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] See more...

Aliases for CDX1 Gene

Aliases for CDX1 Gene

  • Caudal Type Homeobox 1 2 3 5
  • Caudal Type Homeo Box Transcription Factor 1 2 3
  • Caudal-Type Homeobox Protein 1 3 4
  • Homeobox Protein CDX-1 3 4
  • Caudal Type Homeobox Transcription Factor 1 3
  • Caudal-Type Homeobox Protein CDX1 3
  • CDX1 5

External Ids for CDX1 Gene

Previous GeneCards Identifiers for CDX1 Gene

  • GC05P149616
  • GC05P150133
  • GC05P149574
  • GC05P149526
  • GC05P144694

Summaries for CDX1 Gene

Entrez Gene Summary for CDX1 Gene

  • 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]

GeneCards Summary for CDX1 Gene

CDX1 (Caudal Type Homeobox 1) is a Protein Coding gene. Diseases associated with CDX1 include Mesenchymal Chondrosarcoma and Esophagus Melanoma. Among its related pathways are Regulation of Wnt-mediated beta catenin signaling and target gene transcription and Cytoskeleton remodeling Regulation of actin cytoskeleton by Rho GTPases. Gene Ontology (GO) annotations related to this gene include RNA polymerase II distal enhancer sequence-specific DNA binding and distal enhancer DNA-binding transcription activator activity, RNA polymerase II-specific. An important paralog of this gene is CDX2.

UniProtKB/Swiss-Prot Summary for CDX1 Gene

  • Plays a role in transcriptional regulation (PubMed:24623306). Involved in activated KRAS-mediated transcriptional activation of PRKD1 in colorectal cancer (CRC) cells (PubMed:24623306). Binds to the PRKD1 promoter in colorectal cancer (CRC) cells (PubMed:24623306). Could play a role in the terminal differentiation of the intestine. Binds preferentially to methylated DNA (PubMed:28473536).

Gene Wiki entry for CDX1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CDX1 Gene

Genomics for CDX1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CDX1 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
GH05J150149 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 262.7 -6.8 -6838 19.9 BCL11A MNT IKZF1 CTCF BHLHE40 ZEB1 ZIC2 ZNF610 REST GABPA CDX1 PDGFRB lnc-PDGFRB-5 TCOF1 RPL7P1 ZNF300P1 ZNF300 HMGXB3 SLC6A7 SYNPO
GH05J150129 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 24.3 -27.3 -27348 19.8 ZBTB10 CEBPA NR2C1 MNT DEK IKZF1 ZNF217 BRCA1 CTCF BHLHE40 HSALNG0045803 CDX1 SLC6A7 CSF1R TCOF1 CAMK2A ZNF300P1 PDGFRB RPS14 SYNPO
GH05J150316 Enhancer 1.6 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.4 +153.4 153368 8 ZSCAN16 FEZF1 CEBPA BHLHE40 ZEB1 HOMEZ CEBPB FOXA2 ZNF639 MAX lnc-CAMK2A-1 PDGFRB CAMK2A TCOF1 SLC6A7 CDX1 CSF1R SYNPO ARSI
GH05J150065 Promoter/Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 10.6 -100.4 -100412 2.6 ZIC2 VEZF1 EBF1 FOSL1 MAFK MYC MAX JUND ZFP36 EP300 lnc-PDGFRB-2 HMGXB3 TIGD6 CSF1R PDGFRB CDX1 ENSG00000200334 PDE6A TCOF1 CAMK2A
GH05J150291 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.2 +127.6 127623 5.6 MNT IKZF1 ZFP64 ZIC2 ZNF513 ARNT ZNF395 MAX VEZF1 NBN TCOF1 HMGXB3 CDX1 PDGFRB ARSI CAMK2A lnc-CAMK2A-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDX1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CDX1

Top Transcription factor binding sites by QIAGEN in the CDX1 gene promoter:
  • AML1a

Genomic Locations for CDX1 Gene

Latest Assembly
chr5:150,166,778-150,184,558
(GRCh38/hg38)
Size:
17,781 bases
Orientation:
Plus strand

Previous Assembly
chr5:149,546,341-149,564,121
(GRCh37/hg19 by Entrez Gene)
Size:
17,781 bases
Orientation:
Plus strand

chr5:149,546,358-149,564,120
(GRCh37/hg19 by Ensembl)
Size:
17,763 bases
Orientation:
Plus strand

Genomic View for CDX1 Gene

Genes around CDX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDX1 Gene

Proteins for CDX1 Gene

  • Protein details for CDX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P47902-CDX1_HUMAN
    Recommended name:
    Homeobox protein CDX-1
    Protein Accession:
    P47902
    Secondary Accessions:
    • Q4VAU4
    • Q9NYK8

    Protein attributes for CDX1 Gene

    Size:
    265 amino acids
    Molecular mass:
    28138 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for CDX1 Gene

    Alternative splice isoforms for CDX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CDX1 Gene

Post-translational modifications for CDX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CDX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for CDX1

No data available for DME Specific Peptides for CDX1 Gene

Domains & Families for CDX1 Gene

Gene Families for CDX1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for CDX1 Gene

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

Suggested Antigen Peptide Sequences for CDX1 Gene

GenScript: Design optimal peptide antigens:
  • Caudal-type homeobox protein 1 (CDX1_HUMAN)
  • CDX1 protein (Q4VAU3_HUMAN)
  • CDX1 protein (Q4VAU5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P47902

UniProtKB/Swiss-Prot:

CDX1_HUMAN :
  • Belongs to the Caudal homeobox family.
Family:
  • Belongs to the Caudal homeobox family.
genes like me logo Genes that share domains with CDX1: view

Function for CDX1 Gene

Molecular function for CDX1 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in transcriptional regulation (PubMed:24623306). Involved in activated KRAS-mediated transcriptional activation of PRKD1 in colorectal cancer (CRC) cells (PubMed:24623306). Binds to the PRKD1 promoter in colorectal cancer (CRC) cells (PubMed:24623306). Could play a role in the terminal differentiation of the intestine. Binds preferentially to methylated DNA (PubMed:28473536).
GENATLAS Biochemistry:
Drosophila caudal family member 1,murine Cdx1 homolog,homeo domain encoding gene,transcriptional regulator of insulin gene

Phenotypes From GWAS Catalog for CDX1 Gene

Gene Ontology (GO) - Molecular Function for CDX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IDA 24623306
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 15774940
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific IEA,ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 15774940
genes like me logo Genes that share ontologies with CDX1: view
genes like me logo Genes that share phenotypes with CDX1: view

Animal Models for CDX1 Gene

MGI Knock Outs for CDX1:
  • Cdx1 Cdx1<tm4.1(Cdx2)Lhn>
  • Cdx1 Cdx1<tm1Pgr>
  • Cdx1 Cdx1<tm1Lhn>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDX1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CDX1 Gene

Localization for CDX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDX1 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 CDX1 gene
Compartment Confidence
nucleus 5
extracellular 2
cytoskeleton 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for CDX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IEA,IBA 21873635
genes like me logo Genes that share ontologies with CDX1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDX1 Gene

Pathways & Interactions for CDX1 Gene

genes like me logo Genes that share pathways with CDX1: view

Pathways by source for CDX1 Gene

1 GeneGo (Thomson Reuters) pathway for CDX1 Gene
  • Cell adhesion Tight junctions

SIGNOR curated interactions for CDX1 Gene

Activates:

Gene Ontology (GO) - Biological Process for CDX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA,IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0007389 pattern specification process IEA --
GO:0009790 embryo development IBA 21873635
genes like me logo Genes that share ontologies with CDX1: view

Drugs & Compounds for CDX1 Gene

(3) Additional Compounds for CDX1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CDX1: view

Transcripts for CDX1 Gene

mRNA/cDNA for CDX1 Gene

1 REFSEQ mRNAs :
8 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 CDX1

Alternative Splicing Database (ASD) splice patterns (SP) for CDX1 Gene

No ASD Table

Relevant External Links for CDX1 Gene

GeneLoc Exon Structure for
CDX1

Expression for CDX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CDX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CDX1 Gene

This gene is overexpressed in Colon - Transverse (x35.9) and Small Intestine - Terminal Ileum (x13.1).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CDX1

SOURCE GeneReport for Unigene cluster for CDX1 Gene:

Hs.1545

mRNA Expression by UniProt/SwissProt for CDX1 Gene:

P47902-CDX1_HUMAN
Tissue specificity: Intestinal epithelium.

Evidence on tissue expression from TISSUES for CDX1 Gene

  • Intestine(4.6)
  • Stomach(2)
genes like me logo Genes that share expression patterns with CDX1: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDX1 Gene

Orthologs for CDX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CDX1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CDX1 30 31
  • 97.61 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CDX1 30 31
  • 88.55 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CDX1 30 31
  • 87.42 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Cdx1 30 17 31
  • 84.65 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cdx1 30
  • 83.03 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia CDX1 31
  • 74 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CDX1 31
  • 59 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CDX1 31
  • 52 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CDX1 31
  • 67 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii cdx1b 31
  • 51 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta cad 31
  • 21 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea pal-1 31
  • 23 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 21 (a)
OneToMany
Species where no ortholog for CDX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for CDX1 Gene

ENSEMBL:
Gene Tree for CDX1 (if available)
TreeFam:
Gene Tree for CDX1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CDX1: view image

Paralogs for CDX1 Gene

Paralogs for CDX1 Gene

(17) SIMAP similar genes for CDX1 Gene using alignment to 4 proteins:

  • CDX1_HUMAN
  • Q14DX0_HUMAN
  • Q4VAU3_HUMAN
  • Q4VAU5_HUMAN
genes like me logo Genes that share paralogs with CDX1: view

Variants for CDX1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CDX1 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs539576362 Uncertain Significance: not specified 150,167,303(+) G/A
NM_001804.3(CDX1):c.427G>A (p.Gly143Arg)
MISSENSE
rs2302275 - p.Pro130Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CDX1 Gene

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

Structural Variations from Database of Genomic Variants (DGV) for CDX1 Gene

Variant ID Type Subtype PubMed ID
esv2762556 CNV gain 21179565
nsv1022234 CNV loss 25217958
nsv1119045 CNV deletion 24896259
nsv599955 CNV loss 21841781

Variation tolerance for CDX1 Gene

Gene Damage Index Score: 2.17; 39.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDX1 Gene

Human Gene Mutation Database (HGMD)
CDX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDX1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDX1 Gene

Disorders for CDX1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for CDX1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
mesenchymal chondrosarcoma
  • chondrosarcoma mesenchymal
esophagus melanoma
  • melanoma of esophagus
colorectal cancer
  • crc
bartholin's gland carcinoma
  • bartholin gland carcinoma
gastrointestinal carcinoma
  • gastrointestinal neoplasms
- elite association - COSMIC cancer census association via MalaCards
Search CDX1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDX1

genes like me logo Genes that share disorders with CDX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDX1 Gene

Publications for CDX1 Gene

  1. Isolation, characterization, and precise physical localization of human CDX1, a caudal-type homeobox gene. (PMID: 8530027) Bonner CA … Wasmuth JJ (Genomics 1995) 2 3 4 23
  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
  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
  4. A KRAS-directed transcriptional silencing pathway that mediates the CpG island methylator phenotype. (PMID: 24623306) Serra RW … Green MR (eLife 2014) 3 4
  5. Gastrointestinal differentiation marker Cytokeratin 20 is regulated by homeobox gene CDX1. (PMID: 19188603) Chan CW … Bodmer WF (Proceedings of the National Academy of Sciences of the United States of America 2009) 3 23

Products for CDX1 Gene

Sources for CDX1 Gene