TF Info Page for CDX1 (Homeodomain)

Conclusion

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

Description

Description: caudal type homeobox 1 [Source:HGNC Symbol;Acc:HGNC:1805]
Entrez Summary This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded DNA-binding protein regulates intestine-specific gene expression and enterocyte differentiation. It has been shown to induce expression of the intestinal alkaline phosphatase gene, and inhibit beta-catenin/T-cell factor transcriptional activity. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000113722
External Link: CisBP
Interpro IPR000047; IPR001356; IPR006820; IPR009057; IPR017970; IPR020479;
Protein Domain: ENSP00000231656
Protein Domain: ENSP00000477928
Domain:
Protein: ENSP00000231656DBD: HomeodomainOther: Caudal_act
Protein: ENSP00000477928DBD: HomeodomainOther: Caudal_act

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:15677472 15774940 7585967 12954759
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" Yes
GO-Info GO:0001205
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involv
IDA - PMID:15774940
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-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
PBMBerger08Inferred - Cdx1 (100% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - CDX-A (96% AA Identity, Gallus gallus)
TransfacTransfacLicense requiredInferred - CDX-A (96% AA Identity, Gallus gallus)
HT-SELEXYin2017Inferred - CDX2 (94% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - CDX2 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - CDX2 (94% AA Identity, Homo sapiens)
PBMBerger08Inferred - Cdx2 (94% AA Identity, Mus musculus)
ChIP-seqJASPARInferred - CDX2 (94% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - CDX2 (94% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - CDX2 (94% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - CDX2 (94% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - CDX2 (94% AA Identity, Homo sapiens)
MiscHocoMocoInferred - CDX2 (94% AA Identity, Homo sapiens)
MiscHOMERInferred - Cdx2 (94% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - CDX4 (89% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - CDX4 (89% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - CDX4 (89% AA Identity, Homo sapiens)
PBMZoo_01Inferred - Q70LF3_ARTSF (89% AA Identity, Artemia franciscana)
HT-SELEXNitta2015Inferred - cad (85% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - cad (85% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - cad (85% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - cad (85% AA Identity, Drosophila melanogaster)
ChIP-chipJASPARInferred - cad (85% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - cad (85% AA Identity, Drosophila melanogaster)
MiscHOMERInferred - cad (85% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - cad (85% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Q9GP48_9TURB (73% AA Identity, Discocelis tigrina)
PBMZoo_01Inferred - pal-1 (68% AA Identity, Caenorhabditis elegans)

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