LiteFold/GO huggingface dataset:
intronic transcription regulatory region sequence-specific DNA binding (GO:0001161)
Namespace: molecular_function
Definition: Binding to an intronic DNA sequence that regulates the transcription of the transcript it is contained within.
Synonyms: intronic transcription 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 intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)
Namespace: molecular_function
Definition: Binding to an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within.
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 I transcription regulatory region sequence-specific DNA binding (GO:0001163)
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 I.
Synonyms: RNA polymerase I regulatory region DNA binding
RNA polymerase I cis-regulatory region sequence-specific DNA binding (GO:0001165)
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 I. RNA polymerase I elements are referred to either enhancers or upstream control element (UCE, or alternately referred to as the upstream element).
Synonyms: RNA polymerase I enhancer sequence-specific DNA binding; RNA polymerase I upstream control element sequence-specific DNA binding; RNA polymerase I upstream element sequence-specific DNA binding
obsolete RNA polymerase I transcription factor activity, sequence-specific DNA binding (GO:0001167)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a specific DNA sequence in order to modulate transcription by RNA polymerase I. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
Synonyms: sequence-specific DNA binding RNA polymerase I 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 I upstream control element sequence-specific binding (GO:0001168)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a upstream control element (UCE, or alternately referred to as the upstream element, UE), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I in order to modulate transcription by RNA polymerase I.
Synonyms: RNA polymerase I upstream control element sequence-specific DNA 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 I CORE element sequence-specific binding (GO:0001169)
Namespace: molecular_function
Definition: OBSOLETE. Binding to CORE element, a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery in order to modulate transcription by RNA polymerase I.
Synonyms: RNA polymerase I CORE element sequence-specific DNA binding transcription factor activity; RNA polymerase I core promoter sequence-specific DNA binding transcription factor
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 I enhancer sequence-specific binding (GO:0001170)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a RNA polymerase I (Pol I) enhancer in order to modulate transcription by RNA polymerase I.
Synonyms: RNA polymerase I enhancer sequence-specific DNA 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.
reverse transcription (GO:0001171)
Namespace: biological_process
Definition: A DNA synthesis process that uses RNA as the initial template for synthesis of DNA, but which also includes an RNase activity to remove the RNA strand of an RNA-DNA heteroduplex produced by the RNA-dependent synthesis step and use of the initial DNA strand as a template for DNA synthesis.
RNA-templated transcription (GO:0001172)
Namespace: biological_process
Definition: The synthesis of an RNA transcript from an RNA template.
Synonyms: transcription, RNA-dependent; transcription, RNA-templated
transcriptional start site selection at RNA polymerase II promoter (GO:0001174)
Namespace: biological_process
Definition: Any process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
transcriptional start site selection at RNA polymerase III promoter (GO:0001175)
Namespace: biological_process
Definition: Any process involved in the selection of the specific location within the template strand of an RNA polymerase III promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
regulation of transcription open complex formation at RNA polymerase II promoter (GO:0001177)
Namespace: biological_process
Definition: Any process that modulates the rate, frequency or extent of a process involved 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: regulation of transcriptional open complex formation at RNA polymerase II promoter
RNA polymerase I general transcription initiation factor binding (GO:0001179)
Namespace: molecular_function
Definition: Binding to an RNA polymerase I transcription factor, a protein required to initiate or regulate transcription by RNA polymerase I.
Synonyms: RNA polymerase I transcription factor binding
RNA polymerase I general transcription initiation factor activity (GO:0001181)
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 I. Factors required for RNA polymerase I transcription initiation include upstream activation factor (UAF), core factor (CF), TATA binding protein (TBP) and RRN3. In all species characterized, RNA polymerase I transcribes a large polycistronic transcript that is processed into several mature rRNAs (3 or 4 depending on the species), including the large subunit rRNA (28S in humans), the small subunit rRNA (18S in humans), as well as one or two additional smaller rRNAs (the 5.8S rRNA in humans). In most species, this large rRNA transcript is the sole product of RNA polymerase I. However there are rare exceptions, such as Trypanosoma brucei, where RNA polymerase I also transcribes certain mRNAs.
Synonyms: core RNA polymerase I binding transcription factor activity; general RNA polymerase I transcription factor activity; RNA polymerase I transcription general initiation factor activity; transcription factor activity, core RNA polymerase I binding
RNA polymerase I promoter clearance (GO:0001182)
Namespace: biological_process
Definition: A process that mediates the transition from the initiation to the elongation phases of transcription by RNA polymerase I, 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 I promoter; promoter clearance from RNA polymerase I promoter for nuclear large rRNA transcript; RNA polymerase I promoter escape
obsolete RNA polymerase I transcription regulator recruiting activity (GO:0001186)
Namespace: molecular_function
Definition: OBSOLETE. The function of binding to an RNA polymerase I (RNAP I) transcription regulator and recruiting it to the general transcription machinery complex in order to modulate transcription initiation.
Synonyms: RNA polymerase I transcription factor recruiting activity; RNA polymerase I transcription factor recruiting transcription factor activity; transcription factor activity, RNA polymerase I 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'.
RNA polymerase I preinitiation complex assembly (GO:0001188)
Namespace: biological_process
Definition: The formation of a large multiprotein-DNA complex that self-assembles on gene promoter through the sequential recruitment of the general initiation factors that compose the preinitiation complex (PIC) (which includes including UBF, SL1, RRN3 and TBP in human). The PIC engages RNA polymerase I on its DNA template strand and sparks polymerization of the first few RNA nucleotides.
Synonyms: RNA polymerase I transcriptional preinitiation complex assembly; RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript; RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nucleolar primary rRNA transcript
obsolete transcriptional activator activity, RNA polymerase II transcription factor binding (GO:0001190)
Namespace: molecular_function
Definition: OBSOLETE. Binding to an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. 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 transcription factor binding transcription activator activity; RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription
Comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
obsolete transcriptional repressor activity, RNA polymerase II transcription factor binding (GO:0001191)
Namespace: molecular_function
Definition: OBSOLETE. Binding to an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. 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 transcription factor binding transcription factor activity involved in negative regulation of transcription; RNA polymerase II transcription factor binding transcription repressor activity; RNA polymerase II transcription repressor activity
Comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
maintenance of transcriptional fidelity during transcription elongation (GO:0001192)
Namespace: biological_process
Definition: Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation on a DNA template.
Synonyms: maintenance of transcriptional fidelity during DNA-dependent transcription elongation; maintenance of transcriptional fidelity during DNA-dependent transcription elongation from bacterial-type RNA polymerase promoter; maintenance of transcriptional fidelity during DNA-templated transcription elongation; maintenance of transcriptional fidelity during DNA-templated transcription elongation from bacterial-type RNA polymerase promoter
maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II (GO:0001193)
Namespace: biological_process
Definition: Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from an RNA polymerase II promoter.
Synonyms: maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase II promoter; maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter
maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III (GO:0001195)
Namespace: biological_process
Definition: Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a RNA polymerase III promoter.
Synonyms: maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase III promoter; maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase III promoter
obsolete regulation of mating-type specific transcription from RNA polymerase II promoter (GO:0001196)
Namespace: biological_process
Definition: OBSOLETE. Any mating-type specific process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
Comment: This term was obsoleted because it represents a GO-CAM model.
obsolete negative regulation of mating-type specific transcription from RNA polymerase II promoter (GO:0001198)
Namespace: biological_process
Definition: OBSOLETE. Any mating-type specific process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
Synonyms: down regulation of RNA polymerase II transcription, mating-type specific; down-regulation of RNA polymerase II transcription, mating-type specific; downregulation of RNA polymerase II transcription, mating-type specific; inhibition of RNA polymerase II transcription, mating-type specific
Comment: This term was obsoleted because it represents a GO-CAM model.
obsolete histone displacement (GO:0001207)
Namespace: biological_process
Definition: OBSOLETE. The removal of histones, including histone dimers, from nucleosomes within chromatin.
Comment: This term was obsoleted because it represents a molecular function.
obsolete histone H2A-H2B dimer displacement (GO:0001208)
Namespace: biological_process
Definition: OBSOLETE. The removal of a H2A-H2B histone dimer from a nucleosome within chromatin.
Comment: This term was obsoleted because it represents a molecular function.
DNA-binding transcription activator activity (GO:0001216)
Namespace: molecular_function
Definition: A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.
Synonyms: bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription; bacterial-type RNA polymerase transcriptional activator activity, metal ion regulated sequence-specific DNA binding; bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding; metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in positive regulation of transcription; sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in positive regulation of transcription; transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding; transcriptional activator activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding
Comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity.
DNA-binding transcription repressor activity (GO:0001217)
Namespace: molecular_function
Definition: A DNA-binding transcription factor activity that represses or decreases the transcription of specific gene sets.
Synonyms: bacterial-type DNA binding transcription repressor activity; bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription; bacterial-type RNA polymerase transcriptional repressor activity, cadmium ion regulated sequence-specific DNA binding; bacterial-type RNA polymerase transcriptional repressor activity, copper ion regulated sequence-specific DNA binding; bacterial-type RNA polymerase transcriptional repressor activity, metal ion regulated sequence-specific DNA binding; bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding; cadmium ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription; copper ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription; metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription; sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription; transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding; transcriptional repressor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding
Comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity.
transcription coregulator binding (GO:0001221)
Namespace: molecular_function
Definition: Binding to a transcription coregulator, a protein involved in regulation of transcription via protein-protein interactions with transcription factors and other transcription regulatory proteins. Cofactors do not bind DNA directly, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
Synonyms: RNA polymerase II transcription cofactor binding; RNA polymerase II transcription coregulator binding; transcription cofactor binding
transcription corepressor binding (GO:0001222)
Namespace: molecular_function
Definition: Binding to a transcription corepressor, a protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery.
Synonyms: RNA polymerase II transcription corepressor binding
transcription coactivator binding (GO:0001223)
Namespace: molecular_function
Definition: Binding to a transcription coactivator, a protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
Synonyms: RNA polymerase II transcription coactivator binding
DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)
Namespace: molecular_function
Definition: A DNA-binding transcription factor activity that represses or decreases the transcription of specific gene sets transcribed by RNA polymerase II.
Synonyms: distal enhancer DNA-binding transcription repressor activity, RNA polymerase II-specific; metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in negative regulation of transcription; metal ion regulated sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription; proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription; RNA polymerase II distal enhancer sequence-specific DNA-binding transcription factor activity involved in negative regulation of transcription; RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription; RNA polymerase II transcriptional repressor activity, metal ion regulated core promoter proximal region sequence-specific binding; RNA polymerase II transcriptional repressor activity, metal ion regulated proximal promoter sequence-specific DNA binding; sequence-specific distal enhancer binding RNA polymerase II transcription factor activity involved in negative regulation of transcription; transcriptional repressor activity, metal ion regulated sequence-specific DNA binding; transcriptional repressor activity, RNA polymerase II distal enhancer sequence-specific binding; transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding; transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding
Comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity.