Alliance of Genome Resources Gene Biotype Slim
database of genomic structural variation
A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
This relationship is vague and up for discussion.
B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
Example: A splice_junction connects_on exon, exon, mature_transcript.
X contained_by Y iff X starts after start of Y and X ends before end of Y.
The inverse is contains. Example: intein contained_by immature_peptide_region.
X is disconnected_from Y iff it is not the case that X overlaps Y.
B is evidence_for_feature A, if an instance of B supports the existence of A.
This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
X is exemplar of Y if X is the best evidence for Y.
Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
X gained Y if X is a variant_of X' and Y part of X but not X'.
A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may gain a stop codon not present in the reference sequence.
X has_integral_part Y if and only if: X has_part Y and Y part_of X.
The relationship between a feature and an attribute.
X integral_part_of Y if and only if: X part_of Y and Y has_part X.
Example: exon integral_part_of transcript.
R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
Example: region is consecutive_sequence of base.
X lost Y if X is a variant_of X' and Y part of X' but not X.
A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may have lost a stop codon present in the reference sequence.
A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
A relationship between a pseudogenic feature and its functional ancestor.
X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
Example: amino_acid part_of polypeptide.
B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
Example: miRNA processed_from miRNA_primary_transcript.
X is processed_into Y if a region X is modified to create Y.
Example: miRNA_primary_transcript processed into miRNA.
X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
X is transcribed_from Y if X is synthesized from template Y.
Example: primary_transcript transcribed_from gene.
Example: gene transcribed_to primary_transcript.
Example: codon translates_to amino_acid.
X is translation of Y if Y is translated by ribosome to create X.
Example: Polypeptide translation_of CDS.
A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.
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 coding exon that is not the most 3-prime or the most 5-prime in a given transcript.
The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
A small non coding RNA sequence, present in the cytoplasm.
A part of a match, for example an hsp from blast is a match_part.
A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.
A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
Any extent of continuous biological sequence.
An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
A viral sequence which has integrated into a host genome.
A primary transcript that, at least in part, encodes one or more proteins.
Region in mRNA where ribosome assembles.
A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
A region of known length which may be used to manufacture a longer region.
A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
The point at which one or more contiguous nucleotides were excised.
A modified base in which adenine has been methylated.
Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
With spliceosomal introns, the splice sites bind the spliceosomal machinery.
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.
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.
A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter.
A nucleotide match against a sequence from another organism.
The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Definition updated with per Mejia-Almonte et.al Redefining fundamental concepts of transcription initiation in prokaryotes Aug 5 2020.
A region of the gene which is not transcribed.
A transcript that in its initial state requires modification to be functional.
A group of characterized repeat sequences.
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.
A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
restriction fragment length polymorphism
An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
The sequence of the five_prime_coding_exon that codes for protein.
The sequence of the three_prime_coding_exon that codes for protein.
An exon that does not contain any codons.
Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
A primary transcript encoding a ribosomal RNA.
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.
A processed transcript cannot contain introns.
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
A DNA site where a transcription factor binds.
Definition updated along with definitions in Mejia-Almonte et.al PMID:32665585. Added relationship part_of SO:0000727 CRM in place of previous CRM relationship has_part TF_binding_site August 2020 in response to requests from GREEKC initiative. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
The sequences extending on either side of a specific region.
rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.
Definition updated 10 June 2021 as part of restructuring rRNA terms and reforming definitions to have similar structures. Request from EBI. See GitHub Issue #493
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 small nuclear RNA molecule involved in pre-mRNA splicing and processing.
Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing.
Updated the definition of snoRNA (SO:0000275) from "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." to "Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing." to acknowledge that some snoRNAs functionally localize to other compartments (cytoplasm or even secreted). See GitHub Issue #578.
Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites.
Part of the primary transcript that is clipped off during processing.
A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA.
The first base where RNA polymerase begins to synthesize the RNA transcript.
Added relationship is_a SO:0002309 core_promoter_element with the creation of core_promoter_element as part of GREEKC initiative August 2020 - Dave Sant.
A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
First codon to be translated by a ribosome.
In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
A nucleotide sequence that may be used to identify a larger sequence.
A primary transcript encoding a large ribosomal subunit RNA.
A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
Region of sequence similarity by descent from a common ancestor.
Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
Coding region of sequence similarity by descent from a common ancestor.
The boundary between two exons in a processed transcript.
Non-coding region of sequence similarity by descent from a common ancestor.
A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog).
A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.
A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
Region of a transcript that regulates splicing.
A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
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.
The junction where an insertion occurred.
The junction in a genome where a transposable_element has inserted.
A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others).
An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. Moved under ncRNA on 18 Nov 2021. See GitHub Issue #533.
Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.
Dave Sant removed '5_8S rRNA is also found in archaea.' from definition due to lack of references mentioning this on 1 Feb 2021. See GitHub Issue #505. Renamed from rRNA_5_8S to cytosolic_5_8S_rRNA on 10 June 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
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.
Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533.
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.
The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
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.
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.
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.
An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
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.
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.
U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
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.
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.
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.
An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
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.
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.
Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes.
Renamed to cytosolic_18S_rRNA from rRNA_18S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
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.
A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
A region where the sequence differs from that of a specified sequence.
The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
Changed parent term from ncRNA (SO:0000655) to piRNA (SO:0001035). See GitHub Issue #573.
A non-functional descendant of a functional entity.
Does not have to be part of a pseudogene.
One of the pieces of sequence that make up a golden path.
A set of regions which overlap with minimal polymorphism to form a linear sequence.
A piece of sequence that makes up a tiling_path (SO:0000472).
A primary transcript that is never translated into a protein.
The sequence of the 3' exon that is not coding.
three prime coding exon noncoding region
The sequence of the 5' exon preceding the start codon.
A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
A region of chromosome where the spindle fibers attach during mitosis and meiosis.
A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
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.
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.
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'.
Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577.
A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
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.
The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
A regulatory region that 1) when located between a CRM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region.
moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.
Regions of the chromosome that are important for structural elements.
A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
The reverse complement of the primary transcript.
A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. siRNAs trigger the cleavage of their target molecules.
Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes.
Renamed to cytosolic_SSU_rRNA from small_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.
Renamed to cytosolic_LSU_rRNA from large_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes.
Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes.
Renamed from rRNA_28S to cytosolic_28S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
A region of sequence containing one or more repeat units.
A repeat that is located at dispersed sites in the genome.
An intron which is spliced by the spliceosome.
The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020.
A region of nucleotide sequence targeted by a nuclease enzyme.
The space between two bases in a sequence which marks the position where a deletion has occurred.
A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
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.
A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
A sequence_feature with an extent of zero.
A junction is a boundary between regions. A boundary has an extent of zero.
A region of sequence where the validity of the base calling is questionable.
A region of sequence where there may have been an error in the assembly.
A region of sequence implicated in an experimental result.
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.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
Two or more adjacent copies of a region (of length greater than 1).
The 3' splice site of the acceptor primary transcript.
This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
A region of nucleotide sequence corresponding to a known motif.
A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs.
Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534.
A gap in the sequence of known length. The unknown bases are filled in with N's.
A region that is involved in the regulation of transcription of a group of regulated genes.
Merged into transcriptional_cis_regulatory_region (SO:0001055) on 11 Feb 2021 as part of GREEKC reducing redundancy as we prepare to submit several terms to Ensembl. See GitHub Issue #529.
The region of sequence that has been inserted and is being propagated by the clone.
Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
A manufactured term used to allow the parts of a gene to have an is_a path to the root.
This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
Added to allow the polypeptide regions to have is_a paths back to the root.
A terms added to allow the parts of introns to have is_a paths to the root.
A region of a gene that has a specific function.
Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes.
Renamed to cytosolic_16S_rRNA from rRNA_16S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes.
Renamed from rRNA_23S to cytosolic_23S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes.
A variation that increases or decreases the copy number of a given region.
A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
An MGE that is integrated into the host chromosome.
A regulatory_region that modulates the transcription of a gene or genes.
Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527.
A regulatory_region that modulates splicing.
A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
partially characterised change in DNA sequence
Merged with partially characterized change in nucleotide sequence.
An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
The maximal intersection of exon and UTR.
An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
The region of an exon that encodes for protein sequence.
An exon containing either a start or stop codon will be partially coding and partially non coding.
A region containing at least one unique origin of replication and a unique termination site.
A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
A region which is intended for use in an experiment.
A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
A region defined by its disposition to be involved in a biological process.
A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping.
Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
Primary transcript region bordering trans-splice junction.
SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
A regulatory region that is involved in the control of the process of transcription.
Obsoleted by David Sant on 11 Feb 2021 when it was merged with transcriptional_cis_regulatory_region (SO:0001055) to reduce redundancy and be consistent with Gene Ontology. See GitHub Issue #527.
A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification.
Moved from is_a biological_region (SO:0001411) to is_a regulatory_region (SO:0005836) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. 11 Feb 2021 updated definition along with addition of epigenomically_modified_region (SO:0002332). Epigenetically modified region is now not inherited while epigenomically modified region is not annotated as inherited. See GitHub Issue #532 and issue #534.
An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).
A region of sequence that is involved in the control of a biological process.
The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.
A sequence alteration where the length of the change in the variant is the same as that of the reference.
When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.
A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
A continuous nucleotide sequence is inverted in the same position.
A set of units of gene expression directly regulated by a common set of one or more common regulatory gene products.
Definition updated with Mejia-Almonte et.al PMID:32665585 on Aug 5, 2020. Added relationship has_part SO:0002300
The sequence referred to by an entry in a databank such as GenBank or SwissProt.