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 P3 [Source:HGNC Symbol;Acc:HGNC:6106]

Entrez Summary

Ensembl ID:

ENSG00000049768

External Link:

CisBP

Interpro

IPR001766; IPR007087;

Protein Domain:

ENSP00000365380

Protein Domain:

ENSP00000428952

Protein Domain:

ENSP00000365372

Protein Domain:

ENSP00000451208

Domain:

Protein: ENSP00000365380	DBD: Forkhead	Other: FOXP-CC
Protein: ENSP00000428952	DBD: Forkhead	Other: FOXP-CC
Protein: ENSP00000365372	DBD: Forkhead	Other: FOXP-CC
Protein: ENSP00000451208	DBD: Forkhead	Other: FOXP-CC

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:17028180
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.	b
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:11483607 \| NAS - PMID:11138001 GO:0003705 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IEA - GO_REF:0000019 GO:0032088 negative regulation of NF-kappaB transcription factor activity IDA - PMID:16652169 GO:0032792 negative regulation of CREB transcription factor activity IDA - PMID:16652169 GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity IDA - PMID:16873067
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
Methyl-HT-SELEX	Yin2017		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
HT-SELEX	Yin2017		Inferred - FOXP1 (79% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - FOXP1 (79% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - FOXP1 (79% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Foxp1 (79% AA Identity, Mus musculus)
ChIP-seq	JASPAR		Inferred - FOXP1 (79% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - FOXP1 (79% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - FOXP1 (79% AA Identity, Homo sapiens)
SMiLE-seq	Isakova2017		Inferred - FOXP2 (74% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Foxp2 (74% AA Identity, Mus musculus)
ChIP-seq	JASPAR		Inferred - FOXP2 (74% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - FOXP2 (74% AA Identity, Homo sapiens)

Structure

Structure	PDB	3QRF

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": 382, "endStyle": "curved", "aliStart": 302, "text": "Frkh", "colour": "#228B22", "aliEnd": 377, "start": 302, "href": "http://pfam.xfam.org/family/PF00250.16", "type": "pfama", "display": "true", "metadata": {"end": 382, "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": 302, "scoreName": "E-value", "accession": "PF00250.16", "start": 302, "score": 8.3e-27, "identifier": "Forkhead domain", "type": "DBD", "aliEnd": 377}}, {"startStyle": "straight", "end": 226, "endStyle": "straight", "aliStart": 159, "text": "FOXP-CC", "colour": "#9999ff", "aliEnd": 225, "start": 158, "href": "http://pfam.xfam.org/family/PF16159.3", "type": "pfama", "display": "true", "metadata": {"end": 226, "description": "This domain, approximately 60-70 residues in length, is  mainly found in Forkhead box proteins in various Mammalia  species [1]. It is a coiled-coil domain, which modulates  the dimeric associations of FOXP transcription factors.  Several key disease mutations, for instance those found in  the IPEX syndrome are located in this domain [2]", "database": "PfamA", "aliStart": 159, "scoreName": "E-value", "accession": "PF16159.3", "start": 158, "score": 1.8000000000000004e-26, "identifier": "FOXP coiled-coil domain", "type": "DBD", "aliEnd": 225}}], "length": 397}

{"regions": [{"startStyle": "curved", "end": 376, "endStyle": "jagged", "aliStart": 302, "text": "Frkh", "colour": "#228B22", "aliEnd": 349, "start": 302, "href": "http://pfam.xfam.org/family/PF00250.16", "type": "pfama", "display": "true", "metadata": {"end": 376, "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": 302, "scoreName": "E-value", "accession": "PF00250.16", "start": 302, "score": 1.9999999999999999e-22, "identifier": "Forkhead domain", "type": "DBD", "aliEnd": 349}}, {"startStyle": "jagged", "end": 442, "endStyle": "curved", "aliStart": 407, "text": "Frkh", "colour": "#228B22", "aliEnd": 437, "start": 404, "href": "http://pfam.xfam.org/family/PF00250.16", "type": "pfama", "display": "true", "metadata": {"end": 442, "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": 407, "scoreName": "E-value", "accession": "PF00250.16", "start": 404, "score": 1.9999999999999999e-22, "identifier": "Forkhead domain", "type": "DBD", "aliEnd": 437}}, {"startStyle": "straight", "end": 226, "endStyle": "straight", "aliStart": 159, "text": "FOXP-CC", "colour": "#9999ff", "aliEnd": 225, "start": 158, "href": "http://pfam.xfam.org/family/PF16159.3", "type": "pfama", "display": "true", "metadata": {"end": 226, "description": "This domain, approximately 60-70 residues in length, is  mainly found in Forkhead box proteins in various Mammalia  species [1]. It is a coiled-coil domain, which modulates  the dimeric associations of FOXP transcription factors.  Several key disease mutations, for instance those found in  the IPEX syndrome are located in this domain [2]", "database": "PfamA", "aliStart": 159, "scoreName": "E-value", "accession": "PF16159.3", "start": 158, "score": 2.2e-26, "identifier": "FOXP coiled-coil domain", "type": "DBD", "aliEnd": 225}}], "length": 457}

TF Info Page for FOXP3 (Forkhead)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution