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] See more...

Aliases for CDX4 Gene

Aliases for CDX4 Gene

  • Caudal Type Homeobox 4 2 3 5
  • Caudal-Type Homeobox Protein 4 3 4
  • Homeobox Protein CDX-4 3 4
  • Caudal Type Homeo Box Transcription Factor 4 2
  • Caudal Type Homeobox Transcription Factor 4 3
  • CDX4 5

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 Autosomal Dominant Non-Syndromic Intellectual Disability 32 and Adult Acute Lymphocytic Leukemia. Among its related pathways are Regulation of Wnt-mediated beta catenin signaling and target gene transcription and Embryonic and Induced Pluripotent Stem Cells and Lineage-specific Markers. Gene Ontology (GO) annotations related to this gene include RNA polymerase II proximal promoter sequence-specific DNA binding and proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific. An important paralog of this gene is CDX2.

Additional gene information for CDX4 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CDX4 Gene

Genomics for CDX4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CDX4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ073448 Promoter 0.4 EPDnew 600.7 -0.2 -174 0.1 EZH2 CDX4 piR-47086-347 NAP1L2
GH0XJ073447 Enhancer 0.4 ENCODE 600.7 +0.4 426 0.1 EZH2 RAD21 TBP CTCF CDX4 MORF4L1P6 CHIC1
GH0XJ073566 Enhancer 0.4 FANTOM5 Ensembl 2.3 +119.7 119725 0.4 JPX CHIC1 NAP1L2 CDX4 MAP2K4P1 lnc-NAP1L2-3 piR-46677-013 ZCCHC13
GH0XJ073401 Enhancer 0.3 Ensembl 0.3 -45.5 -45453 0.8 RAD21 CTCF JPX CHIC1 RF00026-1177 RNU6-1044P piR-47086-347 CDX4 NAP1L2
GH0XJ073525 Enhancer 0.4 Ensembl ENCODE 0.2 +79.2 79202 1.3 YY1 piR-57750-040 piR-61532-358 lnc-NAP1L2-3 MAP2K4P1 CHIC1 CDX4
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CDX4

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

Genomic Locations for CDX4 Gene

Genomic Locations for CDX4 Gene
chrX:73,447,254-73,455,245
(GRCh38/hg38)
Size:
7,992 bases
Orientation:
Plus strand
chrX:72,667,090-72,675,081
(GRCh37/hg19)
Size:
7,992 bases
Orientation:
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:
    O14627-CDX4_HUMAN
    Recommended name:
    Homeobox protein CDX-4
    Protein Accession:
    O14627
    Secondary Accessions:
    • A1A513
    • Q5JS20

    Protein attributes for CDX4 Gene

    Size:
    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:

No data available for DME Specific Peptides for CDX4 Gene

Domains & Families for CDX4 Gene

Gene Families for CDX4 Gene

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

Protein Domains for CDX4 Gene

InterPro:
Blocks:
  • Lambda and other repressor helix-turn-helix signature
  • Caudal-like activation region
ProtoNet:

Suggested Antigen Peptide Sequences for CDX4 Gene

GenScript: Design optimal peptide antigens:
  • Caudal-type homeobox protein 4 (CDX4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O14627

UniProtKB/Swiss-Prot:

CDX4_HUMAN :
  • Belongs to the Caudal homeobox family.
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 21873635
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 21471217
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific 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

CRISPR 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

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDX4

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

COMPARTMENTS
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 4
plasma membrane 1
extracellular 1
cytoskeleton 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CDX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA 21873635
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

Pathways by source for CDX4 Gene

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:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
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 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDX4

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

No ASD Table

Relevant External Links for CDX4 Gene

GeneLoc Exon Structure for
CDX4

Expression for CDX4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CDX4

SOURCE GeneReport for Unigene cluster for CDX4 Gene:

Hs.553488

Evidence on tissue expression from TISSUES for CDX4 Gene

  • Nervous system(2.2)
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 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
Chimpanzee
(Pan troglodytes)
Mammalia CDX4 30 31
  • 98.83 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cdx4 30
  • 83.57 (n)
Cow
(Bos Taurus)
Mammalia CDX4 30 31
  • 83.57 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CDX4 30 31
  • 83.04 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Cdx4 30 17 31
  • 82.39 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CDX4 31
  • 44 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CDXB 31
  • 53 (a)
OneToMany
-- 31
  • 47 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia CDX4 31
  • 75 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia cdx4-prov 30
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Cdx4 30
Zebrafish
(Danio rerio)
Actinopterygii cdx4 31
  • 44 (a)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12139 30
Worm
(Caenorhabditis elegans)
Secernentea pal-1 31
  • 23 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 24 (a)
OneToMany
Species where no ortholog for CDX4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

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

Paralogs for CDX4 Gene

Paralogs for CDX4 Gene

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

  • CDX4_HUMAN
genes like me logo Genes that share paralogs with CDX4: view

Variants for CDX4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CDX4 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
710287 Likely Benign: not provided 73,447,453(+) C/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CDX4 Gene

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
CDX4

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

(3) MalaCards diseases for CDX4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
autosomal dominant non-syndromic intellectual disability 32
  • autosomal dominant mental retardation 32
adult acute lymphocytic leukemia
  • adult acute lymphoid leukemia
renpenning syndrome 1
  • rens1
- elite association - COSMIC cancer census association via MalaCards
Search CDX4 in MalaCards View complete list of genes associated with diseases
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
  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
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. (PMID: 31515488) Fragoza R … Yu H (Nature communications 2019) 3
  5. Human definitive hematopoietic specification from pluripotent stem cells is regulated by mesodermal expression of CDX4. (PMID: 28408465) Creamer JP … Sturgeon CM (Blood 2017) 3

Products for CDX4 Gene

Sources for CDX4 Gene