Orphan CDS A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence. SO:1001247 Fiat Object Part snap:FiatObjectPart A material entity that is part of an object but is not demarcated by any physical discontinuities. Flanking 3' Quadraplet Recoding Signal Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons. SO:1001281 A phylum of kingdom Animalia. Porifera A class of phylum Chordata. Actinopterygii Platyhelminthes A phylum of kingdom Animalia. A species of genus Sus. Sus scrofa 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. Exemplar mRNA SO:0000734 SO:0000706 The 3' splice site of the acceptor primary transcript. Trans Splice Acceptor Site 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. snap:RealizableEntity Realizable Entity SO:0001654 Nucleotide to Protein Binding Site 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. pre-miRNA Binding GO:0070883 Major TSS SO:0000666 Mobile Intron An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility. SO:0001002 A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes. rRNA 25S SO:0000242 The untranslated sequence separating the 'cistrons' of multicistronic mRNA. Untranslated Region Polycistronic 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. GO:0005575 Cellular Component Saguinus labiatus A species of genus Saguinus. A class of phylum Chordata. Ascidiacea Coding End The last base to be translated into protein. It does not include the stop codon. SO:0000327 A species of genus Medicago. Medicago truncatula Capped mRNA An mRNA that is capped. SO:0000862 A species of genus Pongo. Pongo pygmaeus SO:0001181 Bruno Response Element A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs. SO:0001176 Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues. DHU Loop SO:0000633 An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap. Monocistronic mRNA SO:0000218 Glycine tRNA Primary Transcript A primary transcript encoding glycyl tRNA. A miRNA target site is a binding site where the molecule is a micro RNA. miRNA Target Site SO:0000934 SO:0000225 Proline tRNA Primary Transcript A primary transcript encoding prolyl tRNA. mRNA with Minus 1 Frameshift SO:0000282 An mRNA with a minus 1 frameshift. SO:0001483 SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. SNV Naturally occurring macromolecules that harbor biological information in their structures, e.g. proteins, nucleic acids. Information Biopolymer GRO:InformationBiopolymer Trans Splice Site SO:0001420 Primary transcript region bordering trans-splice junction. Bombyx mori A species of genus Bombyx. A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region. Methionyl tRNA SO:0000266 SO:0000883 Stop Codon Read Through A stop codon redefined to be a new amino acid. Glutaminyl tRNA SO:0000259 A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region. RNA Metabolic Process GO:0016070 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 class of phylum Chordata. Appendicularia An mRNA that is trans-spliced. SO:0000872 Trans Spliced mRNA A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage. SO:0001034 Mirtron A region within an intron. SO:0000841 Spliceosomal Intron Region SO:0000235 Transcription Factor Binding Site A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex. A species of genus Populus. Populus trichocarpa GRO:TranscriptionFactor Transcription Factor 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. Dengue Virus A ssRNA virus of family Flaviviridae. RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. rRNA SO:0000252 Posttranscriptional Gene Silencing by RNA GO:0035194 Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation. A region of guide RNA. Guide RNA Region SO:0000930 SO:0000484 Three Prime Coding Exon Noncoding Region The sequence of the 3' exon that is not coding. A species of genus Haliotis. Haliotis rufescens The recoding stimulatory signal located downstream of the recoding site. 3' Recoding Site SO:1001277 Dictyostelium Discoideum A species of genus Dictyostelium. A species of genus Homo. Homo sapiens Nucleic Acid Binding GO:0003676 Interacting selectively and non-covalently with any nucleic acid. The canonical 3' splice site has the sequence "AG". SO:0000676 Canonical 3' Splice Site Cerebratulus lacteus A species of genus Cerebratulus. A class of phylum Mollusca. Gastropoda A species of genus Branchiostoma. Branchiostoma Floridae The canonical 5' splice site has the sequence "GT". Canonical 5' Splice Site SO:0000677 The recoding stimulatory signal located upstream of the recoding site. 5' Recoding Site SO:1001280 Terminal Loop 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] 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. SO:0000694 SNP SO:0000195 An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon). Coding Exon A species of genus Drosophila. Drosophila willistoni SO:0000275 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 A primary transcript encoding a tmRNA. tmRNA Primary Transcript SO:0000584 An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules. SO:0005843 rRNA Cleavage RNA 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. 5' cis Splice Site SO:0000163 A species of genus Gallus. Gallus gallus Non-canonical Start Codon SO:0000680 A start codon that is not the usual AUG sequence. An intron which is spliced by the spliceosome. Spliceosomal Intron SO:0000662 Lysyl tRNA A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region. SO:0000265 A phylum of kingdom Animalia. Nematoda 5' Intron A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues. SO:0001655 Nucleotide Binding Site SO:0001215 Coding Region of Exon The region of an exon that encodes for protein sequence. The cellular synthesis of RNA on a template of RNA. GO:0001172 Transcription, RNA-dependent SO:0000370 A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. Small Regulatory ncRNA miRNA 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. SO:0000276 SO:0000836 mRNA Region A region of an mRNA. A species of genus Gossypium. Gossypium herbaceum Five Prime Open Reading Frame SO:0000483 A primary transcript that is never translated into a protein. Noncoding Primary Transcript Occurent span:Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. A species of genus Caenorhabditis. Caenorhabditis elegans Chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. GO:0005694 A primary transcript encoding an rRNA cleavage snoRNA. SO:0000582 rRNA cleavage snoRNA Primary Transcript U11 snRNA 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. SO:0000398 Serine tRNA Primary Transcript A primary transcript encoding seryl tRNA. SO:0000226 A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. SO:0000147 Exon A recoded_mRNA that was modified by an alteration of codon meaning. SO:1001265 mRNA Recoded by Codon Redefinition 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. Binding Site SO:0000409 GO:0003677 DNA Binding Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid). A species of genus Glycine. Glycine max SO:0000647 pri-miRNA A primary transcript encoding a micro RNA. SRP 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. SO:0000590 SO:0001035 piRNA A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements. U5 snRNA SO:0000395 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 SO:0000650 Ribosomal RNA transcript that structures the small subunit of the ribosome. SO:0000142 DNA Sequence Secondary Structure A folded DNA sequence. RNAO:0000099 Internal Loop A collection of nucleotide residues that link two given unbroken_stems. A species of genus Apis. Apis mellifera Large Subunit rRNA SO:0000651 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. SO:0000393 U4 snRNA Metabolic Process 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. GO:0008152 A region of a primary transcript, that is removed via trans splicing. Outron SO:0001475 SO:0001171 rRNA 21S A component of the large ribosomal subunit in mitochondrial rRNA. SO:0001212 Plus 2 Translational Frameshift 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. Recursive Splice Site SO:0000998 An RNA with catalytic activity. Ribozyme SO:0000374 The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. SO:0005837 U14 snoRNA Primary Transcript SO:0000630 Upstream AUG Codon A start codon upstream of the ORF. SO:0000204 A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein. Five Prime UTR Methylation Guide snoRNA 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. SO:0005841 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. snap:SpecificallyDependentContinuant Specifically Dependent Continuant mRNA SO:0000234 Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. A ssRNA virus of family Flaviviridae. West Nile Virus Recoded mRNA SO:1001261 The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals. A class of phylum Cnidaria. Hydrozoa A species of genus Schistosoma. Schistosoma mansoni Shine Dalgarno Sequence SO:0000552 A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex. Plants 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). NCIThesaurus:Plant 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'. C/D Box snoRNA SO:0000593 Mature Transcript SO:0000233 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. SO:0000399 U12 snRNA A CDS that is supported by sequence similarity data. CDS Supported by Sequence SImilarity Data SO:1001251 SO:0000479 A transcript that is trans-spliced. Trans-spliced Transcript The loop of the hairpin loop formed by folding of the pre-miRNA. SO:0001246 miRNA Loop Internal UTR A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal. SO:0000241 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. SO:0000001 Region SO:0001419 cis Splice Site Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. Clip SO:0000303 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. SO:0000262 Histidyl tRNA A primary transcript encoding a small nucleolar RNA of the box H/ACA family. H/ACA Box snoRNA Primary Transcript SO:0000596 SO:0000214 A primary transcript encoding aspartyl tRNA. Aspartic acid tRNA Primary Transcript A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. Protein Binding SIte SO:0000410 Translational Frameshift SO:0001210 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. Pyrrolysyl tRNA SO:0000766 Echinoidea A class of phylum Echinodermata. SO:1001287 Distant 3' Recoding SIgnal A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon. Takifugu rubripes A species of genus Takifugu. SO:0001877 A non-coding RNA over 200nucleotides in length. Lnc RNA A species of genus Oryza. Oryza sativa ssRNA Virus Drosophila simulans A species of genus Drosophila. 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. SO:0001752 SL7 Acceptor Site A primary transcript encoding a small temporal mRNA. SO:0000648 stRNA Primary Transcript Polycistronic Transcript SO:0000078 A transcript that is polycistronic. Rattus norvegicus A species of genus Rattus. Echinodermata A phylum of kingdom Animalia. A CDS that is part of a transposable element. Transposable Element CDS SO:0001869 Pan troglodytes A species of genus Pan. Hydra magnipapillata A species of genus Hydra. SO:0000584 tmRNA 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. SO:0000278 Transcript Bound by Nucleic Acid A transcript that is bound by a nucleic acid. SO:0000139 Ribosome Entry Site 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] stRNA SO:0000649 Retro-transcribing Virus A virus that replicates by the reverse transcription of a RNA or DNA intermediate. CDS Supported by Domain Match Data SO:1001249 A CDS that is supported by domain similarity. Drosophila erecta A species of genus Drosophila. A part of a primary transcript. Primary Transcript Region SO:0000835 GO:0035198 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. miRNA Binding A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region. Cysteinyl tRNA SO:0000258 SO:0000989 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. Class II RNA A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough. SO:0000145 Recoded Codon A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA. Recoding Stimulatory Region SO:1001268 A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon. CDS SO:0000316 A primary transcript encoding glutamyl tRNA. Glutamine tRNA Primary Transcript SO:0000217 Locusta migratoria A species of genus Locusta. SO:0001411 Biological Region A region defined by its disposition to be involved in a biological process. Phenylalanine tRNA Primary Transcript SO:0000224 A primary transcript encoding phenylalanyl tRNA. Regulation of Gene Expression 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. GO:0010468 Sorghum bicolor A species of genus Sorghum. SO:0000273 Valyl tRNA A tRNA sequence that has a valine anticodon, and a 3' valine binding region. Regulation of Metabolic Process GO:0019222 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. Anopheles gambiae A species of genus Anopheles. Macaca nemestrina A species of genus Macaca. Drosophila melanogaster A species of genus Drosophila. A binding site that, in the molecule, interacts selectively and non-covalently with DNA. DNA Binding SIte SO:0001429 Processed Transcript SO:0001503 A transcript for which no open reading frame has been identified and for which no other function has been determined. A species of genus Aedes. Aedes aegypti The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure. SO:0001244 pre-miRNA Dengue Virus 1 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. SO:0000386 RNase P RNA Editing Domain SO:0000606 Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602). BFO:MaterialEntity Material Entity 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. Virus NCIThesaurus:Virus 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. RNAO:0000106 Stem Junction 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 A species of genus Lagothrix. A species of genus Vigna. Vigna unguiculata SO:0000407 rRNA 18S A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. SO:1001274 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. SECIS Element Stop Codon Redefined as Selenocysteine A stop codon redefined to be the new amino acid, selenocysteine. SO:0000885 A species of genus Drosophila. Drosophila yakuba A retro-transcribing virus of family Retroviridae. Human Immunodeficiency Virus 1 Interacting selectively and non-covalently with an RNA molecule or a portion thereof. GO:0003723 RNA Binding Human Herpesvirus 1 A dsDNA virus of family Herpesviridae. Solanum lycopersicum A species of genus Solanum. A paired region made up of two contiguous collections of nucleotides, in which each nucleotide forms a base pair. [RNAO:0000097] Unbroken Stem RNAO:0000097 Turbellaria A class of phylum Platyhelminthes. Brassica oleracea A species of genus Brassica. U6atac snRNA U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA. SO:0000397 rRNA Large Subunit Primary Transcript SO:0000325 A primary transcript encoding a large ribosomal subunit RNA. 3'-most region of a precursor transcript that is clipped off during processing. SO:0000557 3' Clip Generically Dependent Continuant 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. snap:GenericallyDependentContinuant SO:0000665 Monocistronic Transcript A transcript that is monocistronic. Pyrrolysine tRNA Primary Transcript SO:0001178 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. Branch Site SO:0000611 SO:0000201 An exon that is bounded by 5' and 3' splice sites. Interior Exon SO:0001180 AU Rich Element 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. Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA. SO:0000638 Transcribed Spacer Region An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. Enzymatic RNA SO:0000372 SO:0000709 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. SL2 Acceptor Site JC Polyomavirus A dsDNA virus of family Polyomaviridae SO:0000323 The first base to be translated into a protein. Coding Start 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. SO:0000990 Class I RNA A species of genus Triticum. Triticum aestivum Noncoding Region of Exon The maximal intersection of exon and UTR. SO:0001214 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. SO:0000387 RprA RNA Oikopleura dioica A species of genus Oikopleura. Protein Coding Primary Transcript SO:0000120 A primary transcript that, at least in part, encodes one or more proteins. RNA 6S 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. SO:0000376 A species of genus Lemur. Lemur catta Insecta A class of phylum Arthropoda. A species of genus Brassica. Brassica rapa SO:0000447 5' UTR Intron An intron located in the 5' UTR. A species of genus Vitis. Vitis vinifera SO:0000392 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. U2 snRNA SO:0000851 CDS Region A region of a CDS. SO:0000232 snoRNA Primary Transcript A primary transcript encoding a small nucleolar mRNA. Mollusca A phylum of kingdom Animalia. Y RNA 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. SO:0000405 Amoebozoa A species of genus Drosophila. Drosophila mojavensis Minor TSS The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488] GO:0005488 Binding 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. Function snap:Function 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. SO:0001016 Internal Guide Sequence tmRNA Region A region of a tmRNA. SO:0000847 A dsDNA virus of family Herpesviridae. Human Herpesvirus 5 Polycistronic mRNA SO:0000634 An mRNA that encodes multiple proteins from at least two non-overlapping regions. Internal Shine Dalgarno Sequence SO:1001260 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. SO:0000770 tmRNA Acceptor Piece 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. Anthozoa A class of phylum Cnidaria. rRNA 28S SO:0000653 A component of the large ribosomal subunit. rRNA 16S A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. SO:0001000 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. tmRNA Coding Piece SO:0000769 A primary transcript encoding a signal recognition particle RNA. SO:0000589 SRP RNA Primary Transcript SO:0000388 RRE RNA 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. Simian Virus 40 A dsDNA virus of family Polyomaviridae. A region of a transcript. Transcript Region SO:0000833 CsrB RsmB RNA 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. SO:0000377 3' Stem-loop Structure A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region. SO:1001279 SO:0000270 A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region. Threonyl tRNA Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA. SO:0001904 Antisense lncRNA SO:0000254 A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region. Alanyl tRNA A class of phylum Chordata. Amphibia Annelida A phylum of kingdom Animalia. GO:0050789 Regulation of Biological Process 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 species of genus Ornithorhynchus. Ornithorhynchus anatinus Interior Intron pre-edited mRNA SO:0000861 Capped Primary Transcript A primary transcript that is capped. SL6 Acceptor Site 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. SO:0001751 Human Herpesvirus 8 A dsDNA virus of family Herpesviridae. SO:0000639 Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs. Internal Transcribed Spacer Region SO:0000229 Tyrosine tRNA Primary Transcript A primary transcript encoding tyrosyl tRNA. A transcript that is bound by a protein. SO:0000279 Transcript Bound by Protein U2 Intron SO:0000184 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. SO:0000383 MicF RNA A dsDNA virus of family Herpesviridae. Murid Herpesvirus 4 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. SL11 Acceptor Site SO:0001756 Cryptic Splice SIte SO:0001533 A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error. Animalia Animals Metazoa Antisense RNA Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. SO:0000644 A collection of one or more adjacent nucleotide residues in which at least one residue is part of a base pair. RNAO:0000095 Paired Region SO:0000264 Leucyl tRNA 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. Pseudouridylation Guide snoRNA SO:0001187 Dengue Virus 3 A species of genus Drosophila. Drosophila persimilis Consensus mRNA SO:0000222 A primary transcript encoding lysyl tRNA. Lysine tRNA Primary Transcript SO:0000274 snRNA 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. Kozak Sequence SO:0001647 Riboswitch SO:0000035 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 Expression GO:0010467 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. SO:0000834 A region of a mature transcript. Mature Transcript Region miRNA Primary Transcript Region SO:0001243 A part of an miRNA primary_transcript. A short ncRNA that is transcribed from an enhancer. May have a regulatory function. SO:0001870 Enhancer RNA Drosophila virilis A species of genus Drosophila. SO:0000655 ncRNA 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. IDO:Disease Disease A species of genus Gossypium. Gossypium raimondii A primary transcript encoding a tasiRNA. tasiRNA Primary Transcript SO:0001801 A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property). Quality snap:Quality A dsDNA virus of family Herpesviridae. Human Herpesvirus 4 A transcript that has been edited by A to I substitution. Edited Transcript by A to I Substitution SO:0000874 SO:0000255 A primary transcript encoding a small ribosomal subunit RNA. rRNA Small Subunit Primary Transcript A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region. Aspartyl tRNA SO:0000257 3' Intron An mRNA that is polyadenylated. Polyadenylated mRNA SO:0000871 Five Prime Coding Exon Noncoding Region SO:0000486 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. SO:0000978 Template Region A primary transcript encoding methionyl tRNA. SO:0000223 Methionine tRNA Primary Transcript A species of genus Zea. Zea mays Disposition snap:Disposition 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 species of genus Gasterosteus. Gasterosteus aculeatus Chordata A phylum of kingdom Animalia. Valine tRNA Primary Transcript A primary transcript encoding valyl tRNA. SO:0000230 The region of an edited transcript that will not be edited. SO:0000607 Unedited Region RNAO:0000096 A collection of one or more nucleotides that are not involved in base pairing. Unpaired Region Dengue Virus 2 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. U3 snoRNA SO:0001179 CHEBI:16991 DNA 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. SO:0000216 Glutamic acid tRNA Primary Transcript A primary transcript encoding a small nucleolar RNA of the box C/D family. C/D Box snoRNA Primary Transcript SO:0000595 Merkel Cell Polyomavirus A dsDNA virus of family Polyomaviridae. Carica papaya A species of genus Carica. The sequence of nucleotide residues along an RNA chain. RNA Sequence NCI Thesaurus:RNA_Sequence NCIThesaurus:DNA_Sequence Physcomitrella patens A species of genus Physcomitrella. A class of phylum Arthropoda. Arachnida Transcript SO:0000673 An RNA synthesized on a DNA or RNA template by an RNA polymerase. SO:0000185 Primary Transcript A transcript that in its initial state requires modification to be functional. BFO:0000141 Immaterial Entity 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 A species of genus Symphalangus. 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. GO:0032774 RNA Biosynthetic Process A stop codon signal for a UAA stop codon redefinition. UAA Stop Codon Signal SO:1001283 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. U14 snoRNA SO:0000403 A class of phylum Porifera. Demospongiae SL1 Acceptor Site A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs. SO:0000708 SO:0000444 Non-coding exon in the 3' UTR. Three Prime Noncoding Exon A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region. Glutamyl tRNA SO:0000260 Dicistronic mRNA An mRNA that has the quality dicistronic. SO:0000716 A subclass of phylum Platyhelminthes. Digenea SO:0000212 Arginine tRNA Primary Transcript A primary transcript encoding arginyl tRNA. Intron Domain Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. Posttranscriptional Regulation of Gene Expression GO:0010608 Non-canonical 5' Splice SIte SO:0000679 A 5' splice site which does not have the sequence "GT". DNA Sequence NCI Thesaurus:DNA_Sequence NCIThesaurus:DNA_Sequence The sequence of nucleotide residues along a DNA chain. SO:0000929 Edited mRNA An mRNA that is edited. SO:1001282 UAG Stop Codon Signal A stop codon signal for a UAG stop codon redefinition. U6 snRNA SO:0000396 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. SO:0000604 Editing Block Edited mRNA sequence mediated by a single guide RNA (SO:0000602). A dsDNA virus of family Herpesviridae.. Human Herpesvirus 2 A class of phylum Chordata. Branchiostomidae Leptocardii UTR Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. SO:0000203 SO:0000935 Edited CDS A CDS that is edited. Aves A class of phylum Chordata. Spermatophyta A subset of Embryophytes. Group IIA Intron GO:0090304 Nucleic Acid Metabolic Process Any cellular metabolic process involving nucleic acids. SO:0001749 SL4 Acceptor Site 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. Transcription, DNA-dependent GO:0006351 The cellular synthesis of RNA on a template of DNA. An mRNA with a plus 1 frameshift. mRNA with Plus 1 Frameshift SO:0000321 Methylation Guide snoRNA Primary Transcript SO:0000580 A primary transcript encoding a methylation guide small nucleolar RNA. Bos taurus A species of genus Bos. Anchor Binding Site SO:0000335 A mRNA with a minus 2 frameshift. mRNA with Minus 2 Frameshift The first base where RNA polymerase begins to synthesize the RNA transcript. TSS SO:0000315 A phylum of kingdom Animalia. Nemertea SO:0001001 rRNA 23S A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. H/ACA Box snoRNA 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. SO:0000594 SO:0000645 The reverse complement of the primary transcript. Antisense Primary Transcript SO:0000202 The coding exon that is most 3-prime on a given transcript. Three Prime Coding Exon SO:0001173 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. Anticodon Loop GO:0065007 Biological Regulation Any process that modulates the frequency, rate or extent of any biological process, quality or function. Monodelphis domestica A species of genus Monodelphis. Intronic lncRNA SO:0001903 A lnc_RNA totally contained within an intron. A phylum of kingdom Animalia. Hemichordata A species of genus Lotus. Lotus japonicus The inactivation of gene expression by a posttranscriptional mechanism. GO:0016441 Posttranscriptional Gene Silencing RNAO_0000000 High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. CHEBI:33697 RNA Telomerase RNA SO:0000390 The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. SO:0000209 A primary transcript encoding a ribosomal RNA. rRNA Primary Transcript CDS Independently Known A CDS with the evidence status of being independently known. SO:1001246 SO:0000652 rRNA 5S 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. SO:0001748 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. SL3 Acceptor Site 3' cis Splice Site 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. SO:0000164 A dsDNA virus of family Polyomaviridae. BK Polyomavirus Human Immunodeficiency Virus 2 A retro-transcribing virus of family Retroviridae. Pinus taeda A species of genus Pinus. A species of genus Drosophila. Drosophila ananassae Collection of Material Entities A dsDNA virus of family Herpesviridae. Gallid Herpesvirus 2 Guide RNA SO:0000602 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. SO:0000406 Twintron An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed. The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote. SO:0000012 scRNA Primary Transcript Start Codon SO:0000318 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. pri-miRNA Binding GO:0070878 Alternatively Spliced Transcript SO:1001187 A transcript that is alternatively spliced. Isoleucyl tRNA SO:0000263 A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region. Tribolium castaneum A species of genus Tribolium. SO:0000253 tRNA 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. A folded RNA sequence. SO:0000122 RNA Sequence Secondary Structure SO:0000243 Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation. Internal Ribosome Entry Site SO:0000635 Mini Exon Donor RNA A primary transcript that donates the spliced leader to other mRNA. OBI:0100026 Organism 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. SO:0001211 Plus 1 Translational Frameshift 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. Anchor Region SO:0000931 A transcript that is edited. Edited Transcript SO:0000873 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. snap:Role Role 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. GO:0008150 Biological Process SL10 Acceptor Site SO:0001755 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. SO:0000013 Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote. scRNA A non-canonical start codon with 4 base pairs. 4bp Start Codon SO:1001269 A collection of nucleotide residues is a part of a nucleic acid consisting of one or more nucleotides. Collection of Nucleotides Residues RNAO:0000108 SO:0001174 A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA. Anticodon span:Process A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. Process SO:0000268 A tRNA sequence that has a proline anticodon, and a 3' proline binding region. Prolyl tRNA SO:1001273 CTG Start Codon A non-canonical start codon of sequence CTG. A primary transcript encoding leucyl tRNA. Leucine tRNA Primary Transcript SO:0000221 Object Schmidtea mediterranea A species of genus Schmidtea. Endonuclease Spliced Intron SO:0001216 An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification. Group IIB Intron Group I Intron SO:0000587 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. Exon of Single Exon Gene SO:0005845 SO:0000404 Vault RNA 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. DsrA RNA 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. SO:0000378 SO:0000228 Tryptophan tRNA Primary Transcript A primary transcript encoding tryptophanyl tRNA. Dengue Virus 4 Saccharum officinarum A species of genus Saccharum. 3' Repeat Recoding Signal SO:1001286 A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements. SO:0005857 Selenocysteinyl tRNA A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region. SO:0000210 tRNA Primary Transcript A primary transcript encoding a transfer RNA. SL12 Acceptor Site 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. SO:0001757 A species of genus Ixodes. Ixodes scapularis SO:0000446 Intron located in the untranslated region. UTR Intron 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. Gene Silencing by miRNA GO:0035195 A class of phylum Chordata. Mammalia CDS Predicted A CDS that is predicted. SO:1001254 A species of genus Cricetulus. Cricetulus griseus Translation GO:0006412 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. Protein CHEBI:36080 A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. A stop codon redefined to be the new amino acid, pyrrolysine. Stop Codon Redefined as Pyrrolysine SO:0000884 Caenorhabditis briggsae A species of genus Caenorhabditis. SO:0000616 Transcription End Site The base where transcription ends. mRNA with Plus 2 Frameshift An mRNA with a plus 2 frameshift. SO:0000329 Monocistronic Primary Transcript A primary transcript encoding for one gene product. SO:0000632 A species of genus Amphimedon. Amphimedon queenslandica An intron located in the 3' UTR. SO:0000448 3' UTR Intron Lycopodiophyta A division of Eukaryota. Five Prime Noncoding Exon Non-coding exon in the 5' UTR. SO:0000445 A primary transcript encoding threonyl tRNA. SO:0000227 Threonine tRNA Primary Transcript UGA Stop Codon Signal A stop codon signal for a UGA stop codon redefinition. SO:1001285 A transcript with a translational frameshift. SO:0000118 Transcript with Translational Frameshift External Transcribed Spacer Region Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA. SO:0000640 A phylum of Eukaryota. Chlorophyta The region of a transcript that will be edited. Pre-edited Region SO:0000583 A region of an rRNA primary transcript. rRNA Primary Transcript Region SO:0000838 Enteropneusta A class of phylum Hemichordata. A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons. SO:0000681 Aberrant Processed Transcript SO:0001463 A multiexonic non-coding RNA transcribed by RNA polymerase II. Linc RNA Polypirimidine Tract The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. SO:0000612 The 5' five prime splice site region of the donor RNA. Trans Splice Donor Site SO:0000707 SO:0000261 A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region. Glycyl tRNA Exon Region A region of an exon. SO:0000852 Stop Codon SO:0000319 In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. snap:DependentContinuant Dependent Continuant 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. A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region. Asparaginyl tRNA SO:0000256 Tetraodon nigroviridis A species of genus Tetraodon. A primary transcript encoding a small nuclear RNA. snRNA Primary Transcript SO:0000231 Archaeal Intron 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. SO:1001271 SO:0000555 5' most region of a precursor transcript that is clipped off during processing. 5' Clip Tyrosyl tRNA SO:0000272 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. GO:0003674 Molecular Function Cysteine tRNA Primary Transcript SO:0000215 A primary transcript encoding cysteinyl tRNA. A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding. SO:1001288 Stop Codon Signal Spliced Leader RNA SO:0000579 Edited Transcript Feature A locatable feature on a transcript that is edited. SO:0001750 SL5 Acceptor Site 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. Protein Metabolic Process GO:0019538 Polycistronic Primary Transcript A primary transcript encoding for more than one gene product. SO:0000631 Cellular Organism CDS Fragment SO:0000162 Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. Splice Site A species of genus Gorilla. Gorilla gorilla 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. OxyS RNA SO:0000384 Selaginella moellendorffii A species of genus Selaginella. Non-canonical 3' Splice Site A 3' splice site that does not have the sequence "AG". SO:0000678 A species of genus Chlamydomonas. Chlamydomonas reinhardtii Xenopus tropicalis A species of genus Xenopus. Five Prime Coding Exon The 5' most coding exon. SO:0000200 Gossypium hirsutum A species of genus Gossypium. Nucleic Acid CHEBI:33696 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. Histidine tRNA Primary Transcript SO:0000219 A primary transcript encoding histidyl tRNA. A species of genus Pan. Pan paniscus Continuant snap:Continuant 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 phylum of Eukaryota. Bryophyta Drosophila pseudoobscura A species of genus Drosophila. SO:0001172 A region of a tRNA. tRNA Region Autocatalutically Spliced Intron A self spliced intron. SO:0000588 Interior Coding Exon A phylum of kingdom Animalia. Cnidaria 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. SO:0000188 Intron SO:0001800 The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene. tasiRNA A primary transcript encoding alanyl tRNA. Alanine tRNA Primary Transcript SO:0000211 A species of genus Capitella. Capitella sp. 1 Tryptophanyl tRNA A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region. SO:0000271 SO:1001197 Dicistronic Primary Transcript A primary transcript that has the quality dicistronic. U1 snRNA SO:0000391 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. A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon. mRNA Recoded by Translation Bypass SO:1001264 A species of genus Ciona. Ciona intestinalis Splice Region A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. SO:0001902 CCA Tail SO:0001175 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 species of genus Schistosoma. Schistosoma japonicum SO:0000385 RNase MRP RNA 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. SO:0001213 Group III Intron 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. Codon SO:0000360 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. U4atac snRNA An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA. SO:0000394 rasiRNA A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. SO:0000454 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. Independent Continuant snap:IndependentContinuant rRNA 5_8S 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. SO:0000375 Gene SO:0000704 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] Strand End RNAO:0000107 Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C. SO:0001177 T Loop A phylum of kingdom Animalia. Arthropoda A species of genus Mus. Mus musculus A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region. Arginyl tRNA SO:0001036 A species of genus Danio. Danio rerio SO:0000198 Noncoding Exon An exon that does not contain any codons. A species of genus Lottia. Lottia gigantea SO:0005856 Selenocysteine tRNA Primary Transcript A primary transcript encoding seryl tRNA. SO:0001754 SL9 Acceptor Site 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. SO:1001259 CDS Supported by EST or cDNA Data A species of genus Pygathrix. Pygathrix bieti Rhinopithecus bieti A species of genus Nematostella. Nematostella vectensis SO:0000379 A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. GcvB RNA SO:0000205 Three Prime UTR A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein. Ateles geoffroyi A species of genus Ateles. A species of genus Drosophila. Drosophila grimshawi dsDNA Virus, no RNA stage 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. SO:0000267 Phenylalanyl tRNA Group II Intron 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. SO:0000603 Murid Herpesvirus 1 A dsDNA virus of family Herpesviridae A species of genus Strongylocentrotus. Strongylocentrotus purpuratus A region of the pri miRNA that basepairs with the guide to form the hairpin. SO:0001473 miRNA Antiguide Brassica napus A species of genus Brassica. SO:0000108 An mRNA with a frameshift. mRNA with Frameshift A primary transcript encoding isoleucyl tRNA. Isoleucine tRNA Primary Transcript SO:0000220 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. Molecular Entity http://en.wikipedia.org/wiki/Molecular_entity tRNA Intron SO:1001272 An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification. A primary transcript encoding asparaginyl tRNA. Asparagine tRNA Primary Transcript SO:0000213 SO:0000389 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. Spot 42 RNA The stem of the hairpin loop formed by folding of the pre-miRNA. SO:0001245 miRNA Stem A species of genus Arabidopsis. Arabidopsis thaliana SO:0000646 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. siRNA A species of genus Saccoglossus. Saccoglossus kowalevskii A species of genus Oryzias. Oryzias latipes Sequences within the intron that modulate splice site selection for some introns. SO:0000320 Intronic Splice Enhancer SL8 Acceptor Site 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. SO:0001753 A species of genus Ciona. Ciona savignyi SO:0001182 Iron Responsive Element 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. Macacine Herpesvirus 4 A dsDNA virus of family Herpesviridae. A region of UTR. UTR Region SO:0000837 Drosophila sechellia A species of genus Drosophila. SO:0000269 Seryl tRNA A tRNA sequence that has a serine anticodon, and a 3' serine binding region. Macaca mulatta A species of genus Macaca. Five Prime Coding Exon Coding Region The sequence of the five_prime_coding_exon that codes for protein. SO:0000196 Canis familiaris A species of genus Canis. A species of genus Xenopus. Xenopus laevis SO:0000295 U12 Intron 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. Three Prime Coding Exon Coding Region SO:0000197 has_part 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. [RO:adjacent_to] adjacent_to 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. [RO:preceded_by] preceded_by 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.) [RO:part_of] part_of has_role As for has_participant, but with the additional condition that the component instance is causally active in the relevant process. [RO:has_agent] has_agent regulates guided_by 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'. [RO:derives_from] derives_from definition_source definition database_cross_reference has_related_synonym has_exact_synonym