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

Gene ID: 1045, updated on 1-Jun-2020

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
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

Genomic context

See CDX2 in Genome Data Viewer
Location:
13q12.2
Exon count:
4
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (27960918..27969368, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (28536205..28543505, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATP synthase F1 subunit epsilon pseudogene 2 Neighboring gene long intergenic non-protein coding RNA 543 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
NHGRI GWA Catalog

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
animal organ morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
anterior/posterior axis specification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
blood vessel development IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
embryo development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome to lysosome transport IEA
Inferred from Electronic Annotation
more info
 
establishment or maintenance of epithelial cell apical/basal polarity IEA
Inferred from Electronic Annotation
more info
 
intestinal epithelial cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
labyrinthine layer development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
regulation of somitogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
somatic stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
trophectodermal cell differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
condensed nuclear chromosome IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcriptional repressor complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

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_001265.6NP_001256.4  homeobox protein CDX-2 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL591024
    Consensus CDS
    CCDS9328.1
    Related
    ENSP00000370408.6, ENST00000381020.8
    Conserved Domains (2) summary
    pfam04731
    Location:13171
    Caudal_act; Caudal like protein activation region
    pfam00046
    Location:190243
    Homeobox; Homeobox domain
  2. NM_001354700.1NP_001341629.1  homeobox protein CDX-2 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AK000205, AL591024, BC014461, KJ081251
    Conserved Domains (2) summary
    pfam00046
    Location:190228
    Homeobox; Homeobox domain
    pfam04731
    Location:13171
    Caudal_act; Caudal like protein activation region

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    27960918..27969368 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (2) summary
    pfam00046
    Location:198250
    Homeobox; Homeobox domain
    pfam04731
    Location:13171
    Caudal_act; Caudal like protein activation region
  2. XM_011534878.2XP_011533180.1  homeobox protein CDX-2 isoform X3

    Conserved Domains (1) summary
    pfam00046
    Location:81133
    Homeobox; Homeobox domain
  3. XM_011534879.2XP_011533181.1  homeobox protein CDX-2 isoform X4

    Conserved Domains (1) summary
    pfam00046
    Location:73125
    Homeobox; Homeobox domain
  4. XM_011534876.2XP_011533178.1  homeobox protein CDX-2 isoform X2

    Conserved Domains (2) summary
    pfam00046
    Location:198236
    Homeobox; Homeobox domain
    pfam04731
    Location:13171
    Caudal_act; Caudal like protein activation region
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