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CDX2 caudal type homeobox 2 [ Homo sapiens (human) ]

Gene ID: 1045, updated on 7-Apr-2024

Summary

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Official Symbol
CDX2provided by HGNC
Official Full Name
caudal type homeobox 2provided by HGNC
Primary source
HGNC:HGNC:1806
See related
Ensembl:ENSG00000165556 MIM:600297; AllianceGenome:HGNC:1806
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CDX3; CDX-3; CDX2/AS
Summary
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]
Expression
Biased expression in colon (RPKM 23.4), small intestine (RPKM 15.9) and 2 other tissues See more
Orthologs
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Genomic context

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Location:
13q12.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (27960918..27969315, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (27182310..27190703, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (28535055..28543452, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATP synthase F1 subunit epsilon pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5205 Neighboring gene long intergenic non-protein coding RNA 543 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:28539919-28540610 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:28540611-28541302 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:28542687-28543378 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:28545455-28546102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28546103-28546749 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:28552766-28553299 Neighboring gene uncharacterized LOC105370132 Neighboring gene ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase Neighboring gene RNA, 7SL, cytoplasmic 272, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Potential predictors for CDX2 expression loss and mismatch repair deficiency in colorectal cancer. Vlahović I, et al. Pathol Oncol Res, 2023. PMID 37325467, Free PMC Article
  2. CDX-2 expression correlates with clinical outcomes in MSI-H metastatic colorectal cancer patients receiving immune checkpoint inhibitors. Ziranu P, et al. Sci Rep, 2023 Mar 16. PMID 36928082, Free PMC Article
  3. Association between Single Nucleotide Polymorphisms Related to Vitamin D Metabolism and the Risk of Developing Asthma. Rojo-Tolosa S, et al. Nutrients, 2023 Feb 5. PMID 36839181, Free PMC Article
  4. Pattern of expression of CDX2 in colorectal cancer and its role in prognosis. Singh J, et al. J Cancer Res Ther, 2022 Dec. PMID 36510997
  5. CDX2 as a Predictive Biomarker Involved in Immunotherapy Response Suppresses Metastasis through EMT in Colorectal Cancer. Wang YS, et al. Dis Markers, 2022. PMID 36277982, Free PMC Article

See all (382) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Combined Use of Helicobacter pylori Genotyping and CDX2 Expression as a Predictor of Malignant Potential in Gastric Intestinal Metaplasia.
    Title: Combined Use of Helicobacter pylori Genotyping and CDX2 Expression as a Predictor of Malignant Potential in Gastric Intestinal Metaplasia.
  2. Loss of SATB2 and CDX2 expression is associated with DNA mismatch repair protein deficiency and BRAF mutation in colorectal cancer.
    Title: Loss of SATB2 and CDX2 expression is associated with DNA mismatch repair protein deficiency and BRAF mutation in colorectal cancer.
  3. Novel inherited CDX2 variant segregating in a family with diverse congenital malformations of the genitourinary system.
    Title: Novel inherited CDX2 variant segregating in a family with diverse congenital malformations of the genitourinary system.
  4. The CDX2 G allele and the FoKI F allele of the VDR gene are more prevalent and related to changes in vitamin D levels in patients with psoriasis vulgaris: A pilot study.
    Title: The CDX2 G allele and the FoKI F allele of the VDR gene are more prevalent and related to changes in vitamin D levels in patients with psoriasis vulgaris: A pilot study.
  5. The prognostic potential of CDX2 in colorectal cancer: Harmonizing biology and clinical practice.
    Title: The prognostic potential of CDX2 in colorectal cancer: Harmonizing biology and clinical practice.
  6. Association of CDX2 and mucin expression with chemotherapeutic benefits in patients with stage II/III gastric cancer.
    Title: Association of CDX2 and mucin expression with chemotherapeutic benefits in patients with stage II/III gastric cancer.
  7. The effect of miR-372-5p regulation on CDX1 and CDX2 in the gastric cancer cell line.
    Title: The effect of miR-372-5p regulation on CDX1 and CDX2 in the gastric cancer cell line.
  8. Relationship between CDX2 rs11568820 and EcoRV rs4516035 polymorphisms on the vitamin D receptor gene with susceptibility to different SARS-CoV-2 variants.
    Title: Relationship between CDX2 rs11568820 and EcoRV rs4516035 polymorphisms on the vitamin D receptor gene with susceptibility to different SARS-CoV-2 variants.
  9. Potential predictors for CDX2 expression loss and mismatch repair deficiency in colorectal cancer.
    Title: Potential predictors for CDX2 expression loss and mismatch repair deficiency in colorectal cancer.
  10. CDX-2 expression correlates with clinical outcomes in MSI-H metastatic colorectal cancer patients receiving immune checkpoint inhibitors.
    Title: CDX-2 expression correlates with clinical outcomes in MSI-H metastatic colorectal cancer patients receiving immune checkpoint inhibitors.
Submit: New GeneRIF Correction See all GeneRIFs (352)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat downregulates caudal type homeobox 2 in HEK 293T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables methyl-CpG binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in animal organ morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in anterior/posterior axis specification IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in blood vessel development IEA
Inferred from Electronic Annotation
more info
  
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in embryo development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosome to lysosome transport IEA
Inferred from Electronic Annotation
more info
  
involved_in establishment or maintenance of epithelial cell apical/basal polarity IEA
Inferred from Electronic Annotation
more info
  
involved_in intestinal epithelial cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in labyrinthine layer development IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of somitogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in somatic stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
  
involved_in stem cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in trophectodermal cell differentiation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in condensed nuclear chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription repressor complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
homeobox protein CDX-2
Names
caudal type homeobox transcription factor 2
caudal-type homeobox protein 2
homeobox protein miniCDX2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001265.6 → NP_001256.4  homeobox protein CDX-2 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL591024
    Consensus CDS
    CCDS9328.1
    UniProtKB/Swiss-Prot
    O00503, Q5VTU7, Q969L8, Q99626, Q9UD92
    Related
    ENSP00000370408.6, ENST00000381020.8
    Conserved Domains (2) summary
    pfam00046
    Location:190 → 243
    Homeobox; Homeobox domain
    pfam04731
    Location:13 → 171
    Caudal_act; Caudal like protein activation region

  2. NM_001354700.2 → NP_001341629.1  homeobox protein CDX-2 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL591024
    UniProtKB/TrEMBL
    A0A076MKN9
    Conserved Domains (2) summary
    pfam04731
    Location:13 → 171
    Caudal_act; Caudal like protein activation region
    cl00084
    Location:190 → 228
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    27960918..27969315 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534876.3 → XP_011533178.1  homeobox protein CDX-2 isoform X2

    UniProtKB/TrEMBL
    A0A076MKN9
    Conserved Domains (2) summary
    pfam00046
    Location:198 → 236
    Homeobox; Homeobox domain
    pfam04731
    Location:13 → 171
    Caudal_act; Caudal like protein activation region

  2. XM_011534875.3 → XP_011533177.1  homeobox protein CDX-2 isoform X1

    Conserved Domains (2) summary
    pfam00046
    Location:198 → 250
    Homeobox; Homeobox domain
    pfam04731
    Location:13 → 171
    Caudal_act; Caudal like protein activation region

  3. XM_011534878.3 → XP_011533180.1  homeobox protein CDX-2 isoform X3

    Conserved Domains (1) summary
    pfam00046
    Location:81 → 133
    Homeobox; Homeobox domain

  4. XM_011534879.2 → XP_011533181.1  homeobox protein CDX-2 isoform X4

    Conserved Domains (1) summary
    pfam00046
    Location:73 → 125
    Homeobox; Homeobox domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    27182310..27190703 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374016.1 → XP_054229991.1  homeobox protein CDX-2 isoform X2

  2. XM_054374015.1 → XP_054229990.1  homeobox protein CDX-2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99626.3 GenPept UniProtKB/Swiss-Prot:Q99626

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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