TF Info Page for ALX3 (Homeodomain)

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 This gene encodes a nuclear protein with a homeobox DNA-binding domain that functions as a transcriptional regulator involved in cell-type differentiation and development. Preferential methylation of this gene's promoter is associated with advanced-stage neuroblastoma tumors. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000156150
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; ;
Protein Domain: ENSP00000358807
Domain:
Protein: ENSP00000358807DBD: HomeodomainOther:

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-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
PBMBerger08Inferred - Alx3 (100% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - ALX4 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (92% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx4 (92% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - ALX4 (92% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ALX1 (89% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX1 (89% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx1 (89% AA Identity, Mus musculus)
PBMBerger08Inferred - Alx1 (89% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - ALX1 (89% AA Identity, Homo sapiens)
MiscHocoMocoInferred - ALX1 (89% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (80% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ARX (80% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ARX (80% AA Identity, Homo sapiens)
PBMBerger08Inferred - Arx (80% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Arx (80% AA Identity, Rattus norvegicus)
PBMBarrera2016Inferred - ARX (78% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (78% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (78% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (78% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (78% AA Identity, Homo sapiens)
B1HJASPARInferred - Pph13 (78% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Pph13 (78% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - CG11294 (77% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (77% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (77% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - al (75% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - al (75% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG2808 (75% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - DRGX (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DRGX (75% AA Identity, Homo sapiens)
B1HJASPARInferred - hbn (75% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - hbn (75% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - PHOX2A (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2A (75% AA Identity, Homo sapiens)
PBMBerger08Inferred - Phox2a (75% AA Identity, Mus musculus)
PBMBarrera2016Inferred - PHOX2B (75% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PHOX2B (75% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PHOX2B (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2B (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2B (75% AA Identity, Homo sapiens)
PBMBerger08Inferred - Phox2b (75% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Drgx (75% AA Identity, Rattus norvegicus)
MiscHOMERInferred - Phox2a (75% AA Identity, Mus musculus)
PBMBarrera2016Inferred - PHOX2B (73% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - UNCX (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - UNCX (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Uncx (73% AA Identity, Mus musculus)
PBMZoo_01Inferred - uncx4.1 (73% AA Identity, Tetraodon nigroviridis)
HT-SELEXYin2017Inferred - DMBX1 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DMBX1 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Dmbx1 (71% AA Identity, Mus musculus)
PBMBarrera2016Inferred - ISX (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ISX (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ISX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RAX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Rax (71% AA Identity, Mus musculus)
B1HJASPARInferred - Rx (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (71% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - si:dkey-43p13.5 (71% AA Identity, Danio rerio)
PBMBarrera2016Inferred - VSX1 (71% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - VSX1 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Vsx1 (71% AA Identity, Mus musculus)
PBMBarrera2016Inferred - VSX2 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Rax (71% AA Identity, Rattus norvegicus)
TransfacTransfacLicense requiredInferred - VSX2 (71% AA Identity, Homo sapiens)
MiscHocoMocoInferred - VSX2 (71% AA Identity, Homo sapiens)
B1HJASPARInferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
SMiLE-seqIsakova2017Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Gsc (70% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - ISX (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Isx (70% AA Identity, Mus musculus)
B1HJASPARInferred - PHDP (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - PHDP (70% AA Identity, Drosophila melanogaster)
PBMBerger08Inferred - Prrx1 (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - VSX1 (70% AA Identity, Homo sapiens)
PBMZoo_01Inferred - vsx2 (70% AA Identity, Danio rerio)
TransfacTransfacLicense requiredInferred - PRRX1 (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Prrx1 (70% AA Identity, Rattus norvegicus)
MiscHocoMocoInferred - PRRX1 (70% AA Identity, Homo sapiens)
B1HJASPARInferred - CG32532 (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG32532 (68% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - CRX (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - CRX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - CRX (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Crx (68% AA Identity, Mus musculus)
PBMBerger08Inferred - Otp (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - PRRX2 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PRRX2 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PRRX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Prrx2 (68% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - CRX (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - CRX (68% AA Identity, Homo sapiens)
ChIP-seqJASPARInferred - Crx (68% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - PRRX2 (68% AA Identity, Homo sapiens)
SELEXJASPARInferred - Prrx2 (68% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Prrx2 (68% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - PRRX2 (68% AA Identity, Sus scrofa)
MiscHocoMocoInferred - CRX (68% AA Identity, Homo sapiens)
MiscHOMERInferred - Crx (68% AA Identity, Mus musculus)
MiscHocoMocoInferred - PRRX2 (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ESX1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ESX1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ESX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ESX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ESX1 (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - PROP1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
B1HJASPARInferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - PROP1 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PROP1 (66% AA Identity, Sus scrofa)
MiscHocoMocoInferred - 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