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

Summary

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
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Genomic context

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_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-U51096 (e-PCR)
- UniSTS:52671

RH48331 (e-PCR)
- UniSTS:11728

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)

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
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

NC_000013.11 Reference GRCh38.p14 Primary Assembly

Range

27960918..27969315 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

pfam00046
Location:81 → 133

Homeobox; Homeobox domain
XM_011534879.2 → XP_011533181.1 homeobox protein CDX-2 isoform X4

Conserved Domains (1) summary

pfam00046
Location:73 → 125

Homeobox; Homeobox domain