The Human Transcription Factors

Conclusion

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

Description

Description:	nuclear receptor subfamily 1 group I member 2 [Source:HGNC Symbol;Acc:HGNC:7968]
Entrez Summary	TBA
Ensembl ID:	ENSG00000144852
External Link:	T132766_1.02
Interpro	IPR000536; IPR001628; IPR001723; IPR001728; IPR008946; ;
Protein Domain:
Protein: ENSP00000336528	DBD: Nuclear Hormone Receptor	Other: Hormone_recep
Protein: ENSP00000377319	DBD: Nuclear Hormone Receptor	Other: Hormone_recep
Protein: ENSP00000420297	DBD: Nuclear Hormone Receptor	Other: Hormone_recep

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:11114890
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"	No
GO-Info	GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor IDA - PMID:11114890 GO:0004879 ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity IDA - PMID:12578355
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
HT-SELEX	Nitta2015		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Misc	HocoMoco		Direct
Misc	HocoMoco		Direct

Structure

Structure	PDB	Not_Covered

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": 148, "endStyle": "curved", "aliStart": 79, "text": "NHR", "colour": "#2cb42c", "aliEnd": 148, "start": 78, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 148, "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": 79, "scoreName": "E-value", "accession": "PF00105.16", "start": 78, "score": 1.1000000000000001e-27, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 148}}, {"startStyle": "straight", "end": 454, "endStyle": "straight", "aliStart": 281, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 450, "start": 276, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 454, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 281, "scoreName": "E-value", "accession": "PF00104.28", "start": 276, "score": 4.9e-18, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 450}}], "length": 474}

{"regions": [{"startStyle": "curved", "end": 109, "endStyle": "curved", "aliStart": 40, "text": "NHR", "colour": "#2cb42c", "aliEnd": 109, "start": 39, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 109, "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": 40, "scoreName": "E-value", "accession": "PF00105.16", "start": 39, "score": 9.400000000000001e-28, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 109}}, {"startStyle": "straight", "end": 415, "endStyle": "straight", "aliStart": 242, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 411, "start": 237, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 415, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 242, "scoreName": "E-value", "accession": "PF00104.28", "start": 237, "score": 4.2e-18, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 411}}], "length": 435}

{"regions": [{"startStyle": "curved", "end": 109, "endStyle": "curved", "aliStart": 40, "text": "NHR", "colour": "#2cb42c", "aliEnd": 109, "start": 39, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 109, "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": 40, "scoreName": "E-value", "accession": "PF00105.16", "start": 39, "score": 8.300000000000001e-28, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 109}}, {"startStyle": "straight", "end": 378, "endStyle": "straight", "aliStart": 205, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 374, "start": 200, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 378, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 205, "scoreName": "E-value", "accession": "PF00104.28", "start": 200, "score": 3.3e-18, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 374}}], "length": 398}

TF Info Page for NR1I2 (Nuclear receptor)