LiteFold/GO huggingface dataset:
nitrogen catabolite repression of transcription from RNA polymerase II promoter (GO:0001081)
Namespace: biological_process
Definition: A transcription regulation process in which the presence of one nitrogen 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 nitrogen sources.
Synonyms: negative regulation of transcription from RNA polymerase II promoter by nitrogen catabolites
obsolete transcription factor activity, RNA polymerase I transcription factor binding (GO:0001082)
Namespace: molecular_function
Definition: OBSOLETE. Binding to an RNA polymerase I 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: RNA polymerase I transcription factor binding transcription factor activity
Comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
obsolete transcription factor activity, RNA polymerase II basal transcription factor binding (GO:0001083)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a basal RNA polymerase II 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: RNA polymerase II basal transcription factor binding transcription factor activity
Comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
obsolete transcription factor activity, TFIID-class binding (GO:0001084)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
Synonyms: TFIID-class binding transcription factor activity
Comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
obsolete transcription factor activity, TFIIA-class binding (GO:0001086)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIA class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
Synonyms: TFIIA-class binding transcription factor activity
Comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
obsolete transcription factor activity, TFIIB-class binding (GO:0001087)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIB class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
Synonyms: TFIIB-class binding transcription factor activity
Comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
obsolete transcription factor activity, TFIIE-class binding (GO:0001088)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIE class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
Synonyms: TFIIE-class binding transcription factor activity
Comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
obsolete transcription factor activity, TFIIF-class transcription factor binding (GO:0001089)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIF class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
Synonyms: TFIIF-class binding transcription factor activity
Comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
obsolete transcription factor activity, TFIIH-class binding (GO:0001090)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIH class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
Synonyms: TFIIH-class binding transcription factor activity
Comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
RNA polymerase II general transcription initiation factor binding (GO:0001091)
Namespace: molecular_function
Definition: Binding to a basal RNA polymerase II transcription factor, any of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
Synonyms: RNA polymerase II basal transcription factor binding
TFIIA-class transcription factor complex binding (GO:0001092)
Namespace: molecular_function
Definition: Binding to a general RNA polymerase II transcription factor belonging to the TFIIA complex, one of the complexes involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
Synonyms: TFIIA-class transcription factor binding
TFIIB-class transcription factor binding (GO:0001093)
Namespace: molecular_function
Definition: Binding to a general RNA polymerase II transcription factor of the TFIIB class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
TFIID-class transcription factor complex binding (GO:0001094)
Namespace: molecular_function
Definition: Binding to a general RNA polymerase II transcription factor belonging to the TFIID complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
Synonyms: TFIID-class transcription factor binding
TFIIF-class transcription factor complex binding (GO:0001096)
Namespace: molecular_function
Definition: Binding to a general RNA polymerase II transcription factor belonging to the TFIIF complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
Synonyms: TFIIF-class transcription factor binding
TFIIH-class transcription factor complex binding (GO:0001097)
Namespace: molecular_function
Definition: Binding to a general RNA polymerase II transcription factor belonging to the TFIIH complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
Synonyms: TFIIH-class transcription factor binding
obsolete basal transcription machinery binding (GO:0001098)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a component of the basal transcription machinery which is composed of the RNA polymerase core enzyme and the basal transcription factor(s), the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase.
Comment: This term was obsoleted because it is an unnecessary grouping term.
obsolete basal RNA polymerase II transcription machinery binding (GO:0001099)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a component of the basal transcription machinery for RNA polymerase II which is composed of the RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits, and the basal RNA polymerase II transcription factors, the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase.
Synonyms: basal RNAP II transcription machinery binding
Comment: This term was obsoleted because it is equivalent to RNA polymerase II complex binding ; GO:0000993.
negative regulation of exit from mitosis (GO:0001100)
Namespace: biological_process
Definition: Any process involved in the inhibition of progression from anaphase/telophase (high mitotic CDK activity) to G1 (low mitotic CDK activity).
Synonyms: down regulation of exit from mitosis; down-regulation of exit from mitosis; downregulation of exit from mitosis; inhibition of exit from mitosis
response to acid chemical (GO:0001101)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form.
Synonyms: response to acid; response to acid anion; response to oxoanion
Comment: This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead.
bacterial-type RNA polymerase holo enzyme binding (GO:0001108)
Namespace: molecular_function
Definition: Binding to a component of the basal transcription machinery which is composed of a bacterial-type RNA polymerase core enzyme and a sigma factor, the minimal set of factors required for formation of the preinitiation complex (PIC) by a bacterial-type RNA polymerase.
Synonyms: basal bacterial-type RNA polymerase transcription machinery binding
promoter clearance during DNA-templated transcription (GO:0001109)
Namespace: biological_process
Definition: Any process involved in the transition from the initiation to the elongation phases of transcription by a DNA-dependent RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors.
Synonyms: promoter clearance during DNA-dependent transcription; promoter clearance from bacterial-type RNA polymerase promoter; promoter escape
RNA polymerase III promoter clearance (GO:0001110)
Namespace: biological_process
Definition: A process that mediates the transition from the initiation to the elongation phases of transcription by RNA polymerase III, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase.
Synonyms: promoter clearance from RNA polymerase III promoter
RNA polymerase II promoter clearance (GO:0001111)
Namespace: biological_process
Definition: A process that mediates the transition from the initiation to the elongation phases of transcription by RNA polymerase II, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors.
Synonyms: promoter clearance from RNA polymerase II promoter; promoter escape from RNA polymerase II promoter; promoter-paused RNA polymerase II release
DNA-templated transcription open complex formation (GO:0001112)
Namespace: biological_process
Definition: Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble.
Synonyms: DNA-dependent transcriptional open complex formation; DNA-templated transcriptional open complex formation; promoter melting; transcription open complex formation at bacterial-type RNA polymerase promoter; transcriptional open complex formation at bacterial-type RNA polymerase promoter
transcription open complex formation at RNA polymerase II promoter (GO:0001113)
Namespace: biological_process
Definition: Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble.
Synonyms: RNA polymerase II promoter melting; transcriptional open complex formation at RNA polymerase II promoter
protein-DNA-RNA complex (GO:0001114)
Namespace: cellular_component
Definition: A macromolecular complex containing protein, DNA, and RNA molecules.
protein-DNA-RNA complex organization (GO:0001115)
Namespace: biological_process
Definition: Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA-RNA complex.
Synonyms: protein-DNA-RNA complex subunit organisation
protein-DNA-RNA complex assembly (GO:0001116)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of proteins, DNA, and RNA molecules to form a protein-DNA-RNA complex.
protein-DNA-RNA complex disassembly (GO:0001117)
Namespace: biological_process
Definition: The disaggregation of a protein-DNA-RNA complex into its constituent components.
transcription ternary complex disassembly (GO:0001118)
Namespace: biological_process
Definition: The disaggregation of a transcription ternary complex, composed of RNA polymerase, template DNA, and an RNA transcript, into its constituent components.
Synonyms: transcription protein-DNA-RNA complex disassembly
protein-DNA-RNA complex remodeling (GO:0001119)
Namespace: biological_process
Definition: The acquisition, loss, or modification of macromolecules within a protein-DNA-RNA complex, resulting in the alteration of an existing complex.
protein-DNA complex remodeling (GO:0001120)
Namespace: biological_process
Definition: The acquisition, loss, or modification of macromolecules within a protein-DNA complex, resulting in the alteration of an existing complex.
Synonyms: protein-DNA complex remodelling
obsolete RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly (GO:0001128)
Namespace: molecular_function
Definition: OBSOLETE. Binding to an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or stability of the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC). Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
Synonyms: RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly
Comment: This term was obsoleted because it represented a mix of function and process and is not annotated consistently
obsolete RNA polymerase II transcription factor activity, TBP-class protein binding, involved in preinitiation complex assembly (GO:0001129)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), to facilitate the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
Synonyms: TATA-binding protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly; TBP-class protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly
Comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
obsolete RNA polymerase II transcription factor activity, TBP-class protein binding (GO:0001132)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
Synonyms: TATA-binding protein binding RNA polymerase II transcription factor activity; TBP-class protein binding RNA polymerase II transcription factor activity; TRF protein binding RNA polymerase II 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 regulator recruiting activity (GO:0001134)
Namespace: molecular_function
Definition: OBSOLETE. The function of binding to an RNA polymerase (RNAP) transcription regulator and recruiting it to the general transcription machinery complex in order to modulate transcription initiation.
Synonyms: transcription factor activity, transcription factor recruiting; transcription factor recruiting activity; transcription factor recruiting transcription factor activity
Comment: The reason for obsoletion is that this function is redundant with other terms, most often 'transcription co-regulator activity; GO:0003712'.
obsolete RNA polymerase II transcription regulator recruiting activity (GO:0001135)
Namespace: molecular_function
Definition: OBSOLETE. The function of binding to an RNA polymerase II (RNAP II) transcription regulator and recruiting it to the general transcription machinery complex in order to modulate transcription initiation.
Synonyms: RNA polymerase II transcription factor recruiting activity; RNA polymerase II transcription factor recruiting transcription factor activity; TFIIE-class transcription factor recruiting transcription factor activity; TFIIF-class transcription factor recruiting transcription factor activity; TFIIH-class transcription factor recruiting transcription factor activity; transcription factor activity, RNA polymerase II transcription factor recruiting; transcription factor activity, TFIIE-class transcription factor recruiting; transcription factor activity, TFIIF-class transcription factor recruiting; transcription factor activity, TFIIH-class transcription factor recruiting
Comment: The reason for obsoletion is that this function is redundant with other terms, most often 'transcription co-regulator activity; GO:0003712'.
obsolete RNA polymerase II complex recruiting activity (GO:0001139)
Namespace: molecular_function
Definition: OBSOLETE. Binding to an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way in order to facilitate the aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
Synonyms: core RNA polymerase II recruiting transcription factor activity; transcription factor activity, core RNA polymerase II recruiting
Comment: This term was obsoleted because it is now represented by transcription coactivator activity ; GO:0003713.
transcription termination site sequence-specific DNA binding (GO:0001147)
Namespace: molecular_function
Definition: Binding to a sequence of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon.
Synonyms: bacterial-type RNA polymerase termination site sequence-specific DNA binding; mitochondrial RNA polymerase termination site sequence-specific DNA binding; mitochondrial RNA polymerase terminator site sequence-specific DNA binding transcription factor activity; transcription factor activity, mitochondrial RNA polymerase terminator site sequence-specific binding; transcription termination site DNA binding
Comment: Transcription termination sites can be recognized by the RNA polymerase (RNAP) itself or by another protein which interacts with the RNAP to promote transcription termination. Note that not all genes have a DNA specific sequence that functions as a termination site; for most mRNAs transcribed by RNAP II termination is not mediated by a specific termination sequence, but is coupled to polyadenylation.
obsolete transcription factor activity, bacterial-type RNA polymerase termination site sequence-specific binding (GO:0001149)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a sequence of DNA that is a termination site for bacterial-type RNA polymerase in order to promote transcription termination by bacterial-type RNA polymerase.
Synonyms: bacterial-type RNA polymerase termination site sequence-specific DNA binding transcription factor activity
obsolete transcription factor activity, RNA polymerase III transcription factor recruiting (GO:0001153)
Namespace: molecular_function
Definition: OBSOLETE. The function of binding to an RNA polymerase III (RNAP III) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP III.
Synonyms: RNA polymerase III transcription factor recruiting transcription factor activity
Comment: This term was made obsolete in the 2018 Transcription branch revision. This term was redundant with other terms.
TFIIIB-class transcription factor complex binding (GO:0001154)
Namespace: molecular_function
Definition: Binding to a general RNA polymerase III transcription factor belonging to the TFIIB complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III.
Synonyms: TFIIIB-class transcription factor binding
TFIIIA-class transcription factor binding (GO:0001155)
Namespace: molecular_function
Definition: Binding to an RNA polymerase III transcription factor of the TFIIIA class, one of the factors involved in formation of the preinitiation complex (PIC) at RNA polymerase III promoters.
TFIIIC-class transcription factor complex binding (GO:0001156)
Namespace: molecular_function
Definition: Binding to a general RNA polymerase III transcription factor belonging to the TFIIC complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III.
Synonyms: TFIIIC-class transcription factor binding