The Human Transcription Factors

Conclusion

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

Description

Description:	RAR related orphan receptor A [Source:HGNC Symbol;Acc:HGNC:10258]
Entrez Summary	TBA
Ensembl ID:	ENSG00000069667
External Link:	T132742_1.02
Interpro	IPR000536; IPR001628; IPR001723; IPR003079; IPR008946; ;
Protein Domain:
Protein: ENSP00000261523	DBD: Nuclear Hormone Receptor	Other: Hormone_recep
Protein: ENSP00000309753	DBD: Nuclear Hormone Receptor	Other: Hormone_recep
Protein: ENSP00000335087	DBD: Nuclear Hormone Receptor	Other: Hormone_recep
Protein: ENSP00000402971	DBD: Nuclear Hormone Receptor	Other: Hormone_recep
Protein: ENSP00000484955	DBD: Nuclear Hormone Receptor	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:7926749 7926749 15941850 15821743 7926749 12467577
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:11053433, PMID:17545671, PMID:18658046, GO:0004879 ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity IEA - GO_REF:0000002 GO:0098531 transcription factor activity, direct ligand regulated sequence-specific DNA binding IDA - PMID:19965867
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	Jolma2013		Direct
SELEX	JASPAR		Direct
SELEX	JASPAR		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
PBM	DREAM_contest		Inferred - Rora (100% AA Identity, Mus musculus)
SMiLE-seq	Isakova2017		Inferred - RORB (92% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - RORB (92% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - RORB (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RORB (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RORB (92% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Rorb (92% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - rorb (92% AA Identity, Tetraodon nigroviridis)
Transfac	Transfac	License required	Inferred - RORB (92% AA Identity, Homo sapiens)
SMiLE-seq	Isakova2017		Inferred - RORC (90% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - RORC (90% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - RORC (90% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RORC (90% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RORC (90% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - RORC (90% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Rorc (90% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - rorc (84% AA Identity, Tetraodon nigroviridis)
PBM	Zoo_01		Inferred - AAEL009588 (77% AA Identity, Aedes aegypti)
HT-SELEX	Nitta2015		Inferred - Hr46 (77% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Hr46 (77% 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

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{"regions": [{"startStyle": "curved", "end": 165, "endStyle": "curved", "aliStart": 97, "text": "NHR", "colour": "#2cb42c", "aliEnd": 165, "start": 96, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 165, "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": 97, "scoreName": "E-value", "accession": "PF00105.16", "start": 96, "score": 4.4e-33, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 165}}, {"startStyle": "straight", "end": 519, "endStyle": "straight", "aliStart": 348, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 517, "start": 333, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 519, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 348, "scoreName": "E-value", "accession": "PF00104.28", "start": 333, "score": 9.5e-24, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 517}}], "length": 549}

{"regions": [{"startStyle": "curved", "end": 140, "endStyle": "curved", "aliStart": 72, "text": "NHR", "colour": "#2cb42c", "aliEnd": 140, "start": 71, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 140, "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": 72, "scoreName": "E-value", "accession": "PF00105.16", "start": 71, "score": 4.099999999999999e-33, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 140}}, {"startStyle": "straight", "end": 494, "endStyle": "straight", "aliStart": 323, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 492, "start": 308, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 494, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 323, "scoreName": "E-value", "accession": "PF00104.28", "start": 308, "score": 8.6e-24, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 492}}], "length": 524}

{"regions": [{"startStyle": "curved", "end": 85, "endStyle": "curved", "aliStart": 17, "text": "NHR", "colour": "#2cb42c", "aliEnd": 85, "start": 16, "href": "http://pfam.xfam.org/family/PF00105.16", "type": "pfama", "display": "true", "metadata": {"end": 85, "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": 17, "scoreName": "E-value", "accession": "PF00105.16", "start": 16, "score": 3.8e-33, "identifier": "Zinc finger, C4 type (two domains)", "type": "DBD", "aliEnd": 85}}, {"startStyle": "straight", "end": 439, "endStyle": "straight", "aliStart": 268, "text": "Hormone_recep", "colour": "#9999ff", "aliEnd": 437, "start": 253, "href": "http://pfam.xfam.org/family/PF00104.28", "type": "pfama", "display": "true", "metadata": {"end": 439, "description": "This all helical domain is involved in binding the hormone in these receptors.", "database": "PfamA", "aliStart": 268, "scoreName": "E-value", "accession": "PF00104.28", "start": 253, "score": 6.8e-24, "identifier": "Ligand-binding domain of nuclear hormone receptor", "type": "DBD", "aliEnd": 437}}], "length": 469}

TF Info Page for RORA (Nuclear receptor)