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 3 [Source:HGNC Symbol;Acc:HGNC:11602]
Entrez Summary	TBA
Ensembl ID:	ENSG00000135111
External Link:	T149482_1.02
Interpro	IPR001699; IPR002070; IPR008967; IPR018186; IPR022582; ;
Protein Domain:
Protein: ENSP00000257566	DBD: T-box	Other: TBX
Protein: ENSP00000257567	DBD: T-box	Other: TBX

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:11689487 12005433
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:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IDA - PMID:11689487
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
Methyl-HT-SELEX	Yin2017		Direct
Misc	HocoMoco		Direct
PBM	DREAM_contest		Inferred - Tbx3 (90% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - TBX2 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - TBX2 (85% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Tbx2 (85% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - TBX2 (85% AA Identity, Homo sapiens)
ChIP-seq	hmCHIP		Inferred - Tbx2 (85% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - TBX2 (85% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - TBX2 (84% AA Identity, Gasterosteus aculeatus)
PBM	Zoo_01		Inferred - TBX2 (84% AA Identity, Takifugu rubripes)
PBM	SebePedros2013		Inferred - XP_008203914.1 (78% AA Identity, Nasonia vitripennis)
PBM	SebePedros2013		Inferred - estExt_fgenesh2_pg.C_1570024 (62% AA Identity, Branchiostoma floridae)
PBM	Zoo_01		Inferred - XP_001195863 (61% AA Identity, Strongylocentrotus purpuratus)

Structure

Structure	PDB	1H6F

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": "curved", "end": 285, "endStyle": "curved", "aliStart": 105, "text": "T-box", "colour": "#009900", "aliEnd": 285, "start": 105, "href": "http://pfam.xfam.org/family/PF00907.20", "type": "pfama", "display": "true", "metadata": {"end": 285, "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": 105, "scoreName": "E-value", "accession": "PF00907.20", "start": 105, "score": 2.4999999999999996e-84, "identifier": "T-box", "type": "DBD", "aliEnd": 285}}, {"startStyle": "straight", "end": 387, "endStyle": "straight", "aliStart": 303, "text": "TBX", "colour": "#9999ff", "aliEnd": 385, "start": 303, "href": "http://pfam.xfam.org/family/PF12598.6", "type": "pfama", "display": "true", "metadata": {"end": 387, "description": "This domain family is found in eukaryotes, and is typically between 77 and 89 amino acids in length. The family is found in association with Pfam:PF00907. There are two completely conserved residues (S and P) that may be functionally important. T-box genes encode transcription factors involved in morphogenesis and organogenesis of vertebrates and invertebrates", "database": "PfamA", "aliStart": 303, "scoreName": "E-value", "accession": "PF12598.6", "start": 303, "score": 5.3e-19, "identifier": "T-box transcription factor", "type": "DBD", "aliEnd": 385}}], "length": 724}

TF Info Page for TBX3 (T-box)