The Human Transcription Factors

Conclusion

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

Description

Description:	homeobox A13 [Source:HGNC Symbol;Acc:HGNC:5102]
Entrez Summary	TBA
Ensembl ID:	ENSG00000106031
External Link:	T093252_1.02
Interpro	IPR001356; IPR009057; IPR017970; IPR022067;
Protein Domain:
Protein: ENSP00000222753	DBD: Homeodomain	Other: HoxA13_N

Previous Annotations

Source	Annotation
TF-CAT classification	No PMIDS:
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
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
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-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	Berger08		Inferred - Hoxa13 (100% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXC13 (92% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC13 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC13 (92% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxc13 (92% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - HOXC13 (92% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXD13 (89% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXD13 (89% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD13 (89% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD13 (89% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD13 (89% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD13 (89% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxd13 (89% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - HOXD13 (89% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXD13 (87% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXD13 (87% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXD13 (87% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXD13 (87% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXD13 (87% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXD13 (87% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB13 (84% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB13 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB13 (84% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - HOXB13 (84% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb13 (84% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - hoxd13a (84% AA Identity, Danio rerio)

Structure

Structure	PDB	2LD5

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": 379, "endStyle": "curved", "aliStart": 323, "text": "HD", "colour": "#228B22", "aliEnd": 379, "start": 323, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 379, "description": "The homeobox domain or homeodomain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [PUBMED:2568852, PUBMED:1357790]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [PUBMED:12445403]. The domain binds DNA through a helix-turn-helix (HTH) structure. ", "database": "PfamA", "aliStart": 323, "scoreName": "E-value", "accession": "PF00046.27", "start": 323, "score": 9.4e-18, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 379}}, {"startStyle": "straight", "end": 224, "endStyle": "straight", "aliStart": 80, "text": "HoxA13_N", "colour": "#9999ff", "aliEnd": 224, "start": 75, "href": "http://pfam.xfam.org/family/PF12284.6", "type": "pfama", "display": "true", "metadata": {"end": 224, "description": "This family of proteins is found in eukaryotes. Proteins in this family are typically between 149 and 306 amino acids in length. The family is found in association with Pfam:PF00046. This family is the N terminal of the Hox gene protein involved in formation of the digital arch of the hands and feet as well as in correct genital formation. Mutation of the protein is associated with hand-foot-genital syndrome.", "database": "PfamA", "aliStart": 80, "scoreName": "E-value", "accession": "PF12284.6", "start": 75, "score": 6.400000000000001e-20, "identifier": "Hox protein A13 N terminal", "type": "DBD", "aliEnd": 224}}], "length": 389}

TF Info Page for HOXA13 (Homeodomain)