The Human Transcription Factors

Conclusion

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

Description

Description:

transcription factor 4 [Source:HGNC Symbol;Acc:HGNC:11634]

Entrez Summary

This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor. The encoded protein recognizes an Ephrussi-box ('E-box ') binding site ('CANNTG') - a motif first identified in immunoglobulin enhancers. This gene is broadly expressed, and may play an important role in nervous system development. Defects in this gene are a cause of Pitt-Hopkins syndrome. In addition, an intronic CTG repeat normally numbering 10-37 repeat units can expand to >50 repeat units and cause Fuchs endothelial corneal dystrophy. Multiple alternatively spliced transcript variants that encode different proteins have been described. [provided by RefSeq, Jul 2016]

Ensembl ID:

ENSG00000196628

External Link:

CisBP

Interpro

IPR011598; ;

Protein Domain:

ENSP00000348374

Protein Domain:

ENSP00000381382

Protein Domain:

ENSP00000409447

Protein Domain:

ENSP00000439656

Protein Domain:

ENSP00000457765

Protein Domain:

ENSP00000455450

Protein Domain:

ENSP00000456802

Protein Domain:

ENSP00000455261

Protein Domain:

ENSP00000455418

Protein Domain:

ENSP00000454366

Protein Domain:

ENSP00000455763

Protein Domain:

ENSP00000440731

Protein Domain:

ENSP00000439827

Protein Domain:

ENSP00000445202

Protein Domain:

ENSP00000441562

Protein Domain:

ENSP00000455179

Protein Domain:

ENSP00000458122

Protein Domain:

ENSP00000468729

Protein Domain:

ENSP00000454647

Protein Domain:

ENSP00000487505

Protein Domain:

ENSP00000486974

Protein Domain:

ENSP00000454866

Protein Domain:

ENSP00000454584

Protein Domain:

ENSP00000456983

Protein Domain:

ENSP00000487419

Protein Domain:

ENSP00000490451

Protein Domain:

ENSP00000490006

Protein Domain:

ENSP00000490883

Protein Domain:

ENSP00000490832

Protein Domain:

ENSP00000490625

Domain:

Protein: ENSP00000348374	DBD: bHLH	Other:
Protein: ENSP00000381382	DBD: bHLH	Other:
Protein: ENSP00000409447	DBD: bHLH	Other:
Protein: ENSP00000439656	DBD: bHLH	Other:
Protein: ENSP00000457765	DBD: bHLH	Other:
Protein: ENSP00000455450	DBD: bHLH	Other:
Protein: ENSP00000456802	DBD: bHLH	Other:
Protein: ENSP00000455261	DBD: bHLH	Other:
Protein: ENSP00000455418	DBD: bHLH	Other:
Protein: ENSP00000454366	DBD: bHLH	Other:
Protein: ENSP00000455763	DBD: bHLH	Other:
Protein: ENSP00000440731	DBD: bHLH	Other:
Protein: ENSP00000439827	DBD: bHLH	Other:
Protein: ENSP00000445202	DBD: bHLH	Other:
Protein: ENSP00000441562	DBD: bHLH	Other:
Protein: ENSP00000455179	DBD: bHLH	Other:
Protein: ENSP00000458122	DBD: bHLH	Other:
Protein: ENSP00000468729	DBD: bHLH	Other:
Protein: ENSP00000454647	DBD: bHLH	Other:
Protein: ENSP00000487505	DBD: bHLH	Other:
Protein: ENSP00000486974	DBD: bHLH	Other:
Protein: ENSP00000454866	DBD: bHLH	Other:
Protein: ENSP00000454584	DBD: bHLH	Other:
Protein: ENSP00000456983	DBD: bHLH	Other:
Protein: ENSP00000487419	DBD: bHLH	Other:
Protein: ENSP00000490451	DBD: bHLH	Other:
Protein: ENSP00000490006	DBD: bHLH	Other:
Protein: ENSP00000490883	DBD: bHLH	Other:
Protein: ENSP00000490832	DBD: bHLH	Other:
Protein: ENSP00000490625	DBD: bHLH	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding TF PPI Transactivation_ PMIDS:8978694
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:0001011 sequence-specific DNA binding RNA polymerase recruiting transcription factor activity ISS - PMID:8978694 GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a ISS - PMID:8978694 GO:0003700 sequence-specific DNA binding transcription factor activity IDA - PMID:11802795, PMID:2105528
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	Jolma2010		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Misc	HocoMoco		Direct
Misc	HOMER		Direct
PBM	Zoo_01		Inferred - Tcf4 (100% AA Identity, Mus musculus)
SELEX	Hallikas2006		Inferred - Tcf4 (100% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - TCF12 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - TCF12 (96% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - Tcf12 (96% AA Identity, Mus musculus)
ChIP-seq	ENCODE		Inferred - TCF12 (96% AA Identity, Homo sapiens)
ChIP-seq	ENCODE		Inferred - TCF12 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF12 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF12 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF12 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF12 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF12 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF12 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF12 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF12 (96% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - Tcf12 (96% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - TCF12 (96% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - TCF12 (96% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Tcf3 (92% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Tcf3 (92% AA Identity, Mus musculus)
SELEX	JASPAR		Inferred - TCF3 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF3 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF3 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF3 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF3 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF3 (88% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - TCF3 (88% AA Identity, Homo sapiens)
PBM	Badis09		Inferred - Tcf3 (87% AA Identity, Mus musculus)
PBM	DREAM_contest		Inferred - Tcf3 (87% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - Tcf3 (87% AA Identity, Mus musculus)
HT-SELEX	Nitta2015		Inferred - da (75% 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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TF Info Page for TCF4 (bHLH)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution