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
  • CDX2 5

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 Sirenomelia and Sacral Defect With Anterior Meningocele. Among its related pathways are Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers and Preimplantation Embryo. 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

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 Pubs

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 257.1 -1.2 -1200 23.4 ZNF600 SSRP1 KLF9 CEBPA ZBTB10 YY1 MXD4 FOXA1 ETS1 TRIM22 CDX2 URAD PLUT PDX1 GSX1 RN7SL272P LNX2 FLT3 HSALNG0095985-001 LOC105370132
GH13J027988 Promoter 0.6 EPDnew 250.4 -19.4 -19376 0.1 CEBPA CEBPG HLF CEBPB HSALNG0095986 RN7SL272P URAD lnc-URAD-1 CDX2 LOC105370132 HSALNG0095985-001 FLT3
GH13J027952 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 38.1 +13.9 13868 6 ZNF654 ZNF207 YY1 REST ZNF592 TARDBP ZNF341 CTCF FOXA2 CTBP1 HSALNG0095981 LINC00543 lnc-CDX2-1 CDX2 PLUT PDX1 GSX1 URAD HSALNG0095983 HSALNG0095979
GH13J027821 Enhancer 1.1 VISTA UCNEbase ENCODE 11.3 +147.0 147016 2.2 EZH2 HDAC2 NANOG MTA2 USF1 KDM1A HSALNG0095971 GSX1 CDX2 RNU6-63P RF00026-270 RNU6-73P PDX1 PLUT
GH13J027928 Enhancer 0.5 ENCODE dbSUPER 12.5 +41.1 41118 0 CBX8 EZH2 CDX2 GSX1 PDX1 PLUT piR-60985-029
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CDX2

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

Latest Assembly
chr13:27,960,918-27,969,337
(GRCh38/hg38)
Size:
8,420 bases
Orientation:
Minus strand

Previous Assembly
chr13:28,535,055-28,543,452
(GRCh37/hg19 by Entrez Gene)
Size:
8,398 bases
Orientation:
Minus strand

chr13:28,536,274-28,545,276
(GRCh37/hg19 by Ensembl)
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

Antibodies for research

  • 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

Protein Domains for CDX2 Gene

InterPro:
Blocks:
  • Lambda and other repressor helix-turn-helix signature
  • Caudal-like activation region

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:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 15677472
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
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:
Targeted motifs for CDX2 Gene
HOMER Transcription Factor Regulatory Elements motif CDX2
  • Consensus sequence: GTCATAAAAN Submotif: canonical Cell Type: mES GEO ID: GSE14586

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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 3
plasma membrane 2
cytoskeleton 2
mitochondrion 2
cytosol 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 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:0000785 chromatin ISA --
GO:0000794 condensed nuclear chromosome IEA --
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA --
GO:0017053 transcriptional repressor 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

1 BioSystems pathway for CDX2 Gene
1 KEGG pathway for CDX2 Gene
2 GeneGo (Thomson Reuters) pathways for CDX2 Gene
  • Cell adhesion Tight junctions
  • Transcription_Role of VDR in regulation of genes involved in osteoporosis
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 IEA,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 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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

Expression for CDX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CDX2

SOURCE GeneReport for Unigene cluster for CDX2 Gene:

Hs.174249

Evidence on tissue expression from TISSUES for CDX2 Gene

  • Intestine(4.7)
  • Blood(4.4)
  • Stomach(2.6)
  • Liver(2.5)
  • Lung(2.3)
  • Pancreas(2.2)
  • Nervous system(2.2)
  • Lymph node(2.2)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with CDX2: view

Primer products for research

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 30
  • 94 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia CDX2 29 30
  • 90.2 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CDX2 29 30
  • 89 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Cdx2 29 16 30
  • 87.03 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cdx2 29
  • 86.67 (n)
Oppossum
(Monodelphis domestica)
Mammalia CDX2 30
  • 83 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CDX2 30
  • 78 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CDX2 29 30
  • 79.44 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CDX2 30
  • 77 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cdx2 29
  • 63.41 (n)
African clawed frog
(Xenopus laevis)
Amphibia xCAD2 29
Zebrafish
(Danio rerio)
Actinopterygii cdx1a 30
  • 60 (a)
ManyToMany
-- 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1956 29
Worm
(Caenorhabditis elegans)
Secernentea pal-1 30
  • 21 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 21 (a)
OneToMany
Species where no ortholog for CDX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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
Alliance of Genome Resources:
Additional Orthologs for CDX2

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CDX2 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
768606 Benign: not provided 27,963,180(-) G/.
NM_001265.6(CDX2):c.877= (p.Pro293=)
NO_SEQUENCE_ALTERATION,THREE_PRIME_UTR
rs1593181774 Likely Pathogenic: Sirenomelia 27,963,117(-) A/G
NM_001265.6(CDX2):c.940T>C (p.Ter314Arg)
STOP_LOST,THREE_PRIME_UTR
rs374108002 Likely Benign: not provided 27,963,375(-) A/T
NM_001265.6(CDX2):c.688-6T>A
rs1805107 -- p.Pro293Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CDX2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
Leiden Open Variation Database (LOVD)
CDX2

SNP Genotyping and Copy Number Assays for research

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

(124) MalaCards diseases for CDX2 Gene - From: CVR, COP, and GCD

Disorder Aliases PubMed IDs
sirenomelia
  • fused legs and feet
sacral defect with anterior meningocele
  • sdam
pseudomyxoma peritonei
  • mucinous ascites
ampulla of vater adenocarcinoma
  • adenocarcinoma of ampulla of vater
ovarian mucinous adenocarcinoma
  • mucinous carcinoma of ovary
- 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

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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 22 40
  2. Cloning and chromosome assignment of the human CDX2 gene. (PMID: 9459001) Drummond F … Edwards YH (Annals of human genetics 1997) 3 4 22
  3. 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 22
  4. 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
  5. Overexpression of Cdx2 inhibits progression of gastric cancer in vitro. (PMID: 20043087) Xie Y … Xiao Q (International journal of oncology 2010) 3 22

Products for CDX2 Gene

  • Addgene plasmids for CDX2

Sources for CDX2 Gene