Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CDX4 Gene

Aliases for CDX4 Gene

  • Caudal Type Homeobox 4 2 3 5
  • Caudal-Type Homeobox Protein 4 3 4
  • Caudal Type Homeo Box Transcription Factor 4 2
  • Caudal Type Homeobox Transcription Factor 4 3
  • Homeobox Protein CDX-4 3

External Ids for CDX4 Gene

Previous GeneCards Identifiers for CDX4 Gene

  • GC0XP068480
  • GC0XP069841
  • GC0XP070881
  • GC0XP071533
  • GC0XP072450
  • GC0XP072583
  • GC0XP066300

Summaries for CDX4 Gene

Entrez Gene Summary for CDX4 Gene

  • This gene encodes a member of a small subfamily of homeobox containing transcription factors. The encoded protein may regulate homeobox gene expression during anteroposterior patterning and hematopoiesis. [provided by RefSeq, Aug 2012]

GeneCards Summary for CDX4 Gene

CDX4 (Caudal Type Homeobox 4) is a Protein Coding gene. Diseases associated with CDX4 include Renpenning Syndrome 1. Among its related pathways are Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers and Regulation of Wnt-mediated beta catenin signaling and target gene transcription. Gene Ontology (GO) annotations related to this gene include RNA polymerase II proximal promoter sequence-specific DNA binding and transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is CDX2.

Additional gene information for CDX4 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDX4 Gene

Genomics for CDX4 Gene

GeneHancer (GH) Regulatory Elements for CDX4 Gene

Promoters and enhancers for CDX4 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ073448 Promoter 0.6 EPDnew 650.7 -0.2 -174 0.1 MAX CDX4 GC0XM073398 RNU6-1044P
GH0XJ073447 Enhancer 0.2 ENCODE 650.7 +0.4 426 0.1 CDX4 MORF4L1P6
GH0XJ073566 Enhancer 0.3 FANTOM5 2.3 +119.6 119588 0.2 CHIC1 NAP1L2 CDX4 PIR39676 GC0XM073547
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDX4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDX4 gene promoter:
  • IRF-7A
  • FOXD3
  • Sox5
  • HTF
  • FOXO1a
  • FOXO1
  • Pax-2
  • Pax-2a
  • Pax-2b
  • Cdc5

Genomic Locations for CDX4 Gene

Genomic Locations for CDX4 Gene
7,992 bases
Plus strand
7,992 bases
Plus strand

Genomic View for CDX4 Gene

Genes around CDX4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDX4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDX4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDX4 Gene

Proteins for CDX4 Gene

  • Protein details for CDX4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein CDX-4
    Protein Accession:
    Secondary Accessions:
    • A1A513
    • Q5JS20

    Protein attributes for CDX4 Gene

    284 amino acids
    Molecular mass:
    30480 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CDX4 Gene

Post-translational modifications for CDX4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CDX4 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for CDX4
  • Boster Bio Antibodies for CDX4

No data available for DME Specific Peptides for CDX4 Gene

Domains & Families for CDX4 Gene

Gene Families for CDX4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for CDX4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Caudal homeobox family.
  • Belongs to the Caudal homeobox family.
genes like me logo Genes that share domains with CDX4: view

Function for CDX4 Gene

Molecular function for CDX4 Gene

GENATLAS Biochemistry:
Drosophila caudal family member 4,murine Cdx4 homolog,homeo domain encoding gene

Gene Ontology (GO) - Molecular Function for CDX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA --
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 21471217
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IMP 21471217
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with CDX4: view
genes like me logo Genes that share phenotypes with CDX4: view

Animal Models for CDX4 Gene

MGI Knock Outs for CDX4:
  • Cdx4 Cdx4<tm1.1Jdes>
  • Cdx4 Cdx4<tm1.1Gqda>

Animal Model Products

miRNA for CDX4 Gene

miRTarBase miRNAs that target CDX4
Targeted motifs for CDX4 Gene
HOMER Transcription Factor Regulatory Elements motif CDX4
  • Consensus sequence: NGYCATAAAWCH Submotif: canonical Cell Type: ZebrafishEmbryos GEO ID: GSE48254

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology and Transcription Factor Targets for CDX4 Gene

Localization for CDX4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDX4 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CDX4 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for CDX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
genes like me logo Genes that share ontologies with CDX4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDX4 Gene

Pathways & Interactions for CDX4 Gene

genes like me logo Genes that share pathways with CDX4: view

Gene Ontology (GO) - Biological Process for CDX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001568 blood vessel development IEA --
GO:0001890 placenta development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with CDX4: view

No data available for SIGNOR curated interactions for CDX4 Gene

Drugs & Compounds for CDX4 Gene

No Compound Related Data Available

Transcripts for CDX4 Gene

mRNA/cDNA for CDX4 Gene

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

Unigene Clusters for CDX4 Gene

Caudal type homeobox 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDX4 Gene

No ASD Table

Relevant External Links for CDX4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDX4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDX4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CDX4 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x27.8), Skin - Sun Exposed (Lower leg) (x17.8), and Testis (x4.4).

NURSA nuclear receptor signaling pathways regulating expression of CDX4 Gene:


SOURCE GeneReport for Unigene cluster for CDX4 Gene:

genes like me logo Genes that share expression patterns with CDX4: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDX4 Gene

Orthologs for CDX4 Gene

This gene was present in the common ancestor of animals.

Orthologs for CDX4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDX4 34 33
  • 98.83 (n)
(Bos Taurus)
Mammalia CDX4 34 33
  • 83.57 (n)
(Rattus norvegicus)
Mammalia Cdx4 33
  • 83.57 (n)
(Canis familiaris)
Mammalia CDX4 34 33
  • 83.04 (n)
(Mus musculus)
Mammalia Cdx4 16 34 33
  • 82.39 (n)
(Monodelphis domestica)
Mammalia CDX4 34
  • 44 (a)
(Gallus gallus)
Aves CDXB 34
  • 53 (a)
-- 34
  • 47 (a)
(Anolis carolinensis)
Reptilia CDX4 34
  • 75 (a)
African clawed frog
(Xenopus laevis)
Amphibia cdx4-prov 33
tropical clawed frog
(Silurana tropicalis)
Amphibia Cdx4 33
(Danio rerio)
Actinopterygii cdx4 34
  • 44 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12139 33
(Caenorhabditis elegans)
Secernentea pal-1 34
  • 23 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 24 (a)
Species where no ortholog for CDX4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • wheat (Triticum aestivum)

Evolution for CDX4 Gene

Gene Tree for CDX4 (if available)
Gene Tree for CDX4 (if available)
Evolutionary constrained regions (ECRs) for CDX4: view image

Paralogs for CDX4 Gene

(2) SIMAP similar genes for CDX4 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CDX4: view

Variants for CDX4 Gene

Sequence variations from dbSNP and Humsavar for CDX4 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000275802 -- 73,448,488(+) C/A intron_variant
rs1000349663 -- 73,452,156(+) G/A intron_variant
rs1001048441 -- 73,445,873(+) G/T upstream_transcript_variant
rs1002110260 -- 73,454,111(+) G/A intron_variant
rs1002742368 -- 73,453,329(+) C/T intron_variant

Variation tolerance for CDX4 Gene

Residual Variation Intolerance Score: 63.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.40; 8.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDX4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for CDX4 Gene

Disorders for CDX4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CDX4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
renpenning syndrome 1
  • rens1
- elite association - COSMIC cancer census association via MalaCards
Search CDX4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDX4

genes like me logo Genes that share disorders with CDX4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDX4 Gene

Publications for CDX4 Gene

  1. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 58
  2. A member of the caudal family of homeobox genes maps to the X-inactivation centre region of the mouse and human X chromosomes. (PMID: 7655457) Horn JM … Ashworth A (Human molecular genetics 1995) 2 3 58
  3. Human definitive hematopoietic specification from pluripotent stem cells is regulated by mesodermal expression of CDX4. (PMID: 28408465) Creamer JP … Sturgeon CM (Blood 2017) 3 58
  4. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. (PMID: 26871637) Yang X … Vidal M (Cell 2016) 3 58
  5. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. (PMID: 24722188) Corominas R … Iakoucheva LM (Nature communications 2014) 3 58

Products for CDX4 Gene

Sources for CDX4 Gene

Loading form....