Fiat Object Part
type: Class
subclass of: Material Entity
definition_source: snap:FiatObjectPart
definition: A material entity that is part of an object but is not demarcated by any physical discontinuities.

Material Entity
type: Class
subclass of: Independent Continuant
definition_source: BFO:MaterialEntity
definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.

Orphan CDS
type: Class
definition: A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.
definition_source: SO:1001247
subclass of: CDS Predicted

CDS Predicted
type: Class
definition: A CDS that is predicted.
definition_source: SO:1001254
subclass of: CDS

Flanking 3' Quadraplet Recoding Signal
type: Class
definition: Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons.
definition_source: SO:1001281
subclass of: 3' Recoding Site

3' Recoding Site
type: Class
definition: The recoding stimulatory signal located downstream of the recoding site.
definition_source: SO:1001277
subclass of: Recoding Stimulatory Region

Porifera
type: Class
definition: A phylum of kingdom Animalia.
subclass of: Metazoa

Metazoa
type: Class
subclass of: Cellular Organism
has_related_synonym: Animals
has_related_synonym: Animalia

Platyhelminthes
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Actinopterygii
type: Class
definition: A class of phylum Chordata.
subclass of: Chordata

Chordata
type: Class
definition: A phylum of kingdom Animalia.
subclass of: Metazoa

Sus scrofa
type: Class
definition: A species of genus Sus.
subclass of: Mammalia
has_exact_synonym: Wild boar
has_exact_synonym: Pig
has_exact_synonym: Swine
has_related_synonym: Sus scrofus

Mammalia
type: Class
definition: A class of phylum Chordata.
subclass of: Chordata

Exemplar mRNA
type: Class
subclass of: mRNA
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.
definition_source: SO:0000734

mRNA
type: Class
subclass of: Mature Transcript
definition_source: SO:0000234
definition: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.

Realizable Entity
type: Class
definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
definition_source: snap:RealizableEntity
subclass of: Specifically Dependent Continuant

Specifically Dependent Continuant
type: Class
definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition_source: snap:SpecificallyDependentContinuant
subclass of: Dependent Continuant

Trans Splice Acceptor Site
type: Class
definition_source: SO:0000706
subclass of: Trans Splice Site
definition: The 3' splice site of the acceptor primary transcript.

Trans Splice Site
type: Class
subclass of: Splice Site
definition_source: SO:0001420
definition: Primary transcript region bordering trans-splice junction.

Bruguiera gymnorhiza
type: Class
subclass of: Spermatophyta
definition: A species of genus Bruguiera.
has_exact_synonym: Burma mangrove
has_related_synonym: Bruguiera gymnorhiza (L.) Savigny
has_related_synonym: Bruguiera gymnorrhizza
has_related_synonym: Bruguiera gymnorrhiza

Spermatophyta
type: Class
subclass of: Plants
definition: A subset of Embryophytes.

Nucleotide to Protein Binding Site
type: Class
definition_source: SO:0001654
subclass of: Protein Binding SIte
definition: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.

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.
definition_source: SO:0000410

pre-miRNA Binding
type: Class
definition: Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA.
definition_source: GO:0070883
subclass of: Restriction
  on property: has_agent
  some values from: pre-miRNA
subclass of: RNA Binding

has_agent
type: ObjectProperty
definition: As for has_participant, but with the additional condition that the component instance is causally active in the relevant process.
range: Material Entity
definition_source: RO:has_agent

pre-miRNA
type: Class
definition: The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
definition_source: SO:0001244
subclass of: Restriction
  on property: has_region
  some values from: Unbroken Stem
subclass of: Restriction
  on property: has_region
  some values from: Internal Loop
subclass of: Restriction
  on property: part_of
  some values from: pri-miRNA
subclass of: miRNA Primary Transcript Region

RNA Binding
type: Class
subclass of: Nucleic Acid Binding
definition: Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
definition_source: GO:0003723

Major TSS
type: Class
subclass of: TSS

TSS
type: Class
definition: The first base where RNA polymerase begins to synthesize the RNA transcript.
definition_source: SO:0000315
subclass of: Primary Transcript Region

Linum usitatissimum
type: Class
has_related_synonym: Linum usitatissimum L.
subclass of: Spermatophyta
definition: A species of genus Linum.

Mobile Intron
type: Class
definition_source: SO:0000666
subclass of: Intron
definition: An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.

Intron
type: Class
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.
subclass of: Primary Transcript Region
definition_source: SO:0000188

rRNA 25S
type: Class
definition_source: SO:0001002
definition: A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
subclass of: Large Subunit rRNA

Large Subunit rRNA
type: Class
definition_source: SO:0000651
subclass of: Restriction
  some values from: rRNA Large Subunit Primary Transcript
  on property: derives_from
subclass of: rRNA
definition: Ribosomal RNA transcript that structures the large subunit of the ribosome.

Untranslated Region Polycistronic mRNA
type: Class
subclass of: UTR
definition_source: SO:0000242
definition: The untranslated sequence separating the 'cistrons' of multicistronic mRNA.

UTR
type: Class
definition: Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
definition_source: SO:0000203
subclass of: mRNA Region

Cellular Component
type: Class
definition: The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
definition_source: GO:0005575
subclass of: Object

Object
type: Class
subclass of: Material Entity

Saguinus labiatus
type: Class
has_exact_synonym: Red-chested mustached tamarin
definition: A species of genus Saguinus.
subclass of: Mammalia

Coding End
type: Class
subclass of: CDS Region
definition: The last base to be translated into protein. It does not include the stop codon.
definition_source: SO:0000327

CDS Region
type: Class
definition_source: SO:0000851
definition: A region of a CDS.
subclass of: Restriction
  some values from: CDS
  on property: part_of
subclass of: mRNA Region

Ascidiacea
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.

Medicago truncatula
type: Class
definition: A species of genus Medicago.
subclass of: Spermatophyta
has_exact_synonym: Barrel medic

Capped mRNA
type: Class
definition: An mRNA that is capped.
definition_source: SO:0000862
subclass of: mRNA

Pongo pygmaeus
type: Class
definition: A species of genus Pongo.
has_exact_synonym: Orangutan
has_exact_synonym: Bornean orangutan
has_exact_synonym: Orang-utan
has_exact_synonym: Orang utan
subclass of: Mammalia

DHU Loop
type: Class
subclass of: tRNA Region
definition_source: SO:0001176
definition: Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.

tRNA Region
type: Class
definition_source: SO:0001172
definition: A region of a tRNA.
subclass of: Restriction
  on property: part_of
  some values from: tRNA
subclass of: Mature Transcript Region

Bruno Response Element
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Three Prime UTR
subclass of: UTR Region
definition_source: SO:0001181
definition: A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.

part_of
type: ObjectProperty
definition: For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
inverse of: has_part
definition_source: RO:part_of

Three Prime UTR
type: Class
definition_source: SO:0000205
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.

UTR Region
type: Class
subclass of: mRNA Region
definition: A region of UTR.
definition_source: SO:0000837

Rhipicephalus microplus
type: Class
subclass of: Arachnida
definition: A species of genus Rhipicephalus.
has_exact_synonym: Cattle tick
has_exact_synonym: Southern cattle tick
has_related_synonym: Boophilus microplus
has_related_synonym: Rhipicephalus (Boophilus) microplus

Arachnida
type: Class
definition: A class of phylum Arthropoda.
subclass of: Arthropoda

Monocistronic mRNA
type: Class
definition_source: SO:0000633
subclass of: mRNA
definition: An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.

Glycine tRNA Primary Transcript
type: Class
definition_source: SO:0000218
definition: A primary transcript encoding glycyl tRNA.
subclass of: tRNA Primary Transcript

tRNA Primary Transcript
type: Class
definition_source: SO:0000210
definition: A primary transcript encoding a transfer RNA.
subclass of: Noncoding Primary Transcript

miRNA Target Site
type: Class
definition: A miRNA target site is a binding site where the molecule is a micro RNA.
subclass of: Nucleotide Binding Site
definition_source: SO:0000934

Nucleotide Binding Site
type: Class
definition: A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.
definition_source: SO:0001655
subclass of: Binding Site

Nasonia longicornis
type: Class
has_related_synonym: Nasonia lonigicornis
subclass of: Insecta
definition: A species of genus Nasonia.

Insecta
type: Class
subclass of: Arthropoda
definition: A class of phylum Arthropoda.

Proline tRNA Primary Transcript
type: Class
definition_source: SO:0000225
definition: A primary transcript encoding prolyl tRNA.
subclass of: tRNA Primary Transcript

mRNA with Minus 1 Frameshift
type: Class
definition_source: SO:0000282
subclass of: mRNA with Frameshift
definition: An mRNA with a minus 1 frameshift.

mRNA with Frameshift
type: Class
subclass of: mRNA
definition_source: SO:0000108
definition: An mRNA with a frameshift.

SNV
type: Class
definition_source: SO:0001483
subclass of: Biological Region
definition: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.

Biological Region
type: Class
definition_source: SO:0001411
subclass of: Region
definition: A region defined by its disposition to be involved in a biological process.

Information Biopolymer
type: Class
subclass of: Molecular Entity
definition: Naturally occurring macromolecules that harbor biological information in their structures, e.g. proteins, nucleic acids.
definition_source: GRO:InformationBiopolymer

Molecular Entity
type: Class
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
definition_source: http://en.wikipedia.org/wiki/Molecular_entity
subclass of: Object

Splice Site
type: Class
definition_source: SO:0000162
definition: Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
subclass of: Primary Transcript Region

Bombyx mori
type: Class
definition: A species of genus Bombyx.
subclass of: Insecta
has_related_synonym: Bombyx mori Linnaeus, 1758
has_exact_synonym: Domestic silkworm
has_exact_synonym: Silk moth
has_exact_synonym: Silkworm

Methionyl tRNA
type: Class
definition: A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
subclass of: Restriction
  on property: derives_from
  some values from: Methionine tRNA Primary Transcript
subclass of: tRNA
definition_source: SO:0000266

derives_from
type: ObjectProperty
definition: Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
definition_source: RO:derives_from

Methionine tRNA Primary Transcript
type: Class
definition: A primary transcript encoding methionyl tRNA.
definition_source: SO:0000223
subclass of: tRNA Primary Transcript

tRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  some values from: tRNA Primary Transcript
  on property: derives_from
definition_source: SO:0000253
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.

Stop Codon Read Through
type: Class
definition_source: SO:0000883
subclass of: Recoded Codon
definition: A stop codon redefined to be a new amino acid.

Recoded Codon
type: Class
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.
subclass of: Codon
definition_source: SO:0000145

Sarcophilus harrisii
type: Class
definition: A species of genus Sarcophilus.
subclass of: Mammalia
has_related_synonym: Sarcophilus laniarius
has_exact_synonym: Tasmanian devil

Glutaminyl tRNA
type: Class
definition_source: SO:0000259
subclass of: Restriction
  on property: derives_from
  some values from: Glutamic acid tRNA Primary Transcript
subclass of: tRNA
definition: A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.

Glutamic acid tRNA Primary Transcript
type: Class
definition: A primary transcript encoding glutaminyl tRNA.
definition_source: SO:0000216
subclass of: tRNA Primary Transcript

RNA Metabolic Process
type: Class
definition_source: GO:0016070
subclass of: Nucleic Acid Metabolic Process
definition: The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.

Nucleic Acid Metabolic Process
type: Class
definition_source: GO:0090304
definition: Any cellular metabolic process involving nucleic acids.
subclass of: Metabolic Process

Appendicularia
type: Class
definition: A class of phylum Chordata.
subclass of: Chordata

Aquilegia coerulea
type: Class
subclass of: Spermatophyta
definition: A species of genus Aquilegia.
has_related_synonym: Aquilegia caerulea

Trans Spliced mRNA
type: Class
definition: An mRNA that is trans-spliced.
subclass of: Restriction
  some values from: Spliced Leader RNA
  on property: adjacent_to
subclass of: mRNA
definition_source: SO:0000872

Spliced Leader RNA
type: Class
subclass of: Primary Transcript Region
subclass of: Restriction
  some values from: Mini Exon Donor RNA
  on property: part_of

adjacent_to
type: ObjectProperty
definition: C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity.
definition_source: RO:adjacent_to

Mirtron
type: Class
definition: A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
subclass of: Intron Domain
definition_source: SO:0001034

Intron Domain
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Intron
subclass of: Primary Transcript Region

Spliceosomal Intron Region
type: Class
definition: A region within an intron.
definition_source: SO:0000841
subclass of: Restriction
  some values from: Spliceosomal Intron
  on property: part_of
subclass of: Primary Transcript Region

Spliceosomal Intron
type: Class
subclass of: Intron
definition: An intron which is spliced by the spliceosome.
definition_source: SO:0000662

Primary Transcript Region
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Primary Transcript
subclass of: Transcript Region
definition: A part of a primary transcript.
definition_source: SO:0000835

Transcription Factor Binding Site
type: Class
subclass of: Nucleotide to Protein Binding Site
definition_source: SO:0000235
definition: A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex.

Populus trichocarpa
type: Class
subclass of: Spermatophyta
has_related_synonym: Populus balsamifera subsp. trichocarpa (Torr. et A.Gray) Brayshaw
has_exact_synonym: Black cottonwood
has_related_synonym: Populus trichocarpa Torr. et A.Gray
has_exact_synonym: Western balsam poplar
has_related_synonym: Populus trichocarpa Torr. & A.Gray
definition: A species of genus Populus.
has_related_synonym: Populus balsamifera subsp. trichocarpa

Transcription Factor
type: Class
subclass of: Role
database_cross_reference: GRO:TranscriptionFactor
definition_source: modified definition from WIkipedia, http://en.wikipedia.org/wiki/Transcription_factor
definition: A role palyed by a protein that binds to specific DNA sequences, thereby controlling the transcription of genetic information from DNA to mRNA.

Role
type: Class
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
subclass of: Realizable Entity
definition_source: snap:Role

Dengue virus
type: Class
subclass of: ssRNA virus
definition: A ssRNA virus of family Flaviviridae.

ssRNA virus
type: Class
subclass of: Virus

Arachis hypogaea
type: Class
subclass of: Spermatophyta
definition: A species of genus Arachis.
has_exact_synonym: Ground-nut
has_exact_synonym: Goober
has_exact_synonym: Peanut
has_related_synonym: Arachis hypogea

rRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA Primary Transcript
definition: RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
definition_source: SO:0000252

ncRNA
type: Class
definition_source: SO:0000655
subclass of: Mature Transcript
definition: 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.

rRNA Primary Transcript
type: Class
definition_source: SO:0000209
definition: A primary transcript encoding a ribosomal RNA.
subclass of: Noncoding Primary Transcript

Posttranscriptional Gene Silencing by RNA
type: Class
definition_source: GO:0035194
definition: Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation.
subclass of: Posttranscriptional Gene Silencing

Posttranscriptional Gene Silencing
type: Class
definition: The inactivation of gene expression by a posttranscriptional mechanism.
definition_source: GO:0016441
subclass of: Posttranscriptional Regulation of Gene Expression

Guide RNA Region
type: Class
definition: A region of guide RNA.
subclass of: Restriction
  some values from: Guide RNA
  on property: part_of
subclass of: Mature Transcript Region
definition_source: SO:0000930

Guide RNA
type: Class
subclass of: ncRNA
definition_source: SO:0000602
definition: A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail) with a stretch of mature edited mRNA.

Mature Transcript Region
type: Class
definition_source: SO:0000834
subclass of: Transcript Region
definition: A region of a mature transcript.

Three Prime Coding Exon Noncoding Region
type: Class
definition_source: SO:0000484
subclass of: Noncoding Region of Exon
subclass of: Restriction
  some values from: Three Prime Noncoding Exon
  on property: part_of
definition: The sequence of the 3' exon that is not coding.

Noncoding Region of Exon
type: Class
subclass of: Exon Region
definition: The maximal intersection of exon and UTR.
definition_source: SO:0001214

Three Prime Noncoding Exon
type: Class
subclass of: Noncoding Exon
definition_source: SO:0000444
definition: Non-coding exon in the 3' UTR.

Xenacoelomorpha
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Haliotis rufescens
type: Class
has_exact_synonym: Red abalone
has_exact_synonym: California red abalone
definition: A species of genus Haliotis.
subclass of: Gastropoda

Gastropoda
type: Class
definition: A class of phylum Mollusca.
subclass of: Mollusca

Recoding Stimulatory Region
type: Class
subclass of: mRNA Region
definition: A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA.
definition_source: SO:1001268

Salvia sclarea
type: Class
definition: A species of genus Salvia.
has_exact_synonym: Clary
has_related_synonym: Salvia sclarea L.
subclass of: Spermatophyta

Dictyostelium discoideum
type: Class
subclass of: Amoebozoa
definition: A species of genus Dictyostelium.

Amoebozoa
type: Class
subclass of: Cellular Organism

Homo sapiens
type: Class
definition: A species of genus Homo.
subclass of: Mammalia
has_exact_synonym: Human
has_exact_synonym: Man

Nucleic Acid Binding
type: Class
definition_source: GO:0003676
definition: Interacting selectively and non-covalently with any nucleic acid.
subclass of: Binding

Binding
type: Class
definition: The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488]
definition_source: GO:0005488
subclass of: Molecular Function

Canonical 3' Splice Site
type: Class
subclass of: 3' cis Splice Site
definition: The canonical 3' splice site has the sequence "AG".
definition_source: SO:0000676

3' cis Splice Site
type: Class
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.
subclass of: cis Splice Site
definition_source: SO:0000164

Taeniopygia guttata
type: Class
definition: A species of genus Taeniopygia.
has_exact_synonym: Zebra finch
subclass of: Aves
has_related_synonym: Taenopygia guttata
has_related_synonym: Poephila guttata

Aves
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.

Cerebratulus lacteus
type: Class
subclass of: Nemertea
definition: A species of genus Cerebratulus.
has_exact_synonym: Milky ribbon-worm
has_exact_synonym: Milky ribbon worm

Nemertea
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Theobroma cacao
type: Class
has_exact_synonym: Cocoa
has_exact_synonym: Cacao
definition: A species of genus Theobroma.
subclass of: Spermatophyta

Mollusca
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Branchiostoma floridae
type: Class
has_exact_synonym: Florida lancelet
definition: A species of genus Branchiostoma.
has_related_synonym: Amphioxus floridae
has_related_synonym: Branchiostoma floridea
subclass of: Branchiostomidae

Branchiostomidae
type: Class
definition: A class of phylum Chordata.
subclass of: Chordata
has_exact_synonym: Leptocardii

Canonical 5' Splice Site
type: Class
definition: The canonical 5' splice site has the sequence "GT".
subclass of: 5' cis Splice Site
definition_source: SO:0000677

5' cis Splice Site
type: Class
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.
definition_source: SO:0000163
subclass of: cis Splice Site

5' Recoding Site
type: Class
definition: The recoding stimulatory signal located upstream of the recoding site.
definition_source: SO:1001280
subclass of: Recoding Stimulatory Region

Meleagrid herpesvirus 1
type: Class
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: herpesvirus of turkey
has_related_synonym: Meleagrid herpesvirus type 1
has_related_synonym: herpesvirus of turkeys
has_related_synonym: turkey herpesvirus HVT
has_exact_synonym: Turkey herpesvirus
subclass of: dsDNA virus, no RNA stage

dsDNA virus, no RNA stage
type: Class
subclass of: Virus
definition: A virus having a dsDNA molecule as genetic material. No RNA intermediate molecules are involved during its replication.

Terminal Loop
type: Class
subclass of: RNA Sequence Secondary Structure
definition: A contiguous sequence of nucleotide residues that directly links the two halves of an unbroken stem (but does not participate in the stem); this structure is also known as a "hairpin loop". Because a terminal loop may also participate in other inter-base interactions, (a) it is defined relative to a particular unbroken_stem, and (b) it is not implicitly defined as unpaired (or paired). [RNAO:0000098]
definition_source: RNAO:0000098

RNA Sequence Secondary Structure
type: Class
definition: A folded RNA sequence.
definition_source: SO:0000122
subclass of: Collection of Nucleotides Residues

SNP
type: Class
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.
definition_source: SO:0000694
subclass of: SNV

Coding Exon
type: Class
definition_source: SO:0000195
subclass of: Exon
definition: An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).

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.
definition_source: SO:0000147

Drosophila willistoni
type: Class
definition: A species of genus Drosophila.
subclass of: Insecta

Brugia malayi
type: Class
definition: A species of genus Brugia.
has_exact_synonym: Agent of lymphatic filariasis
subclass of: Nematoda

Nematoda
type: Class
definition: A phylum of kingdom Animalia.
subclass of: Metazoa

Saccharum sp.
type: Class
definition: A species of genus Saccharum.
subclass of: Spermatophyta

snoRNA
type: Class
definition_source: SO:0000275
subclass of: ncRNA
subclass of: Restriction
  some values from: snoRNA Primary Transcript
  on property: derives_from
definition: 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.

snoRNA Primary Transcript
type: Class
definition_source: SO:0000232
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a small nucleolar mRNA.

tmRNA Primary Transcript
type: Class
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a tmRNA.
definition_source: SO:0000584

Noncoding Primary Transcript
type: Class
definition_source: SO:0000483
definition: A primary transcript that is never translated into a protein.
subclass of: Primary Transcript

rRNA Cleavage RNA
type: Class
subclass of: Restriction
  some values from: rRNA cleavage snoRNA Primary Transcript
  on property: derives_from
subclass of: ncRNA
definition: An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.
definition_source: SO:0005843

rRNA cleavage snoRNA Primary Transcript
type: Class
definition: A primary transcript encoding an rRNA cleavage snoRNA.
definition_source: SO:0000582
subclass of: snoRNA Primary Transcript

cis Splice Site
type: Class
definition_source: SO:0001419
subclass of: Splice Site
definition: Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.

Gallus gallus
type: Class
has_exact_synonym: Chickens
has_exact_synonym: Bantam
has_exact_synonym: Chicken
definition: A species of genus Gallus.
has_related_synonym: Gallus gallus domesticus
has_related_synonym: Gallus domesticus
subclass of: Aves

Citrus reticulata
type: Class
has_related_synonym: Citrus poonensis
has_exact_synonym: Tangerine
has_exact_synonym: Mandarin orange
subclass of: Spermatophyta
definition: A species of genus Citrus.

Non-canonical Start Codon
type: Class
subclass of: Start Codon
definition_source: SO:0000680
definition: A start codon that is not the usual AUG sequence.

Start Codon
type: Class
subclass of: Codon
definition_source: SO:0000318
definition: First codon to be translated by a ribosome.

Helianthus annuus
type: Class
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_exact_synonym: Common sunflower
has_related_synonym: Helianthus annus
has_related_synonym: Helianthus annuus8

Avicennia marina
type: Class
definition: A species of genus Avicennia.
subclass of: Spermatophyta

Lysyl tRNA
type: Class
definition: A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
subclass of: Restriction
  on property: derives_from
  some values from: Lysine tRNA Primary Transcript
subclass of: tRNA
definition_source: SO:0000265

Lysine tRNA Primary Transcript
type: Class
definition_source: SO:0000222
definition: A primary transcript encoding lysyl tRNA.
subclass of: tRNA Primary Transcript

Festuca arundinacea
type: Class
has_related_synonym: Schedonorus phoenix
has_related_synonym: Lolium arundinaceum
has_related_synonym: Schedonorus arundinaceus
has_related_synonym: Festuca elatior
has_exact_synonym: Tall fescue
definition: A species of genus Festuca.
subclass of: Spermatophyta

Citrus sinensis
type: Class
has_exact_synonym: Naranja
has_exact_synonym: Navel orange
definition: A species of genus Citrus.
has_related_synonym: Citrus sinensis (L.) Osbeck
subclass of: Spermatophyta
has_exact_synonym: Apfelsine
has_exact_synonym: Sweet orange
has_exact_synonym: Valencia orange
has_related_synonym: Citrus x sinensis

5' Intron
type: Class
subclass of: Intron

Binding Site
type: Class
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.
definition_source: SO:0000409
subclass of: Biological Region

Coding Region of Exon
type: Class
subclass of: Exon Region
definition_source: SO:0001215
definition: The region of an exon that encodes for protein sequence.

Exon Region
type: Class
definition: A region of an exon.
subclass of: Restriction
  some values from: Exon
  on property: part_of
subclass of: Transcript Region
definition_source: SO:0000852

Transcription, RNA-dependent
type: Class
definition: The cellular synthesis of RNA on a template of RNA.
subclass of: RNA Biosynthetic Process
definition_source: GO:0001172

RNA Biosynthetic Process
type: Class
definition: The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers.
subclass of: RNA Metabolic Process
definition_source: GO:0032774

Small Regulatory ncRNA
type: Class
subclass of: ncRNA
definition_source: SO:0000370
definition: A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.

miRNA
type: Class
definition: Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules that can form local hairpin structures, which ordinarily are processed (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.
subclass of: Small Regulatory ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: pri-miRNA
definition_source: SO:0000276

pri-miRNA
type: Class
definition_source: SO:0000647
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a micro RNA.

Gossypium herbaceum
type: Class
definition: A species of genus Gossypium.
has_exact_synonym: Arabian cotton
subclass of: Spermatophyta
has_related_synonym: Gossypium herbaceum L.

mRNA Region
type: Class
definition_source: SO:0000836
definition: A region of an mRNA.
subclass of: Restriction
  on property: part_of
  some values from: mRNA
subclass of: Mature Transcript Region

Daphnia pulex
type: Class
has_exact_synonym: Common water flea
definition: A species of genus Daphnia.
subclass of: Branchiopoda

Branchiopoda
type: Class
subclass of: Arthropoda
definition: A class of phylum Arthropoda.

Five Prime Open Reading Frame
type: Class
subclass of: mRNA Region
subclass of: Restriction
  on property: part_of
  some values from: Five Prime UTR

Five Prime UTR
type: Class
subclass of: UTR
definition_source: SO:0000204
definition: A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.

Primary Transcript
type: Class
definition_source: SO:0000185
definition: A transcript that in its initial state requires modification to be functional.
subclass of: Transcript

Occurent
type: Class
definition_source: span:Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.

Caenorhabditis elegans
type: Class
has_exact_synonym: Nematode
subclass of: Nematoda
definition: A species of genus Caenorhabditis.
has_related_synonym: Rhabditis elegans

Chromosome
type: Class
definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
definition_source: GO:0005694
subclass of: Cellular Component

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.
definition_source: SO:0000398

snRNA
type: Class
definition_source: SO:0000274
subclass of: ncRNA
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.

Serine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding seryl tRNA.
definition_source: SO:0000226

Transcript Region
type: Class
definition: A region of a transcript.
subclass of: Biological Region
subclass of: Restriction
  on property: part_of
  some values from: Transcript
definition_source: SO:0000833

mRNA Recoded by Codon Redefinition
type: Class
definition: A recoded_mRNA that was modified by an alteration of codon meaning.
definition_source: SO:1001265
subclass of: Recoded mRNA

Recoded mRNA
type: Class
definition_source: SO:1001261
definition: The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.
subclass of: mRNA

DNA Binding
type: Class
definition_source: GO:0003677
subclass of: Nucleic Acid Binding
definition: Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).

Glycine max
type: Class
definition: A species of genus Glycine.
has_exact_synonym: Soybean
has_related_synonym: Glycine max; cv. Wye
subclass of: Spermatophyta

SRP RNA
type: Class
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.
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: SRP RNA Primary Transcript
definition_source: SO:0000590

SRP RNA Primary Transcript
type: Class
definition: A primary transcript encoding a signal recognition particle RNA.
definition_source: SO:0000589
subclass of: Noncoding Primary Transcript

piRNA
type: Class
definition_source: SO:0001035
subclass of: ncRNA
definition: A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.

U5 snRNA
type: Class
definition_source: SO:0000395
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.

Small Subunit rRNA
type: Class
subclass of: Restriction
  some values from: rRNA Small Subunit Primary Transcript
  on property: derives_from
subclass of: rRNA
definition_source: SO:0000650
definition: Ribosomal RNA transcript that structures the small subunit of the ribosome.

rRNA Small Subunit Primary Transcript
type: Class
definition_source: SO:0000255
subclass of: rRNA Primary Transcript
definition: A primary transcript encoding a small ribosomal subunit RNA.

DNA Sequence Secondary Structure
type: Class
definition_source: SO:0000142
subclass of: Collection of Nucleotides Residues
definition: A folded DNA sequence.

Collection of Nucleotides Residues
type: Class
definition: A collection of nucleotide residues is a part of a nucleic acid consisting of one or more nucleotides.
subclass of: Collection of Material Entities
definition_source: RNAO:0000108

Internal Loop
type: Class
subclass of: RNA Sequence Secondary Structure
definition_source: RNAO:0000099
definition: A collection of nucleotide residues that link two given unbroken_stems.

Apis mellifera
type: Class
has_exact_synonym: Honey bee
has_exact_synonym: Honeybee
has_exact_synonym: Bee
subclass of: Insecta
has_related_synonym: Apis mellifica
definition: A species of genus Apis.

rRNA Large Subunit Primary Transcript
type: Class
definition_source: SO:0000325
subclass of: rRNA Primary Transcript
definition: A primary transcript encoding a large ribosomal subunit RNA.

U4 snRNA
type: Class
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.
definition_source: SO:0000393
subclass of: snRNA

Arabidopsis lyrata
type: Class
definition: A species of genus Arabidopsis.
subclass of: Spermatophyta
has_related_synonym: Arabidopsis lyrata (L.) O'Kane & Al-Shehbaz
has_exact_synonym: Lyrate rockcress

rRNA 21S
type: Class
definition_source: SO:0001171
subclass of: Large Subunit rRNA
definition: A component of the large ribosomal subunit in mitochondrial rRNA.

Metabolic Process
type: Class
definition: The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
definition_source: GO:0008152
subclass of: Biological Process

Biological Process
type: Class
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
subclass of: Process
definition_source: GO:0008150

Outron
type: Class
subclass of: Primary Transcript Region
definition: A region of a primary transcript, that is removed via trans splicing.
definition_source: SO:0001475

Plus 2 Translational Frameshift
type: Class
definition_source: SO:0001212
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.

Translational Frameshift
type: Class
subclass of: mRNA Region
definition_source: SO:0001210
definition: The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.

Strigamia maritima
type: Class
subclass of: Chilopoda
definition: A species of genus Strigamia.

Chilopoda
type: Class
definition: A class of phylum Arthropoda.
subclass of: Arthropoda

Ricinus communis
type: Class
has_related_synonym: Ricinus sanguineus
definition: A species of genus Ricinus.
has_related_synonym: Ricinus comunis
has_related_synonym: Ricinis communis
subclass of: Spermatophyta
has_exact_synonym: Castor bean
has_related_synonym: Ricinus communis L.
has_related_synonym: Ricinus sanguineus hort. ex Groenl.
has_related_synonym: Ricimus communis

Ribozyme
type: Class
definition: An RNA with catalytic activity.
definition_source: SO:0000374
subclass of: Enzymatic RNA

Enzymatic RNA
type: Class
definition: An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
definition_source: SO:0000372
subclass of: Transcript

Recursive Splice Site
type: Class
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.
subclass of: cis Splice Site
definition_source: SO:0000998

U14 snoRNA Primary Transcript
type: Class
definition: The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
subclass of: snoRNA Primary Transcript
definition_source: SO:0005837

Upstream AUG Codon
type: Class
subclass of: UTR Region
subclass of: Restriction
  some values from: UTR
  on property: part_of
definition_source: SO:0000630
definition: A start codon upstream of the ORF.

Methylation Guide snoRNA
type: Class
definition: A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.
definition_source: SO:0005841
subclass of: Restriction
  some values from: Methylation Guide snoRNA Primary Transcript
  on property: derives_from
subclass of: C/D Box snoRNA

Methylation Guide snoRNA Primary Transcript
type: Class
definition_source: SO:0000580
subclass of: snoRNA Primary Transcript
definition: A primary transcript encoding a methylation guide small nucleolar RNA.

C/D Box snoRNA
type: Class
subclass of: Restriction
  some values from: C/D Box snoRNA Primary Transcript
  on property: derives_from
subclass of: snoRNA
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'.
definition_source: SO:0000593

Dependent Continuant
type: Class
definition_source: snap:DependentContinuant
definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.
subclass of: Continuant

Haemonchus contortus
type: Class
definition: A species of genus Haemonchus.
has_exact_synonym: Barber pole worm
has_exact_synonym: Red stomach worm
subclass of: Nematoda

Mature Transcript
type: Class
subclass of: Transcript
subclass of: Restriction
  some values from: Primary Transcript
  on property: derives_from
definition_source: SO:0000233
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.

West Nile Virus
type: Class
definition: A ssRNA virus of family Flaviviridae.
subclass of: ssRNA virus

Hydrozoa
type: Class
subclass of: Cnidaria
definition: A class of phylum Cnidaria.

Cnidaria
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Manduca sexta
type: Class
subclass of: Insecta
has_related_synonym: Tobacco hawkmoth
has_exact_synonym: Tobacco hornworm
has_exact_synonym: Tomato hornworm
has_exact_synonym: Hornblower
has_exact_synonym: Carolina sphinx
definition: A species of genus Manduca.

Schistosoma mansoni
type: Class
definition: A species of genus Schistosoma.
subclass of: Digenea

Digenea
type: Class
subclass of: Platyhelminthes
definition: A subclass of phylum Platyhelminthes.

Shine Dalgarno Sequence
type: Class
definition_source: SO:0000552
definition: A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
subclass of: Ribosome Entry Site

Ribosome Entry Site
type: Class
definition_source: SO:0000139
subclass of: mRNA Region
definition: Region in mRNA where ribosome assembles.

Plants
type: Class
subclass of: Cellular Organism
definition: Any living organism that typically synthesizes its food from inorganic substances, possesses cellulose cell walls, responds slowly and often permanently to a stimulus, lacks specialized sense organs and nervous system, and has no powers of locomotion. (EPA Terminology Reference System).
definition_source: NCIThesaurus:Plant

Cellular Organism
type: Class
subclass of: Organism

C/D Box snoRNA Primary Transcript
type: Class
definition: A primary transcript encoding a small nucleolar RNA of the box C/D family.
subclass of: snoRNA Primary Transcript
definition_source: SO:0000595

Transcript
type: Class
subclass of: RNA
definition_source: SO:0000673
definition: An RNA synthesized on a DNA or RNA template by an RNA polymerase.

U12 snRNA
type: Class
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.
subclass of: snRNA
definition_source: SO:0000399

CDS Supported by Sequence SImilarity Data
type: Class
definition: A CDS that is supported by sequence similarity data.
definition_source: SO:1001251
subclass of: CDS Predicted

miRNA Loop
type: Class
definition: The loop of the hairpin loop formed by folding of the pre-miRNA.
definition_source: SO:0001246
subclass of: Restriction
  on property: part_of
  some values from: pre-miRNA
subclass of: miRNA Primary Transcript Region

miRNA Primary Transcript Region
type: Class
definition_source: SO:0001243
definition: A part of an miRNA primary_transcript.
subclass of: Primary Transcript Region

Trans-spliced Transcript
type: Class
subclass of: Transcript
definition_source: SO:0000479
definition: A transcript that is trans-spliced.

Region
type: Class
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.
definition_source: SO:0000001
subclass of: Fiat Object Part

Internal UTR
type: Class
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.
definition_source: SO:0000241
subclass of: UTR

Helianthus ciliaris
type: Class
subclass of: Spermatophyta
has_related_synonym: Helianthus ciliaris DC.
has_related_synonym: Helianthus cilaris
definition: A species of genus Helianthus.

Clip
type: Class
definition_source: SO:0000303
subclass of: Primary Transcript Region
definition: Part of the primary transcript that is clipped off during processing.

Histidyl tRNA
type: Class
definition: A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
subclass of: Restriction
  on property: derives_from
  some values from: Histidine tRNA Primary Transcript
subclass of: tRNA
definition_source: SO:0000262

Histidine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition_source: SO:0000219
definition: A primary transcript encoding histidyl tRNA.

H/ACA Box snoRNA Primary Transcript
type: Class
definition: A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
definition_source: SO:0000596
subclass of: snoRNA Primary Transcript

Aspartic acid tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition_source: SO:0000214
definition: A primary transcript encoding aspartyl tRNA.

Pyrrolysyl tRNA
type: Class
subclass of: Restriction
  some values from: Pyrrolysine tRNA Primary Transcript
  on property: derives_from
subclass of: tRNA
definition: A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
definition_source: SO:0000766

Pyrrolysine tRNA Primary Transcript
type: Class
definition_source: SO:0001178
definition: A primary transcript encoding pyrrolysyl tRNA.
subclass of: tRNA Primary Transcript

Echinoidea
type: Class
definition: A class of phylum Echinodermata.
subclass of: Echinodermata

Echinodermata
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Distant 3' Recoding SIgnal
type: Class
definition_source: SO:1001287
subclass of: 3' Recoding Site
definition: A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.

Takifugu rubripes
type: Class
subclass of: Actinopterygii
has_related_synonym: Takifugu rubripes (Temminck & Schlegel, 1850)
definition: A species of genus Takifugu.
has_related_synonym: Tetraodon rubripes
has_related_synonym: Sphaeroides rubripes
has_related_synonym: Fugu rubripes
has_exact_synonym: Tiger puffer
has_exact_synonym: Torafugu

Calcarea
type: Class
definition: A class of phylum Porifera.
subclass of: Porifera

Hippoglossus hippoglossus
type: Class
has_related_synonym: Hippoglossus hippoglossus (Linnaeus, 1758)
subclass of: Actinopterygii
has_exact_synonym: Atlantic halibut
definition: A species of genus Hippoglossus.

Macacine herpesvirus 1
type: Class
has_related_synonym: Simian herpes B virus
has_related_synonym: Herpes virus B
has_related_synonym: Herpes B virus
has_related_synonym: Cercopithecid herpesvirus 1
has_exact_synonym: Monkey B virus
has_related_synonym: Herpesvirus simiae
has_related_synonym: Simian herpes B virus SHBV
has_related_synonym: Simian herpesvirus B
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Cercopithecine herpesvirus 1
subclass of: dsDNA virus, no RNA stage
has_related_synonym: B virus

Lnc RNA
type: Class
definition_source: SO:0001877
subclass of: ncRNA
definition: A non-coding RNA over 200nucleotides in length.

Oryza sativa
type: Class
subclass of: Spermatophyta
definition: A species of genus Oryza.
has_exact_synonym: Red rice
has_exact_synonym: Rice

Virus
type: Class
definition_source: NCIThesaurus:Virus
definition: An infectious agent which consists of two parts, genetic material and a protein coat. These organisms lack independent metabolism, and they must infect the cells of other types of organisms to reproduce. Most viruses are capable of passing through fine filters that retain bacteria, and are not visible through a light microscope.
subclass of: Organism

Drosophila simulans
type: Class
definition: A species of genus Drosophila.
subclass of: Insecta

SL7 Acceptor Site
type: Class
definition: A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts.
subclass of: SL2 Acceptor Site
definition_source: SO:0001752

SL2 Acceptor Site
type: Class
subclass of: Trans Splice Acceptor Site
definition_source: SO:0000709
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.

stRNA Primary Transcript
type: Class
definition: A primary transcript encoding a small temporal mRNA.
definition_source: SO:0000648
subclass of: pri-miRNA

Polycistronic Transcript
type: Class
subclass of: Transcript
definition_source: SO:0000078
definition: A transcript that is polycistronic.

Rattus norvegicus
type: Class
has_exact_synonym: Norway rat
has_exact_synonym: Rat
has_related_synonym: Rattus norvegicus8
has_related_synonym: Rattus rattiscus
has_related_synonym: Gunn rats
has_related_synonym: Rattus norwegicus
has_exact_synonym: Rattus sp. strain Wistar
subclass of: Mammalia
definition: A species of genus Rattus.
has_exact_synonym: Brown rat

Manihot esculenta
type: Class
definition: A species of genus Manihot.
has_related_synonym: Manihot esculenta Crantz
has_related_synonym: Manihot esculenta0
has_exact_synonym: Manioc
subclass of: Spermatophyta
has_exact_synonym: Tapioca
has_exact_synonym: Yuca
has_related_synonym: Manihot utilissima
has_exact_synonym: Cassava

Terebratulina retusa
type: Class
definition: A species of genus Terebratulina.
subclass of: Brachiopoda

Brachiopoda
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Transposable Element CDS
type: Class
definition: A CDS that is part of a transposable element.
subclass of: CDS
definition_source: SO:0001869

CDS
type: Class
definition: A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon.
subclass of: mRNA Region
definition_source: SO:0000316

Pan troglodytes
type: Class
subclass of: Mammalia
has_related_synonym: Chimpansee troglodytes
definition: A species of genus Pan.
has_exact_synonym: Chimpanzee

tmRNA
type: Class
definition_source: SO:0000584
subclass of: Restriction
  some values from: tmRNA Primary Transcript
  on property: derives_from
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.

Hydra magnipapillata
type: Class
definition: A species of genus Hydra.
subclass of: Hydrozoa

Transcript Bound by Nucleic Acid
type: Class
definition_source: SO:0000278
definition: A transcript that is bound by a nucleic acid.
subclass of: Transcript

stRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: stRNA Primary Transcript
definition: Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. [SO:0000649]
definition_source: SO:0000649

Retro-transcribing virus
type: Class
subclass of: Virus
definition: A virus that replicates by the reverse transcription of a RNA or DNA intermediate.

CDS Supported by Domain Match Data
type: Class
subclass of: CDS Supported by Sequence SImilarity Data
definition_source: SO:1001249
definition: A CDS that is supported by domain similarity.

Drosophila erecta
type: Class
definition: A species of genus Drosophila.
subclass of: Insecta

miRNA Binding
type: Class
definition_source: GO:0035198
subclass of: Restriction
  some values from: mRNA
  on property: has_participant
subclass of: Restriction
  some values from: miRNA
  on property: has_agent
subclass of: RNA Binding
definition: Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.

has_participant
type: ObjectProperty

Cysteinyl tRNA
type: Class
definition: A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
subclass of: Restriction
  some values from: Cysteine tRNA Primary Transcript
  on property: derives_from
subclass of: tRNA
definition_source: SO:0000258

Cysteine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition_source: SO:0000215
definition: A primary transcript encoding cysteinyl tRNA.

Glottidia pyramidata
type: Class
subclass of: Brachiopoda
has_related_synonym: Glottidea pyramidata
definition: A species of genus Glottidia.

Nicotiana tabacum
type: Class
subclass of: Spermatophyta
has_exact_synonym: Common tobacco
has_exact_synonym: Tobacco
has_exact_synonym: American tobacco
has_related_synonym: Nicotania tabacum
has_related_synonym: Nicotiana tabacum var. Samsun
definition: A species of genus Nicotiana.

Class II RNA
type: Class
definition_source: SO:0000989
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.
subclass of: ncRNA

Heliconius melpomene
type: Class
subclass of: Insecta
definition: A species of genus Heliconius.

Codon
type: Class
definition_source: SO:0000360
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.

Glutamine tRNA Primary Transcript
type: Class
definition: A primary transcript encoding glutamyl tRNA.
subclass of: tRNA Primary Transcript
definition_source: SO:0000217

Locusta migratoria
type: Class
definition: A species of genus Locusta.
subclass of: Insecta
has_exact_synonym: Migratory locust

Phenylalanine tRNA Primary Transcript
type: Class
definition_source: SO:0000224
definition: A primary transcript encoding phenylalanyl tRNA.
subclass of: tRNA Primary Transcript

Regulation of Gene Expression
type: Class
subclass of: Regulation of Metabolic Process
subclass of: Restriction
  on property: regulates
  some values from: Gene Expression
definition: Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
definition_source: GO:0010468

Regulation of Metabolic Process
type: Class
subclass of: Regulation of Biological Process
subclass of: Restriction
  on property: regulates
  some values from: Metabolic Process
definition_source: GO:0019222
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.

regulates
type: ObjectProperty

Gene Expression
type: Class
subclass of: Restriction
  some values from: Gene
  on property: has_agent
subclass of: Metabolic Process
definition_source: GO:0010467
definition: The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.

Valyl tRNA
type: Class
definition_source: SO:0000273
subclass of: Restriction
  some values from: Valine tRNA Primary Transcript
  on property: derives_from
subclass of: tRNA
definition: A tRNA sequence that has a valine anticodon, and a 3' valine binding region.

Valine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding valyl tRNA.
definition_source: SO:0000230

Sorghum bicolor
type: Class
subclass of: Spermatophyta
has_related_synonym: Sorghum saccharatum
has_exact_synonym: Sorghum
has_related_synonym: Sorghum bicolor milo
definition: A species of genus Sorghum.
has_exact_synonym: Broomcorn
has_exact_synonym: Milo
has_related_synonym: Sorghum vulgare

Regulation of Biological Process
type: Class
subclass of: Biological Regulation
subclass of: Restriction
  on property: regulates
  some values from: Biological Process
definition_source: GO:0050789
definition: Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.

Anopheles gambiae
type: Class
has_related_synonym: Anopheles gambiae Giles, 1902
has_related_synonym: Anopheles gambia
has_exact_synonym: African malaria mosquito
has_exact_synonym: Anopheles gambiae sensu stricto
subclass of: Insecta
definition: A species of genus Anopheles.

Macaca nemestrina
type: Class
has_exact_synonym: Pigtail macaque
has_exact_synonym: Pigtail monkey
has_exact_synonym: Pig-tailed macaque
subclass of: Mammalia
definition: A species of genus Macaca.

Drosophila melanogaster
type: Class
subclass of: Insecta
has_related_synonym: Drosophila melangaster
has_exact_synonym: Fruit fly
definition: A species of genus Drosophila.

DNA Binding SIte
type: Class
definition: A binding site that, in the molecule, interacts selectively and non-covalently with DNA.
subclass of: Nucleotide Binding Site
definition_source: SO:0001429

Processed Transcript
type: Class
subclass of: Transcript
definition_source: SO:0001503
definition: A transcript for which no open reading frame has been identified and for which no other function has been determined.

Acyrthosiphon pisum
type: Class
definition: A species of genus Acyrthosiphon.
has_exact_synonym: Pea aphid
subclass of: Insecta
has_related_synonym: Acyrthosiphum pisum

Aedes aegypti
type: Class
definition: A species of genus Aedes.
has_related_synonym: Stegomyia aegypti
has_exact_synonym: Yellow fever mosquito
subclass of: Insecta

Malacostraca
type: Class
definition: A class of phylum Arthropoda.
subclass of: Arthropoda

Arthropoda
type: Class
definition: A phylum of kingdom Animalia.
subclass of: Metazoa

has_region
type: ObjectProperty

Unbroken Stem
type: Class
definition: A paired region made up of two contiguous collections of nucleotides, in which each nucleotide forms a base pair. [RNAO:0000097]
subclass of: Paired Region
definition_source: RNAO:0000097

Anatid herpesvirus 1
type: Class
has_related_synonym: Duck enteritis virus
has_related_synonym: Duck plague virus
has_related_synonym: Anatid Herpes virus-1
definition: A dsDNA virus of family Herpesviridae.
subclass of: dsDNA virus, no RNA stage

Dengue virus 1
type: Class
has_related_synonym: dengue type 1 D1 virus
has_related_synonym: dengue virus-1 DEN-1
has_related_synonym: Type 1 dengue virus
has_related_synonym: dengue virus type I
has_related_synonym: Dengue virus type 1
has_related_synonym: dengue virus type 1 DEN1
subclass of: Dengue virus
has_related_synonym: type 1 dengue virus DEN-1

RNase P RNA
type: Class
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.
definition_source: SO:0000386
subclass of: ncRNA

Editing Domain
type: Class
definition_source: SO:0000606
definition: Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
subclass of: Edited Transcript Feature

Edited Transcript Feature
type: Class
definition_source: SO:0000579
subclass of: Transcript Region
definition: A locatable feature on a transcript that is edited.

Acacia auriculiformis
type: Class
subclass of: Spermatophyta
definition: A species of genus Acacia.
has_related_synonym: Acacia auriculiformis A.Cunn. ex Benth.

Independent Continuant
type: Class
definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
subclass of: Continuant
definition_source: snap:IndependentContinuant

Organism
type: Class
definition_source: OBI:0100026
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
subclass of: Object

Pinus densata
type: Class
subclass of: Spermatophyta
definition: A species of genus Pinus.

Stem Junction
type: Class
definition_source: RNAO:0000106
subclass of: RNA Sequence Secondary Structure
definition: A collection of nucleotide residues consisting of all and only the nucleotide regions that link more than two unbroken stems such that each region links exactly two unbroken stems. This term is defined relative to the particular unbroken_stems involved and, again, does not imply anything about the pairedness/unpairedness of the bases in this region. The degree of a junction is a property (e.g. 3-junction, 4-junction), so the different degrees do not get separate entries in the ontology.

Lagothrix lagotricha
type: Class
subclass of: Mammalia
has_exact_synonym: Brown woolly monkey
has_exact_synonym: Common woolly monkey
has_exact_synonym: Humboldt's woolly monkey
has_related_synonym: Lagothrix lagothricha
has_related_synonym: Lagothrix lagotricha lagotricha
definition: A species of genus Lagothrix.

Vigna unguiculata
type: Class
has_exact_synonym: Cowpea
has_related_synonym: Phaseolus unguiculatus
subclass of: Spermatophyta
definition: A species of genus Vigna.

rRNA 18S
type: Class
definition_source: SO:0000407
subclass of: Small Subunit rRNA
definition: A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.

SECIS Element
type: Class
definition_source: SO:1001274
definition: The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes.
subclass of: Recoding Stimulatory Region

Stop Codon Redefined as Selenocysteine
type: Class
definition: A stop codon redefined to be the new amino acid, selenocysteine.
subclass of: Stop Codon Read Through
definition_source: SO:0000885

Drosophila yakuba
type: Class
definition: A species of genus Drosophila.
subclass of: Insecta

Echinococcus granulosus
type: Class
has_related_synonym: Echinococcus granulosus sensu stricto
subclass of: Cestoda
has_related_synonym: Echinococcus granulosus sheep strain
definition: A species of genus Echinococcus.
has_related_synonym: Echinococcus granulosus Tasmanian sheep strain
has_related_synonym: Echinococcus granulosus s. s.
has_related_synonym: Echinococcus granulosus buffalo strain
has_related_synonym: Echinococcus granulosus (Batsch, 1786)
has_related_synonym: Echinococcus granulosus G3 strain
has_related_synonym: Echinococcus granulosus G2 strain
has_related_synonym: Echinococcus granulosus G1 strain

Cestoda
type: Class
definition: A class of phylum Platyhelminthes.
subclass of: Platyhelminthes

Human immunodeficiency virus 1
type: Class
has_related_synonym: AIDS virus
has_related_synonym: human immunodeficiency virus-1 HIV-1
has_related_synonym: human immunodeficiency virus 1 HIV-1
definition: A retro-transcribing virus of family Retroviridae.
has_related_synonym: human immunodeficiency virus type 1 HIV-1
has_related_synonym: Human immundeficiency virus type 1
has_related_synonym: human immunodeficiency virus type 1 ,HIV-1
has_related_synonym: human immunodeficiency virus type 1, HIV-1
has_related_synonym: human immunodeficiency virus type 1 HIV1
subclass of: Retro-transcribing virus
has_related_synonym: human immunodeficiency virus HIV-1
has_related_synonym: human immunodeficiency virus type-1 HIV-1
has_related_synonym: human immunodeficiency virus type 1 HIV 1
has_related_synonym: human immunodeficiency virus type I HIV-1
has_related_synonym: Human immunodeficiencey virus type 1
has_related_synonym: Human immunodeficiency virus type 1

Human herpesvirus 1
type: Class
has_related_synonym: herpes simplex virus 1 HSV-1
subclass of: dsDNA virus, no RNA stage
has_related_synonym: Human herpesvirus type 1
has_related_synonym: herpes simplex virus type-1 HSV-1
has_related_synonym: Herpes simplex virus 1
has_exact_synonym: Herpes simplex virus type 1
has_related_synonym: herpes simplex virus type 1 HSV1
has_related_synonym: herpes simplex virus type 1 HSV-1
has_related_synonym: herpes simplex virus HSV-1
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Human Herpesvirus-1

Solanum lycopersicum
type: Class
has_related_synonym: Solanum esculentum
definition: A species of genus Solanum.
has_related_synonym: Lycopersicon esculentum Mill.
has_related_synonym: Lycopersicum esculentum
has_related_synonym: Solanum lycopersicon
has_related_synonym: Solanum esculentum Dunal
has_related_synonym: Lycopersicon esculentum var. esculentum
has_related_synonym: Lycopersicon lycopersicum
subclass of: Spermatophyta
has_related_synonym: Lycopersicon esculentum
has_exact_synonym: Tomato
has_related_synonym: Solanum lycopersicum L.

Paired Region
type: Class
definition: A collection of one or more adjacent nucleotide residues in which at least one residue is part of a base pair.
subclass of: RNA Sequence Secondary Structure
definition_source: RNAO:0000095

Turbellaria
type: Class
subclass of: Platyhelminthes
definition: A class of phylum Platyhelminthes.

Brassica oleracea
type: Class
subclass of: Spermatophyta
has_related_synonym: Brassica oleracea L.
definition: A species of genus Brassica.

U6atac snRNA
type: Class
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.
definition_source: SO:0000397
subclass of: snRNA

3' Clip
type: Class
definition: 3'-most region of a precursor transcript that is clipped off during processing.
subclass of: Clip
definition_source: SO:0000557

Generically Dependent Continuant
type: Class
subclass of: Dependent Continuant
definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.
definition_source: snap:GenericallyDependentContinuant

Monocistronic Transcript
type: Class
definition_source: SO:0000665
subclass of: Transcript
definition: A transcript that is monocistronic.

Cunninghamia lanceolata
type: Class
has_related_synonym: Cunninghamia lanceolata (Lamb.) Hook.
definition: A species of genus Cunninghamia.
has_exact_synonym: China fir
subclass of: Spermatophyta

Branch Site
type: Class
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.
subclass of: Spliceosomal Intron Region
definition_source: SO:0000611

Interior Exon
type: Class
definition_source: SO:0000201
definition: An exon that is bounded by 5' and 3' splice sites.
subclass of: Exon

AU Rich Element
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Three Prime UTR
subclass of: UTR Region
definition_source: SO:0001180
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.

Transcribed Spacer Region
type: Class
definition: Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
definition_source: SO:0000638
subclass of: rRNA Primary Transcript Region

rRNA Primary Transcript Region
type: Class
subclass of: Restriction
  on property: part_of
  some values from: rRNA Primary Transcript
subclass of: Primary Transcript Region
definition: A region of an rRNA primary transcript.
definition_source: SO:0000838

JC polyomavirus
type: Class
has_related_synonym: polyomavirus JC
has_related_synonym: JC virus
has_related_synonym: Human polyomavirus (type JC)
has_related_synonym: JC polyomavirus JCV
has_related_synonym: human polyomavirus JCV
has_related_synonym: Polyomavirus hominis 2
definition: A dsDNA virus of family Polyomaviridae
subclass of: dsDNA virus, no RNA stage
has_related_synonym: polyoma virus JC JCV

Prunus persica
type: Class
subclass of: Spermatophyta
has_exact_synonym: peach
definition: A species of genus Prunus.
has_related_synonym: Prunus persica var densa
has_related_synonym: Amygdalus persica
has_related_synonym: Persica vulgaris

Coding Start
type: Class
definition_source: SO:0000323
subclass of: CDS Region
definition: The first base to be translated into a protein.

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.
definition_source: SO:0000990

Triticum aestivum
type: Class
has_exact_synonym: Common wheat
has_related_synonym: Triticum aestivum8
definition: A species of genus Triticum.
subclass of: Spermatophyta
has_exact_synonym: Wheat
has_exact_synonym: Bread wheat
has_related_synonym: Triticum vulgare
has_related_synonym: Tricum aestivum
has_related_synonym: Triticum aestivum subsp. aestivum
has_exact_synonym: Canadian hard winter wheat
has_related_synonym: Triticum aestivam

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.
definition_source: SO:0000387

Protein Coding Primary Transcript
type: Class
definition_source: SO:0000120
definition: A primary transcript that, at least in part, encodes one or more proteins.
subclass of: Primary Transcript

Oikopleura dioica
type: Class
subclass of: Appendicularia
definition: A species of genus Oikopleura.

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.
definition_source: SO:0000376

Lemur catta
type: Class
has_exact_synonym: Ring-tailed lemur
definition: A species of genus Lemur.
subclass of: Mammalia

Artibeus jamaicensis
type: Class
definition: A species of genus Artibeus.
has_exact_synonym: Jamaican fruit-eating bat
database_cross_reference: GC_ID:1
subclass of: Mammalia

Branchiostoma belcheri
type: Class
definition: A species of genus Branchiostoma.
subclass of: Branchiostomidae
has_exact_synonym: Belcher's lancelet

Brassica rapa
type: Class
subclass of: Spermatophyta
has_exact_synonym: Field mustard
definition: A species of genus Brassica.
has_related_synonym: Brassica rapa L.

5' UTR Intron
type: Class
definition_source: SO:0000447
subclass of: UTR Intron
definition: An intron located in the 5' UTR.

UTR Intron
type: Class
definition_source: SO:0000446
subclass of: Intron
definition: Intron located in the untranslated region.

Vitis vinifera
type: Class
subclass of: Spermatophyta
definition: A species of genus Vitis.
has_related_synonym: Vitis vinifera subsp. vinifera
has_exact_synonym: Wine grape

Glycine soja
type: Class
subclass of: Spermatophyta
has_exact_synonym: Wild soybean
definition: A species of genus Glycine.

U2 snRNA
type: Class
definition_source: SO:0000392
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.
subclass of: snRNA

Y RNA
type: Class
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.
subclass of: ncRNA
definition_source: SO:0000405

Drosophila mojavensis
type: Class
definition: A species of genus Drosophila.
has_related_synonym: Drosophila mohavensis
subclass of: Insecta

Minor TSS
type: Class
subclass of: TSS

Molecular Function
type: Class
definition: Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
definition_source: GO:0003674
subclass of: Function

Function
type: Class
definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
definition_source: snap:Function
subclass of: Realizable Entity

Internal Guide Sequence
type: Class
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.
subclass of: Restriction
  on property: part_of
  some values from: Group I Intron
subclass of: Intron Domain
definition_source: SO:0001016

Group I Intron
type: Class
subclass of: Autocatalutically Spliced Intron
definition_source: SO:0000587
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.

tmRNA Region
type: Class
definition: A region of a tmRNA.
subclass of: Restriction
  on property: part_of
  some values from: tmRNA
subclass of: Mature Transcript Region
definition_source: SO:0000847

Human herpesvirus 5
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Human cytomegalovirus HCMV
has_related_synonym: human cytomegalovirus CMV
has_related_synonym: human herpesvirus type 5
has_exact_synonym: Human cytomegalovirus

Polycistronic mRNA
type: Class
subclass of: mRNA
definition_source: SO:0000634
definition: An mRNA that encodes multiple proteins from at least two non-overlapping regions.

Internal Shine Dalgarno Sequence
type: Class
subclass of: Recoding Stimulatory Region
subclass of: Internal Ribosome Entry Site
definition_source: SO:1001260
definition: A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria.

Internal Ribosome Entry Site
type: Class
definition_source: SO:0000243
subclass of: Ribosome Entry Site
definition: Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.

Anthozoa
type: Class
definition: A class of phylum Cnidaria.
subclass of: Cnidaria

tmRNA Acceptor Piece
type: Class
definition_source: SO:0000770
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.
subclass of: tmRNA Region

rRNA 28S
type: Class
subclass of: Large Subunit rRNA
definition_source: SO:0000653
definition: A component of the large ribosomal subunit.

rRNA 16S
type: Class
definition: A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
subclass of: Small Subunit rRNA
definition_source: SO:0001000

Culex quinquefasciatus
type: Class
has_related_synonym: Culex quinquifasciatus
has_exact_synonym: Southern house mosquito
has_related_synonym: Culex quiquefasciatus
has_related_synonym: Culex pipiens quinquefasciatus
has_related_synonym: Culex quinquifasiatus
subclass of: Insecta
definition: A species of genus Culex.
has_related_synonym: Culex pipiens quiquefasciatus

tmRNA Coding Piece
type: Class
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.
subclass of: tmRNA Region
definition_source: SO:0000769

Ectocarpus siliculosus
type: Class
subclass of: Stramenopiles
definition: A species of genus Ectocarpus.

Stramenopiles
type: Class
has_exact_synonym: Heterokonts
subclass of: Plants
has_related_synonym: Chromophyta

Bandicoot papillomatosis carcinomatosis virus type 2
type: Class
definition: A dsDNA virus of family Papillomaviridae.
subclass of: dsDNA virus, no RNA stage

RRE RNA
type: Class
definition_source: SO:0000388
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.

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.
definition_source: SO:0000377

Simian virus 40
type: Class
has_related_synonym: Polyomavirus maccacae 1
has_related_synonym: Rhesus macaque polyomavirus
has_related_synonym: Polyomavirus maccacae
has_related_synonym: rhesus polyomavirus
definition: A dsDNA virus of family Polyomaviridae.
subclass of: dsDNA virus, no RNA stage

3' Stem-loop Structure
type: Class
subclass of: 3' Recoding Site
definition: A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region.
definition_source: SO:1001279

Threonyl tRNA
type: Class
definition_source: SO:0000270
definition: A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
subclass of: Restriction
  on property: derives_from
  some values from: Threonine tRNA Primary Transcript
subclass of: tRNA

Threonine tRNA Primary Transcript
type: Class
definition: A primary transcript encoding threonyl tRNA.
definition_source: SO:0000227
subclass of: tRNA Primary Transcript

Antisense lncRNA
type: Class
subclass of: Lnc RNA
definition: Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.
definition_source: SO:0001904

Alanyl tRNA
type: Class
definition_source: SO:0000254
definition: A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
subclass of: Restriction
  some values from: Alanine tRNA Primary Transcript
  on property: derives_from
subclass of: tRNA

Alanine tRNA Primary Transcript
type: Class
definition: A primary transcript encoding alanyl tRNA.
subclass of: tRNA Primary Transcript
definition_source: SO:0000211

Amphibia
type: Class
definition: A class of phylum Chordata.
subclass of: Chordata

Gossypium arboreum
type: Class
definition: A species of genus Gossypium.
has_related_synonym: Gossypium arboreum L.
subclass of: Spermatophyta
has_exact_synonym: Tree cotton

Annelida
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Malus x domestica
type: Class
has_exact_synonym: Cultivated apple
has_related_synonym: Pyrus malus
has_related_synonym: Malus pumila auct.
has_exact_synonym: Apple
has_related_synonym: Malus sylvestris var. domestica
has_exact_synonym: Apple tree
subclass of: Spermatophyta
definition: A species of genus Malus.
has_related_synonym: Malus domestica
has_related_synonym: Malus pumila var. domestica

Suid herpesvirus 1
type: Class
has_related_synonym: Pseudorabies Virus PRV
has_related_synonym: Suid herpesvirus type 1
has_related_synonym: Aujeszky's disease virus
has_related_synonym: Alphaherpesvirus pseudorabies virus PRV
has_exact_synonym: Pseudorabies virus
definition: A dsDNA virus of family Herpesviridae.
subclass of: dsDNA virus, no RNA stage

Biological Regulation
type: Class
definition_source: GO:0065007
definition: Any process that modulates the frequency, rate or extent of any biological process, quality or function.
subclass of: Biological Process

Helianthus petiolaris
type: Class
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_related_synonym: Helianthus petiolaris Nutt.

Ornithorhynchus anatinus
type: Class
has_exact_synonym: Duck-billed platypus
has_exact_synonym: Duckbill platypus
has_exact_synonym: Platypus
definition: A species of genus Ornithorhynchus.
has_related_synonym: Ornythorhynchus anatinus
subclass of: Mammalia

pre-edited mRNA
type: Class
subclass of: Protein Coding Primary Transcript

Interior Intron
type: Class
subclass of: Intron

Capped Primary Transcript
type: Class
subclass of: Primary Transcript
definition_source: SO:0000861
definition: A primary transcript that is capped.

SL6 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts.
definition_source: SO:0001751

Human herpesvirus 8
type: Class
has_related_synonym: Kaposi's sarcoma-associated herpesvirus
has_related_synonym: Karposi's sarcoma-associated herpes-like virus
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Human herpesvirus 8 type P
has_related_synonym: Kaposi's sarcoma-associated herpesvirus - Human herpesvirus 8
subclass of: dsDNA virus, no RNA stage
has_related_synonym: Kaposi's sarcoma-associated herpesvirus KSHV
has_related_synonym: Kaposi's sarcoma-associated human herpes virus
has_related_synonym: Kaposi's sarcoma-associated herpes-like virus

Internal Transcribed Spacer Region
type: Class
definition_source: SO:0000639
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.

Tyrosine tRNA Primary Transcript
type: Class
definition_source: SO:0000229
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding tyrosyl tRNA.

Transcript Bound by Protein
type: Class
definition: A transcript that is bound by a protein.
definition_source: SO:0000279
subclass of: Transcript

U2 Intron
type: Class
definition_source: SO:0000184
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.

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.
definition_source: SO:0000383

Antisense RNA
type: Class
definition: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
definition_source: SO:0000644
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: Antisense Primary Transcript

Rhesus monkey rhadinovirus H26-95
type: Class
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Macaca mulatta rhadinovirus 26-95
subclass of: dsDNA virus, no RNA stage

Aegilops tauschii
type: Class
has_related_synonym: Aegilops tauschii Coss.
has_related_synonym: Aegilops tauschii Cosson
has_related_synonym: Triticum tauschii
definition: A species of genus Aegilops.
has_related_synonym: Aegilops squarrosa subsp. squarrosa
subclass of: Spermatophyta
has_related_synonym: Aegilops squarrosa
has_related_synonym: Patropyrum tauschii subsp. tauschii
has_related_synonym: Patropyrum tauschii
has_related_synonym: Aegilops squarrosa auct.

Murid herpesvirus 4
type: Class
has_exact_synonym: Murine herpesvirus 68
definition: A dsDNA virus of family Herpesviridae.
subclass of: dsDNA virus, no RNA stage
has_related_synonym: mouse herpesvirus 68
has_related_synonym: murine gammaherpesvirus 68
has_related_synonym: murine herpesvirus type 68
has_related_synonym: mouse herpesvirus strain 68

Cryptic Splice SIte
type: Class
subclass of: Splice Site
definition_source: SO:0001533
definition: A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.

SL11 Acceptor Site
type: Class
definition: A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts.
subclass of: SL2 Acceptor Site
definition_source: SO:0001756

Helianthus exilis
type: Class
definition: A species of genus Helianthus.
subclass of: Spermatophyta
has_related_synonym: Helianthus exilis A.Gray

Cynara cardunculus
type: Class
has_related_synonym: Cynara cardunculus L.
has_exact_synonym: Cardoon
has_exact_synonym: Wild artichoke
subclass of: Spermatophyta
definition: A species of genus Cynara.

Antisense Primary Transcript
type: Class
definition_source: SO:0000645
subclass of: Primary Transcript
definition: The reverse complement of the primary transcript.

Leucyl tRNA
type: Class
definition_source: SO:0000264
definition: A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
subclass of: Restriction
  on property: derives_from
  some values from: Leucine tRNA Primary Transcript
subclass of: tRNA

Leucine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding leucyl tRNA.
definition_source: SO:0000221

Pseudouridylation Guide snoRNA
type: Class
definition: A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
subclass of: H/ACA Box snoRNA
definition_source: SO:0001187

H/ACA Box snoRNA
type: Class
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.
subclass of: Restriction
  some values from: H/ACA Box snoRNA Primary Transcript
  on property: derives_from
subclass of: snoRNA
definition_source: SO:0000594

Dengue Virus 3
type: Class
has_related_synonym: Dengue virus type 3
has_related_synonym: dengue 3 virus
subclass of: Dengue virus

Drosophila persimilis
type: Class
definition: A species of genus Drosophila.
subclass of: Insecta

Elaeis guineensis
type: Class
has_related_synonym: Elaeis guineensis var. tenera (Oil palm)
has_related_synonym: Elaeis gunieensis
definition: A species of genus Elaeis.
has_exact_synonym: African oil palm
has_related_synonym: Elaeis guinensi
subclass of: Spermatophyta
has_related_synonym: Elaeis guineensis var. tenera
has_related_synonym: Elaeis guineensis Jacq.

Consensus mRNA
type: Class
subclass of: mRNA

snRNA Primary Transcript
type: Class
definition: A primary transcript encoding a small nuclear RNA.
definition_source: SO:0000231
subclass of: Noncoding Primary Transcript

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.
definition_source: SO:0001647

Riboswitch
type: Class
definition_source: SO:0000035
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.

Gene
type: Class
subclass of: Biological Region
definition_source: SO:0000704
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.

Enhancer RNA
type: Class
definition: A short ncRNA that is transcribed from an enhancer. May have a regulatory function.
subclass of: ncRNA
definition_source: SO:0001870

Drosophila virilis
type: Class
subclass of: Insecta
has_related_synonym: Drosophila irilis
has_related_synonym: Drosophila virilis Sturtevant, 1916
definition: A species of genus Drosophila.

Disease
type: Class
subclass of: Disposition
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
definition_source: IDO:Disease

Disposition
type: Class
definition_source: snap:Disposition
definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
subclass of: Realizable Entity

Rehmannia glutinosa
type: Class
definition: A species of genus Rehmannia.
has_exact_synonym: Chinese foxglove
subclass of: Spermatophyta

Gossypium raimondii
type: Class
definition: A species of genus Gossypium.
subclass of: Spermatophyta
has_related_synonym: Gossypium raimondii Ulbr.

tasiRNA Primary Transcript
type: Class
definition: A primary transcript encoding a tasiRNA.
definition_source: SO:0001801
subclass of: Noncoding Primary Transcript

Quality
type: Class
definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
subclass of: Specifically Dependent Continuant
definition_source: snap:Quality

Human herpesvirus 4
type: Class
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Epstein-Barr virus EBV
has_related_synonym: Human herpesvirus type 4
has_related_synonym: Epstein-Barr-virus EBV
subclass of: dsDNA virus, no RNA stage
has_exact_synonym: Epstein-Barr virus

Edited Transcript by A to I Substitution
type: Class
definition: A transcript that has been edited by A to I substitution.
definition_source: SO:0000874
subclass of: Edited Transcript

Edited Transcript
type: Class
subclass of: Restriction
  on property: has_part
  some values from: Anchor Binding Site
subclass of: Restriction
  some values from: Guide RNA
  on property: guided_by
subclass of: Transcript
definition: A transcript that is edited.
definition_source: SO:0000873

Helianthus paradoxus
type: Class
subclass of: Spermatophyta
has_related_synonym: Helianthus paradoxus Heiser
definition: A species of genus Helianthus.

Aspartyl tRNA
type: Class
subclass of: Restriction
  on property: derives_from
  some values from: Aspartic acid tRNA Primary Transcript
subclass of: tRNA
definition: A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
definition_source: SO:0000257

3' Intron
type: Class
subclass of: Intron

Polyadenylated mRNA
type: Class
definition: An mRNA that is polyadenylated.
definition_source: SO:0000871
subclass of: mRNA

Paralichthys olivaceus
type: Class
has_exact_synonym: Japanese flounder
has_exact_synonym: Bastard halibut
subclass of: Actinopterygii
definition: A species of genus Paralichthys.
has_related_synonym: Paralichtys olivaceus
has_exact_synonym: Paralichthyidae sp. KYJ-2011
has_related_synonym: Hippoglossus olivaceus
has_exact_synonym: Olive flounder
has_exact_synonym: False halibut
has_related_synonym: Paralichthys olivaceus (Temminck & Schlegel, 1846)
has_related_synonym: Paralichthys olivaceous

Five Prime Coding Exon Noncoding Region
type: Class
definition_source: SO:0000486
definition: The sequence of the 5' exon preceding the start codon.
subclass of: Noncoding Region of Exon
subclass of: Restriction
  on property: part_of
  some values from: Five Prime Noncoding Exon

Five Prime Noncoding Exon
type: Class
subclass of: Noncoding Exon
definition: Non-coding exon in the 5' UTR.
definition_source: SO:0000445

Template Region
type: Class
definition: A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
definition_source: SO:0000978
subclass of: Guide RNA Region

Anolis carolinensis
type: Class
has_exact_synonym: Green anole
subclass of: Reptilia
definition: A species of genus Anolis.

Reptilia
type: Class
subclass of: Chordata
definition: Cold-blooded, air-breathing VERTEBRATES belonging to the class Reptilia, usually covered with external scales or bony plates.
definition_source: MSH:D012104

Zea mays
type: Class
definition: A species of genus Zea.
subclass of: Spermatophyta
has_exact_synonym: Maize
has_related_synonym: Zea mays var. japonica
has_related_synonym: Zea mays mays

Gasterosteus aculeatus
type: Class
has_related_synonym: Gasterosteus aculeatus Linnaeus, 1758
definition: A species of genus Gasterosteus.
subclass of: Actinopterygii
has_exact_synonym: Three-spined stickleback
has_exact_synonym: Three spined stickleback

Ascaris suum
type: Class
subclass of: Nematoda
has_exact_synonym: Pig roundworm
definition: A species of genus Ascaris.

Phaseolus vulgaris
type: Class
has_exact_synonym: French bean
has_exact_synonym: Kidney bean
has_exact_synonym: String bean
definition: A species of genus Phaseolus.
subclass of: Spermatophyta

Unedited Region
type: Class
definition: The region of an edited transcript that will not be edited.
subclass of: Edited Transcript Feature
definition_source: SO:0000607

Unpaired Region
type: Class
definition_source: RNAO:0000096
definition: A collection of one or more nucleotides that are not involved in base pairing.
subclass of: RNA Sequence Secondary Structure

Dengue virus 2
type: Class
subclass of: Dengue virus
has_related_synonym: Dengue virus type 2
has_related_synonym: dengue 2 virus DEN-2
has_related_synonym: dengue-2 virus
has_related_synonym: dengue-2 virus DEN-2
has_related_synonym: Dengue virus type II

Ovis aries
type: Class
has_exact_synonym: Sheep
has_related_synonym: Ovis ammon aries
subclass of: Mammalia
definition: A species of genus Ovis.
has_related_synonym: Ovis ovis
has_related_synonym: Ovis orientalis aries
has_exact_synonym: Lambs
has_exact_synonym: Wild sheep
has_exact_synonym: Domestic sheep

U3 snoRNA
type: Class
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.
subclass of: C/D Box snoRNA
definition_source: SO:0001179

DNA
type: Class
subclass of: Nucleic Acid
definition_source: CHEBI:16991
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.

Nucleic Acid
type: Class
definition_source: CHEBI:33696
definition: A macromolecule made up of nucleotide units and hydrolyzable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
subclass of: Information Biopolymer

Merkel cell polyomavirus
type: Class
definition: A dsDNA virus of family Polyomaviridae.
subclass of: dsDNA virus, no RNA stage

Carica papaya
type: Class
subclass of: Spermatophyta
has_exact_synonym: Mamon
has_exact_synonym: Papaya
has_related_synonym: Carica papaya L.
has_related_synonym: Carica payaya
definition: A species of genus Carica.

RNA Sequence
type: Class
definition: The sequence of nucleotide residues along an RNA chain.
subclass of: Generically Dependent Continuant
definition_source: NCI Thesaurus:RNA_Sequence
database_cross_reference: NCIThesaurus:DNA_Sequence

Physcomitrella patens
type: Class
subclass of: Bryophyta
definition: A species of genus Physcomitrella.

Bryophyta
type: Class
subclass of: Plants
definition: A phylum of Eukaryota.

RNA
type: Class
database_cross_reference: RNAO_0000000
subclass of: Nucleic Acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
definition_source: CHEBI:33697

Immaterial Entity
type: Class
definition_source: BFO:0000141
subclass of: Independent Continuant
definition: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth).

Symphalangus syndactylus
type: Class
has_related_synonym: Hylobates syndactylus
definition: A species of genus Symphalangus.
has_exact_synonym: Siamang
subclass of: Mammalia

Petromyzontidae
type: Class
definition: A class of phylum Chordata.
subclass of: Chordata

Leucosolenia complicata
type: Class
definition: A species of genus Leucosolenia.
subclass of: Calcarea

UAA Stop Codon Signal
type: Class
definition: A stop codon signal for a UAA stop codon redefinition.
subclass of: Stop Codon Signal
definition_source: SO:1001283

Stop Codon Signal
type: Class
subclass of: Recoding Stimulatory Region
definition: A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.
definition_source: SO:1001288

Tetranychus urticae
type: Class
has_related_synonym: Tetranychus urticae Koch, 1836
has_exact_synonym: Red spider mite
has_exact_synonym: Twospotted mite
has_exact_synonym: Two-spotted spider mite
definition: A species of genus Tetranychus.
subclass of: Arachnida

Picea abies
type: Class
definition: A species of genus Picea.
subclass of: Spermatophyta
has_related_synonym: Picea excelsa
has_related_synonym: Pinus abies
has_related_synonym: Picea abies L., Karst
has_exact_synonym: Norway spruce

U14 snoRNA
type: Class
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.
subclass of: C/D Box snoRNA
subclass of: Restriction
  some values from: U14 snoRNA Primary Transcript
  on property: derives_from
definition_source: SO:0000403

Demospongiae
type: Class
subclass of: Porifera
definition: A class of phylum Porifera.

Echinococcus multilocularis
type: Class
definition: A species of genus Echinococcus.
subclass of: Cestoda

Noncoding Exon
type: Class
definition_source: SO:0000198
subclass of: Exon
definition: An exon that does not contain any codons.

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.
definition_source: SO:0000708

Glutamyl tRNA
type: Class
definition: A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
subclass of: Restriction
  on property: derives_from
  some values from: Glutamine tRNA Primary Transcript
subclass of: tRNA
definition_source: SO:0000260

Dicistronic mRNA
type: Class
subclass of: Polycistronic mRNA
definition: An mRNA that has the quality dicistronic.
definition_source: SO:0000716

Arginine tRNA Primary Transcript
type: Class
definition_source: SO:0000212
definition: A primary transcript encoding arginyl tRNA.
subclass of: tRNA Primary Transcript

Posttranscriptional Regulation of Gene Expression
type: Class
subclass of: Restriction
  on property: preceded_by
  some values from: Transcription, DNA-dependent
subclass of: Regulation of Gene Expression
definition: Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
definition_source: GO:0010608

preceded_by
type: ObjectProperty
definition_source: RO:preceded_by
definition: P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.

Transcription, DNA-dependent
type: Class
subclass of: RNA Biosynthetic Process
subclass of: Restriction
  on property: part_of
  some values from: Gene Expression
definition_source: GO:0006351
definition: The cellular synthesis of RNA on a template of DNA.

Caenorhabditis remanei
type: Class
definition: A species of genus Caenorhabditis.
has_related_synonym: Caenorhabditis vulgaris Baird, Fitch & Emmons, 1994
has_related_synonym: Caenorhabditis vulgariensis
has_related_synonym: Caenorhabditis vulgaris
has_related_synonym: Caenorhabditis vulgarensis
subclass of: Nematoda

Non-canonical 5' Splice SIte
type: Class
subclass of: 5' cis Splice Site
definition_source: SO:0000679
definition: A 5' splice site which does not have the sequence "GT".

DNA Sequence
type: Class
definition_source: NCI Thesaurus:DNA_Sequence
subclass of: Generically Dependent Continuant
database_cross_reference: NCIThesaurus:DNA_Sequence
definition: The sequence of nucleotide residues along a DNA chain.

Bovine herpesvirus 1
type: Class
has_related_synonym: bovine herpesvirus type 1 BHV-1
subclass of: dsDNA virus, no RNA stage
has_related_synonym: bovine herpesvirus 1 BHV 1
has_related_synonym: bovine herpesvirus type-1 BHV-1
has_related_synonym: bovine herpesvirus 1 BHV-1
has_related_synonym: bovine herpesvirus BHV-1
has_related_synonym: Bovine herpesvirus type 1
has_related_synonym: Bovine rhinotracheitis virus
has_related_synonym: infectious bovine rhinotracheitis virus BHV-1
has_related_synonym: Infectious bovine rhinotracheitis virus
has_related_synonym: bovine herpesvirus 1 BHV1
has_related_synonym: Bovine herpesvirus-1
definition: A dsDNA virus of family Herpesviridae.

UAG Stop Codon Signal
type: Class
definition_source: SO:1001282
definition: A stop codon signal for a UAG stop codon redefinition.
subclass of: Stop Codon Signal

Edited mRNA
type: Class
definition_source: SO:0000929
definition: An mRNA that is edited.
subclass of: mRNA

U6 snRNA
type: Class
definition_source: SO:0000396
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.
subclass of: snRNA

Editing Block
type: Class
definition_source: SO:0000604
subclass of: Edited Transcript Feature
definition: Edited mRNA sequence mediated by a single guide RNA (SO:0000602).

Human herpesvirus 2
type: Class
has_related_synonym: Herpes simplex virus (type 2)
has_related_synonym: Herpes simplex virus 2
has_related_synonym: Herpes simplex virus type 2
has_related_synonym: herpes simplex virus type 2 HSV-2
definition: A dsDNA virus of family Herpesviridae.
subclass of: dsDNA virus, no RNA stage

Helianthus argophyllus
type: Class
definition: A species of genus Helianthus.
has_related_synonym: Helianthus argophyllus Torr. & A.Gray
subclass of: Spermatophyta

Panagrellus redivivus
type: Class
definition: A species of genus Panagrellus.
subclass of: Nematoda

Edited CDS
type: Class
definition_source: SO:0000935
definition: A CDS that is edited.
subclass of: CDS

Digitalis purpurea
type: Class
has_exact_synonym: Common foxglove
definition: A species of genus Digitalis.
subclass of: Spermatophyta
has_related_synonym: Digitalis purpurea L.

Xenoturbella bocki
type: Class
subclass of: Xenacoelomorpha
definition: A species of genus Xenoturbella.

Group IIA Intron
type: Class
subclass of: Group II Intron

Group II Intron
type: Class
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-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.
definition_source: SO:0000603
subclass of: Autocatalutically Spliced Intron

SL4 Acceptor Site
type: Class
definition_source: SO:0001749
subclass of: SL2 Acceptor Site
definition: A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts.

mRNA with Plus 1 Frameshift
type: Class
definition: An mRNA with a plus 1 frameshift.
definition_source: SO:0000321
subclass of: mRNA with Frameshift

Bos taurus
type: Class
has_exact_synonym: Domestic cow
has_exact_synonym: Cattle
has_exact_synonym: Domestic cattle
has_related_synonym: Bos bovis
has_related_synonym: Bos primigenius taurus
definition: A species of genus Bos.
has_related_synonym: Bos tauurus
subclass of: Mammalia
has_exact_synonym: Bovine
has_exact_synonym: Cow

Anchor Binding Site
type: Class
subclass of: Transcript Region

mRNA with Minus 2 Frameshift
type: Class
definition_source: SO:0000335
definition: A mRNA with a minus 2 frameshift.
subclass of: mRNA with Frameshift

rRNA 23S
type: Class
definition_source: SO:0001001
subclass of: Large Subunit rRNA
definition: A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.

Three Prime Coding Exon
type: Class
definition_source: SO:0000202
definition: The coding exon that is most 3-prime on a given transcript.
subclass of: Coding Exon

Anticodon Loop
type: Class
definition_source: SO:0001173
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.
subclass of: tRNA Region

Caenorhabditis brenneri
type: Class
has_exact_synonym: Caenorhabditis n. sp. CB5161
has_exact_synonym: Caenorhabditis sp. 1 CB5161
has_exact_synonym: Caenorhabditis sp. PB2801
has_exact_synonym: Caenorhabditis CB5161
has_exact_synonym: Caenorhabditis sp. CB5161
subclass of: Nematoda
definition: A species of genus Caenorhabditis.

Intronic lncRNA
type: Class
definition_source: SO:0001903
subclass of: Lnc RNA
definition: A lnc_RNA totally contained within an intron.

Monodelphis domestica
type: Class
has_exact_synonym: Gray short-tailed opossum
definition: A species of genus Monodelphis.
has_related_synonym: Monodelphis domesticus
subclass of: Mammalia

Hemichordata
type: Class
definition: A phylum of kingdom Animalia.
subclass of: Metazoa

Lotus japonicus
type: Class
subclass of: Spermatophyta
definition: A species of genus Lotus.
has_related_synonym: Lotus corniculatus var. japonicus

CDS Independently Known
type: Class
definition: A CDS with the evidence status of being independently known.
subclass of: CDS
definition_source: SO:1001246

Telomerase RNA
type: Class
subclass of: ncRNA
definition_source: SO:0000390
definition: The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.

rRNA 5S
type: Class
definition_source: SO:0000652
subclass of: Large Subunit rRNA
definition: 5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription.

SL3 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition_source: SO:0001748
definition: A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts.

BK polyomavirus
type: Class
has_related_synonym: polyomavirus BK
has_related_synonym: Papovavirus BKV
definition: A dsDNA virus of family Polyomaviridae.
subclass of: dsDNA virus, no RNA stage
has_related_synonym: human polyomavirus type BK BKV
has_related_synonym: polyomavirus homonis 1
has_related_synonym: Human polyomavirus BKV
has_related_synonym: Human polyomavirus BK
has_related_synonym: BK virus
has_related_synonym: BK virus BKV
has_related_synonym: Polyomavirus hominis 1
has_related_synonym: Human polyomavirus (type BK)

Human immunodeficiency virus 2
type: Class
has_related_synonym: HIV type 2
subclass of: Retro-transcribing virus
has_related_synonym: human immunodeficiency virus type 2 HIV-2
has_related_synonym: Human immunodeficiency virus-2
has_related_synonym: AIDS virus
definition: A retro-transcribing virus of family Retroviridae.
has_related_synonym: Human immunodeficiency virus type 2
has_related_synonym: human immunodeficiency virus type 2, HIV-2

Drosophila ananassae
type: Class
definition: A species of genus Drosophila.
has_related_synonym: Drosophila annanassae
subclass of: Insecta

Pinus taeda
type: Class
subclass of: Spermatophyta
has_exact_synonym: Loblolly pine
definition: A species of genus Pinus.

Collection of Material Entities
type: Class
subclass of: Material Entity

Gallid herpesvirus 2
type: Class
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Gallid herpesvirus type 2
has_related_synonym: Marek's disease virus MDV1
has_related_synonym: Gallid herpesvirus 1 (serotype 1)
has_related_synonym: Marek's disease virus
subclass of: dsDNA virus, no RNA stage
has_related_synonym: Marek disease virus
has_related_synonym: Marek's disease herpesvirus
has_related_synonym: Marek's disease herpesvirus 1
has_related_synonym: Marek's disease virus type 1 MDV1
has_related_synonym: Marek's disease virus type 1
has_exact_synonym: Marek disease virus type 1
has_related_synonym: Marek's disease virus (MDV)
has_related_synonym: Marek's disease virus MDV
has_related_synonym: Marek's disease virus serotype 1 MDV-1

scRNA Primary Transcript
type: Class
subclass of: Noncoding 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.
definition_source: SO:0000012

Twintron
type: Class
subclass of: Intron
definition_source: SO:0000406
definition: An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.

Ictalurus punctatus
type: Class
has_exact_synonym: Channel catfish
definition: A species of genus Ictalurus.
has_related_synonym: Ictalurus punctatus (Rafinesque, 1818)
has_related_synonym: Silurus punctatus
subclass of: Actinopterygii

pri-miRNA Binding
type: Class
definition: Interacting selectively and non-covalently with a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding.
subclass of: Restriction
  some values from: pri-miRNA
  on property: has_agent
subclass of: RNA Binding
definition_source: GO:0070878

Alternatively Spliced Transcript
type: Class
subclass of: Transcript
definition_source: SO:1001187
definition: A transcript that is alternatively spliced.

Isoleucyl tRNA
type: Class
subclass of: Restriction
  some values from: Isoleucine tRNA Primary Transcript
  on property: derives_from
subclass of: tRNA
definition_source: SO:0000263
definition: A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.

Isoleucine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding isoleucyl tRNA.
definition_source: SO:0000220

Tribolium castaneum
type: Class
definition: A species of genus Tribolium.
has_exact_synonym: Red flour beetle
has_exact_synonym: Rust-red flour beetle
subclass of: Insecta

Gallid herpesvirus 1
type: Class
has_related_synonym: Avian infectious laryngotracheitis virus
has_related_synonym: Infectious laryngotracheitis virus
has_related_synonym: Gallid herpesvirus type 1
has_related_synonym: Laryngotracheitis virus
has_related_synonym: infectious laryngotracheitis virus ILTV
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.

Mini Exon Donor RNA
type: Class
definition_source: SO:0000635
definition: A primary transcript that donates the spliced leader to other mRNA.
subclass of: Primary Transcript

Citrus clementina
type: Class
has_related_synonym: Citrus clementina hort. ex Tanaka
subclass of: Spermatophyta
definition: A species of genus Citrus.

Phaeodactylum tricornutum
type: Class
definition: A species of genus Phaeodactylum.
subclass of: Stramenopiles

Nasonia vitripennis
type: Class
subclass of: Insecta
has_related_synonym: Nasonia vitripennis (Walker, 1836)
definition: A species of genus Nasonia.
has_exact_synonym: Jewel wasp

Plus 1 Translational Frameshift
type: Class
subclass of: Translational Frameshift
definition_source: SO:0001211
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.

Anchor Region
type: Class
definition: A region of a guide_RNA that base-pairs to a target mRNA.
definition_source: SO:0000931
subclass of: Guide RNA Region

has_part
type: ObjectProperty

guided_by
type: ObjectProperty

Process
type: Class
definition_source: span:Process
definition: A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
subclass of: Occurent

Macropus eugenii
type: Class
definition: A species of genus Macropus.
subclass of: Mammalia
has_exact_synonym: Tammar wallaby

scRNA
type: Class
definition_source: SO:0000013
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: scRNA Primary Transcript
definition: Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.

SL10 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition_source: SO:0001755
definition: A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts.

4bp Start Codon
type: Class
definition: A non-canonical start codon with 4 base pairs.
subclass of: Non-canonical Start Codon
definition_source: SO:1001269

Equus caballus
type: Class
has_exact_synonym: Equine
has_related_synonym: Equus przewalskii f. caballus
has_related_synonym: Equus przewalskii forma caballus
has_exact_synonym: Domestic horse
definition: A species of genus Equus.
has_related_synonym: Equus ferus caballus
subclass of: Mammalia
has_exact_synonym: Horse

Hevea brasiliensis
type: Class
has_exact_synonym: Jebe
has_exact_synonym: Rubbertree
has_exact_synonym: Para rubber tree
has_exact_synonym: Siringa
subclass of: Spermatophyta
has_related_synonym: Hevea brasiliensis (Willd. ex A.Juss.) Muell. Arg.
definition: A species of genus Hevea.

Anticodon
type: Class
definition_source: SO:0001174
definition: A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
subclass of: Restriction
  some values from: Anticodon Loop
  on property: part_of
subclass of: tRNA Region

Prolyl tRNA
type: Class
definition_source: SO:0000268
definition: A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
subclass of: Restriction
  on property: derives_from
  some values from: Proline tRNA Primary Transcript
subclass of: tRNA

CTG Start Codon
type: Class
definition_source: SO:1001273
definition: A non-canonical start codon of sequence CTG.
subclass of: Non-canonical Start Codon

Bruguiera cylindrica
type: Class
subclass of: Spermatophyta
has_related_synonym: Bruguiera cylindrica (L.) Blume
definition: A species of genus Bruguiera.

Schmidtea mediterranea
type: Class
has_exact_synonym: Freshwater planarian
definition: A species of genus Schmidtea.
subclass of: Turbellaria
has_related_synonym: Dugesia (Schmidtea) mediterranea
has_related_synonym: Dugesia mediterranea

Endonuclease Spliced Intron
type: Class
definition_source: SO:0001216
subclass of: Intron
definition: An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.

Group IIB Intron
type: Class
subclass of: Group II Intron

Autocatalutically Spliced Intron
type: Class
definition: A self spliced intron.
subclass of: Intron
definition_source: SO:0000588

Exon of Single Exon Gene
type: Class
subclass of: Exon
definition: An exon that is the only exon in a gene.
definition_source: SO:0005845

Vault RNA
type: Class
subclass of: ncRNA
definition_source: SO:0000404
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.

Tryptophan tRNA Primary Transcript
type: Class
definition_source: SO:0000228
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding tryptophanyl tRNA.

DsrA RNA
type: Class
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.
subclass of: Small Regulatory ncRNA
definition_source: SO:0000378

Dengue Virus 4
type: Class
has_related_synonym: Dengue virus type 4
has_related_synonym: dengue type 4 virus DEN4
subclass of: Dengue virus

Human herpesvirus 6B
type: Class
has_related_synonym: Human herpesvirus 6 type B
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.

Saccharum officinarum
type: Class
definition: A species of genus Saccharum.
has_exact_synonym: Sugarcane
has_exact_synonym: Noble cane
subclass of: Spermatophyta

3' Repeat Recoding Signal
type: Class
subclass of: 3' Recoding Site
definition_source: SO:1001286
definition: A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.

Selenocysteinyl tRNA
type: Class
definition_source: SO:0005857
subclass of: Restriction
  on property: derives_from
  some values from: Selenocysteine tRNA Primary Transcript
subclass of: tRNA
definition: A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.

Selenocysteine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition_source: SO:0005856
definition: A primary transcript encoding seryl tRNA.

SL12 Acceptor Site
type: Class
definition: A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts.
definition_source: SO:0001757
subclass of: SL2 Acceptor Site

Ixodes scapularis
type: Class
definition: A species of genus Ixodes.
subclass of: Arachnida
has_related_synonym: Ixodes dammini
has_exact_synonym: Shoulder tick
has_exact_synonym: Blacklegged tick
has_exact_synonym: Black-legged tick
has_exact_synonym: Deer tick

Gene Silencing by miRNA
type: Class
definition: Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
definition_source: GO:0035195
subclass of: Restriction
  on property: has_agent
  some values from: miRNA
subclass of: Posttranscriptional Gene Silencing by RNA

Cricetulus griseus
type: Class
definition: A species of genus Cricetulus.
has_related_synonym: Cricetulus barabensis griseus
has_related_synonym: Cricetus griseus
has_exact_synonym: Cricetulus aureus
has_exact_synonym: Chinese hamster
subclass of: Mammalia

Translation
type: Class
definition_source: GO:0006412
definition: The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome.
subclass of: Protein Metabolic Process
subclass of: Restriction
  on property: part_of
  some values from: Gene Expression

Protein Metabolic Process
type: Class
subclass of: Metabolic Process
definition: The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
definition_source: GO:0019538

Stop Codon Redefined as Pyrrolysine
type: Class
definition: A stop codon redefined to be the new amino acid, pyrrolysine.
definition_source: SO:0000884
subclass of: Stop Codon Read Through

Protein
type: Class
subclass of: Information Biopolymer
subclass of: Restriction
  on property: has_role
  some values from: Transcription Factor
definition_source: CHEBI:36080
definition: A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.

has_role
type: ObjectProperty

Caenorhabditis briggsae
type: Class
subclass of: Nematoda
definition: A species of genus Caenorhabditis.

Transcription End Site
type: Class
definition_source: SO:0000616
subclass of: Primary Transcript Region
definition: The base where transcription ends.

mRNA with Plus 2 Frameshift
type: Class
definition: An mRNA with a plus 2 frameshift.
definition_source: SO:0000329
subclass of: mRNA with Frameshift

Monocistronic Primary Transcript
type: Class
subclass of: Monocistronic Transcript
definition: A primary transcript encoding for one gene product.
definition_source: SO:0000632

Brachypodium distachyon
type: Class
subclass of: Spermatophyta
definition: A species of genus Brachypodium.

3' UTR Intron
type: Class
definition: An intron located in the 3' UTR.
definition_source: SO:0000448
subclass of: UTR Intron

Amphimedon queenslandica
type: Class
subclass of: Demospongiae
definition: A species of genus Amphimedon.
has_related_synonym: Reniera sp. JGI-2005

Lycopodiophyta
type: Class
definition: A division of Eukaryota.
subclass of: Plants

Cucumis melo
type: Class
definition: A species of genus Cucumis.
has_related_synonym: Cucurbita melo L.
has_related_synonym: Cucumis melo var. markuwa Markino
has_exact_synonym: Oriental melon
has_exact_synonym: Muskmelon
subclass of: Spermatophyta

Petromyzon marinus
type: Class
has_exact_synonym: Sea lamprey
has_exact_synonym: Marine lamprey
definition: A species of genus Petromyzon.
subclass of: Petromyzontidae

UGA Stop Codon Signal
type: Class
subclass of: Stop Codon Signal
definition: A stop codon signal for a UGA stop codon redefinition.
definition_source: SO:1001285

Transcript with Translational Frameshift
type: Class
definition: A transcript with a translational frameshift.
definition_source: SO:0000118
subclass of: Transcript

External Transcribed Spacer Region
type: Class
definition: Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
subclass of: Transcribed Spacer Region
definition_source: SO:0000640

Chlorophyta
type: Class
subclass of: Plants
definition: A phylum of Eukaryota.

Pre-edited Region
type: Class
definition: The region of a transcript that will be edited.
subclass of: Edited Transcript Feature
definition_source: SO:0000583

Enteropneusta
type: Class
subclass of: Hemichordata
definition: A class of phylum Hemichordata.

Aberrant Processed Transcript
type: Class
definition: A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
definition_source: SO:0000681
subclass of: Transcript

Linc RNA
type: Class
definition_source: SO:0001463
subclass of: Lnc RNA
definition: A multiexonic non-coding RNA transcribed by RNA polymerase II.

Polypirimidine 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.
definition_source: SO:0000612

Trans Splice Donor Site
type: Class
definition: The 5' five prime splice site region of the donor RNA.
subclass of: Trans Splice Site
definition_source: SO:0000707

Glycyl tRNA
type: Class
subclass of: Restriction
  some values from: Glycine tRNA Primary Transcript
  on property: derives_from
subclass of: tRNA
definition_source: SO:0000261
definition: A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.

Stop Codon
type: Class
subclass of: Codon
definition_source: SO:0000319
definition: In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.

Asparaginyl tRNA
type: Class
definition: A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
subclass of: Restriction
  some values from: Asparagine tRNA Primary Transcript
  on property: derives_from
subclass of: tRNA
definition_source: SO:0000256

Asparagine tRNA Primary Transcript
type: Class
definition: A primary transcript encoding asparaginyl tRNA.
subclass of: tRNA Primary Transcript
definition_source: SO:0000213

Continuant
type: Class
definition_source: snap:Continuant
definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.

Tetraodon nigroviridis
type: Class
subclass of: Actinopterygii
has_exact_synonym: Spotted green pufferfish
has_related_synonym: Tetraodon nigroviridis Marion de Proce, 1822
definition: A species of genus Tetraodon.

Archaeal Intron
type: Class
definition: An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease.
subclass of: Endonuclease Spliced Intron
definition_source: SO:1001271

5' Clip
type: Class
definition_source: SO:0000555
definition: 5' most region of a precursor transcript that is clipped off during processing.
subclass of: Clip

Tyrosyl tRNA
type: Class
definition_source: SO:0000272
subclass of: Restriction
  on property: derives_from
  some values from: Tyrosine tRNA Primary Transcript
subclass of: tRNA
definition: A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.

Sycon ciliatum
type: Class
definition: A species of genus Sycon.
has_related_synonym: Scypha ciliata
subclass of: Calcarea

SL5 Acceptor Site
type: Class
definition_source: SO:0001750
subclass of: SL2 Acceptor Site
definition: A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts.

Polycistronic Primary Transcript
type: Class
definition: A primary transcript encoding for more than one gene product.
definition_source: SO:0000631
subclass of: Primary Transcript

Helianthus tuberosus
type: Class
has_exact_synonym: Jerusalem artichoke
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_related_synonym: Helianthus tuberosus L.

Nasonia giraulti
type: Class
subclass of: Insecta
definition: A species of genus Nasonia.

CDS Fragment
type: Class
subclass of: CDS

Gorilla gorilla
type: Class
has_exact_synonym: Gorilla
has_exact_synonym: Western gorilla
definition: A species of genus Gorilla.
subclass of: Mammalia

OxyS RNA
type: Class
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.
subclass of: Small Regulatory ncRNA
definition_source: SO:0000384

Selaginella moellendorffii
type: Class
subclass of: Lycopodiophyta
definition: A species of genus Selaginella.
has_related_synonym: Selaginella moellendorfii
has_related_synonym: Selaginella moellendorffii Hieron

Non-canonical 3' Splice Site
type: Class
definition: A 3' splice site that does not have the sequence "AG".
subclass of: 3' cis Splice Site
definition_source: SO:0000678

Chlamydomonas reinhardtii
type: Class
subclass of: Chlorophyta
definition: A species of genus Chlamydomonas.
has_related_synonym: Chlamydomonas smithii R.W.Howshaw & H.Ettl
has_related_synonym: Chlamydomonas smithii
has_related_synonym: Chlamydomonas reinhardtii P.A.Dangeard
has_related_synonym: Chlamydomonas reihhardtii

Xenopus (Silurana) tropicalis
type: Class
has_exact_synonym: Western clawed frog
subclass of: Amphibia
definition: A species of genus Xenopus.
has_related_synonym: Xenopus tropicalis
has_related_synonym: Xenopus laevis tropicalis
has_related_synonym: Silurana tropicalis

Five Prime Coding Exon
type: Class
subclass of: Coding Exon
definition: The 5' most coding exon.
definition_source: SO:0000200

Gossypium hirsutum
type: Class
has_exact_synonym: Upland cotton
has_related_synonym: Gossypium hirsutum subsp. mexicanum
subclass of: Spermatophyta
has_related_synonym: Gossypium lanceolatum
has_related_synonym: Gossypium purpurascens
has_exact_synonym: American cotton
definition: A species of genus Gossypium.
has_exact_synonym: Cotton

Bovine leukemia virus
type: Class
subclass of: Retro-transcribing virus
definition: A retro-transcribing virus of family Retroviridae.
has_related_synonym: bovine leukemia virus BLV
has_related_synonym: bovine leukemia virus, BLV

Pan paniscus
type: Class
definition: A species of genus Pan.
has_exact_synonym: Pygmy chimpanzee
has_exact_synonym: Bonobo
subclass of: Mammalia

Drosophila pseudoobscura
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.

Interior Coding Exon
type: Class
subclass of: Coding Exon

tasiRNA
type: Class
definition_source: SO:0001800
definition: The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.
subclass of: Restriction
  some values from: tasiRNA Primary Transcript
  on property: derives_from
subclass of: ncRNA

Hordeum vulgare
type: Class
subclass of: Spermatophyta
has_exact_synonym: Barley
definition: A species of genus Hordeum.
has_related_synonym: Hordeum vulgare L.
has_related_synonym: Horedum vulgare

Capitella sp. 1
type: Class
definition: A species of genus Capitella.
subclass of: Annelida

Tryptophanyl tRNA
type: Class
subclass of: Restriction
  on property: derives_from
  some values from: Tryptophan tRNA Primary Transcript
subclass of: tRNA
definition: A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
definition_source: SO:0000271

Dicistronic Primary Transcript
type: Class
definition_source: SO:1001197
definition: A primary transcript that has the quality dicistronic.
subclass of: Polycistronic Primary Transcript

mRNA Recoded by Translation Bypass
type: Class
definition: A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.
definition_source: SO:1001264
subclass of: Recoded mRNA

U1 snRNA
type: Class
definition_source: SO:0000391
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.

Pristionchus pacificus
type: Class
definition: A species of genus Pristionchus.
subclass of: Nematoda

Cyprinus carpio
type: Class
has_related_synonym: Cyprinus cyprio
has_related_synonym: Cyrpinus carpio
subclass of: Actinopterygii
has_exact_synonym: Common carp
has_exact_synonym: Carp
definition: A species of genus Cyprinus.

Ciona intestinalis
type: Class
definition: A species of genus Ciona.
subclass of: Ascidiacea

CCA Tail
type: Class
subclass of: tRNA Region
definition_source: SO:0001175
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.

Splice Region
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Primary Transcript
subclass of: Primary Transcript Region
definition: A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
definition_source: SO:0001902

Schistosoma japonicum
type: Class
subclass of: Digenea
definition: A species of genus Schistosoma.

RNase MRP RNA
type: Class
subclass of: ncRNA
definition_source: SO:0000385
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.

Group III Intron
type: Class
definition_source: SO:0001213
subclass of: Autocatalutically 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.

U4atac snRNA
type: Class
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.
subclass of: snRNA
definition_source: SO:0000394

rasiRNA
type: Class
subclass of: ncRNA
definition: A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
definition_source: SO:0000454

rRNA 5_8S
type: Class
subclass of: Large Subunit rRNA
definition: 5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.
definition_source: SO:0000375

Strand End
type: Class
subclass of: RNA Sequence Secondary Structure
definition: A sequence_region bounded at one end by the 5' or 3' end of the molecule, and at the other by an unbroken_stem. [RNAO:0000107]
definition_source: RNAO:0000107

T Loop
type: Class
definition: Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
subclass of: tRNA Region
definition_source: SO:0001177

Mus musculus
type: Class
has_exact_synonym: House mouse
has_exact_synonym: Mouse
has_related_synonym: mice C57BL/6xCBA/CaJ hybrid
has_related_synonym: Mus muscaris
definition: A species of genus Mus.
subclass of: Mammalia

Arginyl tRNA
type: Class
definition: A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
subclass of: Restriction
  on property: derives_from
  some values from: Arginine tRNA Primary Transcript
subclass of: tRNA
definition_source: SO:0001036

Acacia mangium
type: Class
subclass of: Spermatophyta
has_related_synonym: Acacia mangium Willd
definition: A species of genus Acacia.

Danio rerio
type: Class
has_related_synonym: Cyprinus rerio Hamilton, 1822
has_related_synonym: Brachydanio rerio
has_exact_synonym: Zebra danio
has_related_synonym: Brachidanio rerio
subclass of: Actinopterygii
has_exact_synonym: Zebrafish
has_related_synonym: Danio rerio frankei
has_related_synonym: Brachydanio rerio frankei
has_related_synonym: Cyprinus rerio
definition: A species of genus Danio.
has_exact_synonym: Leopard danio
has_related_synonym: Danio frankei
has_exact_synonym: Zebra fish
has_related_synonym: Danio rerio (Hamilton, 1822)

Lottia gigantea
type: Class
subclass of: Gastropoda
definition: A species of genus Lottia.

Citrus trifoliata
type: Class
subclass of: Spermatophyta
has_related_synonym: Poncirus trifoliate
has_related_synonym: Citrus trifoliatus
definition: A species of genus Citrus.
has_related_synonym: Poncirus trifoliatus
has_exact_synonym: Trifoliate orange
has_exact_synonym: Hardy orange
has_related_synonym: Poncirus trifoliata

SL9 Acceptor Site
type: Class
definition_source: SO:0001754
definition: A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts.
subclass of: SL2 Acceptor Site

Rhinopithecus bieti
type: Class
subclass of: Mammalia
definition: A species of genus Pygathrix.
has_exact_synonym: Black snub-nosed monkey
has_related_synonym: Pygathrix bieti

CDS Supported by EST or cDNA Data
type: Class
definition: A CDS that is supported by similarity to EST or cDNA data.
definition_source: SO:1001259
subclass of: CDS Supported by Sequence SImilarity Data

GcvB RNA
type: Class
subclass of: DsrA RNA
definition_source: SO:0000379
definition: A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.

Nematostella vectensis
type: Class
definition: A species of genus Nematostella.
subclass of: Anthozoa
has_related_synonym: Nematostella vectensis Stephenson, 1935
has_exact_synonym: Starlet sea anemone

Ateles geoffroyi
type: Class
subclass of: Mammalia
has_related_synonym: Ateles jeoffroyi
has_related_synonym: Ateles geoffreyi
definition: A species of genus Ateles.
has_exact_synonym: Black-handed spider monkey
has_exact_synonym: Central American spider monkey

Drosophila grimshawi
type: Class
definition: A species of genus Drosophila.
has_related_synonym: Idiomyia grimshawi
subclass of: Insecta

Phenylalanyl tRNA
type: Class
subclass of: Restriction
  some values from: Phenylalanine tRNA Primary Transcript
  on property: derives_from
subclass of: tRNA
definition: A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
definition_source: SO:0000267

Solanum tuberosum
type: Class
definition: A species of genus Solanum.
has_related_synonym: Solanum tuberosum subsp. tuberosum
has_exact_synonym: Potato
subclass of: Spermatophyta

Murid herpesvirus 1
type: Class
has_related_synonym: Mouse cytomegalovirus 1
has_related_synonym: murine cytomegalovirus MCMV
has_related_synonym: murine herpesvirus 1
has_related_synonym: murine cytomegalovirus (MCMV)
definition: A dsDNA virus of family Herpesviridae
subclass of: dsDNA virus, no RNA stage
has_exact_synonym: Murine cytomegalovirus

Strongylocentrotus purpuratus
type: Class
subclass of: Echinoidea
has_exact_synonym: Purple sea urchin
has_exact_synonym: Purple urchin
definition: A species of genus Strongylocentrotus.
has_related_synonym: Strongylocentrotus purpuratus (Stimpson, 1857)

Marsupenaeus japonicus
type: Class
subclass of: Malacostraca
definition: A species of genus Marsupenaeus.
has_related_synonym: Penaeus japonicus
has_related_synonym: Penaeus (Marsupenaeus) japonicus
has_related_synonym: Penaeus (Melicertus) japonicus

miRNA Antiguide
type: Class
definition: A region of the pri miRNA that basepairs with the guide to form the hairpin.
definition_source: SO:0001473
subclass of: miRNA Primary Transcript Region

Capitella teleta
type: Class
has_related_synonym: Capitella sp. I ES-2005
definition: A species of genus Capitella.
has_related_synonym: Capitella telata
subclass of: Annelida
has_related_synonym: Capitella sp. I AF-2005
has_related_synonym: Capitella sp. I ECS-2004
has_related_synonym: Capitella sp. I
has_related_synonym: Capitella sp. I Grassle & Grassle, 1976

Brassica napus
type: Class
has_exact_synonym: Rape
has_exact_synonym: Oilseed rape
has_exact_synonym: Rapeseeds
subclass of: Spermatophyta
definition: A species of genus Brassica.

tRNA Intron
type: Class
definition_source: SO:1001272
definition: An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.
subclass of: Endonuclease Spliced Intron

Triticum turgidum
type: Class
definition: A species of genus Triticum.
has_exact_synonym: English wheat
has_related_synonym: Triticum aethiopicum
has_related_synonym: Triticum turgidum8
has_related_synonym: Triticum turgidum L.
subclass of: Spermatophyta
has_exact_synonym: Cone wheat
has_exact_synonym: Poulard wheat
has_related_synonym: Triticum aethiopicum Jakubz.
has_exact_synonym: Rivet wheat

Spot 42 RNA
type: Class
definition_source: SO:0000389
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.
subclass of: Small Regulatory ncRNA

miRNA Stem
type: Class
subclass of: Restriction
  on property: part_of
  some values from: pre-miRNA
subclass of: miRNA Primary Transcript Region
definition: The stem of the hairpin loop formed by folding of the pre-miRNA.
definition_source: SO:0001245

Arabidopsis thaliana
type: Class
definition: A species of genus Arabidopsis.
subclass of: Spermatophyta
has_exact_synonym: Mouse-ear cress
has_exact_synonym: Thale cress
has_exact_synonym: Thale-cress
has_related_synonym: Arbisopsis thaliana
has_related_synonym: Arabidopsis thaliana (thale cress)

siRNA
type: Class
subclass of: ncRNA
definition_source: SO:0000646
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. SRNAs trigger the cleavage of their target molecules.

Bandicoot papillomatosis carcinomatosis virus type 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Papillomaviridae.
has_related_synonym: Bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1)

Populus euphratica
type: Class
definition: A species of genus Populus.
has_related_synonym: Populus diversifolia
has_related_synonym: Popolus euphratica
subclass of: Spermatophyta

Saccoglossus kowalevskii
type: Class
subclass of: Enteropneusta
definition: A species of genus Saccoglossus.
has_related_synonym: Saccoglossus kowalevskyi
has_related_synonym: Saccoglossus kowalesvskii

Panax ginseng
type: Class
has_exact_synonym: Chinese ginseng
has_exact_synonym: ginseng
has_exact_synonym: ren seng
has_exact_synonym: insam
definition: A species of genus Panax.
has_exact_synonym: hong shen
subclass of: Spermatophyta
has_exact_synonym: Korean ginseng
has_exact_synonym: ninjin

Oryzias latipes
type: Class
definition: A species of genus Oryzias.
has_exact_synonym: Japanese rice fish
has_exact_synonym: Japanese medaka
has_exact_synonym: Medaka
subclass of: Actinopterygii

Intronic Splice Enhancer
type: Class
definition: Sequences within the intron that modulate splice site selection for some introns.
subclass of: Spliceosomal Intron Region
definition_source: SO:0000320

SL8 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts.
definition_source: SO:0001753

Ciona savignyi
type: Class
definition: A species of genus Ciona.
subclass of: Ascidiacea

Iron Responsive Element
type: Class
definition_source: SO:0001182
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.
subclass of: Restriction
  some values from: UTR
  on property: part_of
subclass of: UTR Region

Macacine herpesvirus 4
type: Class
has_related_synonym: Cercopithecine herpesvirus 1
has_related_synonym: Herpesvirus simiae
subclass of: dsDNA virus, no RNA stage
has_related_synonym: Simian herpesvirus B
has_exact_synonym: monkey B virus
has_related_synonym: herpes B virus
has_related_synonym: Cercopithecid herpesvirus 1
has_related_synonym: herpes virus B
has_related_synonym: Simian herpes B virus
has_related_synonym: simian herpes B virus SHBV
has_related_synonym: B virus
definition: A dsDNA virus of family Herpesviridae.

Drosophila sechellia
type: Class
has_related_synonym: Drosophila sechellia Tsacas and Bachli, 1981
definition: A species of genus Drosophila.
subclass of: Insecta

Seryl tRNA
type: Class
subclass of: Restriction
  on property: derives_from
  some values from: Serine tRNA Primary Transcript
subclass of: tRNA
definition_source: SO:0000269
definition: A tRNA sequence that has a serine anticodon, and a 3' serine binding region.

Macaca mulatta
type: Class
subclass of: Mammalia
has_exact_synonym: Rhesus monkey
has_exact_synonym: Rhesus macaque
definition: A species of genus Macaca.

Five Prime Coding Exon Coding Region
type: Class
definition: The sequence of the five_prime_coding_exon that codes for protein.
definition_source: SO:0000196
subclass of: Coding Region of Exon
subclass of: Restriction
  some values from: Five Prime Coding Exon
  on property: part_of

Canis lupus familiaris
type: Class
has_exact_synonym: Dog
definition: A species of genus Canis.
has_related_synonym: Canis domesticus
has_related_synonym: Canis canis
has_related_synonym: Canis familiaris
subclass of: Mammalia

Xenopus laevis
type: Class
has_exact_synonym: Clawed frog
has_related_synonym: Bufo laevis
has_related_synonym: Xenopus leavis
has_exact_synonym: African clawed frog
has_exact_synonym: Platanna
subclass of: Amphibia
definition: A species of genus Xenopus.
has_exact_synonym: Common platanna
has_related_synonym: Xenopus laevis (Daudin, 1802)

U12 Intron
type: Class
definition_source: SO:0000295
subclass of: Spliceosomal Intron
definition: A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.

Three Prime Coding Exon Coding Region
type: Class
subclass of: Coding Region of Exon
subclass of: Restriction
  some values from: Three Prime Coding Exon
  on property: part_of
definition: The sequence of the three_prime_coding_exon that codes for protein.
definition_source: SO:0000197

Herpesvirus saimiri (strain 11)
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.

results_in
type: ObjectProperty

has_structure
type: ObjectProperty

definition_source
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

definition
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty