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 D3 [Source:HGNC Symbol;Acc:HGNC:5137]
Entrez Summary	TBA
Ensembl ID:	ENSG00000128652
External Link:	T093296_1.02
Interpro	IPR001356; IPR001827; IPR009057; IPR017970; IPR020479; IPR025281;
Protein Domain:
Protein: ENSP00000249440	DBD: Homeodomain	Other: DUF4074
Protein: ENSP00000392615	DBD: Homeodomain	Other:
Protein: ENSP00000386498	DBD: Homeodomain	Other: DUF4074

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:14610084
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	GO:0003700 sequence-specific DNA binding transcription factor activity IEA - GO_REF:0000002
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
Methyl-HT-SELEX	Yin2017		Direct
PBM	Berger08		Inferred - Hoxd3 (100% AA Identity, Mus musculus)
PBM	Badis09		Inferred - Hoxa3 (98% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Hoxa3 (98% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - HOXA3 (98% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb3 (96% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - PDX1 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PDX1 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PDX1 (78% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Pdx1 (78% AA Identity, Mus musculus)
SELEX	JASPAR		Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (78% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - PDX1 (78% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Pdx1 (78% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXA2 (77% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA2 (77% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - HOXA2 (77% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa2 (77% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB2 (77% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - SPU_026099 (77% AA Identity, Strongylocentrotus purpuratus)
Misc	HOMER		Inferred - Hoxa2 (77% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXA5 (75% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA5 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA5 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA5 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA5 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA5 (75% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa5 (75% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB4 (75% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb4 (75% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB5 (75% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB5 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB5 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB5 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB5 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB5 (75% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb5 (75% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Hoxc5 (75% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXD4 (75% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD4 (75% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - Q0N4M8_NEMVE (75% AA Identity, Nematostella vectensis)
B1H	JASPAR		Inferred - Scr (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Scr (75% AA Identity, Drosophila melanogaster)
COMPILED	JASPAR		Inferred - HOXA5 (75% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA5 (75% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXA5 (75% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Hoxb4 (75% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - HOXD4 (75% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - Antp (73% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Dfd (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Dfd (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Dfd (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - HOXA4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA4 (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa4 (73% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXA6 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA6 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA6 (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa6 (73% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXA7 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA7 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA7 (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa7 (73% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Hoxa7 (73% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - HOXC4 (73% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC4 (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxc4 (73% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - pb (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - pb (73% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - Antp (73% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - Dfd (73% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - HOXA4 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA7 (73% AA Identity, Homo sapiens)
Misc	iDMMPMM		Inferred - Antp (73% AA Identity, Drosophila melanogaster)
Misc	iDMMPMM		Inferred - Dfd (73% AA Identity, Drosophila melanogaster)
Misc	HocoMoco		Inferred - HOXA7 (73% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXB7 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB7 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB7 (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb7 (71% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - HOXC4 (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxc6 (71% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - HOXB7 (71% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXC6 (71% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - abd-A (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - abd-A (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - abd-A (70% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - ftz (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - ftz (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - HOXB6 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB6 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB6 (70% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb6 (70% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - HOXB7 (70% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXB7 (70% AA Identity, Homo sapiens)
PBM	BusserDevelopment2012		Inferred - Ubx (70% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Ubx (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Ubx (70% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - zen (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - zen (70% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - abd-A (70% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - ftz (70% AA Identity, Drosophila melanogaster)
ChIP-seq	modENCODE		Inferred - lin-39 (70% AA Identity, Caenorhabditis elegans)
Transfac	Transfac	License required	Inferred - Ubx (70% AA Identity, Drosophila melanogaster)
Misc	iDMMPMM		Inferred - abd-A (70% AA Identity, Drosophila melanogaster)
Misc	iDMMPMM		Inferred - ftz (70% AA Identity, Drosophila melanogaster)
Misc	HocoMoco		Inferred - HOXB6 (70% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - lin-39 (70% AA Identity, Caenorhabditis elegans)
Misc	iDMMPMM		Inferred - Ubx (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - HOXA1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA1 (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa1 (68% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa9 (68% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - lab (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - lab (68% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - NEMVEDRAFT_v1g205636 (68% AA Identity, Nematostella vectensis)
PBM	Zoo_01		Inferred - Q24782_9CNID (68% AA Identity, Eleutheria dichotoma)
B1H	JASPAR		Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA9 (68% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - Hoxa9 (68% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - HOXA1 (68% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Hoxa9 (68% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - GSX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - GSX1 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - GSX2 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - GSX2 (66% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Gsx2 (66% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB1 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB9 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB9 (66% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb9 (66% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXC9 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC9 (66% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxc9 (66% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXD9 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD9 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD9 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD9 (66% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - ind (66% AA Identity, Drosophila melanogaster)
ChIP-seq	JASPAR		Inferred - Hoxc9 (66% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXB1 (66% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Hoxc9 (66% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - HOXD9 (66% AA Identity, Homo sapiens)

Structure

Structure	PDB	Not_Covered

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": 251, "endStyle": "curved", "aliStart": 195, "text": "HD", "colour": "#228B22", "aliEnd": 251, "start": 195, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 251, "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": 195, "scoreName": "E-value", "accession": "PF00046.27", "start": 195, "score": 4.1999999999999995e-21, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 251}}, {"startStyle": "straight", "end": 430, "endStyle": "straight", "aliStart": 370, "text": "DUF4074", "colour": "#9999ff", "aliEnd": 430, "start": 369, "href": "http://pfam.xfam.org/family/PF13293.4", "type": "pfama", "display": "true", "metadata": {"end": 430, "description": "This family is found at the C-terminal of Homeobox proteins in Metazoa.", "database": "PfamA", "aliStart": 370, "scoreName": "E-value", "accession": "PF13293.4", "start": 369, "score": 9.2e-31, "identifier": "Domain of unknown function (DUF4074)", "type": "DBD", "aliEnd": 430}}], "length": 433}

TF Info Page for HOXD3 (Homeodomain)