The Human Transcription Factors

Conclusion

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

Description

Description:

T-box 5 [Source:HGNC Symbol;Acc:HGNC:11604]

Entrez Summary

This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene is closely linked to related family member T-box 3 (ulnar mammary syndrome) on human chromosome 12. The encoded protein may play a role in heart development and specification of limb identity. Mutations in this gene have been associated with Holt-Oram syndrome, a developmental disorder affecting the heart and upper limbs. Several transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

Ensembl ID:

ENSG00000089225

External Link:

CisBP

Interpro

IPR001699; IPR008967; IPR018186; ;

Protein Domain:

ENSP00000309913

Protein Domain:

ENSP00000337723

Protein Domain:

ENSP00000384152

Protein Domain:

ENSP00000433292

Domain:

Protein: ENSP00000309913	DBD: T-box	Other:
Protein: ENSP00000337723	DBD: T-box	Other:
Protein: ENSP00000384152	DBD: T-box	Other:
Protein: ENSP00000433292	DBD: T-box	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:11555635
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:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor IEA - GO_REF:0000019 GO:0003700 sequence-specific DNA binding transcription factor activity IDA - PMID:11431700, PMID:12499378, PMID:16332960
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
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 - Tbx5 (100% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Tbx5 (100% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Tbx5 (100% AA Identity, Mus musculus)
PBM	DREAM_contest		Inferred - Tbx4 (92% AA Identity, Mus musculus)
PBM	SebePedros2013		Inferred - estExt_fgenesh2_pg.C_1570024 (62% AA Identity, Branchiostoma floridae)
PBM	Zoo_01		Inferred - XP_001195863 (62% AA Identity, Strongylocentrotus purpuratus)
HT-SELEX	Yin2017		Inferred - TBX2 (61% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - TBX2 (61% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Tbx2 (61% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - TBX2 (61% AA Identity, Homo sapiens)
ChIP-seq	hmCHIP		Inferred - Tbx2 (61% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - TBX2 (61% AA Identity, Homo sapiens)

Structure

Structure	PDB	2X6V

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

{"regions": [{"startStyle": "curved", "end": 238, "endStyle": "curved", "aliStart": 57, "text": "T-box", "colour": "#009900", "aliEnd": 237, "start": 56, "href": "http://pfam.xfam.org/family/PF00907.20", "type": "pfama", "display": "true", "metadata": {"end": 238, "description": "The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations [2].", "database": "PfamA", "aliStart": 57, "scoreName": "E-value", "accession": "PF00907.20", "start": 56, "score": 1.4e-81, "identifier": "T-box", "type": "DBD", "aliEnd": 237}}], "length": 519}

{"regions": [{"startStyle": "curved", "end": 188, "endStyle": "curved", "aliStart": 7, "text": "T-box", "colour": "#009900", "aliEnd": 187, "start": 6, "href": "http://pfam.xfam.org/family/PF00907.20", "type": "pfama", "display": "true", "metadata": {"end": 188, "description": "The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations [2].", "database": "PfamA", "aliStart": 7, "scoreName": "E-value", "accession": "PF00907.20", "start": 6, "score": 1.0999999999999997e-81, "identifier": "T-box", "type": "DBD", "aliEnd": 187}}], "length": 469}

{"regions": [{"startStyle": "curved", "end": 238, "endStyle": "curved", "aliStart": 57, "text": "T-box", "colour": "#009900", "aliEnd": 237, "start": 56, "href": "http://pfam.xfam.org/family/PF00907.20", "type": "pfama", "display": "true", "metadata": {"end": 238, "description": "The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations [2].", "database": "PfamA", "aliStart": 57, "scoreName": "E-value", "accession": "PF00907.20", "start": 56, "score": 6.599999999999999e-82, "identifier": "T-box", "type": "DBD", "aliEnd": 237}}], "length": 350}

TF Info Page for TBX5 (T-box)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution