U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 1045, updated on 28-Oct-2024

    Summary

    Go to the top of the page Help
    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
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See CDX2 in Genome Data Viewer
    Location:
    13q12.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (27960918..27969315, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (27182310..27190703, complement)
    RS_2024_09 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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: HPA RNA-seq normal tissues 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Primary ovarian carcinoid tumors may express CDX-2: a potential pitfall in distinction from metastatic intestinal carcinoid tumors involving the ovary. Rabban JT, et al. Int J Gynecol Pathol, 2009 Jan. PMID 19047909
    2. Aberrant CDX2 expression in hepatocellular carcinomas: an important diagnostic pitfall. Shah SS, et al. Hum Pathol, 2017 Jun. PMID 28089540
    3. Expression of homeodomain protein CDX2 in colorectal adenoma and adenocarcinoma. Bakaris S, et al. Histol Histopathol, 2008 Sep. PMID 18581275
    4. CDX2 expression in columnar variant of papillary thyroid carcinoma. Bongiovanni M, et al. Thyroid, 2013 Nov. PMID 23734674
    5. Morules in endometrioid proliferations of the uterus and ovary consistently express the intestinal transcription factor CDX2. Houghton O, et al. Histopathology, 2008 Aug. PMID 18752499

    See all (396) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Knockdown of CDX2 Induces microRNA-221 Up-regulation in Human Colon Cancer Cells.
      Title: Knockdown of CDX2 Induces microRNA-221 Up-regulation in Human Colon Cancer Cells.
    2. CDX2 alleviates hypoxia-induced apoptosis and oxidative stress in spermatogenic cells through suppression of reactive oxygen species-mediated Wnt/beta-catenin pathway.
      Title: CDX2 alleviates hypoxia-induced apoptosis and oxidative stress in spermatogenic cells through suppression of reactive oxygen species-mediated Wnt/β-catenin pathway.
    3. Concomitant expression patterns of CDX2 and SATB2 as prognostic factors in stage III colorectal cancers.
      Title: Concomitant expression patterns of CDX2 and SATB2 as prognostic factors in stage III colorectal cancers.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (355)

    Phenotypes

    Go to the top of the page Help

    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

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

    Go to the top of the page Help

    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

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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 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 digestive tract development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryonic pattern specification 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
    located_in 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

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_2024_08

    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.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools