LiteFold/GO huggingface dataset:
branched-chain amino acid catabolic process to alcohol via Ehrlich pathway (GO:0000950)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the catabolism of branched chain amino acids to produce branched chain alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanol, 2-methylbutanol, or 2-methylpropanol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols.
Synonyms: branched chain family amino acid catabolic process to alcohol via Ehrlich pathway
obsolete L-methionine catabolic process to 3-methylthiopropanol (GO:0000951)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving the catabolism of branched chain amino acids to produce branched chain alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When L-methionine is used as the substrate, 3-methylthiopropanol is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols.
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
aromatic amino acid family catabolic process to carboxylic acid via Ehrlich pathway (GO:0000952)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanoate, 4-hydroxyphenylethanoate, or 2-(Indol-3-yl)-ethanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids.
branched-chain amino acid catabolic process to carboxylic acid via Ehrlich pathway (GO:0000953)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanoate, 2-methylbutanoate, or 2-methylpropanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids.
Synonyms: branched chain family amino acid catabolic process to carboxylic acid via Ehrlich pathway
amino acid catabolic process via Ehrlich pathway (GO:0000955)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols or carboxylic acids containing one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives, sometimes referred to as fusel acids, may be produced instead of alcohols.
nuclear-transcribed mRNA catabolic process (GO:0000956)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells.
Synonyms: nuclear mRNA breakdown; nuclear mRNA catabolism; nuclear mRNA degradation
mitochondrial RNA catabolic process (GO:0000957)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of RNA transcribed from the mitochondrial genome and occurring in the mitochondrion.
mitochondrial mRNA catabolic process (GO:0000958)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of mRNA transcribed from the mitochondrial genome and occurring in the mitochondrion.
mitochondrial RNA metabolic process (GO:0000959)
Namespace: biological_process
Definition: The chemical reactions and pathways involving RNA transcribed from the mitochondrial genome and occurring in the mitochondrion.
negative regulation of mitochondrial RNA catabolic process (GO:0000961)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome.
positive regulation of mitochondrial RNA catabolic process (GO:0000962)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome.
mitochondrial RNA processing (GO:0000963)
Namespace: biological_process
Definition: The conversion of a primary RNA molecule transcribed from a mitochondrial genome into one or more mature RNA molecules; occurs in the mitochondrion.
mitochondrial RNA 5'-end processing (GO:0000964)
Namespace: biological_process
Definition: Any process involved in forming the mature 5' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion.
Synonyms: mitochondrial RNA 5' end processing
mitochondrial RNA 3'-end processing (GO:0000965)
Namespace: biological_process
Definition: Any process involved in forming the mature 3' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion.
Synonyms: mitochondrial RNA 3' end processing
rRNA 5'-end processing (GO:0000967)
Namespace: biological_process
Definition: Any process involved in forming the mature 5' end of an rRNA molecule.
Synonyms: rRNA 5' end processing
tRNA exon ligation (GO:0000968)
Namespace: biological_process
Definition: An RNA exon ligation process that rejoins two exons of a pre-tRNA which has had the intron removed.
obsolete tRNA exon ligation utilizing GTP as source of linkage phosphate (GO:0000970)
Namespace: biological_process
Definition: OBSOLETE. A tRNA exon ligation process in which the splice junction phosphate is derived from exogenous GTP. This type of ligation to rejoin the 5' and 3' exons of a tRNA is observed in the yeast Saccharomyces cerevisiae where the ligation reaction also produces a 2'-phosphate at the splice junction which is subsequently removed as part of the ligation process.
Comment: The reason for obsoletion is that this term is a molecular function
obsolete tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate (GO:0000971)
Namespace: biological_process
Definition: OBSOLETE. A tRNA exon ligation process in which the splice junction phosphate is derived from the 2',3' cyclic phosphate at the 3'-end of the 5'-exon. This type of ligation to rejoin the 5' and 3' exons of a tRNA is observed in wheat, Chlamydomonas, and vertebrate species including humans.
Comment: The reason for obsoletion is that this term is a molecular function.
transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)
Namespace: biological_process
Definition: The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery. In S. cerevisiae, this process involves cis-acting DNA sequences such as the TATA box and upstream activating sequence (UAS) elements, trans-acting transcriptional activators, and also the 3'-UTR of the transcript.
post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000973)
Namespace: biological_process
Definition: The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed.
Synonyms: posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery
Prp19 complex (GO:0000974)
Namespace: cellular_component
Definition: A protein complex consisting of Prp19 and associated proteins that is involved in the transition from the precatalytic spliceosome to the activated form that catalyzes step 1 of splicing, and which remains associated with the spliceosome through the second catalytic step. It is widely conserved, found in both yeast and mammals, though the exact composition varies. In S. cerevisiae, it contains Prp19p, Ntc20p, Snt309p, Isy1p, Syf2p, Cwc2p, Prp46p, Clf1p, Cef1p, and Syf1p.
Synonyms: MOS4-Associated Complex; nineteen complex; NTC; Prp19/CDC5 complex
transcription cis-regulatory region binding (GO:0000976)
Namespace: molecular_function
Definition: Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
Synonyms: bacterial-type RNA polymerase regulatory region DNA binding; bacterial-type RNA polymerase transcription regulatory region sequence-specific DNA binding; eubacterial-type RNA polymerase regulatory region DNA binding; eubacterial-type RNA polymerase regulatory region sequence-specific DNA binding; regulatory region DNA binding; transcription regulatory region DNA binding; transcription regulatory region sequence-specific DNA binding
Comment: Note that this term is meant to also capture non-specific binding to regulatory regions. Also, to minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription.
RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)
Namespace: molecular_function
Definition: Binding to a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
Synonyms: RNA polymerase II regulatory region DNA binding
Comment: To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription.
RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)
Namespace: molecular_function
Definition: Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase II.
Synonyms: RNA polymerase II core promoter proximal region sequence-specific DNA binding; RNA polymerase II distal enhancer sequence-specific DNA binding; RNA polymerase II promoter proximal region sequence-specific DNA binding; RNA polymerase II proximal promoter sequence-specific DNA binding; RNA polymerase II upstream activating sequence (UAS) sequence-specific DNA binding
Comment: Note that the phrase "upstream activating sequence", or UAS is often used in S. cerevisiae literature to refer to cis-regulatory sequences. In bacteria such as E. coli, the phrase "upstream activating sequence", or UAS is usually a synonym for "enhancer".
RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)
Namespace: molecular_function
Definition: Binding to a DNA sequence that is part of the core promoter of a RNA polymerase II-transcribed gene.
DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)
Namespace: molecular_function
Definition: A DNA-binding transcription factor activity that modulates the transcription of specific gene sets transcribed by RNA polymerase II.
Synonyms: copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity; metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity; metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity; RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity; RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity; RNA polymerase II transcription factor activity, copper ion regulated core promoter proximal region sequence-specific binding; RNA polymerase II transcription factor activity, copper ion regulated proximal promoter sequence-specific DNA binding; RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding; RNA polymerase II transcription factor activity, metal ion regulated proximal promoter sequence-specific DNA binding; RNA polymerase II transcription factor activity, metal ion regulated sequence-specific DNA binding; RNA polymerase II transcription factor activity, sequence-specific DNA binding; RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region DNA binding; RNA polymerase II transcription factor activity, zinc ion regulated core promoter proximal region sequence-specific DNA binding; RNA polymerase II transcription factor activity, zinc ion regulated proximal promoter sequence-specific DNA binding; sequence-specific distal enhancer binding RNA polymerase II transcription factor activity; sequence-specific DNA binding RNA polymerase II transcription factor activity; sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity; transcription factor; transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding; transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding; transcription factor activity, RNA polymerase II proximal promoter sequence-specific DNA binding; zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity
Comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity.
cis-regulatory region sequence-specific DNA binding (GO:0000987)
Namespace: molecular_function
Definition: Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers.
Synonyms: bacterial-type cis-regulatory region sequence-specific DNA binding; bacterial-type proximal promoter sequence-specific DNA binding; bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding; bacterial-type RNA polymerase enhancer sequence-specific DNA binding; bacterial-type RNA polymerase upstream activating sequence (UAS) sequence-specific DNA binding; cis-regulatory region binding; core promoter proximal region DNA binding; core promoter proximal region sequence-specific DNA binding; enhancer binding; enhancer sequence-specific DNA binding; eubacterial-type RNA polymerase regulatory transcription factor sequence-specific DNA binding; promoter proximal region sequence-specific DNA binding; proximal promoter sequence-specific DNA binding
obsolete transcription factor activity, protein binding (GO:0000988)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a protein or protein complex, to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
Synonyms: protein binding transcription factor activity; transcription factor activity
Comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
obsolete transcription factor activity, transcription factor binding (GO:0000989)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
Synonyms: transcription factor binding transcription factor activity
Comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
obsolete transcription factor activity, core RNA polymerase binding (GO:0000990)
Namespace: molecular_function
Definition: OBSOLETE. Binding to an RNA polymerase in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
Synonyms: core RNA polymerase binding transcription factor activity
Comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
obsolete transcription factor activity, core RNA polymerase II binding (GO:0000991)
Namespace: molecular_function
Definition: OBSOLETE. Binding to an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
Synonyms: core RNA polymerase II binding transcription factor activity
Comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
RNA polymerase III cis-regulatory region sequence-specific DNA binding (GO:0000992)
Namespace: molecular_function
Definition: Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase III. The transcribed region might be contain a single gene or a cistron containing multiple genes.
RNA polymerase II complex binding (GO:0000993)
Namespace: molecular_function
Definition: Binding to an RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
Synonyms: RNA polymerase II core binding; RNAP II core binding
RNA polymerase III core binding (GO:0000994)
Namespace: molecular_function
Definition: Binding to an RNA polymerase III core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of seventeen subunits.
RNA polymerase III general transcription initiation factor activity (GO:0000995)
Namespace: molecular_function
Definition: A general transcription initiation factor activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase III. Factors required for RNA polymerase III transcription initiation include TFIIIA, TFIIIB and TFIIIC. RNA polymerase III transcribes genes encoding short RNAs, including tRNAs, 5S rRNA, U6 snRNA, the short ncRNA component of RNases P, the mitochondrial RNA processing (MRP) RNA, the signal recognition particle SRP RNA, and in higher eukaryotes a number of micro and other small RNAs, though there is some variability across species as to whether a given small noncoding RNA is transcribed by RNA polymerase II or RNA polymerase III.
Synonyms: core RNA polymerase III binding transcription factor activity; RNA polymerase III general initiation factor activity; RNA polymerase III transcription factor activity, sequence-specific DNA binding; sequence-specific DNA binding RNA polymerase III transcription factor activity; transcription factor activity, core RNA polymerase III binding
bacterial-type RNA polymerase core enzyme binding (GO:0001000)
Namespace: molecular_function
Definition: Binding to a bacterial-type RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one omega subunit.
Synonyms: eubacterial-type RNA polymerase core enzyme binding
Comment: Should omega be included here?
mitochondrial single-subunit type RNA polymerase binding (GO:0001001)
Namespace: molecular_function
Definition: Binding to a single subunit mitochondrial RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6.
RNA polymerase III type 1 promoter sequence-specific DNA binding (GO:0001002)
Namespace: molecular_function
Definition: Binding to a sequence of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition.
Synonyms: RNA polymerase III type 1 promoter DNA binding
RNA polymerase III type 2 promoter sequence-specific DNA binding (GO:0001003)
Namespace: molecular_function
Definition: Binding to a sequence of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs.
Synonyms: RNA polymerase III type 2 promoter DNA binding