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 7 (T-cell specific, HMG-box) [Source:HGNC Symbol;Acc:HGNC:11639]

Entrez Summary

Ensembl ID:

ENSG00000081059

External Link:

CisBP

Interpro

IPR009071; IPR013558;

Protein Domain:

ENSP00000340347

Protein Domain:

ENSP00000367822

Protein Domain:

ENSP00000378469

Protein Domain:

ENSP00000430179

Protein Domain:

ENSP00000430617

Protein Domain:

ENSP00000429935

Protein Domain:

ENSP00000429547

Domain:

Protein: ENSP00000340347	DBD: HMG	Other: CTNNB1_binding
Protein: ENSP00000367822	DBD: HMG	Other: CTNNB1_binding
Protein: ENSP00000378469	DBD: HMG	Other: CTNNB1_binding
Protein: ENSP00000430179	DBD: HMG	Other: CTNNB1_binding
Protein: ENSP00000430617	DBD: HMG	Other: CTNNB1_binding
Protein: ENSP00000429935	DBD: HMG	Other:
Protein: ENSP00000429547	DBD: HMG	Other: CTNNB1_binding

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:7579399
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:0001227 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor IEA - GO_REF:0000019
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
SMiLE-seq	Isakova2017		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
PBM	Badis09		Inferred - Tcf7 (100% AA Identity, Mus musculus)
PBM	Badis09		Inferred - Tcf7l2 (98% AA Identity, Mus musculus)
ChIP-seq	JASPAR		Inferred - TCF7L2 (98% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF7L2 (98% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF7L2 (98% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF7L2 (98% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF7L2 (98% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TCF7L2 (98% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - TCF7L2 (98% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - TCF7L2 (98% AA Identity, Homo sapiens)
SMiLE-seq	Isakova2017		Inferred - LEF1 (97% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - LEF1 (97% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - LEF1 (97% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - LEF1 (97% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - LEF1 (97% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - LEF1 (97% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - LEF1 (97% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - LEF1 (97% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - LEF1 (97% AA Identity, Homo sapiens)
PBM	Badis09		Inferred - Lef1 (97% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - LEF1 (97% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - LEF1 (97% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - LEF1 (97% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - LEF1 (97% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - LEF1 (97% AA Identity, Homo sapiens)

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": "jagged", "end": 62, "endStyle": "curved", "aliStart": 2, "text": "HMG", "colour": "#228B22", "aliEnd": 61, "start": 2, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 62, "description": "High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.", "database": "PfamA", "aliStart": 2, "scoreName": "E-value", "accession": "PF00505.17", "start": 2, "score": 1.8e-17, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 61}}], "length": 106}

{"regions": [{"startStyle": "curved", "end": 222, "endStyle": "curved", "aliStart": 154, "text": "HMG", "colour": "#228B22", "aliEnd": 221, "start": 154, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 222, "description": "High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.", "database": "PfamA", "aliStart": 154, "scoreName": "E-value", "accession": "PF00505.17", "start": 154, "score": 3.4e-22, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 221}}, {"startStyle": "jagged", "end": 97, "endStyle": "straight", "aliStart": 1, "text": "CTNNB1_binding", "colour": "#9999ff", "aliEnd": 97, "start": 1, "href": "http://pfam.xfam.org/family/PF08347.9", "type": "pfama", "display": "true", "metadata": {"end": 97, "description": "This region tends to appear at the N-terminus of proteins also containing DNA-binding HMG (high mobility group) boxes (Pfam:PF00505) and appears to bind the armadillo repeat of CTNNB1 (beta-catenin), forming a stable complex. Signaling by Wnt through TCF/LCF is involved in developmental patterning, induction of neural tissues, cell fate decisions and stem cell differentiation [3].  Isoforms of HMG T-cell factors lacking the N-terminal CTNNB1-binding domain cannot fulfill their role as transcriptional activators in T-cell differentiation [1,2].", "database": "PfamA", "aliStart": 1, "scoreName": "E-value", "accession": "PF08347.9", "start": 1, "score": 4.9e-15, "identifier": "N-terminal CTNNB1 binding", "type": "DBD", "aliEnd": 97}}], "length": 270}

TF Info Page for TCF7 (HMG/Sox)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution