The Human Transcription Factors

Conclusion

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

Description

Description:	forkhead box A3 [Source:HGNC Symbol;Acc:HGNC:5023]
Entrez Summary	TBA
Ensembl ID:	ENSG00000170608
External Link:	T081607_1.02
Interpro	IPR001766; IPR013638; IPR018122; IPR018533;
Protein Domain:
Protein: ENSP00000304004	DBD: Forkhead	Other: Forkhead_N, HNF_C
Protein: ENSP00000470816	DBD: Forkhead	Other: Forkhead_N

Previous Annotations

Source	Annotation
TF-CAT classification	No PMIDS:
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:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity IBA - GO_REF:0000033 GO:0003700 sequence-specific DNA binding transcription factor activity IDA - PMID:12695546 \| TAS - PMID:9369482
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	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
HT-SELEX	Yin2017		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
ChIP-seq	ENCODE		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
ChIP-seq	ENCODE		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
ChIP-seq	ENCODE		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
ChIP-seq	hmCHIP		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
ChIP-seq	modENCODE		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - FOXA1 (95% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - FOXA2 (90% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - FOXA2 (90% AA Identity, Homo sapiens)
PBM	Badis09		Inferred - Foxa2 (90% AA Identity, Mus musculus)
ChIP-seq	ENCODE		Inferred - FOXA2 (90% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA2 (90% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXA2 (90% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - Foxa2 (90% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Foxa2 (90% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Foxa2 (90% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - P33205 (90% AA Identity, Xenopus laevis)
Transfac	Transfac	License required	Inferred - Q91765 (90% AA Identity, Xenopus laevis)
Misc	HocoMoco		Inferred - FOXA2 (90% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - FOXA2 (90% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - fkh (85% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - fkh (85% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - fkh (85% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Q2L6N7_PELSI (85% AA Identity, Trionyx sinensis)
ChIP-seq	modENCODE		Inferred - fkh (85% AA Identity, Drosophila melanogaster)
Misc	iDMMPMM		Inferred - fkh (85% AA Identity, Drosophila melanogaster)
ChIP-seq	JASPAR		Inferred - pha-4 (84% AA Identity, Caenorhabditis elegans)
ChIP-seq	modENCODE		Inferred - pha-4 (84% AA Identity, Caenorhabditis elegans)
Misc	HOMER		Inferred - pha-4 (84% AA Identity, Caenorhabditis elegans)
HT-SELEX	Yin2017		Inferred - FOXB1 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - FOXB1 (73% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - Foxb1 (73% AA Identity, Mus musculus)

Structure

Structure	PDB	1VTN

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": 102, "endStyle": "jagged", "aliStart": 84, "text": "Frkh", "colour": "#228B22", "aliEnd": 101, "start": 84, "href": "http://pfam.xfam.org/family/PF00250.16", "type": "pfama", "display": "true", "metadata": {"end": 102, "description": "The fork head domain is a conserved DNA-binding domain (also known as a \"winged helix\") of about 100 amino-acid residues.", "database": "PfamA", "aliStart": 84, "scoreName": "E-value", "accession": "PF00250.16", "start": 84, "score": 0.00042, "identifier": "Forkhead domain", "type": "DBD", "aliEnd": 101}}, {"startStyle": "jagged", "end": 83, "endStyle": "straight", "aliStart": 4, "text": "Forkhead_N", "colour": "#9999ff", "aliEnd": 83, "start": 1, "href": "http://pfam.xfam.org/family/PF08430.10", "type": "pfama", "display": "true", "metadata": {"end": 83, "description": "The region described in this family is found towards the N-terminus of various eukaryotic forkhead/HNF-3-related transcription factors (which contain the Pfam:PF00250 domain). These proteins play key roles in embryogenesis, maintenance of differentiated cell states, and tumourigenesis [1].", "database": "PfamA", "aliStart": 4, "scoreName": "E-value", "accession": "PF08430.10", "start": 1, "score": 1.8e-05, "identifier": "Forkhead N-terminal region", "type": "DBD", "aliEnd": 83}}], "length": 102}

TF Info Page for FOXA3 (Forkhead)