotated source: stop_gained
annotated property: has_exact_synonym
annotated target: Jannovar:stop_gained
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: stop_gained
annotated property: has_exact_synonym
annotated target: Seattleseq:stop-gained
has_synonym_type: variant annotation term

Axiom
annotated source: stop_gained
annotated property: has_exact_synonym
annotated target: VAAST:stop_gained
has_synonym_type: variant annotation term

Axiom
annotated source: stop_gained
annotated property: has_exact_synonym
annotated target: VAT:prematureStop
has_synonym_type: variant annotation term

Axiom
annotated source: stop_gained
annotated property: has_exact_synonym
annotated target: VEP:stop_gained
has_synonym_type: variant annotation term

Axiom
annotated source: stop_gained
annotated property: has_exact_synonym
annotated target: nonsense
database_cross_reference: ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
has_synonym_type: dbsnp variant terms

Axiom
annotated source: stop_gained
annotated property: has_exact_synonym
annotated target: snpEff:STOP_GAINED
has_synonym_type: variant annotation term

Axiom
annotated source: stop_gained
annotated property: has_exact_synonym
annotated target: stop gained
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: stop_gained
annotated property: has_related_synonym
annotated target: Seattleseq:stop-gained-near-splice
has_synonym_type: variant annotation term

SO_0001588
type: Class
IAO_0000231: IAO_0000227
term replaced by: SO_0001819
deprecated: true

frameshift_variant
type: Class
subclass of: SO_0001818
definition: A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
created by: kareneilbeck
creation date: 2010-03-22T02:40:19Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http://vat.gersteinlab.org/formats.php
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
database_cross_reference: loinc:LA6694-9
has_exact_synonym: Jannovar:frameshift_variant
has_exact_synonym: Seattleseq:frameshift
has_exact_synonym: VAAST:frameshift_variant
has_exact_synonym: VEP:frameshift_variant
has_exact_synonym: frameshift variant
has_exact_synonym: frameshift_
has_exact_synonym: frameshift_coding
has_exact_synonym: snpEff:FRAME_SHIFT
has_narrow_synonym: VAT:deletionFS
has_narrow_synonym: VAT:insertionFS
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:frameshift block substitution
has_related_synonym: ANNOVAR:frameshift substitution
has_related_synonym: Seattleseq:frameshift-near-splice
id: SO:0001589
comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.

Axiom
annotated source: frameshift_variant
annotated property: definition
annotated target: A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: frameshift_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

VAT
type: Axiom
annotated source: frameshift_variant
annotated property: database_cross_reference
annotated target: http://vat.gersteinlab.org/formats.php

Frameshift
type: Axiom
annotated source: frameshift_variant
annotated property: database_cross_reference
annotated target: loinc:LA6694-9

Axiom
annotated source: frameshift_variant
annotated property: has_exact_synonym
annotated target: Jannovar:frameshift_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: frameshift_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:frameshift
has_synonym_type: variant annotation term

Axiom
annotated source: frameshift_variant
annotated property: has_exact_synonym
annotated target: VAAST:frameshift_variant
has_synonym_type: variant annotation term

Axiom
annotated source: frameshift_variant
annotated property: has_exact_synonym
annotated target: VEP:frameshift_variant
has_synonym_type: variant annotation term

Axiom
annotated source: frameshift_variant
annotated property: has_exact_synonym
annotated target: frameshift_
database_cross_reference: ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
has_synonym_type: dbsnp variant terms

Axiom
annotated source: frameshift_variant
annotated property: has_exact_synonym
annotated target: frameshift_coding
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: frameshift_variant
annotated property: has_exact_synonym
annotated target: snpEff:FRAME_SHIFT
has_synonym_type: variant annotation term

Axiom
annotated source: frameshift_variant
annotated property: has_narrow_synonym
annotated target: VAT:deletionFS
has_synonym_type: variant annotation term

Axiom
annotated source: frameshift_variant
annotated property: has_narrow_synonym
annotated target: VAT:insertionFS
has_synonym_type: variant annotation term

Axiom
annotated source: frameshift_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:frameshift block substitution
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

Axiom
annotated source: frameshift_variant
annotated property: has_related_synonym
annotated target: Seattleseq:frameshift-near-splice
has_synonym_type: variant annotation term

terminator_codon_variant
type: Class
subclass of: coding_sequence_variant
definition: A sequence variant whereby at least one of the bases in the terminator codon is changed.
created by: kareneilbeck
creation date: 2010-03-22T02:40:37Z
has_alternative_id: SO:0001625
database_cross_reference: http://vat.gersteinlab.org/formats.php
database_cross_reference: loinc:LA6700-2
has_exact_synonym: VAT:endOverlap
has_exact_synonym: terminal codon variant
has_exact_synonym: terminal_codon_variant
has_exact_synonym: terminator codon variant
has_obo_namespace: sequence
id: SO:0001590
comment: The terminal codon may be the terminator, or in an incomplete transcript the last available codon.

Axiom
annotated source: terminator_codon_variant
annotated property: definition
annotated target: A sequence variant whereby at least one of the bases in the terminator codon is changed.
database_cross_reference: SO:ke

VAT
type: Axiom
annotated source: terminator_codon_variant
annotated property: database_cross_reference
annotated target: http://vat.gersteinlab.org/formats.php

Stop Codon Mutation
type: Axiom
annotated source: terminator_codon_variant
annotated property: database_cross_reference
annotated target: loinc:LA6700-2

Axiom
annotated source: terminator_codon_variant
annotated property: has_exact_synonym
annotated target: VAT:endOverlap
has_synonym_type: variant annotation term

frame_restoring_variant
type: Class
subclass of: frameshift_variant
definition: A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame.
created by: kareneilbeck
creation date: 2010-03-22T02:41:09Z
has_exact_synonym: frame restoring variant
has_obo_namespace: sequence
id: SO:0001591

Axiom
annotated source: frame_restoring_variant
annotated property: definition
annotated target: A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame.
database_cross_reference: SO:ke

minus_1_frameshift_variant
type: Class
subclass of: frameshift_variant
definition: A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead.
created by: kareneilbeck
creation date: 2010-03-22T02:41:30Z
has_exact_synonym: -1 frameshift variant
has_exact_synonym: minus 1 frameshift variant
has_obo_namespace: sequence
id: SO:0001592

Axiom
annotated source: minus_1_frameshift_variant
annotated property: definition
annotated target: A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead.
database_cross_reference: http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535

minus_2_frameshift_variant
type: Class
subclass of: frameshift_variant
definition: A sequence variant which causes a disruption of the translational reading frame, by shifting two bases forward.
created by: kareneilbeck
creation date: 2010-03-22T02:41:52Z
has_exact_synonym: -2 frameshift variant
has_exact_synonym: minus 2 frameshift variant
has_obo_namespace: sequence
id: SO:0001593

plus_1_frameshift_variant
type: Class
subclass of: frameshift_variant
definition: A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward.
created by: kareneilbeck
creation date: 2010-03-22T02:42:06Z
has_exact_synonym: +1 frameshift variant
has_exact_synonym: plus 1 frameshift variant
has_obo_namespace: sequence
id: SO:0001594

Axiom
annotated source: plus_1_frameshift_variant
annotated property: definition
annotated target: A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward.
database_cross_reference: http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535

plus_2_frameshift_variant
type: Class
subclass of: frameshift_variant
definition: A sequence variant which causes a disruption of the translational reading frame, by shifting two bases backward.
created by: kareneilbeck
creation date: 2010-03-22T02:42:23Z
has_exact_synonym: +2 frameshift variant
has_exact_synonym: plus 2 frameshift variant
has_obo_namespace: sequence
id: SO:0001595

transcript_secondary_structure_variant
type: Class
subclass of: transcript_variant
definition: A sequence variant within a transcript that changes the secondary structure of the RNA product.
created by: kareneilbeck
creation date: 2010-03-22T02:43:18Z
has_exact_synonym: transcript secondary structure variant
has_obo_namespace: sequence
id: SO:0001596

Axiom
annotated source: transcript_secondary_structure_variant
annotated property: definition
annotated target: A sequence variant within a transcript that changes the secondary structure of the RNA product.
database_cross_reference: SO:ke

compensatory_transcript_secondary_structure_variant
type: Class
subclass of: transcript_secondary_structure_variant
definition: A secondary structure variant that compensate for the change made by a previous variant.
created by: kareneilbeck
creation date: 2010-03-22T02:43:54Z
has_exact_synonym: compensatory transcript secondary structure variant
has_obo_namespace: sequence
id: SO:0001597

Axiom
annotated source: compensatory_transcript_secondary_structure_variant
annotated property: definition
annotated target: A secondary structure variant that compensate for the change made by a previous variant.
database_cross_reference: SO:ke

translational_product_structure_variant
type: Class
subclass of: gene_variant
definition: A sequence variant within the transcript that changes the structure of the translational product.
created by: kareneilbeck
creation date: 2010-03-22T02:44:17Z
has_exact_synonym: translational product structure variant
has_obo_namespace: sequence
id: SO:0001598

Axiom
annotated source: translational_product_structure_variant
annotated property: definition
annotated target: A sequence variant within the transcript that changes the structure of the translational product.
database_cross_reference: SO:ke

3D_polypeptide_structure_variant
type: Class
subclass of: translational_product_function_variant
definition: A sequence variant that changes the resulting polypeptide structure.
created by: kareneilbeck
creation date: 2010-03-22T02:44:46Z
has_exact_synonym: 3D polypeptide structure variant
has_obo_namespace: sequence
id: SO:0001599

Axiom
annotated source: 3D_polypeptide_structure_variant
annotated property: definition
annotated target: A sequence variant that changes the resulting polypeptide structure.
database_cross_reference: SO:ke

complex_3D_structural_variant
type: Class
subclass of: 3D_polypeptide_structure_variant
definition: A sequence variant that changes the resulting polypeptide structure.
created by: kareneilbeck
creation date: 2010-03-22T02:45:13Z
has_exact_synonym: complex 3D structural variant
has_obo_namespace: sequence
id: SO:0001600

Axiom
annotated source: complex_3D_structural_variant
annotated property: definition
annotated target: A sequence variant that changes the resulting polypeptide structure.
database_cross_reference: SO:ke

conformational_change_variant
type: Class
subclass of: 3D_polypeptide_structure_variant
definition: A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence.
created by: kareneilbeck
creation date: 2010-03-22T02:45:48Z
has_exact_synonym: conformational change variant
has_obo_namespace: sequence
id: SO:0001601

Axiom
annotated source: conformational_change_variant
annotated property: definition
annotated target: A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence.
database_cross_reference: SO:ke

complex_change_of_translational_product_variant
type: Class
subclass of: translational_product_function_variant
definition: A variant that changes the translational product with respect to the reference.
created by: kareneilbeck
creation date: 2010-03-22T02:46:54Z
has_exact_synonym: complex change of translational product variant
has_obo_namespace: sequence
id: SO:0001602

polypeptide_sequence_variant
type: Class
subclass of: translational_product_structure_variant
definition: A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence.
created by: kareneilbeck
creation date: 2010-03-22T02:47:13Z
has_exact_synonym: polypeptide sequence variant
has_obo_namespace: sequence
id: SO:0001603

Axiom
annotated source: polypeptide_sequence_variant
annotated property: definition
annotated target: A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence.
database_cross_reference: SO:ke

amino_acid_deletion
type: Class
subclass of: polypeptide_sequence_variant
definition: A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide.
created by: kareneilbeck
creation date: 2010-03-22T02:47:36Z
has_exact_synonym: amino acid deletion
has_obo_namespace: sequence
id: SO:0001604

Axiom
annotated source: amino_acid_deletion
annotated property: definition
annotated target: A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide.
database_cross_reference: SO:ke

amino_acid_insertion
type: Class
subclass of: polypeptide_sequence_variant
definition: A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide.
created by: kareneilbeck
creation date: 2010-03-22T02:47:56Z
has_exact_synonym: amino acid insertion
has_obo_namespace: sequence
id: SO:0001605

Axiom
annotated source: amino_acid_insertion
annotated property: definition
annotated target: A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide.
database_cross_reference: SO:ke

amino_acid_substitution
type: Class
subclass of: polypeptide_sequence_variant
definition: A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide.
created by: kareneilbeck
creation date: 2010-03-22T02:48:17Z
has_exact_synonym: VAAST:amino_acid_substitution
has_exact_synonym: amino acid substitution
has_obo_namespace: sequence
id: SO:0001606

Axiom
annotated source: amino_acid_substitution
annotated property: definition
annotated target: A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide.
database_cross_reference: SO:ke

Axiom
annotated source: amino_acid_substitution
annotated property: has_exact_synonym
annotated target: VAAST:amino_acid_substitution
has_synonym_type: variant annotation term

conservative_amino_acid_substitution
type: Class
subclass of: amino_acid_substitution
definition: A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide.
created by: kareneilbeck
creation date: 2010-03-22T02:48:57Z
has_exact_synonym: conservative amino acid substitution
has_obo_namespace: sequence
id: SO:0001607

Axiom
annotated source: conservative_amino_acid_substitution
annotated property: definition
annotated target: A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide.
database_cross_reference: SO:ke

non_conservative_amino_acid_substitution
type: Class
subclass of: amino_acid_substitution
definition: A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide.
created by: kareneilbeck
creation date: 2010-03-22T02:49:23Z
has_exact_synonym: non conservative amino acid substitution
has_obo_namespace: sequence
id: SO:0001608

Axiom
annotated source: non_conservative_amino_acid_substitution
annotated property: definition
annotated target: A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide.
database_cross_reference: SO:ke

elongated_polypeptide
type: Class
subclass of: polypeptide_sequence_variant
definition: An elongation of a polypeptide sequence deriving from a sequence variant extending the CDS.
created by: kareneilbeck
creation date: 2010-03-22T02:49:52Z
has_exact_synonym: elongated polypeptide
has_obo_namespace: sequence
id: SO:0001609

Axiom
annotated source: elongated_polypeptide
annotated property: definition
annotated target: An elongation of a polypeptide sequence deriving from a sequence variant extending the CDS.
database_cross_reference: SO:ke

elongated_polypeptide_C_terminal
type: Class
subclass of: elongated_polypeptide
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002229
definition: An elongation of a polypeptide sequence at the C terminus deriving from a sequence variant extending the CDS.
created by: kareneilbeck
creation date: 2010-03-22T02:50:20Z
has_exact_synonym: elongated polypeptide C terminal
has_obo_namespace: sequence
id: SO:0001610

Axiom
annotated source: elongated_polypeptide_C_terminal
annotated property: definition
annotated target: An elongation of a polypeptide sequence at the C terminus deriving from a sequence variant extending the CDS.
database_cross_reference: SO:ke

elongated_polypeptide_N_terminal
type: Class
subclass of: elongated_polypeptide
subclass of: Restriction
  on property: derives_from
  some values from: SO_0002228
definition: An elongation of a polypeptide sequence at the N terminus deriving from a sequence variant extending the CDS.
created by: kareneilbeck
creation date: 2010-03-22T02:50:31Z
has_exact_synonym: elongated polypeptide N terminal
has_obo_namespace: sequence
id: SO:0001611

Axiom
annotated source: elongated_polypeptide_N_terminal
annotated property: definition
annotated target: An elongation of a polypeptide sequence at the N terminus deriving from a sequence variant extending the CDS.
database_cross_reference: SO:ke

elongated_in_frame_polypeptide_C_terminal
type: Class
subclass of: elongated_polypeptide_C_terminal
definition: A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus.
created by: kareneilbeck
creation date: 2010-03-22T02:51:05Z
has_exact_synonym: elongated in frame polypeptide C terminal
has_obo_namespace: sequence
id: SO:0001612

Axiom
annotated source: elongated_in_frame_polypeptide_C_terminal
annotated property: definition
annotated target: A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus.
database_cross_reference: SO:ke

elongated_out_of_frame_polypeptide_C_terminal
type: Class
subclass of: elongated_polypeptide_C_terminal
definition: A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus.
created by: kareneilbeck
creation date: 2010-03-22T02:51:20Z
has_exact_synonym: elongated polypeptide out of frame C terminal
has_obo_namespace: sequence
id: SO:0001613

Axiom
annotated source: elongated_out_of_frame_polypeptide_C_terminal
annotated property: definition
annotated target: A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus.
database_cross_reference: SO:ke

elongated_in_frame_polypeptide_N_terminal_elongation
type: Class
subclass of: elongated_polypeptide_N_terminal
definition: A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus.
created by: kareneilbeck
creation date: 2010-03-22T02:51:49Z
has_exact_synonym: elongated in frame polypeptide N terminal
has_obo_namespace: sequence
id: SO:0001614

Axiom
annotated source: elongated_in_frame_polypeptide_N_terminal_elongation
annotated property: definition
annotated target: A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus.
database_cross_reference: SO:ke

elongated_out_of_frame_polypeptide_N_terminal
type: Class
subclass of: elongated_polypeptide_N_terminal
definition: A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus.
created by: kareneilbeck
creation date: 2010-03-22T02:52:05Z
has_exact_synonym: elongated out of frame N terminal
has_obo_namespace: sequence
id: SO:0001615

Axiom
annotated source: elongated_out_of_frame_polypeptide_N_terminal
annotated property: definition
annotated target: A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus.
database_cross_reference: SO:ke

polypeptide_fusion
type: Class
subclass of: polypeptide_sequence_variant
definition: A sequence variant that causes a fusion of two polypeptide sequences.
created by: kareneilbeck
creation date: 2010-03-22T02:52:43Z
has_exact_synonym: polypeptide fusion
has_obo_namespace: sequence
id: SO:0001616

Axiom
annotated source: polypeptide_fusion
annotated property: definition
annotated target: A sequence variant that causes a fusion of two polypeptide sequences.
database_cross_reference: SO:ke

polypeptide_truncation
type: Class
subclass of: polypeptide_sequence_variant
definition: A sequence variant of the CD that causes a truncation of the resulting polypeptide.
created by: kareneilbeck
creation date: 2010-03-22T02:53:07Z
has_exact_synonym: polypeptide truncation
has_obo_namespace: sequence
id: SO:0001617

Axiom
annotated source: polypeptide_truncation
annotated property: definition
annotated target: A sequence variant of the CD that causes a truncation of the resulting polypeptide.
database_cross_reference: SO:ke

inactive_catalytic_site
type: Class
subclass of: inactive_ligand_binding_site
definition: A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence.
created by: kareneilbeck
creation date: 2010-03-22T03:06:14Z
has_exact_synonym: inactive catalytic site
has_obo_namespace: sequence
id: SO:0001618

Axiom
annotated source: inactive_catalytic_site
annotated property: definition
annotated target: A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence.
database_cross_reference: SO:ke

non_coding_transcript_variant
type: Class
subclass of: transcript_variant
definition: A transcript variant of a non coding RNA gene.
created by: kareneilbeck
creation date: 2010-03-23T11:16:23Z
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:non_coding_transcript_variant
has_exact_synonym: VEP:non_coding_transcript_variant
has_exact_synonym: nc transcript variant
has_exact_synonym: non coding transcript variant
has_exact_synonym: within_non_coding_gene
has_narrow_synonym: ANNOVAR:ncRNA
has_obo_namespace: sequence
id: SO:0001619
comment: Within non-coding gene - Located within a gene that does not code for a protein.

Axiom
annotated source: non_coding_transcript_variant
annotated property: definition
annotated target: A transcript variant of a non coding RNA gene.
database_cross_reference: SO:ke

Axiom
annotated source: non_coding_transcript_variant
annotated property: has_exact_synonym
annotated target: Jannovar:non_coding_transcript_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: non_coding_transcript_variant
annotated property: has_exact_synonym
annotated target: VEP:non_coding_transcript_variant
has_synonym_type: variant annotation term

Axiom
annotated source: non_coding_transcript_variant
annotated property: has_exact_synonym
annotated target: within_non_coding_gene
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: dbsnp variant terms

Axiom
annotated source: non_coding_transcript_variant
annotated property: has_narrow_synonym
annotated target: ANNOVAR:ncRNA
database_cross_reference: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/
has_synonym_type: variant annotation term

mature_miRNA_variant
type: Class
subclass of: non_coding_transcript_variant
definition: A transcript variant located with the sequence of the mature miRNA.
created by: kareneilbeck
creation date: 2010-03-23T11:16:58Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
has_exact_synonym: VEP:mature_miRNA_variant
has_exact_synonym: mature miRNA variant
has_exact_synonym: snpEff:MICRO_RNA
has_exact_synonym: within_mature_miRNA
has_obo_namespace: sequence
id: SO:0001620
comment: EBI term: Within mature miRNA - Located within a microRNA.

Axiom
annotated source: mature_miRNA_variant
annotated property: definition
annotated target: A transcript variant located with the sequence of the mature miRNA.
database_cross_reference: SO:ke

Axiom
annotated source: mature_miRNA_variant
annotated property: has_exact_synonym
annotated target: VEP:mature_miRNA_variant
has_synonym_type: variant annotation term

Axiom
annotated source: mature_miRNA_variant
annotated property: has_exact_synonym
annotated target: snpEff:MICRO_RNA
has_synonym_type: variant annotation term

Axiom
annotated source: mature_miRNA_variant
annotated property: has_exact_synonym
annotated target: within_mature_miRNA
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

NMD_transcript_variant
type: Class
subclass of: transcript_variant
definition: A variant in a transcript that is the target of nonsense-mediated mRNA decay.
created by: kareneilbeck
creation date: 2010-03-23T11:20:40Z
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: NMD transcript variant
has_exact_synonym: NMD_transcript
has_exact_synonym: Nonsense mediated decay transcript variant
has_exact_synonym: VEP:NMD_transcript_variant
has_obo_namespace: sequence
id: SO:0001621

Axiom
annotated source: NMD_transcript_variant
annotated property: definition
annotated target: A variant in a transcript that is the target of nonsense-mediated mRNA decay.
database_cross_reference: SO:ke

Axiom
annotated source: NMD_transcript_variant
annotated property: has_exact_synonym
annotated target: NMD_transcript
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: NMD_transcript_variant
annotated property: has_exact_synonym
annotated target: VEP:NMD_transcript_variant
has_synonym_type: variant annotation term

UTR_variant
type: Class
subclass of: SO_0001791
subclass of: SO_0001968
definition: A transcript variant that is located within the UTR.
created by: kareneilbeck
creation date: 2010-03-23T11:22:58Z
has_exact_synonym: UTR variant
has_exact_synonym: UTR_
has_obo_namespace: sequence
id: SO:0001622

Axiom
annotated source: UTR_variant
annotated property: definition
annotated target: A transcript variant that is located within the UTR.
database_cross_reference: SO:ke

Axiom
annotated source: UTR_variant
annotated property: has_exact_synonym
annotated target: UTR_
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

5_prime_UTR_variant
type: Class
subclass of: UTR_variant
definition: A UTR variant of the 5' UTR.
created by: kareneilbeck
creation date: 2010-03-23T11:23:29Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: 5'UTR variant
has_exact_synonym: 5PRIME_UTR
has_exact_synonym: Jannovar:5_prime_utr_variant
has_exact_synonym: Seattleseq:5-prime-UTR
has_exact_synonym: VAAST:5_prime_UTR_variant
has_exact_synonym: VAAST:five_prime_UTR_variant
has_exact_synonym: VEP:5_prime_UTR_variant
has_exact_synonym: five prime UTR variant
has_exact_synonym: snpEff:UTR_5_PRIME
has_exact_synonym: untranslated-5
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:UTR5
id: SO:0001623
comment: EBI term: 5prime UTR variations - In 5prime UTR (untranslated region).

Axiom
annotated source: 5_prime_UTR_variant
annotated property: definition
annotated target: A UTR variant of the 5' UTR.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: 5_prime_UTR_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: 5_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: 5PRIME_UTR
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: 5_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: Jannovar:5_prime_utr_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: 5_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:5-prime-UTR
has_synonym_type: variant annotation term

Axiom
annotated source: 5_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: VAAST:5_prime_UTR_variant
has_synonym_type: variant annotation term

Axiom
annotated source: 5_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: VAAST:five_prime_UTR_variant
has_synonym_type: variant annotation term

Axiom
annotated source: 5_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: VEP:5_prime_UTR_variant
has_synonym_type: variant annotation term

Axiom
annotated source: 5_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: snpEff:UTR_5_PRIME
has_synonym_type: variant annotation term

Axiom
annotated source: 5_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: untranslated-5
database_cross_reference: ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
has_synonym_type: dbsnp variant terms

Axiom
annotated source: 5_prime_UTR_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:UTR5
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

3_prime_UTR_variant
type: Class
subclass of: UTR_variant
definition: A UTR variant of the 3' UTR.
created by: kareneilbeck
creation date: 2010-03-23T11:23:54Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: 3'UTR variant
has_exact_synonym: 3PRIME_UTR
has_exact_synonym: Jannovar:3_prime_utr_variant
has_exact_synonym: Seattleseq:3-prime-UTR
has_exact_synonym: VAAST:3_prime_UTR_variant
has_exact_synonym: VAAST:three_prime_UTR_variant
has_exact_synonym: VEP:3_prime_UTR_variant
has_exact_synonym: snpEff:UTR_3_PRIME
has_exact_synonym: three prime UTR variant
has_exact_synonym: untranslated-3
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:UTR3
id: SO:0001624
comment: EBI term 3prime UTR variations - In 3prime UTR.

Axiom
annotated source: 3_prime_UTR_variant
annotated property: definition
annotated target: A UTR variant of the 3' UTR.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: 3_prime_UTR_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: 3_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: 3PRIME_UTR
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: 3_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: Jannovar:3_prime_utr_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: 3_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:3-prime-UTR
has_synonym_type: variant annotation term

Axiom
annotated source: 3_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: VAAST:3_prime_UTR_variant
has_synonym_type: variant annotation term

Axiom
annotated source: 3_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: VAAST:three_prime_UTR_variant
has_synonym_type: variant annotation term

Axiom
annotated source: 3_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: VEP:3_prime_UTR_variant
has_synonym_type: variant annotation term

Axiom
annotated source: 3_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: snpEff:UTR_3_PRIME
has_synonym_type: variant annotation term

Axiom
annotated source: 3_prime_UTR_variant
annotated property: has_exact_synonym
annotated target: untranslated-3
database_cross_reference: ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
has_synonym_type: dbsnp variant terms

Axiom
annotated source: 3_prime_UTR_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:UTR3
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

SO_0001625
type: Class
IAO_0000231: IAO_0000227
term replaced by: terminator_codon_variant
deprecated: true

incomplete_terminal_codon_variant
type: Class
subclass of: terminator_codon_variant
subclass of: inframe_variant
definition: A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed.
created by: kareneilbeck
creation date: 2010-03-23T03:51:15Z
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: VEP:incomplete_terminal_codon_variant
has_exact_synonym: incomplete terminal codon variant
has_exact_synonym: partial_codon
has_obo_namespace: sequence
id: SO:0001626
comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.

Axiom
annotated source: incomplete_terminal_codon_variant
annotated property: definition
annotated target: A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed.
database_cross_reference: SO:ke

Axiom
annotated source: incomplete_terminal_codon_variant
annotated property: has_exact_synonym
annotated target: VEP:incomplete_terminal_codon_variant
has_synonym_type: variant annotation term

Axiom
annotated source: incomplete_terminal_codon_variant
annotated property: has_exact_synonym
annotated target: partial_codon
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

intron_variant
type: Class
subclass of: transcript_variant
definition: A transcript variant occurring within an intron.
created by: kareneilbeck
creation date: 2010-03-23T03:52:38Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:intron_variant
has_exact_synonym: Seattleseq:intron
has_exact_synonym: VAAST:intron_variant
has_exact_synonym: VEP:intron_variant
has_exact_synonym: intron variant
has_exact_synonym: intron_
has_exact_synonym: intronic
has_exact_synonym: snpEff:INTRON
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:intronic
has_related_synonym: Seattleseq:intron-near-splice
id: SO:0001627
comment: EBI term: Intronic variations - In intron.

Axiom
annotated source: intron_variant
annotated property: definition
annotated target: A transcript variant occurring within an intron.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: intron_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: intron_variant
annotated property: has_exact_synonym
annotated target: Jannovar:intron_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: intron_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:intron
has_synonym_type: variant annotation term

Axiom
annotated source: intron_variant
annotated property: has_exact_synonym
annotated target: VAAST:intron_variant
has_synonym_type: variant annotation term

Axiom
annotated source: intron_variant
annotated property: has_exact_synonym
annotated target: VEP:intron_variant
has_synonym_type: variant annotation term

Axiom
annotated source: intron_variant
annotated property: has_exact_synonym
annotated target: intron_
database_cross_reference: ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
has_synonym_type: dbsnp variant terms

Axiom
annotated source: intron_variant
annotated property: has_exact_synonym
annotated target: intronic
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: intron_variant
annotated property: has_exact_synonym
annotated target: snpEff:INTRON
has_synonym_type: variant annotation term

Axiom
annotated source: intron_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:intronic
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

Axiom
annotated source: intron_variant
annotated property: has_related_synonym
annotated target: Seattleseq:intron-near-splice
has_synonym_type: variant annotation term

intergenic_variant
type: Class
subclass of: SO_0001878
definition: A sequence variant located in the intergenic region, between genes.
created by: kareneilbeck
creation date: 2010-03-23T05:07:37Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:intergenic_variant
has_exact_synonym: Seattleseq:intergenic
has_exact_synonym: VEP:intergenic_variant
has_exact_synonym: intergenic
has_exact_synonym: intergenic variant
has_exact_synonym: snpEff:INTERGENIC
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:intergenic
id: SO:0001628
comment: EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript.

Axiom
annotated source: intergenic_variant
annotated property: definition
annotated target: A sequence variant located in the intergenic region, between genes.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: intergenic_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: intergenic_variant
annotated property: has_exact_synonym
annotated target: Jannovar:intergenic_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: intergenic_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:intergenic
has_synonym_type: variant annotation term

Axiom
annotated source: intergenic_variant
annotated property: has_exact_synonym
annotated target: VEP:intergenic_variant
has_synonym_type: variant annotation term

Axiom
annotated source: intergenic_variant
annotated property: has_exact_synonym
annotated target: intergenic
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: intergenic_variant
annotated property: has_exact_synonym
annotated target: snpEff:INTERGENIC
has_synonym_type: variant annotation term

Axiom
annotated source: intergenic_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:intergenic
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

splice_site_variant
type: Class
subclass of: splicing_variant
subclass of: intron_variant
definition: A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript.
created by: kareneilbeck
creation date: 2010-03-24T09:42:00Z
database_cross_reference: http://vat.gersteinlab.org/formats.php
has_exact_synonym: VAT:spliceOverlap
has_exact_synonym: essential_splice_site
has_exact_synonym: splice site variant
has_obo_namespace: sequence
id: SO:0001629
comment: EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger.

Axiom
annotated source: splice_site_variant
annotated property: definition
annotated target: A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript.
database_cross_reference: http://ensembl.org/info/docs/variation/index.html

VAT
type: Axiom
annotated source: splice_site_variant
annotated property: database_cross_reference
annotated target: http://vat.gersteinlab.org/formats.php

Axiom
annotated source: splice_site_variant
annotated property: has_exact_synonym
annotated target: VAT:spliceOverlap
has_synonym_type: variant annotation term

Axiom
annotated source: splice_site_variant
annotated property: has_exact_synonym
annotated target: essential_splice_site
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

splice_region_variant
type: Class
subclass of: splicing_variant
definition: A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
created by: kareneilbeck
creation date: 2010-03-24T09:46:02Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:splice_region_variant
has_exact_synonym: VAAST:splice_region_variant
has_exact_synonym: VEP:splice_region_variant
has_exact_synonym: snpEff:SPLICE_SITE_REGION
has_exact_synonym: splice region variant
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:splicing
has_related_synonym: snpEff:SPLICE_SITE_BRANCH
has_related_synonym: snpEff:SPLICE_SITE_BRANCH_U12
id: SO:0001630
comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.

Axiom
annotated source: splice_region_variant
annotated property: definition
annotated target: A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
database_cross_reference: http://ensembl.org/info/docs/variation/index.html

Axiom
annotated source: splice_region_variant
annotated property: has_exact_synonym
annotated target: Jannovar:splice_region_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: splice_region_variant
annotated property: has_exact_synonym
annotated target: VAAST:splice_region_variant
has_synonym_type: variant annotation term

Axiom
annotated source: splice_region_variant
annotated property: has_exact_synonym
annotated target: VEP:splice_region_variant
has_synonym_type: variant annotation term

Axiom
annotated source: splice_region_variant
annotated property: has_exact_synonym
annotated target: snpEff:SPLICE_SITE_REGION
has_synonym_type: variant annotation term

Axiom
annotated source: splice_region_variant
annotated property: has_exact_synonym
annotated target: splice region variant
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

Axiom
annotated source: splice_region_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:splicing
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

Axiom
annotated source: splice_region_variant
annotated property: has_related_synonym
annotated target: snpEff:SPLICE_SITE_BRANCH
has_synonym_type: variant annotation term

Axiom
annotated source: splice_region_variant
annotated property: has_related_synonym
annotated target: snpEff:SPLICE_SITE_BRANCH_U12
has_synonym_type: variant annotation term

upstream_gene_variant
type: Class
subclass of: intergenic_variant
definition: A sequence variant located 5' of a gene.
created by: kareneilbeck
creation date: 2010-03-24T09:49:13Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:upstream_gene_variant
has_exact_synonym: VEP:upstream_gene_variant
has_exact_synonym: snpEff:UPSTREAM
has_exact_synonym: upstream gene variant
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:upstream
id: SO:0001631
comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.

Axiom
annotated source: upstream_gene_variant
annotated property: definition
annotated target: A sequence variant located 5' of a gene.
database_cross_reference: SO:ke

Axiom
annotated source: upstream_gene_variant
annotated property: has_exact_synonym
annotated target: Jannovar:upstream_gene_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: upstream_gene_variant
annotated property: has_exact_synonym
annotated target: VEP:upstream_gene_variant
has_synonym_type: variant annotation term

Axiom
annotated source: upstream_gene_variant
annotated property: has_exact_synonym
annotated target: snpEff:UPSTREAM
has_synonym_type: variant annotation term

Axiom
annotated source: upstream_gene_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:upstream
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

downstream_gene_variant
type: Class
subclass of: intergenic_variant
definition: A sequence variant located 3' of a gene.
created by: kareneilbeck
creation date: 2010-03-24T09:49:38Z
database_cross_reference: http://snpeff.sourceforge.net/SnpEff_manual.html
database_cross_reference: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
has_exact_synonym: Jannovar:downstream_gene_variant
has_exact_synonym: VEP:downstream_gene_variant
has_exact_synonym: downstream gene variant
has_exact_synonym: snpEff:DOWNSTREAM
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:downstream
id: SO:0001632
comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.

Axiom
annotated source: downstream_gene_variant
annotated property: definition
annotated target: A sequence variant located 3' of a gene.
database_cross_reference: SO:ke

Axiom
annotated source: downstream_gene_variant
annotated property: has_exact_synonym
annotated target: Jannovar:downstream_gene_variant
database_cross_reference: http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
has_synonym_type: variant annotation term

Axiom
annotated source: downstream_gene_variant
annotated property: has_exact_synonym
annotated target: VEP:downstream_gene_variant
has_synonym_type: variant annotation term

Axiom
annotated source: downstream_gene_variant
annotated property: has_exact_synonym
annotated target: snpEff:DOWNSTREAM
has_synonym_type: variant annotation term

Axiom
annotated source: downstream_gene_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:downstream
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

5KB_downstream_variant
type: Class
subclass of: downstream_gene_variant
definition: A sequence variant located within 5 KB of the end of a gene.
created by: kareneilbeck
creation date: 2010-03-24T09:50:16Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
has_exact_synonym: 5KB downstream variant
has_exact_synonym: Seattleseq:downstream-gene
has_exact_synonym: downstream
has_obo_namespace: sequence
has_related_synonym: within 5KB downstream
id: SO:0001633
comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.

Axiom
annotated source: 5KB_downstream_variant
annotated property: definition
annotated target: A sequence variant located within 5 KB of the end of a gene.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: 5KB_downstream_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: 5KB_downstream_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:downstream-gene
has_synonym_type: variant annotation term

Axiom
annotated source: 5KB_downstream_variant
annotated property: has_exact_synonym
annotated target: downstream
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

500B_downstream_variant
type: Class
subclass of: downstream_gene_variant
definition: A sequence variant located within a half KB of the end of a gene.
created by: kareneilbeck
creation date: 2010-03-24T09:50:42Z
has_exact_synonym: 500B downstream variant
has_exact_synonym: near-gene-3
has_obo_namespace: sequence
id: SO:0001634

Axiom
annotated source: 500B_downstream_variant
annotated property: definition
annotated target: A sequence variant located within a half KB of the end of a gene.
database_cross_reference: SO:ke

Axiom
annotated source: 500B_downstream_variant
annotated property: has_exact_synonym
annotated target: near-gene-3
database_cross_reference: ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
has_synonym_type: dbsnp variant terms

5KB_upstream_variant
type: Class
subclass of: upstream_gene_variant
definition: A sequence variant located within 5KB 5' of a gene.
created by: kareneilbeck
creation date: 2010-03-24T09:51:06Z
database_cross_reference: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp
has_exact_synonym: 5kb upstream variant
has_exact_synonym: Seattleseq:upstream-gene
has_exact_synonym: upstream
has_obo_namespace: sequence
id: SO:0001635
comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.

Axiom
annotated source: 5KB_upstream_variant
annotated property: definition
annotated target: A sequence variant located within 5KB 5' of a gene.
database_cross_reference: SO:ke

Seattleseq
type: Axiom
annotated source: 5KB_upstream_variant
annotated property: database_cross_reference
annotated target: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp

Axiom
annotated source: 5KB_upstream_variant
annotated property: has_exact_synonym
annotated target: Seattleseq:upstream-gene
has_synonym_type: variant annotation term

Axiom
annotated source: 5KB_upstream_variant
annotated property: has_exact_synonym
annotated target: upstream
database_cross_reference: http://ensembl.org/info/docs/variation/index.html
has_synonym_type: ensembl variant terms

2KB_upstream_variant
type: Class
subclass of: upstream_gene_variant
definition: A sequence variant located within 2KB 5' of a gene.
created by: kareneilbeck
creation date: 2010-03-24T09:51:22Z
has_exact_synonym: 2KB upstream variant
has_exact_synonym: near-gene-5
has_obo_namespace: sequence
id: SO:0001636

Axiom
annotated source: 2KB_upstream_variant
annotated property: definition
annotated target: A sequence variant located within 2KB 5' of a gene.
database_cross_reference: SO:ke

Axiom
annotated source: 2KB_upstream_variant
annotated property: has_exact_synonym
annotated target: near-gene-5
database_cross_reference: ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
has_synonym_type: dbsnp variant terms

rRNA_gene
type: Class
subclass of: ncRNA_gene
definition: A gene that encodes for ribosomal RNA.
created by: kareneilbeck
creation date: 2010-04-21T10:10:32Z
has_exact_synonym: rDNA
has_exact_synonym: rRNA gene
has_obo_namespace: sequence
id: SO:0001637
comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).

Axiom
annotated source: rRNA_gene
annotated property: definition
annotated target: A gene that encodes for ribosomal RNA.
database_cross_reference: SO:ke

piRNA_gene
type: Class
subclass of: SO_0002342
definition: A gene that encodes for an piwi associated RNA.
created by: kareneilbeck
creation date: 2010-04-21T10:11:36Z
has_exact_synonym: piRNA gene
has_obo_namespace: sequence
id: SO:0001638
comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.

Axiom
annotated source: piRNA_gene
annotated property: definition
annotated target: A gene that encodes for an piwi associated RNA.
database_cross_reference: SO:ke

RNase_P_RNA_gene
type: Class
subclass of: SO_0002180
definition: A gene that encodes an RNase P RNA.
created by: kareneilbeck
creation date: 2010-04-21T10:13:23Z
has_exact_synonym: RNase P RNA gene
has_obo_namespace: sequence
id: SO:0001639
comment: Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533.

Axiom
annotated source: RNase_P_RNA_gene
annotated property: definition
annotated target: A gene that encodes an RNase P RNA.
database_cross_reference: SO:ke

RNase_MRP_RNA_gene
type: Class
subclass of: SO_0002180
definition: A gene that encodes a RNase_MRP_RNA.
created by: kareneilbeck
creation date: 2010-04-21T10:13:58Z
has_obo_namespace: sequence
has_related_synonym: RNase MRP RNA gene
id: SO:0001640
comment: Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533.

Axiom
annotated source: RNase_MRP_RNA_gene
annotated property: definition
annotated target: A gene that encodes a RNase_MRP_RNA.
database_cross_reference: SO:ke

lincRNA_gene
type: Class
subclass of: SO_0002127
definition: A gene that encodes a long, intervening non-coding RNA.
created by: kareneilbeck
creation date: 2010-04-21T10:14:24Z
has_exact_synonym: lincRNA gene
has_obo_namespace: sequence
id: SO:0001641

Axiom
annotated source: lincRNA_gene
annotated property: definition
annotated target: A gene that encodes a long, intervening non-coding RNA.
database_cross_reference: PMID:23463798
database_cross_reference: SO:ke
database_cross_reference: http://www.gencodegenes.org/gencode_biotypes.html

mathematically_defined_repeat
type: Class
subclass of: experimental_feature
definition: A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness.
created by: kareneilbeck
creation date: 2010-05-03T11:50:14Z
has_exact_synonym: mathematically defined repeat
has_obo_namespace: sequence
id: SO:0001642
comment: Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.).

Axiom
annotated source: mathematically_defined_repeat
annotated property: definition
annotated target: A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness.
database_cross_reference: SO:jestill

telomerase_RNA_gene
type: Class
subclass of: ncRNA_gene
definition: A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.
created by: kareneilbeck
creation date: 2010-05-18T05:26:38Z
database_cross_reference: http:http://en.wikipedia.org/wiki/Telomerase_RNA_component
has_exact_synonym: TERC
has_exact_synonym: Telomerase RNA component
has_exact_synonym: telomerase RNA gene
has_obo_namespace: sequence
id: SO:0001643

Axiom
annotated source: telomerase_RNA_gene
annotated property: definition
annotated target: A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.
database_cross_reference: SO:ke

wikipedia
type: Axiom
annotated source: telomerase_RNA_gene
annotated property: database_cross_reference
annotated target: http:http://en.wikipedia.org/wiki/Telomerase_RNA_component

targeting_vector
type: Class
equivalent class: Class
  intersection of: vector_replicon
  intersection of: Restriction
    on property: has_part
    some values from: homologous_region
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: vector_replicon
subclass of: engineered_region
subclass of: Restriction
  on property: has_part
  some values from: homologous_region
subclass of: Restriction
  on property: has_quality
  some values from: engineered
definition: An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications.
created by: kareneilbeck
creation date: 2010-05-28T02:05:25Z
has_obo_namespace: sequence
has_related_synonym: targeting vector
id: SO:0001644

Axiom
annotated source: targeting_vector
annotated property: definition
annotated target: An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications.
database_cross_reference: MGD:tm
database_cross_reference: PMID:10354467

genetic_marker
type: Class
subclass of: biological_region
definition: A measurable sequence feature that varies within a population.
created by: kareneilbeck
creation date: 2010-05-28T02:33:07Z
has_obo_namespace: sequence
has_related_synonym: genetic marker
id: SO:0001645

Axiom
annotated source: genetic_marker
annotated property: definition
annotated target: A measurable sequence feature that varies within a population.
database_cross_reference: SO:db

DArT_marker
type: Class
subclass of: genetic_marker
definition: A genetic marker, discovered using Diversity Arrays Technology (DArT) technology.
created by: kareneilbeck
creation date: 2010-05-28T02:34:43Z
has_exact_synonym: DArT marker
has_obo_namespace: sequence
id: SO:0001646

Axiom
annotated source: DArT_marker
annotated property: definition
annotated target: A genetic marker, discovered using Diversity Arrays Technology (DArT) technology.
database_cross_reference: SO:ke

kozak_sequence
type: Class
subclass of: ribosome_entry_site
definition: A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
created by: kareneilbeck
creation date: 2010-06-07T03:12:20Z
database_cross_reference: http://en.wikipedia.org/wiki/Kozak_consensus_sequence
has_exact_synonym: kozak consensus
has_exact_synonym: kozak consensus sequence
has_exact_synonym: kozak sequence
has_obo_namespace: sequence
id: SO:0001647
in_subset: SOFA

Axiom
annotated source: kozak_sequence
annotated property: definition
annotated target: A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
database_cross_reference: SO:ke

wikipedia
type: Axiom
annotated source: kozak_sequence
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Kozak_consensus_sequence

nested_transposon
type: Class
subclass of: transposable_element
definition: A transposon that is disrupted by the insertion of another element.
created by: kareneilbeck
creation date: 2010-06-23T03:22:57Z
has_exact_synonym: nested transposon
has_obo_namespace: sequence
id: SO:0001648

Axiom
annotated source: nested_transposon
annotated property: definition
annotated target: A transposon that is disrupted by the insertion of another element.
database_cross_reference: SO:ke

nested_repeat
type: Class
subclass of: repeat_region
definition: A repeat that is disrupted by the insertion of another element.
created by: kareneilbeck
creation date: 2010-06-23T03:24:55Z
has_broad_synonym: INSDC_feature:repeat_region
has_exact_synonym: INSDC_qualifier:nested
has_exact_synonym: nested repeat
has_obo_namespace: sequence
id: SO:0001649

Axiom
annotated source: nested_repeat
annotated property: definition
annotated target: A repeat that is disrupted by the insertion of another element.
database_cross_reference: SO:ke

inframe_variant
type: Class
subclass of: SO_0001818
definition: A sequence variant which does not cause a disruption of the translational reading frame.
created by: kareneilbeck
creation date: 2010-07-19T01:24:44Z
has_exact_synonym: VAAST:inframe_variant
has_exact_synonym: cds-indel
has_exact_synonym: inframe variant
has_obo_namespace: sequence
has_related_synonym: ANNOVAR:nonframeshift block substitution
has_related_synonym: ANNOVAR:nonframeshift substitution
id: SO:0001650

Axiom
annotated source: inframe_variant
annotated property: definition
annotated target: A sequence variant which does not cause a disruption of the translational reading frame.
database_cross_reference: SO:ke

Axiom
annotated source: inframe_variant
annotated property: has_exact_synonym
annotated target: VAAST:inframe_variant
has_synonym_type: variant annotation term

Axiom
annotated source: inframe_variant
annotated property: has_exact_synonym
annotated target: cds-indel
has_synonym_type: dbsnp variant terms

Axiom
annotated source: inframe_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:nonframeshift block substitution
database_cross_reference: http://www.openbioinformatics.org/annovar/annovar_download.html
has_synonym_type: variant annotation term

Axiom
annotated source: inframe_variant
annotated property: has_related_synonym
annotated target: ANNOVAR:nonframeshift substitution
has_synonym_type: variant annotation term

SO_0001651
type: Class
IAO_0000231: IAO_0000227
term replaced by: SO_0001821
deprecated: true

SO_0001652
type: Class
IAO_0000231: IAO_0000227
term replaced by: SO_0001822
deprecated: true

retinoic_acid_responsive_element
type: Class
subclass of: TF_binding_site
definition: A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.
created by: kareneilbeck
creation date: 2010-08-03T10:46:12Z
has_exact_synonym: RARE
has_exact_synonym: retinoic acid responsive element
has_obo_namespace: sequence
id: SO:0001653

Axiom
annotated source: retinoic_acid_responsive_element
annotated property: definition
annotated target: A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.
database_cross_reference: PMID:11327309
database_cross_reference: PMID:19917671

nucleotide_to_protein_binding_site
type: Class
subclass of: protein_binding_site
definition: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
created by: kareneilbeck
creation date: 2010-08-03T12:26:05Z
has_obo_namespace: sequence
has_related_synonym: nucleotide to protein binding site
id: SO:0001654
in_subset: SOFA

Axiom
annotated source: nucleotide_to_protein_binding_site
annotated property: definition
annotated target: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
database_cross_reference: SO:ke

nucleotide_binding_site
type: Class
subclass of: binding_site
definition: A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.
created by: kareneilbeck
creation date: 2010-08-03T12:30:04Z
has_exact_synonym: np_bind
has_exact_synonym: nucleotide binding site
has_obo_namespace: sequence
id: SO:0001655
comment: See GO:0000166 : nucleotide binding.

Axiom
annotated source: nucleotide_binding_site
annotated property: definition
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.
database_cross_reference: SO:cb

Axiom
annotated source: nucleotide_binding_site
annotated property: has_exact_synonym
annotated target: np_bind
database_cross_reference: uniprot:feature
has_synonym_type: biosapiens

metal_binding_site
type: Class
subclass of: binding_site
definition: A binding site that, in the molecule, interacts selectively and non-covalently with metal ions.
created by: kareneilbeck
creation date: 2010-08-03T12:31:42Z
has_obo_namespace: sequence
has_related_synonym: metal binding site
id: SO:0001656
comment: See GO:0046872 : metal ion binding.

Axiom
annotated source: metal_binding_site
annotated property: definition
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with metal ions.
database_cross_reference: SO:cb

ligand_binding_site
type: Class
subclass of: binding_site
definition: A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone.
created by: kareneilbeck
creation date: 2010-08-03T12:32:58Z
has_exact_synonym: ligand binding site
has_obo_namespace: sequence
id: SO:0001657

Axiom
annotated source: ligand_binding_site
annotated property: definition
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone.
database_cross_reference: SO:ke

nested_tandem_repeat
type: Class
subclass of: nested_repeat
definition: An NTR is a nested repeat of two distinct tandem motifs interspersed with each other.
created by: kareneilbeck
creation date: 2010-08-26T09:36:16Z
has_exact_synonym: NTR
has_exact_synonym: nested tandem repeat
has_obo_namespace: sequence
id: SO:0001658
comment: Tracker ID: 3052459.

Axiom
annotated source: nested_tandem_repeat
annotated property: definition
annotated target: An NTR is a nested repeat of two distinct tandem motifs interspersed with each other.
database_cross_reference: SO:AF

promoter_element
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: overlaps
  some values from: TF_binding_site
subclass of: Restriction
  on property: part_of
  some values from: promoter
definition: An element that can exist within the promoter region of a gene.
created by: kareneilbeck
creation date: 2010-10-01T11:48:32Z
has_exact_synonym: promoter element
has_obo_namespace: sequence
id: SO:0001659
comment: Mmoved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.

core_eukaryotic_promoter_element
type: Class
subclass of: SO_0002309
subclass of: Restriction
  on property: part_of
  some values from: SO_0002221
definition: An element that only exists within the promoter region of a eukaryotic gene.
created by: kareneilbeck
creation date: 2010-10-01T11:49:03Z
has_exact_synonym: core eukaryotic promoter element
has_obo_namespace: sequence
has_related_synonym: general transcription factor binding site
id: SO:0001660

Axiom
annotated source: core_eukaryotic_promoter_element
annotated property: definition
annotated target: An element that only exists within the promoter region of a eukaryotic gene.
database_cross_reference: GREEKC:cl

RNA_polymerase_II_TATA_box
type: Class
subclass of: TATA_box
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_core_promoter
definition: A TATA box core promoter of a gene transcribed by RNA polymerase II.
created by: kareneilbeck
creation date: 2010-10-01T02:42:12Z
has_exact_synonym: RNA polymerase II TATA box
has_obo_namespace: sequence
id: SO:0001661

Axiom
annotated source: RNA_polymerase_II_TATA_box
annotated property: definition
annotated target: A TATA box core promoter of a gene transcribed by RNA polymerase II.
database_cross_reference: PMID:16858867

RNA_polymerase_III_TATA_box
type: Class
subclass of: TATA_box
subclass of: Restriction
  on property: part_of
  some values from: RNApol_III_promoter
definition: A TATA box core promoter of a gene transcribed by RNA polymerase III.
created by: kareneilbeck
creation date: 2010-10-01T02:43:16Z
has_exact_synonym: RNA polymerase III TATA box
has_obo_namespace: sequence
id: SO:0001662

Axiom
annotated source: RNA_polymerase_III_TATA_box
annotated property: definition
annotated target: A TATA box core promoter of a gene transcribed by RNA polymerase III.
database_cross_reference: SO:ke

BREd_motif
type: Class
subclass of: core_eukaryotic_promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_core_promoter
definition: A core RNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G).
created by: kareneilbeck
creation date: 2010-10-01T02:49:55Z
has_exact_synonym: BREd
has_obo_namespace: sequence
has_related_synonym: BREd motif
id: SO:0001663

Axiom
annotated source: BREd_motif
annotated property: definition
annotated target: A core RNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G).
database_cross_reference: PMID:16858867

DCE
type: Class
subclass of: core_eukaryotic_promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_core_promoter
definition: A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII.
created by: kareneilbeck
creation date: 2010-10-01T02:56:41Z
has_obo_namespace: sequence
has_related_synonym: downstream core element
id: SO:0001664

Axiom
annotated source: DCE
annotated property: definition
annotated target: A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII.
database_cross_reference: PMID:16858867

DCE_SI
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: DCE
definition: A sub element of the DCE core promoter element, with consensus sequence CTTC.
created by: kareneilbeck
creation date: 2010-10-01T03:00:10Z
has_obo_namespace: sequence
has_related_synonym: DCE SI
id: SO:0001665

Axiom
annotated source: DCE_SI
annotated property: definition
annotated target: A sub element of the DCE core promoter element, with consensus sequence CTTC.
database_cross_reference: PMID:16858867
database_cross_reference: SO:ke

DCE_SII
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: DCE
definition: A sub element of the DCE core promoter element with consensus sequence CTGT.
created by: kareneilbeck
creation date: 2010-10-01T03:00:30Z
has_exact_synonym: DCE SII
has_obo_namespace: sequence
id: SO:0001666

Axiom
annotated source: DCE_SII
annotated property: definition
annotated target: A sub element of the DCE core promoter element with consensus sequence CTGT.
database_cross_reference: PMID:16858867
database_cross_reference: SO:ke

DCE_SIII
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: DCE
definition: A sub element of the DCE core promoter element with consensus sequence AGC.
created by: kareneilbeck
creation date: 2010-10-01T03:00:44Z
has_exact_synonym: DCE SIII
has_obo_namespace: sequence
id: SO:0001667

Axiom
annotated source: DCE_SIII
annotated property: definition
annotated target: A sub element of the DCE core promoter element with consensus sequence AGC.
database_cross_reference: PMID:16858867
database_cross_reference: SO:ke

proximal_promoter_element
type: Class
subclass of: regulatory_promoter_element
definition: DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor).
created by: kareneilbeck
creation date: 2010-10-01T03:10:23Z
has_obo_namespace: sequence
has_related_synonym: proximal promoter element
has_related_synonym: specific transcription factor binding site
id: SO:0001668

Axiom
annotated source: proximal_promoter_element
annotated property: definition
annotated target: DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor).
database_cross_reference: PMID:12515390
database_cross_reference: PMID:9679020
database_cross_reference: SO:ml

RNApol_II_core_promoter
type: Class
subclass of: RNApol_II_promoter
definition: The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
created by: kareneilbeck
creation date: 2010-10-01T03:13:41Z
has_exact_synonym: RNApol II core promoter
has_obo_namespace: sequence
id: SO:0001669

Axiom
annotated source: RNApol_II_core_promoter
annotated property: definition
annotated target: The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
database_cross_reference: PMID:16858867

distal_promoter_element
type: Class
subclass of: regulatory_promoter_element
definition: A regulatory promoter element that is distal from the TSS.
created by: kareneilbeck
creation date: 2010-10-01T03:21:08Z
has_obo_namespace: sequence
has_related_synonym: distal promoter element
id: SO:0001670

bacterial_RNApol_promoter_sigma_70_element
type: Class
subclass of: bacterial_RNApol_promoter
definition: A DNA sequence to which bacterial RNA polymerase sigma 70 binds, to begin transcription.
created by: kareneilbeck
creation date: 2010-10-06T01:41:34Z
has_exact_synonym: bacterial RNA polymerase promoter sigma 70
has_obo_namespace: sequence
id: SO:0001671

bacterial_RNApol_promoter_sigma54_element
type: Class
subclass of: bacterial_RNApol_promoter
definition: A DNA sequence to which bacterial RNA polymerase sigma 54 binds, to begin transcription.
created by: kareneilbeck
creation date: 2010-10-06T01:42:37Z
has_exact_synonym: bacterial RNA polymerase promoter sigma54
has_obo_namespace: sequence
has_related_synonym: <new synonym>
id: SO:0001672

minus_12_signal
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: bacterial_RNApol_promoter_sigma54_element
definition: A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
created by: kareneilbeck
creation date: 2010-10-06T01:44:57Z
has_exact_synonym: minus 12 signal
has_obo_namespace: sequence
id: SO:0001673

Axiom
annotated source: minus_12_signal
annotated property: definition
annotated target: A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
database_cross_reference: PMID:18331472

minus_24_signal
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: bacterial_RNApol_promoter_sigma54_element
definition: A conserved region about 24-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
created by: kareneilbeck
creation date: 2010-10-06T01:45:24Z
has_obo_namespace: sequence
has_related_synonym: minus 24 signal
id: SO:0001674

Axiom
annotated source: minus_24_signal
annotated property: definition
annotated target: A conserved region about 24-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
database_cross_reference: PMID:18331472

A_box_type_1
type: Class
subclass of: A_box
subclass of: Restriction
  on property: part_of
  some values from: RNApol_III_promoter_type_1
definition: An A box within an RNA polymerase III type 1 promoter.
created by: kareneilbeck
creation date: 2010-10-06T05:43:43Z
has_obo_namespace: sequence
has_related_synonym: A box type 1
id: SO:0001675
comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.

Axiom
annotated source: A_box_type_1
annotated property: definition
annotated target: An A box within an RNA polymerase III type 1 promoter.
database_cross_reference: SO:ke

A_box_type_2
type: Class
subclass of: A_box
subclass of: Restriction
  on property: part_of
  some values from: RNApol_III_promoter_type_2
definition: An A box within an RNA polymerase III type 2 promoter.
created by: kareneilbeck
creation date: 2010-10-06T05:44:18Z
has_obo_namespace: sequence
has_related_synonym: A box type 2
id: SO:0001676
comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.

Axiom
annotated source: A_box_type_2
annotated property: definition
annotated target: An A box within an RNA polymerase III type 2 promoter.
database_cross_reference: SO:ke

intermediate_element
type: Class
subclass of: core_eukaryotic_promoter_element
subclass of: Restriction
  on property: part_of
  some values from: RNApol_III_promoter_type_1
definition: A core promoter region of RNA polymerase III type 1 promoters.
created by: kareneilbeck
creation date: 2010-10-06T05:52:03Z
has_exact_synonym: IE
has_obo_namespace: sequence
has_related_synonym: intermediate element
id: SO:0001677

Axiom
annotated source: intermediate_element
annotated property: definition
annotated target: A core promoter region of RNA polymerase III type 1 promoters.
database_cross_reference: PMID:12381659

regulatory_promoter_element
type: Class
subclass of: promoter_element
definition: A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region.
created by: kareneilbeck
creation date: 2010-10-07T04:39:48Z
has_obo_namespace: sequence
has_related_synonym: regulatory promoter element
id: SO:0001678

Axiom
annotated source: regulatory_promoter_element
annotated property: definition
annotated target: A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region.
database_cross_reference: PMID:12381659

transcription_regulatory_region
type: Class
definition: A regulatory region that is involved in the control of the process of transcription.
created by: kareneilbeck
creation date: 2010-10-12T03:49:35Z
has_exact_synonym: transcription regulatory region
has_obo_namespace: sequence
id: SO:0001679
in_subset: SOFA
comment: Obsoleted by David Sant on 11 Feb 2021 when it was merged with transcriptional_cis_regulatory_region (SO:0001055) to reduce redundancy and be consistent with Gene Ontology. See GitHub Issue #527.
deprecated: true

Axiom
annotated source: transcription_regulatory_region
annotated property: definition
annotated target: A regulatory region that is involved in the control of the process of transcription.
database_cross_reference: SO:ke

translation_regulatory_region
type: Class
subclass of: SO_0005836
definition: A regulatory region that is involved in the control of the process of translation.
created by: kareneilbeck
creation date: 2010-10-12T03:52:45Z
has_exact_synonym: translation regulatory region
has_obo_namespace: sequence
id: SO:0001680

Axiom
annotated source: translation_regulatory_region
annotated property: definition
annotated target: A regulatory region that is involved in the control of the process of translation.
database_cross_reference: SO:ke

recombination_regulatory_region
type: Class
subclass of: SO_0005836
definition: A regulatory region that is involved in the control of the process of recombination.
created by: kareneilbeck
creation date: 2010-10-12T03:53:35Z
has_exact_synonym: recombination regulatory region
has_obo_namespace: sequence
id: SO:0001681

Axiom
annotated source: recombination_regulatory_region
annotated property: definition
annotated target: A regulatory region that is involved in the control of the process of recombination.
database_cross_reference: SO:ke

replication_regulatory_region
type: Class
subclass of: SO_0005836
definition: A regulatory region that is involved in the control of the process of nucleotide replication.
created by: kareneilbeck
creation date: 2010-10-12T03:54:09Z
has_broad_synonym: INSDC_feature:regulatory
has_exact_synonym: INSDC_qualifier:replication_regulatory_region
has_exact_synonym: replication regulatory region
has_obo_namespace: sequence
id: SO:0001682

Axiom
annotated source: replication_regulatory_region
annotated property: definition
annotated target: A regulatory region that is involved in the control of the process of nucleotide replication.
database_cross_reference: SO:ke

sequence_motif
type: Class
subclass of: biological_region
definition: A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
created by: kareneilbeck
creation date: 2010-10-14T04:13:22Z
database_cross_reference: http://en.wikipedia.org/wiki/Sequence_motif
has_obo_namespace: sequence
has_related_synonym: sequence motif
id: SO:0001683
in_subset: SOFA

Axiom
annotated source: sequence_motif
annotated property: definition
annotated target: A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
database_cross_reference: http://en.wikipedia.org/wiki/Sequence_motif

wikipedia
type: Axiom
annotated source: sequence_motif
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Sequence_motif

experimental_feature_attribute
type: Class
subclass of: feature_attribute
definition: An attribute of an experimentally derived feature.
created by: kareneilbeck
creation date: 2010-10-28T02:22:23Z
has_obo_namespace: sequence
has_related_synonym: experimental feature attribute
id: SO:0001684

Axiom
annotated source: experimental_feature_attribute
annotated property: definition
annotated target: An attribute of an experimentally derived feature.
database_cross_reference: SO:ke

score
type: Class
subclass of: experimental_feature_attribute
definition: The score of an experimentally derived feature such as a p-value.
created by: kareneilbeck
creation date: 2010-10-28T02:23:16Z
has_obo_namespace: sequence
id: SO:0001685

Axiom
annotated source: score
annotated property: definition
annotated target: The score of an experimentally derived feature such as a p-value.
database_cross_reference: SO:ke

quality_value
type: Class
subclass of: experimental_feature_attribute
definition: An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score.
created by: kareneilbeck
creation date: 2010-10-28T02:24:11Z
has_obo_namespace: sequence
has_related_synonym: quality value
id: SO:0001686

Axiom
annotated source: quality_value
annotated property: definition
annotated target: An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score.
database_cross_reference: SO:ke

restriction_enzyme_recognition_site
type: Class
subclass of: SO_0001954
definition: The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.
created by: kareneilbeck
creation date: 2010-10-29T12:29:57Z
has_exact_synonym: restriction endonuclease recognition site
has_exact_synonym: restriction enzyme recognition site
has_obo_namespace: sequence
id: SO:0001687

Axiom
annotated source: restriction_enzyme_recognition_site
annotated property: definition
annotated target: The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.
database_cross_reference: SO:ke

restriction_enzyme_cleavage_junction
type: Class
subclass of: SO_0002204
definition: The boundary at which a restriction enzyme breaks the nucleotide sequence.
created by: kareneilbeck
creation date: 2010-10-29T12:35:02Z
has_exact_synonym: restriction enzyme cleavage junction
has_obo_namespace: sequence
id: SO:0001688

Axiom
annotated source: restriction_enzyme_cleavage_junction
annotated property: definition
annotated target: The boundary at which a restriction enzyme breaks the nucleotide sequence.
database_cross_reference: SO:ke

five_prime_restriction_enzyme_junction
type: Class
subclass of: single_strand_restriction_enzyme_cleavage_site
subclass of: Restriction
  on property: part_of
  some values from: sticky_end_restriction_enzyme_cleavage_site
definition: The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence.
created by: kareneilbeck
creation date: 2010-10-29T12:36:24Z
has_exact_synonym: 5' restriction enzyme junction
has_obo_namespace: sequence
id: SO:0001689

Axiom
annotated source: five_prime_restriction_enzyme_junction
annotated property: definition
annotated target: The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence.
database_cross_reference: SO:ke

three_prime_restriction_enzyme_junction
type: Class
subclass of: single_strand_restriction_enzyme_cleavage_site
subclass of: Restriction
  on property: part_of
  some values from: sticky_end_restriction_enzyme_cleavage_site
definition: The restriction enzyme cleavage junction on the 3' strand of the nucleotide sequence.
created by: kareneilbeck
creation date: 2010-10-29T12:37:52Z
has_exact_synonym: 3' restriction enzyme junction
has_obo_namespace: sequence
id: SO:0001690

blunt_end_restriction_enzyme_cleavage_site
type: Class
subclass of: restriction_enzyme_recognition_site
definition: A restriction enzyme recognition site that, when cleaved, results in no overhangs.
created by: kareneilbeck
creation date: 2010-10-29T12:39:53Z
has_exact_synonym: blunt end restriction enzyme cleavage site
has_obo_namespace: sequence
id: SO:0001691

Axiom
annotated source: blunt_end_restriction_enzyme_cleavage_site
annotated property: definition
annotated target: A restriction enzyme recognition site that, when cleaved, results in no overhangs.
database_cross_reference: SBOL:jgquinn
database_cross_reference: SO:ke

sticky_end_restriction_enzyme_cleavage_site
type: Class
subclass of: restriction_enzyme_recognition_site
definition: A site where restriction enzymes can cleave that will produce an overhang or 'sticky end'.
created by: kareneilbeck
creation date: 2010-10-29T12:40:50Z
has_obo_namespace: sequence
has_related_synonym: sticky end restriction enzyme cleavage site
id: SO:0001692

blunt_end_restriction_enzyme_cleavage_junction
type: Class
subclass of: restriction_enzyme_cleavage_junction
subclass of: Restriction
  on property: part_of
  some values from: blunt_end_restriction_enzyme_cleavage_site
definition: A restriction enzyme cleavage site where both strands are cut at the same position.
created by: kareneilbeck
creation date: 2010-10-29T12:43:14Z
has_obo_namespace: sequence
has_related_synonym: blunt end restriction enzyme cleavage site
id: SO:0001693

Axiom
annotated source: blunt_end_restriction_enzyme_cleavage_junction
annotated property: definition
annotated target: A restriction enzyme cleavage site where both strands are cut at the same position.
database_cross_reference: SO:ke

single_strand_restriction_enzyme_cleavage_site
type: Class
subclass of: restriction_enzyme_cleavage_junction
definition: A restriction enzyme cleavage site whereby only one strand is cut.
created by: kareneilbeck
creation date: 2010-10-29T12:44:48Z
has_obo_namespace: sequence
has_related_synonym: single strand restriction enzyme cleavage site
id: SO:0001694

Axiom
annotated source: single_strand_restriction_enzyme_cleavage_site
annotated property: definition
annotated target: A restriction enzyme cleavage site whereby only one strand is cut.
database_cross_reference: SO:ke

restriction_enzyme_single_strand_overhang
type: Class
subclass of: SO_0001954
subclass of: Restriction
  on property: part_of
  some values from: sticky_end_restriction_enzyme_cleavage_site
definition: A terminal region of DNA sequence where the end of the region is not blunt ended.
created by: kareneilbeck
creation date: 2010-10-29T12:48:35Z
has_exact_synonym: single strand overhang
has_obo_namespace: sequence
has_related_synonym: sticky end
id: SO:0001695

Axiom
annotated source: restriction_enzyme_single_strand_overhang
annotated property: definition
annotated target: A terminal region of DNA sequence where the end of the region is not blunt ended.
database_cross_reference: SO:ke

experimentally_defined_binding_region
type: Class
subclass of: experimental_feature
definition: A region that has been implicated in binding although the exact coordinates of binding may be unknown.
created by: kareneilbeck
creation date: 2010-11-02T11:39:59Z
has_obo_namespace: sequence
has_related_synonym: experimentally defined binding region
id: SO:0001696

Axiom
annotated source: experimentally_defined_binding_region
annotated property: definition
annotated target: A region that has been implicated in binding although the exact coordinates of binding may be unknown.
database_cross_reference: SO:ke

ChIP_seq_region
type: Class
subclass of: experimentally_defined_binding_region
subclass of: Restriction
  on property: contains
  some values from: protein_binding_site
definition: A region of sequence identified by CHiP seq technology to contain a protein binding site.
created by: kareneilbeck
creation date: 2010-11-02T11:43:07Z
has_obo_namespace: sequence
has_related_synonym: ChIP seq region
id: SO:0001697

Axiom
annotated source: ChIP_seq_region
annotated property: definition
annotated target: A region of sequence identified by CHiP seq technology to contain a protein binding site.
database_cross_reference: SO:ke

ASPE_primer
type: Class
subclass of: primer
definition: "A primer containing an SNV at the 3' end for accurate genotyping.
created by: kareneilbeck
creation date: 2010-11-11T03:25:21Z
has_exact_synonym: ASPE primer
has_exact_synonym: allele specific primer extension primer
has_obo_namespace: sequence
id: SO:0001698

Axiom
annotated source: ASPE_primer
annotated property: definition
annotated target: "A primer containing an SNV at the 3' end for accurate genotyping.
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/11252801

dCAPS_primer
type: Class
subclass of: primer
definition: A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site.
created by: kareneilbeck
creation date: 2010-11-11T03:27:09Z
has_exact_synonym: dCAPS primer
has_exact_synonym: derived cleaved amplified polymorphic primer
has_obo_namespace: sequence
id: SO:0001699

Axiom
annotated source: dCAPS_primer
annotated property: definition
annotated target: A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site.
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/9628033

histone_modification
type: Class
equivalent class: Class
  intersection of: post_translationally_modified_region
  intersection of: Restriction
    on property: has_quality
    some values from: epigenetically_modified
subclass of: post_translationally_modified_region
subclass of: epigenetically_modified_region
subclass of: Restriction
  on property: has_quality
  some values from: epigenetically_modified
definition: Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation.
created by: kareneilbeck
creation date: 2010-03-31T10:22:08Z
has_exact_synonym: histone modification
has_obo_namespace: sequence
has_related_synonym: histone modification site
id: SO:0001700

Axiom
annotated source: histone_modification
annotated property: definition
annotated target: Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation.
database_cross_reference: http:en.wikipedia.org/wiki/Histone

histone_methylation_site
type: Class
subclass of: histone_modification
definition: A histone modification site where the modification is the methylation of the residue.
created by: kareneilbeck
creation date: 2010-03-31T10:23:02Z
has_exact_synonym: histone methylation
has_exact_synonym: histone methylation site
has_obo_namespace: sequence
id: SO:0001701

Axiom
annotated source: histone_methylation_site
annotated property: definition
annotated target: A histone modification site where the modification is the methylation of the residue.
database_cross_reference: SO:ke

histone_acetylation_site
type: Class
subclass of: histone_modification
definition: A histone modification where the modification is the acylation of the residue.
created by: kareneilbeck
creation date: 2010-03-31T10:23:27Z
has_exact_synonym: histone acetylation
has_exact_synonym: histone acetylation site
has_obo_namespace: sequence
id: SO:0001702

Axiom
annotated source: histone_acetylation_site
annotated property: definition
annotated target: A histone modification where the modification is the acylation of the residue.
database_cross_reference: SO:ke

H3K9_acetylation_site
type: Class
subclass of: SO_0001973
definition: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated.
created by: kareneilbeck
creation date: 2010-03-31T10:25:05Z
has_exact_synonym: H3K9 acetylation site
has_exact_synonym: H3K9ac
has_obo_namespace: sequence
id: SO:0001703

Axiom
annotated source: H3K9_acetylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H3K14_acetylation_site
type: Class
subclass of: SO_0001973
definition: A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated.
created by: kareneilbeck
creation date: 2010-03-31T10:25:53Z
has_exact_synonym: H3K14 acetylation site
has_exact_synonym: H3K14ac
has_obo_namespace: sequence
id: SO:0001704

Axiom
annotated source: H3K14_acetylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H3K4_monomethylation_site
type: Class
subclass of: H3K4_methylation_site
definition: A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:28:14Z
has_exact_synonym: H3K4 mono-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K4me1
id: SO:0001705

Axiom
annotated source: H3K4_monomethylation_site
annotated property: definition
annotated target: A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H3K4_trimethylation
type: Class
subclass of: H3K4_methylation_site
definition: A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:29:12Z
has_exact_synonym: H3K4 tri-methylation
has_obo_namespace: sequence
has_related_synonym: H3K4me3
id: SO:0001706

Axiom
annotated source: H3K4_trimethylation
annotated property: definition
annotated target: A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H3K9_trimethylation_site
type: Class
subclass of: H3K9_methylation_site
definition: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:30:34Z
has_exact_synonym: H3K9 tri-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K9Me3
id: SO:0001707

Axiom
annotated source: H3K9_trimethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H3K27_monomethylation_site
type: Class
subclass of: H3K27_methylation_site
definition: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:31:54Z
has_exact_synonym: H2K27 mono-methylation site
has_obo_namespace: sequence
has_related_synonym: H2K27Me1
id: SO:0001708

Axiom
annotated source: H3K27_monomethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H3K27_trimethylation_site
type: Class
subclass of: H3K27_methylation_site
definition: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:32:41Z
has_exact_synonym: H3K27 tri-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K27Me3
id: SO:0001709

Axiom
annotated source: H3K27_trimethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H3K79_monomethylation_site
type: Class
subclass of: H3K79_methylation_site
definition: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:33:42Z
has_exact_synonym: H3K79 mono-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K79me1
id: SO:0001710

Axiom
annotated source: H3K79_monomethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H3K79_dimethylation_site
type: Class
subclass of: H3K79_methylation_site
definition: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:34:39Z
has_exact_synonym: H3K79 di-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K79Me2
id: SO:0001711

Axiom
annotated source: H3K79_dimethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H3K79_trimethylation_site
type: Class
subclass of: H3K79_methylation_site
definition: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:35:30Z
has_exact_synonym: H3K79 tri-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K79Me3
id: SO:0001712

Axiom
annotated source: H3K79_trimethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H4K20_monomethylation_site
type: Class
subclass of: histone_methylation_site
definition: A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:36:43Z
has_exact_synonym: H4K20 mono-methylation site
has_obo_namespace: sequence
has_related_synonym: H4K20Me1
id: SO:0001713

Axiom
annotated source: H4K20_monomethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

H2BK5_monomethylation_site
type: Class
subclass of: histone_methylation_site
definition: A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated.
created by: kareneilbeck
creation date: 2010-03-31T10:38:12Z
has_exact_synonym: H2BK5 mono-methylation site
has_obo_namespace: sequence
id: SO:0001714

Axiom
annotated source: H2BK5_monomethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated.
database_cross_reference: http://en.wikipedia.org/wiki/Histone

ISRE
type: Class
subclass of: TF_binding_site
definition: An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.
created by: kareneilbeck
creation date: 2010-04-05T11:15:08Z
has_exact_synonym: interferon stimulated response element
has_obo_namespace: sequence
id: SO:0001715
comment: Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021.

Axiom
annotated source: ISRE
annotated property: definition
annotated target: An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.
database_cross_reference: http://genesdev.cshlp.org/content/2/4/383.abstrac

histone_ubiqitination_site
type: Class
subclass of: histone_modification
definition: A histone modification site where ubiquitin may be added.
created by: kareneilbeck
creation date: 2010-04-13T10:12:18Z
has_obo_namespace: sequence
has_related_synonym: histone ubiquitination site
id: SO:0001716

Axiom
annotated source: histone_ubiqitination_site
annotated property: definition
annotated target: A histone modification site where ubiquitin may be added.
database_cross_reference: SO:ke

H2B_ubiquitination_site
type: Class
subclass of: histone_ubiqitination_site
definition: A histone modification site on H2B where ubiquitin may be added.
created by: kareneilbeck
creation date: 2010-04-13T10:13:28Z
has_obo_namespace: sequence
has_related_synonym: H2BUbiq
id: SO:0001717

Axiom
annotated source: H2B_ubiquitination_site
annotated property: definition
annotated target: A histone modification site on H2B where ubiquitin may be added.
database_cross_reference: SO:ke

H3K18_acetylation_site
type: Class
subclass of: SO_0001973
definition: A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated.
created by: kareneilbeck
creation date: 2010-04-13T10:39:35Z
has_exact_synonym: H3K18 acetylation site
has_exact_synonym: H3K18ac
has_obo_namespace: sequence
id: SO:0001718

Axiom
annotated source: H3K18_acetylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated.
database_cross_reference: SO:ke

H3K23_acetylation_site
type: Class
subclass of: SO_0001973
definition: A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated.
created by: kareneilbeck
creation date: 2010-04-13T10:42:45Z
has_exact_synonym: H3K23 acetylation site
has_exact_synonym: H3K23ac
has_obo_namespace: sequence
id: SO:0001719

Axiom
annotated source: H3K23_acetylation_site
annotated property: definition
annotated target: A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated.
database_cross_reference: SO:ke

epigenetically_modified_region
type: Class
equivalent class: Class
  intersection of: biological_region
  intersection of: Restriction
    on property: has_quality
    some values from: epigenetically_modified
subclass of: SO_0005836
subclass of: Restriction
  on property: has_quality
  some values from: epigenetically_modified
definition: A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification.
created by: kareneilbeck
creation date: 2010-03-27T12:02:29Z
has_obo_namespace: sequence
has_related_synonym: epigenetically modified region
id: SO:0001720
in_subset: SOFA
comment: Moved from is_a biological_region (SO:0001411) to is_a regulatory_region (SO:0005836) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. 11 Feb 2021 updated definition along with addition of epigenomically_modified_region (SO:0002332). Epigenetically modified region is now not inherited while epigenomically modified region is not annotated as inherited. See GitHub Issue #532 and issue #534.

Axiom
annotated source: epigenetically_modified_region
annotated property: definition
annotated target: A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification.
database_cross_reference: SO:ke
database_cross_reference: http://en.wikipedia.org/wiki/Epigenetics

H3K27_acylation_site
type: Class
definition: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated.
created by: kareneilbeck
creation date: 2010-04-13T10:44:09Z
has_exact_synonym: H3K27 acylation site
has_obo_namespace: sequence
has_related_synonym: H3K27Ac
id: SO:0001721
deprecated: true

Axiom
annotated source: H3K27_acylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated.
database_cross_reference: SO:ke

H3K36_monomethylation_site
type: Class
subclass of: H3K36_methylation_site
definition: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
created by: kareneilbeck
creation date: 2010-04-13T10:46:32Z
has_exact_synonym: H3K36 mono-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K36Me1
id: SO:0001722

Axiom
annotated source: H3K36_monomethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
database_cross_reference: SO:ke

H3K36_dimethylation_site
type: Class
subclass of: H3K36_methylation_site
definition: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated.
created by: kareneilbeck
creation date: 2010-04-13T10:59:35Z
has_exact_synonym: H3K36 di-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K36Me2
id: SO:0001723

Axiom
annotated source: H3K36_dimethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated.
database_cross_reference: SO:ke

H3K36_trimethylation_site
type: Class
subclass of: H3K36_methylation_site
definition: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
created by: kareneilbeck
creation date: 2010-04-13T11:01:58Z
has_exact_synonym: H3K36 tri-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K36Me3
id: SO:0001724

Axiom
annotated source: H3K36_trimethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
database_cross_reference: SO:ke

H3K4_dimethylation_site
type: Class
subclass of: H3K4_methylation_site
definition: A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated.
created by: kareneilbeck
creation date: 2010-04-13T11:03:15Z
has_exact_synonym: H3K4 di-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K4Me2
id: SO:0001725

Axiom
annotated source: H3K4_dimethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated.
database_cross_reference: SO:ke

H3K27_dimethylation_site
type: Class
subclass of: H3K27_methylation_site
definition: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated.
created by: kareneilbeck
creation date: 2010-04-13T01:45:41Z
has_exact_synonym: H3K27 di-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K27Me2
id: SO:0001726

Axiom
annotated source: H3K27_dimethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated.
database_cross_reference: SO:ke

H3K9_monomethylation_site
type: Class
subclass of: H3K9_methylation_site
definition: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
created by: kareneilbeck
creation date: 2010-04-13T11:06:17Z
has_exact_synonym: H3K9 mono-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K9Me1
id: SO:0001727

Axiom
annotated source: H3K9_monomethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
database_cross_reference: SO:ke

H3K9_dimethylation_site
type: Class
subclass of: H3K9_methylation_site
definition: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated.
created by: kareneilbeck
creation date: 2010-04-13T11:08:19Z
has_exact_synonym: H3K9 di-methylation site
has_obo_namespace: sequence
has_related_synonym: H3K9Me2
id: SO:0001728

Axiom
annotated source: H3K9_dimethylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated.
database_cross_reference: SO:ke

H4K16_acetylation_site
type: Class
subclass of: SO_0001972
definition: A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated.
created by: kareneilbeck
creation date: 2010-04-13T11:09:41Z
has_exact_synonym: H4K16 acetylation site
has_exact_synonym: H4K16ac
has_obo_namespace: sequence
id: SO:0001729

Axiom
annotated source: H4K16_acetylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated.
database_cross_reference: SO:ke

H4K5_acetylation_site
type: Class
subclass of: SO_0001972
definition: A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated.
created by: kareneilbeck
creation date: 2010-04-13T11:13:00Z
has_exact_synonym: H4K5 acetylation site
has_exact_synonym: H4K5ac
has_obo_namespace: sequence
id: SO:0001730

Axiom
annotated source: H4K5_acetylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated.
database_cross_reference: SO:ke

H4K8_acetylation_site
type: Class
subclass of: SO_0001972
definition: A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated.
created by: kareneilbeck
creation date: 2010-04-13T11:14:24Z
has_exact_synonym: H4K8 acetylation site
has_exact_synonym: H4K8ac
has_obo_namespace: sequence
id: SO:0001731

Axiom
annotated source: H4K8_acetylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated.
database_cross_reference: SO:KE

H3K27_methylation_site
type: Class
subclass of: histone_methylation_site
definition: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated.
created by: kareneilbeck
creation date: 2010-04-13T11:26:22Z
has_exact_synonym: H3K27 methylation site
has_obo_namespace: sequence
id: SO:0001732

Axiom
annotated source: H3K27_methylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated.
database_cross_reference: SO:ke

H3K36_methylation_site
type: Class
subclass of: histone_methylation_site
definition: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated.
created by: kareneilbeck
creation date: 2010-04-13T11:27:28Z
has_exact_synonym: H3K36 methylation site
has_obo_namespace: sequence
id: SO:0001733

Axiom
annotated source: H3K36_methylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated.
database_cross_reference: SO:ke

H3K4_methylation_site
type: Class
subclass of: histone_methylation_site
definition: A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated.
created by: kareneilbeck
creation date: 2010-04-13T11:28:14Z
has_exact_synonym: H3K4 methylation site
has_obo_namespace: sequence
id: SO:0001734

Axiom
annotated source: H3K4_methylation_site
annotated property: definition
annotated target: A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated.
database_cross_reference: SO:ke

H3K79_methylation_site
type: Class
subclass of: histone_methylation_site
definition: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated.
created by: kareneilbeck
creation date: 2010-04-13T11:29:16Z
has_exact_synonym: H3K79 methylation site
has_obo_namespace: sequence
id: SO:0001735

Axiom
annotated source: H3K79_methylation_site
annotated property: definition
annotated target: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated.
database_cross_reference: SO:ke

H3K9_methylation_site
type: Class
subclass of: histone_methylation_site
definition: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated.
created by: kareneilbeck
creation date: 2010-04-13T11:31:37Z
has_exact_synonym: H3K9 methylation site
has_obo_namespace: sequence
id: SO:0001736