The Human Transcription Factors

Conclusion

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

Description

Description:

ALX homeobox 4 [Source:HGNC Symbol;Acc:HGNC:450]

Entrez Summary

This gene encodes a paired-like homeodomain transcription factor expressed in the mesenchyme of developing bones, limbs, hair, teeth, and mammary tissue. Mutations in this gene cause parietal foramina 2 (PFM2); an autosomal dominant disease characterized by deficient ossification of the parietal bones. Mutations in this gene also cause a form of frontonasal dysplasia with alopecia and hypogonadism; suggesting a role for this gene in craniofacial development, mesenchymal-epithelial communication, and hair follicle development. Deletion of a segment of chromosome 11 containing this gene, del(11)(p11p12), causes Potocki-Shaffer syndrome (PSS); a syndrome characterized by craniofacial anomalies, cognitive disability, multiple exostoses, and genital abnormalities in males. In mouse, this gene has been shown to use dual translation initiation sites located 16 codons apart. [provided by RefSeq, Oct 2009]

Ensembl ID:

ENSG00000052850

External Link:

CisBP

Interpro

IPR001356; IPR003654; IPR009057; IPR017970;

Protein Domain:

ENSP00000332744

Domain:

Protein: ENSP00000332744	DBD: Homeodomain	Other: OAR

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	GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor IEA - GO_REF:0000019
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	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Transfac	Transfac	License required	Direct
PBM	Berger08		Inferred - Alx4 (100% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - ALX3 (92% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ALX3 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX3 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX3 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX3 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX3 (92% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Alx3 (92% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - ALX1 (91% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX1 (91% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Alx1 (91% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Alx1 (91% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - ALX1 (91% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - ALX1 (91% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (87% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ARX (87% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ARX (87% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Arx (87% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Arx (87% AA Identity, Rattus norvegicus)
PBM	Barrera2016		Inferred - ARX (85% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (85% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (85% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (85% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (85% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - al (78% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - al (78% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG2808 (78% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - DRGX (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - DRGX (78% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - VSX2 (78% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - VSX2 (78% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - VSX2 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX2 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX2 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX2 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX2 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Drgx (78% AA Identity, Rattus norvegicus)
Transfac	Transfac	License required	Inferred - VSX2 (78% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - VSX2 (78% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - CG11294 (77% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG11294 (77% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG11294 (77% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - PHOX2A (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2A (77% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Phox2a (77% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - PHOX2B (77% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PHOX2B (77% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PHOX2B (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2B (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2B (77% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Phox2b (77% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - Pph13 (77% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Pph13 (77% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - vsx2 (77% AA Identity, Danio rerio)
Misc	HOMER		Inferred - Phox2a (77% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - DMBX1 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - DMBX1 (75% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Dmbx1 (75% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - hbn (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - hbn (75% AA Identity, Drosophila melanogaster)
PBM	Barrera2016		Inferred - PHOX2B (75% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - Rx (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rx (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rx (75% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - PHDP (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - PHDP (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - RAX (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RAX (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RAX (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Rax (73% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - UNCX (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - UNCX (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Uncx (73% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - uncx4.1 (73% AA Identity, Tetraodon nigroviridis)
PBM	Barrera2016		Inferred - VSX1 (73% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - VSX1 (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Vsx1 (73% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Rax (73% AA Identity, Rattus norvegicus)
PBM	Barrera2016		Inferred - ISX (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ISX (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ISX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ISX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ISX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ISX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ISX (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Prrx1 (71% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - VSX1 (71% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PRRX1 (71% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Prrx1 (71% AA Identity, Rattus norvegicus)
Misc	HocoMoco		Inferred - PRRX1 (71% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - CG32532 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG32532 (70% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
SMiLE-seq	Isakova2017		Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
PBM	Barrera2016		Inferred - ISX (70% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Isx (70% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Prrx2 (70% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - si:dkey-43p13.5 (70% AA Identity, Danio rerio)
B1H	JASPAR		Inferred - Vsx1 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Vsx1 (70% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Vsx1 (70% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Vsx2 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Vsx2 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Vsx2 (70% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Vsx2 (70% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - PRRX2 (70% AA Identity, Homo sapiens)
SELEX	JASPAR		Inferred - Prrx2 (70% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Prrx2 (70% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - PRRX2 (70% AA Identity, Sus scrofa)
Misc	HocoMoco		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - CRX (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - CRX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - CRX (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Crx (68% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - otp (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - otp (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - otp (68% AA Identity, Drosophila melanogaster)
PBM	Berger08		Inferred - Otp (68% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - repo (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - repo (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - repo (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - repo (68% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - unc-4 (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - unc-4 (68% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - CRX (68% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - CRX (68% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - Crx (68% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - CRX (68% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Crx (68% AA Identity, Mus musculus)
HT-SELEX	Nitta2015		Inferred - CG5369 (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG5369 (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG5369 (66% AA Identity, Drosophila melanogaster)
PBM	Barrera2016		Inferred - CRX (66% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - CRX (66% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - CRX (66% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - CRX (66% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ESX1 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ESX1 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ESX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ESX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ESX1 (66% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - OdsH (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - OdsH (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - OdsH (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - SHOX (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - SHOX (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - SHOX (66% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - SHOX (66% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Shox2 (66% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Shox2 (66% AA Identity, Rattus norvegicus)
PBM	BusserDevelopment2012		Inferred - Ptx1 (65% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Ptx1 (65% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Ptx1 (65% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Ptx1 (65% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Ptx1 (65% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Ptx1 (65% AA Identity, Drosophila melanogaster)

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": 271, "endStyle": "curved", "aliStart": 215, "text": "HD", "colour": "#228B22", "aliEnd": 271, "start": 215, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 271, "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": 215, "scoreName": "E-value", "accession": "PF00046.27", "start": 215, "score": 3.6e-25, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 271}}, {"startStyle": "straight", "end": 405, "endStyle": "straight", "aliStart": 387, "text": "OAR", "colour": "#9999ff", "aliEnd": 405, "start": 387, "href": "http://pfam.xfam.org/family/PF03826.15", "type": "pfama", "display": "true", "metadata": {"end": 405, "description": NaN, "database": "PfamA", "aliStart": 387, "scoreName": "E-value", "accession": "PF03826.15", "start": 387, "score": 5.8e-10, "identifier": "OAR domain", "type": "DBD", "aliEnd": 405}}], "length": 412}

TF Info Page for ALX4 (Homeodomain)