LiteFold/GO huggingface dataset:
molecular_function (GO:0003674)
Namespace: molecular_function
Definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
Synonyms: molecular function
Comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
obsolete protein (GO:0003675)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: protein
Comment: Note that this term was deleted from GO and was restored to the ontology in Feb 2003 to ensure that the ID is not reused.
nucleic acid binding (GO:0003676)
Namespace: molecular_function
Definition: Binding to a nucleic acid.
Synonyms: base pairing
DNA binding (GO:0003677)
Namespace: molecular_function
Definition: Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
Synonyms: microtubule/chromatin interaction; plasmid binding; structure specific DNA binding; structure-specific DNA binding
DNA helicase activity (GO:0003678)
Namespace: molecular_function
Definition: Unwinding of a DNA helix, driven by ATP hydrolysis.
Synonyms: ATP-dependent DNA helicase activity
bent DNA binding (GO:0003681)
Namespace: molecular_function
Definition: Binding to DNA in a bent conformation.
chromatin binding (GO:0003682)
Namespace: molecular_function
Definition: Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
Synonyms: lamin/chromatin binding; microtubule/chromatin interaction; nuclear membrane vesicle binding to chromatin
obsolete lamin/chromatin binding (GO:0003683)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: lamin/chromatin binding
Comment: This term was made obsolete because it represents two functions.
damaged DNA binding (GO:0003684)
Namespace: molecular_function
Definition: Binding to damaged DNA.
Synonyms: DNA repair enzyme; DNA repair protein
obsolete DNA repair protein (GO:0003685)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: DNA repair protein
Comment: This term was made obsolete because it includes a process term.
obsolete DNA replication factor (GO:0003687)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: DNA replication factor
Comment: This term was made obsolete because it does not represent a true molecular function.
DNA replication origin binding (GO:0003688)
Namespace: molecular_function
Definition: Binding to a DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
Synonyms: ARS binding
DNA clamp loader activity (GO:0003689)
Namespace: molecular_function
Definition: Facilitating the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their closing around the DNA duplex, driven by ATP hydrolysis.
Synonyms: DNA clamp loading ATPase activity; DNA-protein loading ATPase activity; PCNA loading activity; PCNA loading complex activity; protein-DNA loading ATPase activity
double-stranded DNA binding (GO:0003690)
Namespace: molecular_function
Definition: Binding to double-stranded DNA.
Synonyms: dsDNA binding
double-stranded telomeric DNA binding (GO:0003691)
Namespace: molecular_function
Definition: Binding to double-stranded telomere-associated DNA.
left-handed Z-DNA binding (GO:0003692)
Namespace: molecular_function
Definition: Binding to DNA in the Z form, i.e. a left-handed helix in which the phosphate backbone zigzags.
P-element binding (GO:0003693)
Namespace: molecular_function
Definition: Binding to a P-element, a class of Drosophila transposon responsible for hybrid dysgenesis.
obsolete plasmid binding (GO:0003694)
Namespace: molecular_function
Definition: OBSOLETE. Interacting selectively with a plasmid, an extrachromosomal genetic element usually characterized as a covalently continuous double stranded DNA molecule found in bacteria and some other microorganisms.
Synonyms: plasmid binding; plasmid-associated protein
Comment: This term was made obsolete because it refers to component information.
obsolete random coil DNA binding (GO:0003695)
Namespace: molecular_function
Definition: OBSOLETE. Binding to DNA in a random coil configuration.
Synonyms: random coil binding
Comment: This term was obsoleted because the definition was not clear enough as to what is directing specificity of the binding to the DNA.
satellite DNA binding (GO:0003696)
Namespace: molecular_function
Definition: Binding to satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
single-stranded DNA binding (GO:0003697)
Namespace: molecular_function
Definition: Binding to single-stranded DNA.
Synonyms: ssDNA binding
Comment: Note that this term is restricted to those cases where the binding is to a single-stranded DNA molecule, not to one of the stands of double-stranded DNA.
DNA-binding transcription factor activity (GO:0003700)
Namespace: molecular_function
Definition: A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
Synonyms: bacterial-type DNA binding transcription factor activity; bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity; bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity; bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding; bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding; DNA binding transcription factor activity; gene-specific transcription factor activity; metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity; metal ion regulated sequence-specific DNA binding transcription factor activity; nucleic acid binding transcription factor activity; sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity; sequence-specific DNA binding transcription factor activity; transcription factor activity; transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding; transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding; transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding; transcription factor activity, metal ion regulated sequence-specific DNA binding
Comment: Usage guidance: Most DNA-binding transcription factors do not have enzymatic activity. The presence of specific DNA-binding domains known to be present in DNA-binding transcription factors (HOX, GATA etc) should be used to help decide whether a protein is a DNA binding transcription factor or a coregulator. If a protein has an enzymatic activity (for example, ubiquitin ligase, histone acetyl transferase) and no known DNA binding domain, consider annotating to GO:0003712 transcription coregulator activity. Special care should be taken with proteins containing zinc fingers, Myb/SANT and ARID domains, since only a subset of proteins containing these domains directly and selectively bind to regulatory DNA motifs in cis-regulatory regions.
obsolete RNA polymerase I transcription factor activity (GO:0003701)
Namespace: molecular_function
Definition: OBSOLETE. Functions to initiate or regulate RNA polymerase I transcription.
Synonyms: RNA polymerase I transcription factor activity
Comment: This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete RNA polymerase II transcription factor activity (GO:0003702)
Namespace: molecular_function
Definition: OBSOLETE. Functions to initiate or regulate RNA polymerase II transcription.
Synonyms: RNA polymerase II transcription factor activity
Comment: This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete specific RNA polymerase II transcription factor activity (GO:0003704)
Namespace: molecular_function
Definition: OBSOLETE. Functions to enable the transcription of specific, or specific sets, of genes by RNA polymerase II.
Synonyms: specific RNA polymerase II transcription factor activity
Comment: This term was obsoleted because "general/nonspecific/basal" transcription vs "specific" transcription were determined not to be separable, distinct process. Thus, terms trying to distinguish "general/nonspecific/basal" transcription from "specific" transcription were removed from both the Molecular Function and the Biological Process ontologies. In addition, this Molecular Function term was defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
nuclear steroid receptor activity (GO:0003707)
Namespace: molecular_function
Definition: A nuclear receptor activity regulated by steroid binding and modulating the transcription of specific gene sets transcribed by RNA polymerase II.
Synonyms: steroid hormone receptor activity
obsolete RNA polymerase III transcription factor activity (GO:0003709)
Namespace: molecular_function
Definition: OBSOLETE. Functions to initiate or regulate RNA polymerase III transcription.
Synonyms: RNA polymerase III transcription factor activity
Comment: This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
transcription elongation factor activity (GO:0003711)
Namespace: molecular_function
Definition: A molecular function that stimulates the elongation properties of the RNA polymerase during the elongation phase of transcription. A subclass of transcription elongation factors enable the transition from transcription initiation to elongation, while another class rescue stalled RNA polymerases.
Synonyms: transcription elongation regulator activity; transcriptional elongation regulator activity
Comment: Restored term from obsolete.
transcription coregulator activity (GO:0003712)
Namespace: molecular_function
Definition: A transcription regulator activity that modulates the transcription of specific gene sets via binding to a DNA-binding transcription factor at a specific genomic locus, either on its own or as part of a complex. Coregulators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators.
Synonyms: nuclear receptor coreceptor activity; RNA polymerase II transcriptional cofactor activity; transcription cofactor activity; transcription coreceptor activity; transcriptional co-regulator
Comment: Usage guidance: Most transcription coregulators do not bind DNA. Those that do usually bind DNA either in a non-specific or non-direct manner. If a protein binds DNA specifically, consider annotating to GO:0003700 DNA binding transcription factor activity.
transcription coactivator activity (GO:0003713)
Namespace: molecular_function
Definition: A transcription coregulator activity that activates or increases the transcription of specific gene sets via binding to a DNA-binding transcription factor at a specific genomic locus, either on its own or as part of a complex. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coactivators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators. A fourth class of coactivator activity is the bridging of a DNA-binding transcription factor to the general (basal) transcription machinery. The Mediator complex, which bridges sequence-specific DNA binding transcription factors and RNA polymerase, is also a transcription coactivator.
Synonyms: RNA polymerase II transcription co-activator activity; RNA polymerase II transcription coactivator activity; RNA polymerase II transcription mediator activity; transcription co-activator activity
Comment: For usage guidance, see comment in GO:0003712 ; transcription coregulator activity.
transcription corepressor activity (GO:0003714)
Namespace: molecular_function
Definition: A transcription coregulator activity that represses or decreases the transcription of specific gene sets via binding to a DNA-binding transcription factor at a specific genomic locus, either on its own or as part of a complex. Corepressors often act by altering chromatin structure and modifications. For example, one class of transcription corepressors modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators.
Synonyms: RNA polymerase II transcription co-repressor activity; RNA polymerase II transcription corepressor activity; transcription co-repressor activity
Comment: For usage guidance, see comment in GO:0003712 ; transcription coregulator activity.
obsolete transcription termination factor activity (GO:0003715)
Namespace: molecular_function
Definition: OBSOLETE. Any activity that brings about termination of transcription.
Synonyms: transcription termination factor activity; transcriptional termination factor activity
Comment: This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete RNA polymerase I transcription termination factor activity (GO:0003716)
Namespace: molecular_function
Definition: OBSOLETE. Any activity that brings about termination of transcription by RNA polymerase I.
Synonyms: Pol I transcription termination factor activity; RNA polymerase I transcription termination factor activity
Comment: This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.