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 3 [Source:HGNC Symbol;Acc:HGNC:449]

Entrez Summary

Ensembl ID:

ENSG00000156150

External Link:

CisBP

Interpro

IPR001356; IPR009057; IPR017970; ;

Protein Domain:

ENSP00000358807

Domain:

Protein: ENSP00000358807	DBD: Homeodomain	Other:

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	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
PBM	Berger08		Inferred - Alx3 (100% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - ALX4 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX4 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX4 (92% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Alx4 (92% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - ALX4 (92% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ALX1 (89% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX1 (89% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Alx1 (89% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Alx1 (89% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - ALX1 (89% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - ALX1 (89% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (80% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ARX (80% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ARX (80% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Arx (80% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Arx (80% AA Identity, Rattus norvegicus)
PBM	Barrera2016		Inferred - ARX (78% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (78% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (78% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (78% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (78% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - Pph13 (78% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Pph13 (78% AA Identity, Drosophila melanogaster)
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)
B1H	JASPAR		Inferred - al (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - al (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG2808 (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - DRGX (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - DRGX (75% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - hbn (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - hbn (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - PHOX2A (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2A (75% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Phox2a (75% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - PHOX2B (75% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PHOX2B (75% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PHOX2B (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2B (75% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2B (75% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Phox2b (75% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Drgx (75% AA Identity, Rattus norvegicus)
Misc	HOMER		Inferred - Phox2a (75% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - PHOX2B (73% AA Identity, Homo sapiens)
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)
HT-SELEX	Yin2017		Inferred - DMBX1 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - DMBX1 (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Dmbx1 (71% AA Identity, Mus musculus)
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)
HT-SELEX	Yin2017		Inferred - RAX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RAX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RAX (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Rax (71% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - Rx (71% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rx (71% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rx (71% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - si:dkey-43p13.5 (71% AA Identity, Danio rerio)
PBM	Barrera2016		Inferred - VSX1 (71% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - VSX1 (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Vsx1 (71% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - VSX2 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - VSX2 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX2 (71% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Rax (71% AA Identity, Rattus norvegicus)
Transfac	Transfac	License required	Inferred - VSX2 (71% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - VSX2 (71% AA Identity, Homo sapiens)
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)
B1H	JASPAR		Inferred - PHDP (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - PHDP (70% AA Identity, Drosophila melanogaster)
PBM	Berger08		Inferred - Prrx1 (70% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - VSX1 (70% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - vsx2 (70% AA Identity, Danio rerio)
Transfac	Transfac	License required	Inferred - PRRX1 (70% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Prrx1 (70% AA Identity, Rattus norvegicus)
Misc	HocoMoco		Inferred - PRRX1 (70% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - CG32532 (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG32532 (68% AA Identity, Drosophila melanogaster)
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)
PBM	Berger08		Inferred - Otp (68% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - PRRX2 (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PRRX2 (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PRRX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Prrx2 (68% AA Identity, Mus musculus)
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)
Transfac	Transfac	License required	Inferred - PRRX2 (68% AA Identity, Homo sapiens)
SELEX	JASPAR		Inferred - Prrx2 (68% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Prrx2 (68% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - PRRX2 (68% AA Identity, Sus scrofa)
Misc	HocoMoco		Inferred - CRX (68% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Crx (68% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - PRRX2 (68% 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 - 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)
PBM	Barrera2016		Inferred - PROP1 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - PROP1 (66% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PROP1 (66% AA Identity, Sus scrofa)
Misc	HocoMoco		Inferred - PROP1 (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 ALX3 (Homeodomain)