The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	High-throughput in vitro

Description

Description:	vitamin D (1,25- dihydroxyvitamin D3) receptor [Source:HGNC Symbol;Acc:HGNC:12679]
Entrez Summary	TBA
Ensembl ID:	ENSG00000111424
External Link:	T132747_1.02
Interpro	IPR000324; IPR000536; IPR001628; IPR001723; IPR008946; ;
Protein Domain:
Protein: ENSP00000449573	DBD: Nuclear Hormone Receptor	Other: Hormone_recep
Protein: ENSP00000447173	DBD: Nuclear Hormone Receptor	Other: Hormone_recep
Protein: ENSP00000449561	DBD: Nuclear Hormone Receptor	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene Candidate_DNA-Binding sequence-specific Transcription Factor Binding tf co-factor binding_Co-activation DNA Binding_ PMIDS:16750418 8674817
Vaquerizas 2009 TF classification "a" Has direct evidence of TF function; "b" Has evidence for an orthologous TF; "c" contains likely DBDs, but has no functional evidence; "x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription; "other" category contains proteins without clear DBDs they curated from external sources.	a
CisBP considers it as a TF?	Yes
TFclass considers it as a TF?	Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"	Yes
GO-Info	GO:0003700 sequence-specific DNA binding transcription factor activity IDA - PMID:17426122 GO:0008434 vitamin D3 receptor activity IDA - PMID:12016314, PMID:16549446, PMID:17082781
Initial Assessment 1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding; 1a2 There is high confidence data for a close ortholog (as defined in CisBP); 2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model; 2a2 There is lower confidence evidence for an close ortholog; 3a There is decent circumstantial evidence for its role as a TF or not; 4a Two or more datasets predict it as a TF; 5a One of the source datasets predicts is as a TF	1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
SMiLE-seq	Isakova2017		Direct
HT-SELEX	Jolma2013		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
Misc	HocoMoco		Direct
Misc	HOMER		Direct
PBM	Zoo_01		Inferred - ENSPMAG00000000180 (85% AA Identity, Petromyzon marinus)

Structure

Structure	PDB	1KB2

Experimental History

Method	Constructs
Tried in PBM? (Whether the protein was tried in PBM or not)
Tried in HT-SELEX (Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information? (Tried with another method and failed?)

External Contribution

Name
Email
Comment
Reference

{"regions": [{"startStyle": "curved", "end": 91, "endStyle": "curved", "aliStart": 23, "text": "NHR", "colour": "#2cb42c", "aliEnd": 91, "start": 22, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 91, "description": "In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.", "database": "PfamA", "aliStart": 23, "scoreName": "E-value", "accession": "PF00105.16", "start": 22, "score": 8.3e-29, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 91}}, {"startStyle": "straight", "end": 406, "endStyle": "straight", "aliStart": 226, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 401, "start": 216, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 406, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 226, "scoreName": "E-value", "accession": "PF00104.28", "start": 216, "score": 7.5e-24, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 401}}], "length": 428}

{"regions": [{"startStyle": "curved", "end": 141, "endStyle": "curved", "aliStart": 73, "text": "NHR", "colour": "#2cb42c", "aliEnd": 141, "start": 72, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 141, "description": "In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.", "database": "PfamA", "aliStart": 73, "scoreName": "E-value", "accession": "PF00105.16", "start": 72, "score": 1e-28, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 141}}, {"startStyle": "straight", "end": 456, "endStyle": "straight", "aliStart": 276, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 451, "start": 266, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 456, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 276, "scoreName": "E-value", "accession": "PF00104.28", "start": 266, "score": 1.1000000000000001e-23, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 451}}], "length": 478}

TF Info Page for VDR (Nuclear receptor)