The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	High-throughput in vitro		Has been shown to bind both as a homodimer and with several nuclear receptor homodimerization partners

Description

Description:	retinoid X receptor beta [Source:HGNC Symbol;Acc:HGNC:10478]
Entrez Summary	TBA
Ensembl ID:	ENSG00000204231
External Link:	T132784_1.02
Interpro	IPR000003; IPR000536; IPR001628; IPR001723; IPR008946; ;
Protein Domain:
Protein: ENSP00000363812	DBD: Nuclear Hormone Receptor	Other: Hormone_recep, Nuc_recep-AF1
Protein: ENSP00000363817	DBD: Nuclear Hormone Receptor	Other: Hormone_recep, Nuc_recep-AF1

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene Candidate_DNA-Binding sequence-specific_DNA Binding_ PMIDS:2554307 10393558
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:12767074 GO:0003700 sequence-specific DNA binding transcription factor activity NAS - PMID:1662118 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 TAS - PMID:1662118
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	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Misc	HocoMoco		Direct
HT-SELEX	Yin2017		Inferred - RXRB (100% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - RXRB (100% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RXRB (100% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RXRB (100% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - Rxrb (100% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - RXRB (100% AA Identity, Homo sapiens)
SMiLE-seq	Isakova2017		Inferred - RXRA (90% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - RXRA (90% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RXRA (90% AA Identity, Homo sapiens)
PBM	Badis09		Inferred - Rxra (90% AA Identity, Mus musculus)
ChIP-seq	ENCODE		Inferred - RXRA (90% AA Identity, Homo sapiens)
ChIP-seq	ENCODE		Inferred - RXRA (90% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RXRA (90% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RXRA (90% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RXRA (90% AA Identity, Homo sapiens)
SELEX	JASPAR		Inferred - Rxra (90% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - RXRA (90% AA Identity, Homo sapiens)
SMiLE-seq	Isakova2017		Inferred - RXRG (88% AA Identity, Homo sapiens)
HT-SELEX	Jolma2010		Inferred - RXRG (88% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - RXRG (88% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - RXRG (88% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RXRG (88% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RXRG (88% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - Rxrg (88% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - RXRG (88% AA Identity, Homo sapiens)
HT-SELEX	Nitta2015		Inferred - usp (82% AA Identity, Drosophila melanogaster)
SELEX	JASPAR		Inferred - usp (82% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - usp (82% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - usp (82% AA Identity, Drosophila melanogaster)
Misc	iDMMPMM		Inferred - usp (82% AA Identity, Drosophila melanogaster)

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": 272, "endStyle": "curved", "aliStart": 204, "text": "NHR", "colour": "#2cb42c", "aliEnd": 272, "start": 203, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 272, "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": 204, "scoreName": "E-value", "accession": "PF00105.16", "start": 203, "score": 8.599999999999999e-32, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 272}}, {"startStyle": "straight", "end": 513, "endStyle": "straight", "aliStart": 336, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 513, "start": 331, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 513, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 336, "scoreName": "E-value", "accession": "PF00104.28", "start": 331, "score": 1.4e-39, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 513}}, {"startStyle": "jagged", "end": 197, "endStyle": "jagged", "aliStart": 128, "text": "Nuc_recep-AF1", "colour": "#9999ff", "aliEnd": 189, "start": 98, "href": "http://pfam.xfam.org/family/PF11825.6", "type": "pfama", "display": "true", "metadata": {"end": 197, "description": "Nuclear receptors (NRs) are a family of ligand-inducible transcription factors, and, like other transcription factors, they contain a distinct DNA binding domain that allows for target gene recognition and several activation domains that possess the ability to activate transcription [1]. One of these activation domains is at the N-terminal, although there are two distinct motifs within this domain, between residues 20-36 and between 74 and the end of this domain, which are the binding regions. One of the co-activators is TIF1beta, which appears to bind at the first motif [2].", "database": "PfamA", "aliStart": 128, "scoreName": "E-value", "accession": "PF11825.6", "start": 98, "score": 4.6e-06, "identifier": "Nuclear/hormone receptor activator site AF-1", "type": "DBD", "aliEnd": 189}}], "length": 534}

{"regions": [{"startStyle": "curved", "end": 272, "endStyle": "curved", "aliStart": 204, "text": "NHR", "colour": "#2cb42c", "aliEnd": 272, "start": 203, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 272, "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": 204, "scoreName": "E-value", "accession": "PF00105.16", "start": 203, "score": 9.999999999999999e-33, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 272}}, {"startStyle": "straight", "end": 517, "endStyle": "straight", "aliStart": 336, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 517, "start": 331, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 517, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 336, "scoreName": "E-value", "accession": "PF00104.28", "start": 331, "score": 5.5e-40, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 517}}, {"startStyle": "jagged", "end": 197, "endStyle": "jagged", "aliStart": 128, "text": "Nuc_recep-AF1", "colour": "#9999ff", "aliEnd": 189, "start": 98, "href": "http://pfam.xfam.org/family/PF11825.6", "type": "pfama", "display": "true", "metadata": {"end": 197, "description": "Nuclear receptors (NRs) are a family of ligand-inducible transcription factors, and, like other transcription factors, they contain a distinct DNA binding domain that allows for target gene recognition and several activation domains that possess the ability to activate transcription [1]. One of these activation domains is at the N-terminal, although there are two distinct motifs within this domain, between residues 20-36 and between 74 and the end of this domain, which are the binding regions. One of the co-activators is TIF1beta, which appears to bind at the first motif [2].", "database": "PfamA", "aliStart": 128, "scoreName": "E-value", "accession": "PF11825.6", "start": 98, "score": 4.5e-06, "identifier": "Nuclear/hormone receptor activator site AF-1", "type": "DBD", "aliEnd": 189}}], "length": 538}

TF Info Page for RXRB (Nuclear receptor)