LiteFold/GO huggingface dataset:
contractile vacuole (GO:0000331)
Namespace: cellular_component
Definition: A specialized vacuole of eukaryotic cells, especially Protozoa, that fills with water from the cytoplasm and then discharges this externally by the opening of contractile vacuole pores. One of its functions is osmoregulatory.
Synonyms: central bladder; central vacuole
template for synthesis of G-rich strand of telomere DNA activity (GO:0000332)
Namespace: molecular_function
Definition: Provision of the template used by reverse transcriptase to synthesize the G-rich strand of telomeric DNA.
Synonyms: telomerase RNA; telomerase, template
Comment: Note that this term describes the activity of an RNA gene product that interacts with other nucleic acid molecules via base pairing; it should not be used to annotate proteins.
telomerase catalytic core complex (GO:0000333)
Namespace: cellular_component
Definition: The minimal catalytic core of telomerase is a ribonucleoprotein complex composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition.
Synonyms: TERT-TERC complex
3-hydroxyanthranilate 3,4-dioxygenase activity (GO:0000334)
Namespace: molecular_function
Definition: Catalysis of the reaction: 3-hydroxyanthranilate + O2 = cis,cis-2-amino-3-(3-oxoprop-1-enyl)but-2-enedioate + H+.
Synonyms: 3-hydroxyanthranilate oxygenase activity; 3-hydroxyanthranilate:oxygen 3,4-oxidoreductase (decyclizing); 3-hydroxyanthranilic acid dioxygenase activity; 3-hydroxyanthranilic acid oxygenase activity; 3-hydroxyanthranilic oxygenase activity; 3HAO
obsolete negative regulation of transposition, DNA-mediated (GO:0000335)
Namespace: biological_process
Definition: OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of DNA transposition.
Synonyms: down regulation of DNA transposition; down-regulation of DNA transposition; downregulation of DNA transposition; inhibition of DNA transposition; negative regulation of DNA transposition
Comment: This term was obsoleted because there is no evidence that this process exists.
obsolete regulation of transposition, DNA-mediated (GO:0000337)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of DNA transposition, the process of transposing (moving to a different location) a segment of a chromosome or a piece of a DNA molecule.
Synonyms: regulation of DNA transposition
Comment: This term was obsoleted because there is no evidence that this process exists.
protein deneddylation (GO:0000338)
Namespace: biological_process
Definition: The removal of a ubiquitin-like protein of the NEDD8 type from a protein.
Synonyms: cullin deneddylation
RNA cap binding (GO:0000339)
Namespace: molecular_function
Definition: Binding to a 7-methylguanosine (m7G) group or derivative located at the 5' end of an RNA molecule.
Synonyms: binding to mRNA cap; mRNA cap binding; snRNA cap binding
RNA 7-methylguanosine cap binding (GO:0000340)
Namespace: molecular_function
Definition: Binding to a 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II.
Synonyms: RNA m7G cap binding
RNA trimethylguanosine cap binding (GO:0000341)
Namespace: molecular_function
Definition: Binding to the trimethylguanosine (m(3)(2,2,7)-GTP) group located at the 5' end of some RNA molecules. Such trimethylated cap structures, generally produced by posttranscriptional modification of a 7-methylguanosine cap, are often found on snRNAs and snoRNAs transcribed by RNA polymerase II, but have also be found on snRNAs transcribed by RNA polymerase III. They have also been found on a subset of the mRNA population in some species, e.g. C. elegans.
Synonyms: RNA m2,2,7G cap binding
RNA cap 4 binding (GO:0000342)
Namespace: molecular_function
Definition: Binding to a hypermethylated cap structure consisting of 7-methylguanosine (m(7)G) followed by four methylated nucleotides (cap 4): 7-methylguanosine-ppp-N6, N6, 2'-O-trimethyladenosine-p-2'-O-methyladenosine-p-2'-O-methylcytosine-p-N3, 2'-O-dimethyluridine Such caps are known to be found at the 5' ends of SL RNAs of trypanosomatid protozoa.
plastid-encoded plastid RNA polymerase complex B (GO:0000344)
Namespace: cellular_component
Definition: A plastid-encoded DNA-directed RNA polymerase complex that resembles eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-B is distinguished from PEP-A by its sensitivity to the antibiotic rifampicin. PEP-B is found in both etioplasts and chloroplasts, but is the predominate form in etioplasts. It forms the core of the PEP-A form; the conversion from PEP-B to PEP-A occurs during chloroplast maturation.
Synonyms: PEP-B
cytosolic DNA-directed RNA polymerase complex (GO:0000345)
Namespace: cellular_component
Definition: The eubacterial DNA-directed RNA polymerase is a multisubunit complex with a core composed of the essential subunits beta-prime, beta, and two copies of alpha and a fifth nonessential subunit called omega. An additional subunit, a sigma factor, is required for promoter recognition and specificity.
transcription export complex (GO:0000346)
Namespace: cellular_component
Definition: The transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans.
Synonyms: TREX complex
THO complex (GO:0000347)
Namespace: cellular_component
Definition: The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1p, Tho2p, Thp1p, and Mft1p, while the human complex is composed of 7 subunits.
mRNA branch site recognition (GO:0000348)
Namespace: biological_process
Definition: Recognition of the pre-mRNA branch site sequence by components of the assembling spliceosome.
Synonyms: nuclear mRNA branch site recognition; spliceosomal A complex biosynthesis; spliceosomal A complex formation; spliceosomal B complex biosynthesis; spliceosomal B complex formation; U12-type nuclear mRNA branch site recognition; U2-type nuclear mRNA branch site recognition
Comment: Note that this step represents the formation of the B complex (yeast) or the A complex (mammalian).
generation of catalytic spliceosome for first transesterification step (GO:0000349)
Namespace: biological_process
Definition: Formation of a catalytic spliceosome complex ready to perform the first splicing reaction. This occurs by an ATP-dependent conformational change of the pre-catalytic spliceosome.
Synonyms: catalytic spliceosome assembly for first transesterification step; formation of catalytic spliceosome for first transesterification step; spliceosomal A2-2 complex biosynthesis; spliceosomal A2-2 complex formation; spliceosomal C1 complex biosynthesis; spliceosomal C1 complex formation; U12-type catalytic spliceosome formation for first transesterification step; U2-type catalytic spliceosome formation for first transesterification step
Comment: Note that this step represents the formation of the A2-2 complex (yeast) or the C1 complex (mammalian).
trans assembly of SL-containing precatalytic spliceosome (GO:0000352)
Namespace: biological_process
Definition: Assembly of a spliceosomal complex containing the SL RNA and the pre-mRNA to be joined, as well as all the spliceosomal snRNPs involved in trans leader splicing. Formation of the trans leader spliceosome brings together the quadruple SL/U4/U5/U6 snRNP and the complex of the U2 snRNP with the splice site of the pre-mRNA.
Synonyms: trans assembly of spliced leader-containing precatalytic spliceosome
formation of quadruple SL/U4/U5/U6 snRNP (GO:0000353)
Namespace: biological_process
Definition: Formation of a quadruple snRNP complex composed of the spliced leader (SL) RNA along with the U4/U6-U5 tri-snRNP complex. Interactions that may facilitate this include a duplex between the SL and U6 RNAs and interactions between the U5 RNA and the exon sequence at the 5' splice site within the SL RNA.
Comment: Note that this step is analogous to 5' splice site selection in cis-splicing.
cis assembly of pre-catalytic spliceosome (GO:0000354)
Namespace: biological_process
Definition: Assembly of a spliceosomal complex containing the intact pre-mRNA and all of the spliceosomal snRNPs. This occurs when the tri-snRNP associates with the pre-mRNA and associated snRNPs in an ATP-dependent manner.
Synonyms: cis assembly of U12-type pre-catalytic spliceosome; cis assembly of U2-type pre-catalytic spliceosome; formation of spliceosomal A2-1 complex; formation of spliceosomal B1 complex; spliceosomal A2-1 complex biosynthesis; spliceosomal A2-1 complex formation; spliceosomal B1 complex biosynthesis; spliceosomal B1 complex formation
Comment: Note that this step represents formation of the A2-1 complex (yeast) or the B1 complex (mammals).
obsolete second U2-type spliceosomal transesterification activity (GO:0000364)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the second transesterification reaction of U2-type spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure. The catalytic site is thought to be formed by U6 and/or U2 snRNAs and/or associated proteins.
Synonyms: 3'-splice site cleavage, exon ligation; second U2-type spliceosomal transesterification activity
Comment: This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not.
mRNA trans splicing, via spliceosome (GO:0000365)
Namespace: biological_process
Definition: The joining together of exons from two different primary transcripts of messenger RNA (mRNA) via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
Synonyms: nuclear mRNA trans splicing, via spliceosome; nuclear mRNA trans splicing, via U2-type spliceosome
mRNA alternative trans-splicing (GO:0000366)
Namespace: biological_process
Definition: The joining together of two independently transcribed RNAs from two different genes, each of which also produces mRNA(s) via cis-splicing.
Synonyms: intergenic mRNA trans splicing; intergenic nuclear mRNA trans splicing
obsolete second U12-type spliceosomal transesterification activity (GO:0000367)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the second transesterification reaction of U12-type spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure. The catalytic site is thought to be formed by U6 and/or U2 snRNAs and/or associated proteins.
Synonyms: 3'-splice site cleavage, exon ligation; second U12-type spliceosomal transesterification activity
Comment: This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not.
Group II intron splicing (GO:0000373)
Namespace: biological_process
Definition: The splicing of Group II introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group II introns and containing splice site consensus sequences, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions (mechanistically similar to those for splicing of nuclear mRNAs) initiated by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat.
Synonyms: mRNA splicing
Comment: Note that Group II introns are known to be found in a number of places: rRNA, mRNA, and tRNA in organelles of fungi, plants, and protists; and mRNA of bacteria.
Group III intron splicing (GO:0000374)
Namespace: biological_process
Definition: The splicing of Group III introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group III introns, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions begun by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat. Though very similar in structure and mechanism to Group II introns, Group III introns are smaller and more streamlined and the splice site consensus sequences are not as well conserved.
Synonyms: mRNA splicing
Comment: Note that Group III introns are known to be found in mRNA of plastids of euglenoid protists.
RNA splicing, via transesterification reactions (GO:0000375)
Namespace: biological_process
Definition: Splicing of RNA via a series of two transesterification reactions.
Synonyms: pre-mRNA splicing factor activity; RNA splicing factor activity, transesterification mechanism; spliceosomal catalysis
Comment: Note that nuclear mRNA, Group I, Group II, and Group III introns are all spliced by a series of two transesterification reactions that occur within the RNA itself, or between two RNAs in trans splicing. Some of these require one or more proteins to stabilize the catalytic conformation, while others are autocatalytic. Note that tRNA introns are spliced by a different catalytic mechanism.
RNA splicing, via transesterification reactions with guanosine as nucleophile (GO:0000376)
Namespace: biological_process
Definition: Splicing of RNA via a series of two transesterification reactions with exogenous guanosine as the initiating nucleophile.
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile (GO:0000377)
Namespace: biological_process
Definition: Splicing of RNA via a series of two transesterification reactions with a bulged adenosine residue from the intron branch point as the initiating nucleophile. When the initial RNA for the splicing reaction is a single molecule (cis splicing), the excised intron is released in a lariat structure.
Synonyms: lariat RNA biosynthesis; lariat RNA formation
RNA exon ligation (GO:0000378)
Namespace: biological_process
Definition: The RNA metabolic process that joins two exons, each of which has free ends that were generated by endonucleolytic cleavages, by a ligation reaction.
Comment: Note that this is not a part of spliceosomal RNA splicing.
tRNA-type intron splice site recognition and cleavage (GO:0000379)
Namespace: biological_process
Definition: RNA processing that begins when the tertiary structure of a tRNA type intron is recognized, and ends when the endonucleolytic cleavage of the RNA at both the 5' and 3' splice sites occurs.
alternative mRNA splicing, via spliceosome (GO:0000380)
Namespace: biological_process
Definition: The process of generating multiple mRNA molecules from a given set of exons by differential use of exons from the primary transcript(s) to form multiple mature mRNAs that vary in their exon composition.
Synonyms: alternative nuclear mRNA splicing, via spliceosome; splice site selection
Comment: Note that this process most commonly occurs in cis, selecting or skipping exons from the same primary transcript, but it has also been observed to occur in trans at low frequency, at least in some mammals.
regulation of alternative mRNA splicing, via spliceosome (GO:0000381)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
Synonyms: regulation of alternative nuclear mRNA splicing, via spliceosome; splice site selection
first spliceosomal transesterification activity (GO:0000384)
Namespace: molecular_function
Definition: Catalysis of the first transesterification reaction of spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, while it is still joined to the 3' exon.
Synonyms: lariat formation, 5'-splice site cleavage
second spliceosomal transesterification activity (GO:0000386)
Namespace: molecular_function
Definition: Catalysis of the second transesterification reaction of spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure.
Synonyms: 3'-splice site cleavage, exon ligation; lariat formation, 5'-splice site cleavage
spliceosomal snRNP assembly (GO:0000387)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.
Synonyms: spliceosomal snRNP biogenesis
spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) (GO:0000388)
Namespace: biological_process
Definition: Rearrangement of the pre-catalytic spliceosome containing U4 (or U4atac) and U1 (or U11) snRNPs to unpair U4 (or U4atac) from U6 (or U6atac) and release it from the spliceosomal complex along with U1 (or U11).
Synonyms: 3'-splice site cleavage, exon ligation; spliceosomal A1 complex biosynthesis; spliceosomal A1 complex formation; spliceosomal B2 complex biosynthesis; spliceosomal B2 complex formation; U12-type spliceosome conformational change to release U4atac and U11; U2-type spliceosome conformational change to release U4 and U1
Comment: Note that this step represents formation of the A1 complex (yeast) or the B2 complex (mammalian).
mRNA 3'-splice site recognition (GO:0000389)
Namespace: biological_process
Definition: Recognition of the intron 3'-splice site by components of the assembling U2- or U12-type spliceosome.
Synonyms: nuclear mRNA 3'-splice site recognition; U12-type nuclear mRNA 3'-splice site recognition; U2-type nuclear mRNA 3'-splice site recognition
spliceosomal complex disassembly (GO:0000390)
Namespace: biological_process
Definition: Disassembly of a spliceosomal complex with the ATP-dependent release of the product RNAs, one of which is composed of the joined exons. In cis splicing, the other product is the excised sequence, often a single intron, in a lariat structure.
Synonyms: spliceosome complex disassembly; spliceosome disassembly; U12-type spliceosome disassembly; U2-type spliceosome disassembly
spliceosomal conformational changes to generate catalytic conformation (GO:0000393)
Namespace: biological_process
Definition: Structural rearrangements of the spliceosome complex, containing RNA to be spliced, to generate a catalytic conformation.
Synonyms: 3'-splice site cleavage, exon ligation
RNA splicing, via endonucleolytic cleavage and ligation (GO:0000394)
Namespace: biological_process
Definition: Splicing of RNA via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
Synonyms: mRNA splicing
Comment: Note that while typically associated with tRNA splicing, this mechanism of splicing is known to be used for some non-tRNA substrates, e.g. HAC1 (YFL031W) in S. cerevisiae and an intron in the 23S rRNA of the Archaeal species Desulfurococcus mobilis.
mRNA splicing, via spliceosome (GO:0000398)
Namespace: biological_process
Definition: The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
Synonyms: mRNA splicing; nuclear mRNA splicing via U12-type spliceosome; nuclear mRNA splicing via U2-type spliceosome; nuclear mRNA splicing, via spliceosome; pre-mRNA splicing; splicing AT-AC intron; splicing GT-AG intron
Comment: Note that although the many U12-type introns have the sequence AT-AC at the intron termini, some introns with these terminal sequences are spliced by the U2-type spliceosome. The distinguishing characteristics are sequences near the 5' splice site and the branch point sequences of the intron. Note that although the majority of U2-type introns have the sequence GU-AG at the intron termini, some introns with these terminal sequences are spliced by the U12-type spliceosome. The distinguishing characteristics are sequences near the 5' splice site and the branch point sequences of the intron.
cellular bud neck septin structure (GO:0000399)
Namespace: cellular_component
Definition: Any of a series of septin structures that are localized in the bud neck of a budding fungal cell during the cell cycle.
four-way junction DNA binding (GO:0000400)
Namespace: molecular_function
Definition: Binding to a DNA segment containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.
Synonyms: forked DNA binding; Holliday junction binding
open form four-way junction DNA binding (GO:0000401)
Namespace: molecular_function
Definition: Binding to a DNA segment containing the open form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The open form of a four-way junction can be diagrammed without any of the strands crossing over.
Synonyms: open form Holliday junction binding
crossed form four-way junction DNA binding (GO:0000402)
Namespace: molecular_function
Definition: Binding to a DNA segment containing the crossed form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The crossed form of a four-way junction cannot be diagrammed without any of the strands crossing over, and instead contains a single crossover between two of the strands.
Synonyms: crossed form Holliday junction binding
Y-form DNA binding (GO:0000403)
Namespace: molecular_function
Definition: Binding to a DNA segment shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end.
Synonyms: forked DNA binding; splayed Y-form DNA binding
heteroduplex DNA loop binding (GO:0000404)
Namespace: molecular_function
Definition: Binding to a DNA segment containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration.
Synonyms: loop DNA binding
bubble DNA binding (GO:0000405)
Namespace: molecular_function
Definition: Binding to DNA segment that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA.