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Aliases for CDX1 Gene

Aliases for CDX1 Gene

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

External Ids for CDX1 Gene

Previous GeneCards Identifiers for CDX1 Gene

  • GC05P149616
  • 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 colon adenocarcinoma and bile reflux. Among its related pathways are Regulation of Wnt-mediated beta catenin signaling and target gene transcription and Cell adhesion Integrin-mediated cell adhesion and migration. GO annotations related to this gene include RNA polymerase II distal enhancer sequence-specific DNA binding and RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription. An important paralog of this gene is CDX4.

UniProtKB/Swiss-Prot for CDX1 Gene

  • Could play a role in the terminal differentiation of the intestine

Gene Wiki entry for CDX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDX1 Gene

Genomics for CDX1 Gene

Regulatory Elements for CDX1 Gene

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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for CDX1 Gene

Start:
150,166,781 bp from pter
End:
150,184,558 bp from pter
Size:
17,778 bases
Orientation:
Plus strand

Genomic View for CDX1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

    Alternative splice isoforms for CDX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CDX1 Gene

Proteomics data for CDX1 Gene at MOPED

Post-translational modifications for CDX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CDX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CDX1 Gene

Domains for CDX1 Gene

Gene Families for CDX1 Gene

HGNC:
  • HOXL :Homeoboxes / ANTP class : HOXL subclass

Suggested Antigen Peptide Sequences for CDX1 Gene

Graphical View of Domain Structure for InterPro Entry

P47902

UniProtKB/Swiss-Prot:

CDX1_HUMAN :
  • P47902
Domain:
  • Contains 1 homeobox DNA-binding domain.
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

GENATLAS Biochemistry: Drosophila caudal family member 1,murine Cdx1 homolog,homeo domain encoding gene,transcriptional regulator of insulin gene
UniProtKB/Swiss-Prot Function: Could play a role in the terminal differentiation of the intestine

Gene Ontology (GO) - Molecular Function for CDX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IDA 15774940
GO:0001205 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IDA 15774940
GO:0003677 DNA binding --
GO:0005515 protein binding IPI 19059241
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:

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for CDX1 Gene

Localization for CDX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDX1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CDX1 Gene COMPARTMENTS Subcellular localization image for CDX1 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for CDX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with CDX1: view

Pathways 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

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for CDX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated --
GO:0007275 multicellular organismal development --
GO:0007389 pattern specification process --
GO:0009887 organ morphogenesis TAS 8530027
GO:0009952 anterior/posterior pattern specification IEA --
genes like me logo Genes that share ontologies with CDX1: view

Compounds for CDX1 Gene

(3) Novoseek inferred chemical compound relationships for CDX1 Gene

Compound -log(P) Hits PubMed IDs
crcs 46.7 2
5-aza-2deoxycytidine 32.8 3
retinoic acid 20.4 3
genes like me logo Genes that share compounds with CDX1: view

Transcripts for CDX1 Gene

mRNA/cDNA for CDX1 Gene

(19) Selected AceView cDNA sequences:
(9) Additional mRNA sequences :
(1) REFSEQ mRNAs :
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CDX1 Gene

Caudal type homeobox 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CDX1

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

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

No ASD Table

Relevant External Links for CDX1 Gene

GeneLoc Exon Structure for
CDX1
ECgene alternative splicing isoforms for
CDX1

Expression for CDX1 Gene

mRNA expression in normal human tissues 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 (35.9) and Small Intestine - Terminal Ileum (13.1).

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

In Situ Assay Products

No data available for Protein expression 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 35
  • 97.61 (n)
  • 97.74 (a)
CDX1 36
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CDX1 35
  • 87.42 (n)
  • 87.92 (a)
CDX1 36
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CDX1 35
  • 88.55 (n)
  • 89.06 (a)
CDX1 36
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Cdx1 35
  • 84.65 (n)
  • 85.66 (a)
Cdx1 16
Cdx1 36
  • 84 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CDX1 36
  • 59 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CDX1 36
  • 74 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cdx1 35
  • 83.03 (n)
  • 84.68 (a)
chicken
(Gallus gallus)
Aves CDX1 36
  • 52 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CDX1 36
  • 67 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii cdx1b 36
  • 51 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta cad 36
  • 21 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea pal-1 36
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 21 (a)
OneToMany
Species with no ortholog for CDX1:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for CDX1 Gene

Paralogs for CDX1 Gene

Selected SIMAP similar genes for CDX1 Gene using alignment to 4 proteins:

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

Variants for CDX1 Gene

Sequence variations from dbSNP and Humsavar for CDX1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type MAF
rs717746 -- 150,176,995(-) CCCCC(A/C)AGGCC intron-variant
rs887343 -- 150,169,260(+) GGCAC(A/G)AGAGC intron-variant
rs887344 -- 150,169,459(+) TCTTC(C/T)GCAGA intron-variant
rs2237090 -- 150,170,058(+) TCCCC(A/G)GCTGC intron-variant
rs2237091 -- 150,170,234(+) TCATC(A/G)TCACC intron-variant

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

Variant ID Type Subtype PubMed ID
nsv883027 CNV Loss 21882294
nsv883030 CNV Loss 21882294

Relevant External Links for CDX1 Gene

HapMap Linkage Disequilibrium report
CDX1
Human Gene Mutation Database (HGMD)
CDX1

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

Disorders for CDX1 Gene

(1) University of Copenhagen DISEASES for CDX1 Gene

(17) Novoseek inferred disease relationships for CDX1 Gene

Disease -log(P) Hits PubMed IDs
metaplasia 72.1 31
colon cancer 57.7 18
colorectal carcinoma 47.4 8
colorectal cancer 44.8 18
adenocarcinoma 43.5 11
genes like me logo Genes that share disorders with CDX1: view

No data available for UniProtKB/Swiss-Prot 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 C.A. … Wasmuth J.J. (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 G.V. … Iovanna J.L. (Int. J. Cancer 1997) 3 4 23
  3. DNA methylation down-regulates CDX1 gene expression in colorectal cancer cell lines. (PMID: 12124393) Suh E.R. … Traber P.G. (J. Biol. Chem. 2002) 3 23
  4. Expression of Cdx1 and Cdx2 mRNAs and relevance of this expression to differentiation in human gastrointestinal mucosa--with special emphasis on participation in intestinal metaplasia of the human stomach. (PMID: 11846061) Mizoshita T. … Tatematsu M. (Gastric Cancer 2001) 3 23
  5. Cdx1 homeobox gene during human colon cancer progression. (PMID: 12970739) Domon-Dell C. … Freund J.N. (Oncogene 2003) 3 23

Products for CDX1 Gene

Sources for CDX1 Gene

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