TF Info Page for T (T-box)

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 The protein encoded by this gene is an embryonic nuclear transcription factor that binds to a specific DNA element, the palindromic T-site. It binds through a region in its N-terminus, called the T-box, and effects transcription of genes required for mesoderm formation and differentiation. The protein is localized to notochord-derived cells. Variation in this gene was associated with susceptibility to neural tube defects and chordoma. A mutation in this gene was found in a family with sacral agenesis with vertebral anomalies. [provided by RefSeq, Sep 2018]
Ensembl ID: ENSG00000164458
External Link: CisBP
Interpro IPR001699; IPR002070; IPR008967; IPR018186;
Protein Domain: ENSP00000355836
Protein Domain: ENSP00000355841
Protein Domain: ENSP00000296946
Protein Domain: ENSP00000453512
Domain:
Protein: ENSP00000355836DBD: T-boxOther:
Protein: ENSP00000355841DBD: T-boxOther:
Protein: ENSP00000296946DBD: T-boxOther:
Protein: ENSP00000453512DBD: T-boxOther:

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-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
SELEXJASPARDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
MiscHOMERInferred - T (99% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - TBX19 (82% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - TBX19 (82% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - byn (72% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - byn (72% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - byn (72% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - 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