This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded protein is a major regulator of intestine-specific genes involved in cell growth an differentiation. This protein also plays a role in early embryonic development of the intestinal tract. Aberrant expression of this gene is associated with intestinal inflammation and tumorigenesis... See more...

Aliases for CDX2 Gene

Aliases for CDX2 Gene

  • Caudal Type Homeobox 2 2 3 5
  • Caudal-Type Homeobox Protein 2 3 4
  • Homeobox Protein CDX-2 3 4
  • CDX-3 3 4
  • CDX3 3 4
  • Caudal Type Homeo Box Transcription Factor 2 2
  • Caudal Type Homeobox Transcription Factor 2 3
  • Homeobox Protein MiniCDX2 3
  • CDX2/AS 3

External Ids for CDX2 Gene

Previous HGNC Symbols for CDX2 Gene

  • CDX3

Previous GeneCards Identifiers for CDX2 Gene

  • GC13M026516
  • GC13M022516
  • GC13M027466
  • GC13M026334
  • GC13M027434
  • GC13M028536
  • GC13M009356

Summaries for CDX2 Gene

Entrez Gene Summary for CDX2 Gene

  • This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded protein is a major regulator of intestine-specific genes involved in cell growth an differentiation. This protein also plays a role in early embryonic development of the intestinal tract. Aberrant expression of this gene is associated with intestinal inflammation and tumorigenesis. [provided by RefSeq, Jan 2012]

CIViC Summary for CDX2 Gene

GeneCards Summary for CDX2 Gene

CDX2 (Caudal Type Homeobox 2) is a Protein Coding gene. Diseases associated with CDX2 include Ampulla Of Vater Adenocarcinoma and Ovarian Mucinous Adenocarcinoma. Among its related pathways are Incretin synthesis, secretion, and inactivation and Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and transcription corepressor activity. An important paralog of this gene is CDX1.

UniProtKB/Swiss-Prot Summary for CDX2 Gene

  • Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine. Binds preferentially to methylated DNA (PubMed:28473536).

Gene Wiki entry for CDX2 Gene

Additional gene information for CDX2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CDX2 Gene

Genomics for CDX2 Gene

GeneHancer (GH) Regulatory Elements for CDX2 Gene

Promoters and enhancers for CDX2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J027958 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 757 +0.6 602 23.4 CTCF ZBTB6 FOXA1 MLX RBPJ NR2F1 NR2F6 MIXL1 MYC HLF CDX2 URAD SNORA27 PAN3 PLUT PDX1 GSX1 RN7SL272P POLR1D LNX2
GH13J027988 Promoter 0.6 EPDnew 750.4 -17.6 -17574 0.1 HLF CEBPG CEBPA RN7SL272P RF00017-1374 URAD lnc-URAD-1 CDX2
GH13J027952 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 38.1 +15.7 15670 6 CTCF GATA3 TCF7L2 ZNF217 MYC MAX RAD21 POLR2A NKRF SP1 LINC00543 lnc-CDX2-1 CDX2 PLUT PDX1 GSX1 URAD lnc-CDX2-3
GH13J027821 Enhancer 1.1 VISTA UCNEbase ENCODE 11.3 +148.8 148818 2.2 HDAC2 MTA2 USF1 EZH2 NANOG GSX1 CDX2 RNU6-63P RF00026-281 RNU6-73P piR-35674-123 PLUT
GH13J027850 Enhancer 0.7 Ensembl ENCODE 11.2 +118.9 118906 3.1 MYC MAX CTBP1 CEBPB TCF7L2 FOS GSX1 CDX2 PDX1 PLUT USP12-AS2 AB330789-010 piR-48209-147
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDX2 gene promoter:
  • AP-1
  • ATF-2
  • c-Fos
  • c-Jun
  • COUP
  • COUP-TF
  • COUP-TF1
  • HNF-4alpha1

Genomic Locations for CDX2 Gene

Genomic Locations for CDX2 Gene
chr13:27,960,057-27,971,139
(GRCh38/hg38)
Size:
11,083 bases
Orientation:
Minus strand
chr13:28,536,274-28,545,276
(GRCh37/hg19)
Size:
9,003 bases
Orientation:
Minus strand

Genomic View for CDX2 Gene

Genes around CDX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDX2 Gene

Proteins for CDX2 Gene

  • Protein details for CDX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q99626-CDX2_HUMAN
    Recommended name:
    Homeobox protein CDX-2
    Protein Accession:
    Q99626
    Secondary Accessions:
    • O00503
    • Q5VTU7
    • Q969L8
    • Q9UD92

    Protein attributes for CDX2 Gene

    Size:
    313 amino acids
    Molecular mass:
    33520 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for CDX2 Gene

neXtProt entry for CDX2 Gene

Post-translational modifications for CDX2 Gene

  • Phosphorylation of Ser-60 mediates the transactivation capacity.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CDX2 Gene

Antibody Products

  • Abcam antibodies for CDX2

No data available for DME Specific Peptides for CDX2 Gene

Domains & Families for CDX2 Gene

Gene Families for CDX2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for CDX2 Gene

GenScript: Design optimal peptide antigens:
  • Caudal-type homeobox protein 2 (CDX2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q99626

UniProtKB/Swiss-Prot:

CDX2_HUMAN :
  • Belongs to the Caudal homeobox family.
Family:
  • Belongs to the Caudal homeobox family.
genes like me logo Genes that share domains with CDX2: view

Function for CDX2 Gene

Molecular function for CDX2 Gene

UniProtKB/Swiss-Prot Function:
Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine. Binds preferentially to methylated DNA (PubMed:28473536).
GENATLAS Biochemistry:
Drosophila caudal family member 2,murine Cdx2 homolog,homeo domain encoding gene,expressed in the intestine,involved in the proliferation and differentiation of intestinal epithelial cells,mutated in colorectal carcinoma with normal APC/CTNNB signaling pathway,fused with ETV6 in acute myeloid leukemia,

Phenotypes From GWAS Catalog for CDX2 Gene

Gene Ontology (GO) - Molecular Function for CDX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IDA 15677472
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 15677472
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with CDX2: view
genes like me logo Genes that share phenotypes with CDX2: view

Animal Models for CDX2 Gene

MGI Knock Outs for CDX2:

Animal Model Products

CRISPR Products

Targeted motifs for CDX2 Gene
HOMER Transcription Factor Regulatory Elements motif CDX2
  • Consensus sequence: GTCATAAAAN Submotif: canonical Cell Type: mES GEO ID: GSE14586

Clone Products

  • Addgene plasmids for CDX2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for CDX2 Gene

Localization for CDX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDX2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CDX2 gene
Compartment Confidence
nucleus 5
extracellular 2
cytoskeleton 2
plasma membrane 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CDX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000794 condensed nuclear chromosome IEA --
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA --
GO:0017053 transcriptional repressor complex IEA --
GO:0032991 protein-containing complex IEA --
genes like me logo Genes that share ontologies with CDX2: view

Pathways & Interactions for CDX2 Gene

genes like me logo Genes that share pathways with CDX2: view

Pathways by source for CDX2 Gene

2 Qiagen pathways for CDX2 Gene
  • Oct4 in Mammalian ESC Pluripotency
  • Transcriptional Regulatory Network in Embryonic Stem Cell
1 Cell Signaling Technology pathway for CDX2 Gene

SIGNOR curated interactions for CDX2 Gene

Activates:
Is activated by:
Is inactivated by:
Other effect:

Gene Ontology (GO) - Biological Process for CDX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 15677472
GO:0001568 blood vessel development IEA --
GO:0001824 blastocyst development IEA --
GO:0001829 trophectodermal cell differentiation IEA --
GO:0001890 placenta development IEA --
genes like me logo Genes that share ontologies with CDX2: view

Drugs & Compounds for CDX2 Gene

(8) Drugs for CDX2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(7) Additional Compounds for CDX2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CDX2: view

Transcripts for CDX2 Gene

mRNA/cDNA for CDX2 Gene

(2) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(35) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for CDX2

Alternative Splicing Database (ASD) splice patterns (SP) for CDX2 Gene

No ASD Table

Relevant External Links for CDX2 Gene

GeneLoc Exon Structure for
CDX2
ECgene alternative splicing isoforms for
CDX2

Expression for CDX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDX2 Gene

mRNA differential expression in normal tissues according to GTEx for CDX2 Gene

This gene is overexpressed in Colon - Transverse (x37.2) and Small Intestine - Terminal Ileum (x12.6).

NURSA nuclear receptor signaling pathways regulating expression of CDX2 Gene:

CDX2

SOURCE GeneReport for Unigene cluster for CDX2 Gene:

Hs.174249

Evidence on tissue expression from TISSUES for CDX2 Gene

  • Intestine(4.7)
  • Blood(4.2)
  • Stomach(2.6)
  • Liver(2.1)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with CDX2: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDX2 Gene

Orthologs for CDX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CDX2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CDX2 33
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CDX2 33 32
  • 90.2 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CDX2 33 32
  • 89 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Cdx2 17 33 32
  • 87.03 (n)
rat
(Rattus norvegicus)
Mammalia Cdx2 32
  • 86.67 (n)
oppossum
(Monodelphis domestica)
Mammalia CDX2 33
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CDX2 33
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves CDX2 33 32
  • 79.44 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CDX2 33
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cdx2 32
  • 63.41 (n)
African clawed frog
(Xenopus laevis)
Amphibia xCAD2 32
zebrafish
(Danio rerio)
Actinopterygii cdx1a 33
  • 60 (a)
ManyToMany
-- 32
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1956 32
worm
(Caenorhabditis elegans)
Secernentea pal-1 33
  • 21 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 21 (a)
OneToMany
Species where no ortholog for CDX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CDX2 Gene

ENSEMBL:
Gene Tree for CDX2 (if available)
TreeFam:
Gene Tree for CDX2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CDX2: view image

Paralogs for CDX2 Gene

Paralogs for CDX2 Gene

(2) SIMAP similar genes for CDX2 Gene using alignment to 1 proteins:

  • CDX2_HUMAN
genes like me logo Genes that share paralogs with CDX2: view

Variants for CDX2 Gene

Sequence variations from dbSNP and Humsavar for CDX2 Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs1000356367 -- 27,960,670(-) T/C downstream_transcript_variant
rs1000662860 -- 27,965,609(-) C/T intron_variant
rs1000803534 -- 27,965,524(-) G/A intron_variant
rs1000886841 -- 27,960,640(-) G/C downstream_transcript_variant
rs1001266346 -- 27,971,317(-) C/A upstream_transcript_variant

Variation tolerance for CDX2 Gene

Residual Variation Intolerance Score: 52.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.61; 56.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDX2 Gene

Human Gene Mutation Database (HGMD)
CDX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDX2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for CDX2 Gene

Disorders for CDX2 Gene

MalaCards: The human disease database

(104) MalaCards diseases for CDX2 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
ampulla of vater adenocarcinoma
  • adenocarcinoma of ampulla of vater
ovarian mucinous adenocarcinoma
  • mucinous carcinoma of ovary
ampulla of vater cancer
  • malignant tumour of ampulla of vater
pseudomyxoma peritonei
  • mucinous ascites
chronic cholangitis
- elite association - COSMIC cancer census association via MalaCards
Search CDX2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDX2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CDX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDX2 Gene

Publications for CDX2 Gene

  1. CDX2 polymorphisms, RNA expression, and risk of colorectal cancer. (PMID: 15994917) Rozek LS … Gruber SB (Cancer research 2005) 3 23 43 56
  2. Molecular cloning, sequencing and expression of the mRNA encoding human Cdx1 and Cdx2 homeobox. Down-regulation of Cdx1 and Cdx2 mRNA expression during colorectal carcinogenesis. (PMID: 9036867) Mallo GV … Iovanna JL (International journal of cancer 1997) 3 4 23 56
  3. Impact of cytosine methylation on DNA binding specificities of human transcription factors. (PMID: 28473536) Yin Y … Taipale J (Science (New York, N.Y.) 2017) 3 4 56
  4. Overexpression of Cdx2 inhibits progression of gastric cancer in vitro. (PMID: 20043087) Xie Y … Xiao Q (International journal of oncology 2010) 3 23 56
  5. CDX2 expression in the intestinal-type gastric epithelial neoplasia: frequency and significance. (PMID: 19820687) Park DY … Lauwers GY (Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2010) 3 23 56

Products for CDX2 Gene

Sources for CDX2 Gene