TF Info Page for RXRA (Nuclear receptor)

Conclusion

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

Description

Description: retinoid X receptor alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Entrez Summary Retinoid X receptors (RXRs) and retinoic acid receptors (RARs) are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]
Ensembl ID: ENSG00000186350
External Link: CisBP
Interpro IPR000003; IPR000536; IPR001628; IPR001723; IPR008946; IPR021780;
Protein Domain: ENSP00000419692
Domain:
Protein: ENSP00000419692DBD: Nuclear Hormone ReceptorOther: Hormone_recep, Nuc_recep-AF1

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_Transcription Factor Binding
tf co-factor binding
DNA-Binding
sequence-specific_DNA Binding
TF PPI_
PMIDS:7838715 15544927
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:12037571, PMID:17426122, PMID:20219900
GO:0003708
retinoic acid receptor activity
TAS - PMID:19374686
GO:0004879
ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity
IDA - PMID:7990953
GO:0004886
9-cis retinoic acid receptor 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
1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source Annotation Motif Evidence
SMiLE-seqIsakova2017Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
ChIP-seqENCODEDirect
ChIP-seqENCODEDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
PBMBadis09Inferred - Rxra (100% AA Identity, Mus musculus)
SELEXJASPARInferred - Rxra (100% AA Identity, Mus musculus)
SMiLE-seqIsakova2017Inferred - RXRG (95% AA Identity, Homo sapiens)
HT-SELEXJolma2010Inferred - RXRG (95% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RXRG (95% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RXRG (95% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RXRG (95% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RXRG (95% AA Identity, Homo sapiens)
PBMZoo_01Inferred - Rxrg (95% AA Identity, Mus musculus)
MiscHocoMocoInferred - RXRG (95% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RXRB (90% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RXRB (90% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RXRB (90% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RXRB (90% AA Identity, Homo sapiens)
PBMZoo_01Inferred - Rxrb (90% AA Identity, Mus musculus)
MiscHocoMocoInferred - RXRB (90% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - usp (85% AA Identity, Drosophila melanogaster)
SELEXJASPARInferred - usp (85% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - usp (85% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - usp (85% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - usp (85% AA Identity, Drosophila melanogaster)

Structure

Structure PDB 1BY4

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