A material entity that is part of an object but is not demarcated by any physical discontinuities.
A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.
Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons.
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.
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.
The 3' splice site of the acceptor primary transcript.
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA.
An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
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.
The last base to be translated into protein. It does not include the stop codon.
Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
A primary transcript encoding glycyl tRNA.
A miRNA target site is a binding site where the molecule is a micro RNA.
A primary transcript encoding prolyl tRNA.
SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
Naturally occurring macromolecules that harbor biological information in their structures, e.g. proteins, nucleic acids.
Primary transcript region bordering trans-splice junction.
A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
A stop codon redefined to be a new amino acid.
A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
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.
A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex.
Populus balsamifera subsp. trichocarpa (Torr. et A.Gray) Brayshaw
modified definition from WIkipedia, http://en.wikipedia.org/wiki/Transcription_factor
A role palyed by a protein that binds to specific DNA sequences, thereby controlling the transcription of genetic information from DNA to mRNA.
RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
Posttranscriptional Gene Silencing by RNA
Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation.
Three Prime Coding Exon Noncoding Region
The sequence of the 3' exon that is not coding.
The recoding stimulatory signal located downstream of the recoding site.
Interacting selectively and non-covalently with any nucleic acid.
The canonical 3' splice site has the sequence "AG".
The canonical 5' splice site has the sequence "GT".
The recoding stimulatory signal located upstream of the recoding site.
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]
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.
An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
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.
An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.
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.
A start codon that is not the usual AUG sequence.
An intron which is spliced by the spliceosome.
A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.
The region of an exon that encodes for protein sequence.
The cellular synthesis of RNA on a template of RNA.
A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
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.
A primary transcript that is never translated into a protein.
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
A primary transcript encoding an rRNA cleavage snoRNA.
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
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.
A primary transcript encoding seryl tRNA.
A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
A recoded_mRNA that was modified by an alteration of codon meaning.
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.
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
A primary transcript encoding a micro RNA.
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.
A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
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.
Ribosomal RNA transcript that structures the small subunit of the ribosome.
A collection of nucleotide residues that link two given unbroken_stems.
Ribosomal RNA transcript that structures the large subunit of the ribosome.
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.
Arabidopsis lyrata (L.) O'Kane & Al-Shehbaz
A component of the large ribosomal subunit in mitochondrial rRNA.
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.
A region of a primary transcript, that is removed via trans splicing.
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.
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.
The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
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.
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.
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.
A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
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).
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'.
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.
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.
A CDS that is supported by sequence similarity data.
CDS Supported by Sequence SImilarity Data
The loop of the hairpin loop formed by folding of the pre-miRNA.
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.
A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.
Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
Part of the primary transcript that is clipped off during processing.
A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
A primary transcript encoding aspartyl tRNA.
A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
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.
A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.
Takifugu rubripes (Temminck & Schlegel, 1850)
Hippoglossus hippoglossus (Linnaeus, 1758)
A non-coding RNA over 200nucleotides in length.
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.
A primary transcript encoding a small temporal mRNA.
A CDS that is part of a transposable element.
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.
A transcript that is bound by a nucleic acid.
Region in mRNA where ribosome assembles.
Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. [SO:0000649]
A virus that replicates by the reverse transcription of a RNA or DNA intermediate.
A CDS that is supported by domain similarity.
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.
A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
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.
A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.
A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA.
A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon.
A primary transcript encoding glutamyl tRNA.
A region defined by its disposition to be involved in a biological process.
A primary transcript encoding phenylalanyl tRNA.
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.
A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
A binding site that, in the molecule, interacts selectively and non-covalently with DNA.
A transcript for which no open reading frame has been identified and for which no other function has been determined.
The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
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.
Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
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.
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.
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.
A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.
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.
A stop codon redefined to be the new amino acid, selenocysteine.
Echinococcus granulosus Tasmanian sheep strain
A retro-transcribing virus of family Retroviridae.
human immunodeficiency virus type 1 HIV-1
human immunodeficiency virus type 1 ,HIV-1
human immunodeficiency virus type 1, HIV-1
human immunodeficiency virus type 1 HIV1
human immunodeficiency virus type-1 HIV-1
human immunodeficiency virus type 1 HIV 1
human immunodeficiency virus type I HIV-1
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
A paired region made up of two contiguous collections of nucleotides, in which each nucleotide forms a base pair. [RNAO:0000097]
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.
3'-most region of a precursor transcript that is clipped off during processing.
A primary transcript encoding a large ribosomal subunit RNA.
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.
A primary transcript encoding pyrrolysyl tRNA.
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.
An exon that is bounded by 5' and 3' splice sites.
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.
An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
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.
The first base to be translated into a protein.
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.
The maximal intersection of exon and UTR.
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.
A primary transcript that, at least in part, encodes one or more proteins.
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.
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.
A primary transcript encoding a small nucleolar mRNA.
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.
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488]
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.
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.
An mRNA that encodes multiple proteins from at least two non-overlapping regions.
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.
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.
A component of the large ribosomal subunit.
A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
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.
A primary transcript encoding a signal recognition particle RNA.
Bandicoot papillomatosis carcinomatosis virus type 2
A dsDNA virus of family Papillomaviridae.
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.
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.
A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region.
A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.
A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
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.
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.
Karposi's sarcoma-associated herpes-like virus
Kaposi's sarcoma-associated herpesvirus - Human herpesvirus 8
Kaposi's sarcoma-associated herpesvirus KSHV
Kaposi's sarcoma-associated human herpes virus
Kaposi's sarcoma-associated herpes-like virus
Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
A primary transcript encoding tyrosyl tRNA.
A transcript that is bound by a protein.
A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
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.
A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.
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.
Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
A collection of one or more adjacent nucleotide residues in which at least one residue is part of a base pair.
A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
Elaeis guineensis var. tenera (Oil palm)
A primary transcript encoding lysyl tRNA.
A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
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.
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.
A short ncRNA that is transcribed from an enhancer. May have a regulatory function.
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.
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A primary transcript encoding a tasiRNA.
A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
A transcript that has been edited by A to I substitution.
Edited Transcript by A to I Substitution
A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
A primary transcript encoding a small ribosomal subunit RNA.
Paralichthys olivaceus (Temminck & Schlegel, 1846)
The sequence of the 5' exon preceding the start codon.
A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
A primary transcript encoding methionyl tRNA.
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.
A primary transcript encoding valyl tRNA.
The region of an edited transcript that will not be edited.
A collection of one or more nucleotides that are not involved in base pairing.
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.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
A primary transcript encoding glutaminyl tRNA.
A primary transcript encoding a small nucleolar RNA of the box C/D family.
The sequence of nucleotide residues along an RNA chain.
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
A transcript that in its initial state requires modification to be functional.
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).
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.
A stop codon signal for a UAA stop codon redefinition.
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.
A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
An mRNA that has the quality dicistronic.
A primary transcript encoding arginyl tRNA.
Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
Posttranscriptional Regulation of Gene Expression
Caenorhabditis vulgaris Baird, Fitch & Emmons, 1994
A 5' splice site which does not have the sequence "GT".
The sequence of nucleotide residues along a DNA chain.
infectious bovine rhinotracheitis virus BHV-1
A stop codon signal for a UAG stop codon redefinition.
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.
Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
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.
Any cellular metabolic process involving nucleic acids.
The cellular synthesis of RNA on a template of DNA.
Methylation Guide snoRNA Primary Transcript
A primary transcript encoding a methylation guide small nucleolar RNA.
The first base where RNA polymerase begins to synthesize the RNA transcript.
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.
A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.
The reverse complement of the primary transcript.
The coding exon that is most 3-prime on a given transcript.
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.
Any process that modulates the frequency, rate or extent of any biological process, quality or function.
A lnc_RNA totally contained within an intron.
The inactivation of gene expression by a posttranscriptional mechanism.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
A primary transcript encoding a ribosomal RNA.
A CDS with the evidence status of being independently known.
The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
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.
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.
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.
human immunodeficiency virus type 2 HIV-2
human immunodeficiency virus type 2, HIV-2
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.
The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote.
An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
First codon to be translated by a ribosome.
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.
A transcript that is alternatively spliced.
A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
Avian infectious laryngotracheitis virus
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.
Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
A primary transcript that donates the spliced leader to other mRNA.
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.
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.
A region of a guide_RNA that base-pairs to a target mRNA.
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.
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.
Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.
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.
A non-canonical start codon with 4 base pairs.
A collection of nucleotide residues is a part of a nucleic acid consisting of one or more nucleotides.
Hevea brasiliensis (Willd. ex A.Juss.) Muell. Arg.
A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
A non-canonical start codon of sequence CTG.
A primary transcript encoding leucyl tRNA.
An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
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.
An exon that is the only exon in a gene.
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.
A primary transcript encoding tryptophanyl tRNA.
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.
Cold-blooded, air-breathing VERTEBRATES belonging to the class Reptilia, usually covered with external scales or bony plates.
A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.
A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.
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.
A primary transcript encoding a transfer RNA.
Intron located in the untranslated region.
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.
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.
A stop codon redefined to be the new amino acid, pyrrolysine.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
A primary transcript encoding for one gene product.
A primary transcript encoding threonyl tRNA.
A stop codon signal for a UGA stop codon redefinition.
A transcript with a translational frameshift.
Transcript with Translational Frameshift
Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
The region of a transcript that will be edited.
A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
A multiexonic non-coding RNA transcribed by RNA polymerase II.
The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
The 5' five prime splice site region of the donor RNA.
A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
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.
Tetraodon nigroviridis Marion de Proce, 1822
A primary transcript encoding a small nuclear RNA.
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.
5' most region of a precursor transcript that is clipped off during processing.
A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
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.
A primary transcript encoding cysteinyl tRNA.
A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.
A locatable feature on a transcript that is edited.
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.
The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
A primary transcript encoding for more than one gene product.
Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
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.
A 3' splice site that does not have the sequence "AG".
Chlamydomonas smithii R.W.Howshaw & H.Ettl
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.
A primary transcript encoding histidyl tRNA.
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.
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.
The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.
A primary transcript encoding alanyl tRNA.
A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
A primary transcript that has the quality dicistronic.
A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.
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.
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.
A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
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 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.
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.
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.
A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
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.
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.
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.
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]
Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
An exon that does not contain any codons.
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.
A CDS that is supported by similarity to EST or cDNA data.
A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
A virus having a dsDNA molecule as genetic material. No RNA intermediate molecules are involved during its replication.
A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
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.
Strongylocentrotus purpuratus (Stimpson, 1857)
A region of the pri miRNA that basepairs with the guide to form the hairpin.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
A primary transcript encoding isoleucyl tRNA.
An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.
A primary transcript encoding asparaginyl tRNA.
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.
The stem of the hairpin loop formed by folding of the pre-miRNA.
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 (BPCV1)
Bandicoot papillomatosis carcinomatosis virus type 1
Sequences within the intron that modulate splice site selection for some introns.
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.
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.
Drosophila sechellia Tsacas and Bachli, 1981
A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
The sequence of the five_prime_coding_exon that codes for protein.
A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
The sequence of the three_prime_coding_exon that codes for protein.
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'.
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.
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.
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.)
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process.