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	TBA
Ensembl ID:	ENSG00000052850
External Link:
Interpro	IPR001356; IPR003654; IPR009057; IPR017970;
Protein 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

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TF Info Page for ALX4 (Homeodomain)