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 NA
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