TF Info Page for ISX (Homeodomain)

Conclusion

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

Description

Description: intestine specific homeobox [Source:HGNC Symbol;Acc:HGNC:28084]
Entrez Summary Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain. This gene is a member of the RAXLX homeobox gene family. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000175329
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; ;
Protein Domain: ENSP00000311492
Protein Domain: ENSP00000386037
Domain:
Protein: ENSP00000311492DBD: HomeodomainOther:
Protein: ENSP00000386037DBD: 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.
b
CisBP considers it as a TF? Yes
TFclass considers it as a TF? Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding" Yes
GO-Info GO:0001227
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
PBMBarrera2016Direct
PBMBarrera2016Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
PBMBerger08Inferred - Isx (91% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - ALX1 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX1 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx1 (71% AA Identity, Mus musculus)
PBMBerger08Inferred - Alx1 (71% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx3 (71% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - ALX4 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx4 (71% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - ALX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - ALX4 (71% AA Identity, Homo sapiens)
MiscHocoMocoInferred - ALX1 (71% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - CG2808 (70% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - ENSCING00000016045 (70% AA Identity, Ciona intestinalis)
B1HJASPARInferred - Pph13 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Pph13 (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - al (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - al (68% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - ARX (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ARX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ARX (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Arx (68% AA Identity, Mus musculus)
B1HJASPARInferred - CG11294 (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (68% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - DRGX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DRGX (68% AA Identity, Homo sapiens)
B1HJASPARInferred - hbn (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - hbn (68% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - RAX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Rax (68% AA Identity, Mus musculus)
B1HJASPARInferred - Rx (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (68% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - Arx (68% AA Identity, Rattus norvegicus)
TransfacTransfacLicense requiredInferred - Drgx (68% AA Identity, Rattus norvegicus)
TransfacTransfacLicense requiredInferred - Rax (68% AA Identity, Rattus norvegicus)
PBMBarrera2016Inferred - ARX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (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