LiteFold/GO huggingface dataset:
double-strand/single-strand DNA junction binding (GO:0000406)
Namespace: molecular_function
Definition: Binding to a DNA segment that contains double-stranded DNA flanked by a region of single-stranded DNA.
phagophore assembly site (GO:0000407)
Namespace: cellular_component
Definition: Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction.
Synonyms: PAS; perivacuolar space; pre-autophagosomal structure
EKC/KEOPS complex (GO:0000408)
Namespace: cellular_component
Definition: A protein complex involved in t6A tRNA modification. For example, in Saccharomyces cerevisiae the complex contains Bud32p, Kae1p, Gon7p, Cgi121p, and Pcc1p.
Synonyms: endopeptidase-like kinase chromatin-associated protein complex; KEOPS/EKC complex; kinase, putative endopeptidase and other proteins of small size protein complex; TCTC; threonyl-carbamoly transferase complex
Comment: Originally proposed to be involved in transcription as well as promoting telomere uncapping and telomere elongation.
regulation of transcription by galactose (GO:0000409)
Namespace: biological_process
Definition: Any process involving galactose that modulates the frequency, rate or extent or transcription.
carbon catabolite repression of transcription by galactose (GO:0000410)
Namespace: biological_process
Definition: A transcription regulation process in which the presence of galactose that leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.
Synonyms: down regulation of transcription by galactose; down-regulation of transcription by galactose; downregulation of transcription by galactose; inhibition of transcription by galactose
positive regulation of transcription by galactose (GO:0000411)
Namespace: biological_process
Definition: Any process involving galactose that activates or increases the rate of transcription.
Synonyms: activation of transcription by galactose; stimulation of transcription by galactose; up regulation of transcription by galactose; up-regulation of transcription by galactose; upregulation of transcription by galactose
obsolete histone peptidyl-prolyl isomerization (GO:0000412)
Namespace: biological_process
Definition: OBSOLETE. The modification of a histone by cis-trans isomerization of a proline residue.
Synonyms: histone proline isomerization
Comment: This term was obsoleted because it represents a molecular function.
protein peptidyl-prolyl isomerization (GO:0000413)
Namespace: biological_process
Definition: The modification of a protein by cis-trans isomerization of a proline residue.
Synonyms: protein proline isomerization
obsolete regulation of histone H3-K36 methylation (GO:0000414)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3.
Comment: This term was obsoleted because it represents a molecular function.
obsolete negative regulation of histone H3-K36 methylation (GO:0000415)
Namespace: biological_process
Definition: OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3.
Synonyms: down regulation of histone H3-K36 methylation; down-regulation of histone H3-K36 methylation; downregulation of histone H3-K36 methylation; inhibition of histone H3-K36 methylation
Comment: This term was obsoleted because it represents a molecular function.
obsolete positive regulation of histone H3-K36 methylation (GO:0000416)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3.
Synonyms: activation of histone H3-K36 methylation; stimulation of histone H3-K36 methylation; up regulation of histone H3-K36 methylation; up-regulation of histone H3-K36 methylation; upregulation of histone H3-K36 methylation
Comment: This term was obsoleted because it represents a molecular function.
HIR complex (GO:0000417)
Namespace: cellular_component
Definition: A protein complex proposed to be involved in replication-independent nucleosome assembly, by promoting histone deposition onto DNA. For example, in Saccharomyces, the complex contains Hir1p, Hir2p, Hir3p, and Hpc2p.
Synonyms: HIRA complex
RNA polymerase IV complex (GO:0000418)
Namespace: cellular_component
Definition: RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase V, while the largest subunit is found only in RNAP IV complex.
Synonyms: DNA-directed RNA polymerase IV complex; DNA-directed RNA polymerase IVa complex
RNA polymerase V complex (GO:0000419)
Namespace: cellular_component
Definition: RNA polymerase V is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol V is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits.
Synonyms: DNA-directed RNA polymerase IVb complex; DNA-directed RNA polymerase V complex
autophagosome membrane (GO:0000421)
Namespace: cellular_component
Definition: The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered.
Synonyms: autophagic vacuole membrane
mitophagy (GO:0000423)
Namespace: biological_process
Definition: The selective autophagy process in which a mitochondrion is degraded by macroautophagy.
Synonyms: macromitophagy
Comment: Note that this terms refers to the macroautophagy process and is named by common usage. Be aware that there are a separate micromitophagy and mitophagy by induced vacuole formation processes.
micromitophagy (GO:0000424)
Namespace: biological_process
Definition: Degradation of a mitochondrion by microautophagy.
Comment: Note that this term is not a child of mitophagy because the community generally uses the latter to refer to the macroautophagy of mitochondria.
pexophagy (GO:0000425)
Namespace: biological_process
Definition: The selective autophagy process in which a peroxisome is degraded by macroautophagy.
Synonyms: macropexophagy
micropexophagy (GO:0000426)
Namespace: biological_process
Definition: Degradation of a peroxisome by microautophagy.
Comment: Note that this term is not a child of pexophagy because the community usually uses the latter to refer to the macroautohagy process.
plastid-encoded plastid RNA polymerase complex (GO:0000427)
Namespace: cellular_component
Definition: An RNA polymerase complex containing polypeptides encoded by the plastid genome. Plastid-encoded DNA-directed RNA polymerases resemble eubacterial multisubunit RNA polymerases, with a core composed of alpha, beta, and beta-prime subunits. Some forms contain multiple additional subunits. An additional sigma factor subunit is required for promoter recognition.
DNA-directed RNA polymerase complex (GO:0000428)
Namespace: cellular_component
Definition: A protein complex that possesses DNA-directed RNA polymerase activity.
carbon catabolite regulation of transcription from RNA polymerase II promoter (GO:0000429)
Namespace: biological_process
Definition: A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources.
Synonyms: regulation of transcription from RNA polymerase II promoter by carbon catabolites
regulation of transcription from RNA polymerase II promoter by galactose (GO:0000431)
Namespace: biological_process
Definition: Any process involving galactose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)
Namespace: biological_process
Definition: Any process involving glucose that activates or increases the rate of transcription from an RNA polymerase II promoter.
Synonyms: activation of transcription from RNA polymerase II promoter by glucose; stimulation of transcription from RNA polymerase II promoter by glucose; up regulation of transcription from RNA polymerase II promoter by glucose; up-regulation of transcription from RNA polymerase II promoter by glucose; upregulation of transcription from RNA polymerase II promoter by glucose
carbon catabolite repression of transcription from RNA polymerase II promoter by glucose (GO:0000433)
Namespace: biological_process
Definition: A transcription regulation process in which the presence of glucose leads to a decrease in the frequency, rate, or extent of transcription of specific RNA polymerase II-transcribed genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.
Synonyms: down regulation of transcription from RNA polymerase II promoter by glucose; down-regulation of transcription from RNA polymerase II promoter by glucose; downregulation of transcription from RNA polymerase II promoter by glucose; inhibition of transcription from RNA polymerase II promoter by glucose
carbon catabolite repression of transcription from RNA polymerase II promoter by galactose (GO:0000434)
Namespace: biological_process
Definition: Any process involving galactose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
Synonyms: down regulation of transcription from RNA polymerase II promoter by galactose; down-regulation of transcription from RNA polymerase II promoter by galactose; downregulation of transcription from RNA polymerase II promoter by galactose; inhibition of transcription from RNA polymerase II promoter by galactose
positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)
Namespace: biological_process
Definition: Any process involving galactose that activates or increases the rate of transcription from an RNA polymerase II promoter.
Synonyms: activation of transcription from RNA polymerase II promoter by galactose; stimulation of transcription from RNA polymerase II promoter by galactose; up regulation of transcription from RNA polymerase II promoter by galactose; up-regulation of transcription from RNA polymerase II promoter by galactose; upregulation of transcription from RNA polymerase II promoter by galactose
carbon catabolite activation of transcription from RNA polymerase II promoter (GO:0000436)
Namespace: biological_process
Definition: Any process involving carbon catabolites that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
Synonyms: positive regulation of transcription from RNA polymerase II promoter by carbon catabolites
carbon catabolite repression of transcription from RNA polymerase II promoter (GO:0000437)
Namespace: biological_process
Definition: A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources.
Synonyms: negative regulation of transcription from RNA polymerase II promoter by carbon catabolites
core TFIIH complex portion of holo TFIIH complex (GO:0000438)
Namespace: cellular_component
Definition: The core TFIIH complex when it is part of the general transcription factor TFIIH.
Synonyms: SSL2-core TFIIH complex portion of holo TFIIH complex
transcription factor TFIIH core complex (GO:0000439)
Namespace: cellular_component
Definition: The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD.
Synonyms: core TFIIH complex; SSL2-core TFIIH complex
MIS12/MIND type complex (GO:0000444)
Namespace: cellular_component
Definition: A multiprotein kinetochore subcomplex that binds to centromeric chromatin and forms part of the outer kinetochore. It helps to recruit outer kinetochore subunits that will bind to microtubules. In humans, it consists of MIS12, DSN1, NSL1 and PMF1.
Synonyms: MIND complex; Mis12 complex; Mtw1p Including Nnf1p-Nsl1p-Dsn1p complex; nuclear MIS12/MIND complex
endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)
Namespace: biological_process
Definition: Endonucleolytic cleavage between the SSU-rRNA and the 5.8S rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript.
Synonyms: endonucleolytic cleavage at A2
cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000448)
Namespace: biological_process
Definition: Endonucleolytic cleavage within ITS2 between the 5.8S rRNA and the LSU-rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript.
Synonyms: cleavage at C2; cleavage in ITS2 of tricistronic rRNA transcript to separate 5.8S and LSU rRNAs (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) (GO:0000449)
Namespace: biological_process
Definition: Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the Large Subunit (LSU) rRNA, and the 5S rRNA, in that order, from 5' to 3' along the primary transcript. For example, primary ribosomal RNA transcripts containing three genes, in this order, are produced in E. coli and other prokaryotic species. Note that the use of the word tricistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript.
cleavage of bicistronic rRNA transcript (SSU-rRNA, LSU-rRNA) (GO:0000450)
Namespace: biological_process
Definition: Endonucleolytic cleavage of pre-rRNAs originally produced as a bicistronic rRNA transcript that contains the SSU-rRNA and the LSU-rRNA in that order from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with two genes in this order are produced in Archaeal species.
rRNA 2'-O-methylation (GO:0000451)
Namespace: biological_process
Definition: The addition of a methyl group to the 2'-oxygen atom of a nucleotide residue in an rRNA molecule during ribosome biogenesis.
snoRNA guided rRNA 2'-O-methylation (GO:0000452)
Namespace: biological_process
Definition: The posttranscriptional addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis using a snoRNA guide that targets the position of methylation.
Synonyms: snoRNA guided rRNA 2'-O-ribose methylation
obsolete enzyme-directed rRNA 2'-O-methylation (GO:0000453)
Namespace: biological_process
Definition: OBSOLETE. The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA.
Comment: This term was obsoleted because it represents a molecular function.
snoRNA guided rRNA pseudouridine synthesis (GO:0000454)
Namespace: biological_process
Definition: The intramolecular conversion of uridine to pseudouridine in an rRNA molecule during ribosome biogenesis using a snoRNA guide that targets the position of pseudouridylation.
enzyme-directed rRNA pseudouridine synthesis (GO:0000455)
Namespace: biological_process
Definition: The intramolecular conversion of uridine to pseudouridine during ribosome biogenesis where the enzyme specifies the site that becomes pseudouridylated without using a guide RNA.
endonucleolytic cleavage between SSU-rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) (GO:0000457)
Namespace: biological_process
Definition: Endonucleolytic cleavage to separate a pre-SSU-rRNA from a pre-LSU-rRNA originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the Large Subunit (LSU) rRNA, and the 5S rRNA, in that order, from 5' to 3' along the primary transcript. Note that the use of the word tricistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript.
obsolete exonucleolytic trimming involved in rRNA processing (GO:0000459)
Namespace: biological_process
Definition: OBSOLETE. Exonucleolytic digestion of a pre-rRNA molecule in the process to generate a mature rRNA molecule.
Synonyms: exonucleolytic trimming during rRNA processing
Comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
maturation of 5.8S rRNA (GO:0000460)
Namespace: biological_process
Definition: Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule.
endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000461)
Namespace: biological_process
Definition: Endonucleolytic cleavage at the 3'-end of the SSU-rRNA from an originally tricistronic rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA.
Synonyms: endonucleolytic cleavage at site D
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)
Namespace: biological_process
Definition: Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript.
Synonyms: maturation of 18S rRNA
maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000463)
Namespace: biological_process
Definition: Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript.
endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000464)
Namespace: biological_process
Definition: Endonucleolytic cleavage within Internal Transcribed Spacer 1 (ITS1) upstream of the 5.8S rRNA derived from an originally tricistronic rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. In S. cerevisiae, this endonucleolytic cleavage within ITS1 initiates the maturation of the LSU and the 5.8S rRNAs.
Synonyms: endonucleolytic cleavage at A3
exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000465)
Namespace: biological_process
Definition: Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 5'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript.
exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000467)
Namespace: biological_process
Definition: Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 3'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript.
generation of mature 3'-end of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000468)
Namespace: biological_process
Definition: Any process involved in generating the mature 3'-end of an LSU-rRNA derived from a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript.
Synonyms: processing at B2
obsolete cleavage involved in rRNA processing (GO:0000469)
Namespace: biological_process
Definition: OBSOLETE. Any phosphodiester bond hydrolysis involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule.
Synonyms: cleavage during rRNA processing
Comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
maturation of LSU-rRNA (GO:0000470)
Namespace: biological_process
Definition: Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule.
endonucleolytic cleavage in 3'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000471)
Namespace: biological_process
Definition: Endonucleolytic cleavage within the 3'-External Transcribed Spacer (ETS) of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. In S. cerevisiae, endonucleolytic cleavage within the 3'-ETS of the pre-RNA, which may occur cotranscriptionally, is the first step in rRNA processing, and initiates a cascade of subsequent processing and modification events.
endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)
Namespace: biological_process
Definition: Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA.
Synonyms: endonucleolytic cleavage at A1