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 brachyury transcription factor [Source:HGNC Symbol;Acc:HGNC:11515]
Entrez Summary	TBA
Ensembl ID:	ENSG00000164458
External Link:	T149487_1.02
Interpro	IPR001699; IPR002070; IPR008967; IPR018186;
Protein Domain:
Protein: ENSP00000355836	DBD: T-box	Other:
Protein: ENSP00000355841	DBD: T-box	Other:
Protein: ENSP00000296946	DBD: T-box	Other:
Protein: ENSP00000453512	DBD: T-box	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_Transactivation_ PMIDS:7588606 8344258
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:0003700 sequence-specific DNA binding transcription factor activity NAS - PMID:8963900 GO:0003705 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IDA - PMID:21632880
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
SELEX	JASPAR		Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
Misc	HOMER		Inferred - T (99% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - TBX19 (82% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - TBX19 (82% AA Identity, Homo sapiens)
HT-SELEX	Nitta2015		Inferred - byn (72% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - byn (72% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - byn (72% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - byn (72% AA Identity, Drosophila melanogaster)

Structure

Structure	PDB	1XBR

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": 219, "endStyle": "curved", "aliStart": 44, "text": "T-box", "colour": "#009900", "aliEnd": 219, "start": 44, "href": "http://pfam.xfam.org/family/PF00907.20", "type": "pfama", "display": "true", "metadata": {"end": 219, "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": 44, "scoreName": "E-value", "accession": "PF00907.20", "start": 44, "score": 2.6999999999999996e-73, "identifier": "T-box", "type": "DBD", "aliEnd": 219}}], "length": 378}

{"regions": [{"startStyle": "curved", "end": 219, "endStyle": "curved", "aliStart": 44, "text": "T-box", "colour": "#009900", "aliEnd": 219, "start": 44, "href": "http://pfam.xfam.org/family/PF00907.20", "type": "pfama", "display": "true", "metadata": {"end": 219, "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": 44, "scoreName": "E-value", "accession": "PF00907.20", "start": 44, "score": 3.2e-73, "identifier": "T-box", "type": "DBD", "aliEnd": 219}}], "length": 404}

{"regions": [{"startStyle": "curved", "end": 219, "endStyle": "curved", "aliStart": 44, "text": "T-box", "colour": "#009900", "aliEnd": 219, "start": 44, "href": "http://pfam.xfam.org/family/PF00907.20", "type": "pfama", "display": "true", "metadata": {"end": 219, "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": 44, "scoreName": "E-value", "accession": "PF00907.20", "start": 44, "score": 3.7999999999999996e-73, "identifier": "T-box", "type": "DBD", "aliEnd": 219}}], "length": 436}

{"regions": [{"startStyle": "curved", "end": 219, "endStyle": "curved", "aliStart": 44, "text": "T-box", "colour": "#009900", "aliEnd": 219, "start": 44, "href": "http://pfam.xfam.org/family/PF00907.20", "type": "pfama", "display": "true", "metadata": {"end": 219, "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": 44, "scoreName": "E-value", "accession": "PF00907.20", "start": 44, "score": 8.999999999999998e-74, "identifier": "T-box", "type": "DBD", "aliEnd": 219}}], "length": 243}

TF Info Page for T (T-box)