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 D4 [Source:HGNC Symbol;Acc:HGNC:5138]
Entrez Summary	TBA
Ensembl ID:	ENSG00000170166
External Link:	T093364_1.02
Interpro	IPR001356; IPR001827; IPR009057; IPR017970; IPR017995; IPR020479;
Protein Domain:
Protein: ENSP00000302548	DBD: Homeodomain	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:1756725
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
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Misc	HocoMoco		Direct
HT-SELEX	Yin2017		Inferred - HOXA4 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA4 (98% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa4 (98% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - HOXA4 (98% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXC4 (96% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC4 (96% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxc4 (96% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB4 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB4 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB4 (94% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb4 (94% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - HOXC4 (94% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Hoxb4 (94% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXA5 (92% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA5 (92% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa5 (92% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB5 (92% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB5 (92% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb5 (92% AA Identity, Mus musculus)
COMPILED	JASPAR		Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXA5 (92% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - Dfd (91% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Dfd (91% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Dfd (91% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - Dfd (91% AA Identity, Drosophila melanogaster)
Misc	iDMMPMM		Inferred - Dfd (91% AA Identity, Drosophila melanogaster)
PBM	Berger08		Inferred - Hoxc5 (89% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - Scr (89% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Scr (89% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Antp (87% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - HOXA7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA7 (87% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa7 (87% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Hoxa7 (87% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - HOXB7 (87% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB7 (87% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB7 (87% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb7 (87% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Antp (87% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - HOXA7 (87% AA Identity, Homo sapiens)
Misc	iDMMPMM		Inferred - Antp (87% AA Identity, Drosophila melanogaster)
Misc	HocoMoco		Inferred - HOXA7 (87% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXB7 (87% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXB7 (85% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - HOXB7 (85% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA6 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA6 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA6 (84% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa6 (84% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB6 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB6 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB6 (84% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb6 (84% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - HOXB6 (84% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - abd-A (82% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - abd-A (82% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - abd-A (82% AA Identity, Drosophila melanogaster)
PBM	Berger08		Inferred - Hoxc6 (82% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - abd-A (82% AA Identity, Drosophila melanogaster)
Misc	iDMMPMM		Inferred - abd-A (82% AA Identity, Drosophila melanogaster)
Misc	HocoMoco		Inferred - HOXC6 (82% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - ftz (80% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - ftz (80% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - ftz (80% AA Identity, Drosophila melanogaster)
Misc	iDMMPMM		Inferred - ftz (80% AA Identity, Drosophila melanogaster)
PBM	BusserDevelopment2012		Inferred - Ubx (78% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Ubx (78% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Ubx (78% AA Identity, Drosophila melanogaster)
ChIP-seq	modENCODE		Inferred - lin-39 (78% AA Identity, Caenorhabditis elegans)
Transfac	Transfac	License required	Inferred - Ubx (78% AA Identity, Drosophila melanogaster)
Misc	HOMER		Inferred - lin-39 (78% AA Identity, Caenorhabditis elegans)
Misc	iDMMPMM		Inferred - Ubx (78% AA Identity, Drosophila melanogaster)
PBM	Berger08		Inferred - Hoxb3 (77% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - SPU_026099 (77% AA Identity, Strongylocentrotus purpuratus)
PBM	Badis09		Inferred - Hoxa3 (75% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Hoxa3 (75% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXD3 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD3 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD3 (75% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxd3 (75% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - Q0N4M8_NEMVE (75% AA Identity, Nematostella vectensis)
Transfac	Transfac	License required	Inferred - HOXA3 (75% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxd8 (73% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - PDX1 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PDX1 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PDX1 (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Pdx1 (73% AA Identity, Mus musculus)
SELEX	JASPAR		Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PDX1 (73% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - PDX1 (73% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Pdx1 (73% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB8 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB8 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB8 (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb8 (71% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXD8 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD8 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD8 (71% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - lab (71% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - lab (71% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - pb (71% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - pb (71% AA Identity, Drosophila melanogaster)
Misc	HocoMoco		Inferred - HOXB8 (71% AA Identity, Homo sapiens)
PBM	TF_Evolution	Unpublished Data	Inferred - Cbr-mab-5 (70% AA Identity, Caenorhabditis briggsae)
HT-SELEX	Yin2017		Inferred - HOXA2 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA2 (70% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - HOXA2 (70% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa2 (70% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB2 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC8 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC8 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC8 (70% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxc8 (70% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - zen (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - zen (70% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - HOXC8 (70% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Hoxa2 (70% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - HOXC8 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - GSX1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - GSX1 (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - GSX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - GSX2 (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Gsx2 (68% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB9 (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB9 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB9 (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb9 (68% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - ind (68% AA Identity, Drosophila melanogaster)
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)
HT-SELEX	Yin2017		Inferred - HOXA1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA1 (66% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa1 (66% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXA9 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA9 (66% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa9 (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 - 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)
PBM	Zoo_01		Inferred - O76842_CUPSA (66% AA Identity, Cupiennius salei)
PBM	Zoo_01		Inferred - Q7M3U4_ACRFO (66% AA Identity, Acropora formosa)
Transfac	Transfac	License required	Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA9 (66% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - Hoxa9 (66% AA Identity, Mus musculus)
ChIP-seq	JASPAR		Inferred - Hoxc9 (66% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXA1 (66% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Hoxa9 (66% AA Identity, Mus musculus)
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

TF Info Page for HOXD4 (Homeodomain)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution