TF Info Page for NR1H4 (Nuclear receptor)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer High-throughput in vitro Also binds DNA as heterodimer with RXRA (PMID: 11870371)

Description

Description: nuclear receptor subfamily 1 group H member 4 [Source:HGNC Symbol;Acc:HGNC:7967]
Entrez Summary This gene encodes a ligand-activated transcription factor that shares structural features in common with nuclear hormone receptor family members. This protein functions as a receptor for bile acids, and when bound to bile acids, binds to DNA and regulates the expression of genes involved in bile acid synthesis and transport. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Feb 2016]
Ensembl ID: ENSG00000012504
External Link: CisBP
Interpro IPR000536; IPR001628; IPR001723; IPR001728; IPR008946; ;
Protein Domain: ENSP00000188403
Protein Domain: ENSP00000376712
Protein Domain: ENSP00000448506
Protein Domain: ENSP00000448978
Protein Domain: ENSP00000447149
Protein Domain: ENSP00000446760
Protein Domain: ENSP00000446861
Domain:
Protein: ENSP00000188403DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000376712DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000448506DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000448978DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000447149DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000446760DBD: Nuclear Hormone ReceptorOther:
Protein: ENSP00000446861DBD: Nuclear Hormone ReceptorOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific
Transcription Factor Binding
tf co-factor binding_Co-activation_
PMIDS:11533040
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:0001077
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a
IDA - PMID:24211198
GO:0003700
sequence-specific DNA binding transcription factor activity
TAS - PMID:10334992, PMID:9223286
GO:0003705
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity
IDA - PMID:21757002
GO:0004879
ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity
ISS - PMID:21757002
GO:0004887
thyroid hormone receptor activity
IEA - GO_REF:0000002
GO:0032088
negative regulation of NF-kappaB transcription factor activity
IEA - GO_REF:0000019
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
2a1, Lower confidence direct evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source Annotation Motif Evidence
PBMBarrera2016Direct
PBMBarrera2016Direct
SMiLE-seqIsakova2017Direct
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
MiscHOMERInferred - Nr1h4 (100% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - AAM33367 (90% AA Identity, Xenopus laevis)

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