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Aliases for HOXC4 Gene

Aliases for HOXC4 Gene

  • Homeobox C4 2 3 5
  • Homeobox Protein Hox-3E 3 4
  • Homeobox Protein CP19 3 4
  • Homeo Box C4 2 3
  • HOX3E 3 4
  • Homeo Box 3E 3
  • HOX3 3
  • Cp19 3

External Ids for HOXC4 Gene

Previous HGNC Symbols for HOXC4 Gene

  • HOX3
  • HOX3E

Previous GeneCards Identifiers for HOXC4 Gene

  • GC12M054370
  • GC12P054523
  • GC12P054127
  • GC12P052696
  • GC12P054410
  • GC12P051448

Summaries for HOXC4 Gene

Entrez Gene Summary for HOXC4 Gene

  • This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene, HOXC4, is one of several homeobox HOXC genes located in a cluster on chromosome 12. Three genes, HOXC5, HOXC4 and HOXC6, share a 5' non-coding exon. Transcripts may include the shared exon spliced to the gene-specific exons, or they may include only the gene-specific exons. Two alternatively spliced variants that encode the same protein have been described for HOXC4. Transcript variant one includes the shared exon, and transcript variant two includes only gene-specific exons. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXC4 Gene

HOXC4 (Homeobox C4) is a Protein Coding gene. Among its related pathways are Developmental Biology and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and HMG box domain binding. An important paralog of this gene is HOXA7.

UniProtKB/Swiss-Prot for HOXC4 Gene

  • Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Gene Wiki entry for HOXC4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXC4 Gene

Genomics for HOXC4 Gene

Regulatory Elements for HOXC4 Gene

Enhancers for HOXC4 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around HOXC4 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the HOXC4 gene promoter:

Genomic Location for HOXC4 Gene

54,016,852 bp from pter
54,056,030 bp from pter
39,179 bases
Plus strand

Genomic View for HOXC4 Gene

Genes around HOXC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXC4 Gene

Proteins for HOXC4 Gene

  • Protein details for HOXC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-C4
    Protein Accession:

    Protein attributes for HOXC4 Gene

    264 amino acids
    Molecular mass:
    29811 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXC4 Gene

Proteomics data for HOXC4 Gene at MOPED

Post-translational modifications for HOXC4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXC4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXC4 Gene

Domains & Families for HOXC4 Gene

Gene Families for HOXC4 Gene

Suggested Antigen Peptide Sequences for HOXC4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the Antp homeobox family. Deformed subfamily.
  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the Antp homeobox family. Deformed subfamily.
genes like me logo Genes that share domains with HOXC4: view

Function for HOXC4 Gene

Molecular function for HOXC4 Gene

GENATLAS Biochemistry:
homeo box C4(3E),Drosophila Dfd,expressed in first trimester trophoblast,involved in mouse anterior limb patterning,expressed in anterior limb
UniProtKB/Swiss-Prot Function:
Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Gene Ontology (GO) - Molecular Function for HOXC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 23455924
genes like me logo Genes that share ontologies with HOXC4: view
genes like me logo Genes that share phenotypes with HOXC4: view

Animal Models for HOXC4 Gene

MGI Knock Outs for HOXC4:

Animal Model Products

miRNA for HOXC4 Gene

miRTarBase miRNAs that target HOXC4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXC4 Gene

Localization for HOXC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXC4 Gene

Subcellular locations from

Jensen Localization Image for HOXC4 Gene COMPARTMENTS Subcellular localization image for HOXC4 gene
Compartment Confidence
nucleus 5
plasma membrane 1

No data available for Gene Ontology (GO) - Cellular Components for HOXC4 Gene

Pathways & Interactions for HOXC4 Gene

genes like me logo Genes that share pathways with HOXC4: view

Gene Ontology (GO) - Biological Process for HOXC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009952 anterior/posterior pattern specification IEA --
genes like me logo Genes that share ontologies with HOXC4: view

No data available for SIGNOR curated interactions for HOXC4 Gene

Drugs & Compounds for HOXC4 Gene

No Compound Related Data Available

Transcripts for HOXC4 Gene

mRNA/cDNA for HOXC4 Gene

Unigene Clusters for HOXC4 Gene

Homeobox C4:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HOXC4 Gene

No ASD Table

Relevant External Links for HOXC4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXC4 Gene

mRNA expression in normal human tissues for HOXC4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXC4 Gene

This gene is overexpressed in Fallopian Tube (x7.0), Kidney - Cortex (x4.2), and Artery - Tibial (x4.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HOXC4 Gene

SOURCE GeneReport for Unigene cluster for HOXC4 Gene Hs.549040

genes like me logo Genes that share expression patterns with HOXC4: view

Primer Products

No data available for Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for HOXC4 Gene

Orthologs for HOXC4 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXC4 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia HOXC4 35
  • 98.48 (n)
  • 99.62 (a)
HOXC4 36
  • 100 (a)
(Canis familiaris)
Mammalia HOXC4 35
  • 97.85 (n)
  • 99.24 (a)
HOXC4 36
  • 99 (a)
(Mus musculus)
Mammalia Hoxc4 35
  • 97.35 (n)
  • 98.86 (a)
Hoxc4 16
Hoxc4 36
  • 99 (a)
(Pan troglodytes)
Mammalia HOXC4 35
  • 99.75 (n)
  • 100 (a)
HOXC4 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Hoxc4 35
  • 97.47 (n)
  • 99.24 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 76 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxc4 35
  • 72.03 (n)
  • 74.51 (a)
Str.7417 35
African clawed frog
(Xenopus laevis)
Amphibia hoxc6-A-prov 35
(Danio rerio)
Actinopterygii hoxc4a 35
  • 67.94 (n)
  • 70.5 (a)
hoxc4a 36
  • 59 (a)
fruit fly
(Drosophila melanogaster)
Insecta Dfd 37
  • 81 (a)
Scr 37
  • 68 (a)
Dfd 36
  • 19 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 27 (a)
Species with no ortholog for HOXC4:
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for HOXC4 Gene

Gene Tree for HOXC4 (if available)
Gene Tree for HOXC4 (if available)

Paralogs for HOXC4 Gene

(16) SIMAP similar genes for HOXC4 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with HOXC4: view

Variants for HOXC4 Gene

Sequence variations from dbSNP and Humsavar for HOXC4 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs11835301 - 54,054,883(+) CAAGC(G/T)CTCGA reference, missense
rs35406888 - 54,054,943(+) TTACA(A/G)CCGCT reference, missense
rs7134677 -- 54,047,714(+) GCGCG(C/T)GGAGG intron-variant
rs7136889 -- 54,043,968(+) TGTGT(G/T)TAGGG intron-variant
rs7297416 -- 54,049,306(+) AGTGA(A/C)CTATT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HOXC4 Gene

Variant ID Type Subtype PubMed ID
nsv826379 CNV Gain 20364138
nsv899100 CNV Loss 21882294
dgv512e1 CNV Complex 17122850
nsv428282 CNV Gain 18775914
nsv899102 CNV Loss 21882294
esv2672088 CNV Deletion 23128226
nsv832418 CNV Loss 17160897
nsv716 CNV Insertion 18451855

Variation tolerance for HOXC4 Gene

Residual Variation Intolerance Score: 33.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.62; 78.23% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for HOXC4 Gene

Disorders for HOXC4 Gene

Relevant External Links for HOXC4

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for HOXC4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HOXC4 Gene

Publications for HOXC4 Gene

  1. Analysis of single nucleotide polymorphisms and haplotypes in HOXC gene cluster within susceptible region 12q13 of simple congenital heart disease. (PMID: 16215934) Gong L.G. … Sun K.L. (Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2005) 3 23 48 67
  2. [Effect of human cytomegalovirus infection on the expression of hoxc4 and hoxc6 genes in the proliferation of lymphocytic progenitor cells]. (PMID: 19236766) Feng J.Q. … Chen S.Q. (Zhongguo Shi Yan Xue Ye Xue Za Zhi 2009) 3 23
  3. Selective inhibition of class switching to IgG and IgE by recruitment of the HoxC4 and Oct-1 homeodomain proteins and Ku70/Ku86 to newly identified ATTT cis-elements. (PMID: 12672812) Schaffer A. … Casali P. (J. Biol. Chem. 2003) 3 23
  4. HOXC4, HOXC5, and HOXC6 expression in primary cutaneous lymphoid lesions. High expression of HOXC5 in anaplastic large-cell lymphomas. (PMID: 9327740) Bijl J.J. … Meijer C.J. (Am. J. Pathol. 1997) 3 23
  5. Expression of HOXC4 homeoprotein in the nucleus of activated human lymphocytes. (PMID: 7718879) Meazza R. … Corte G. (Blood 1995) 3 23

Products for HOXC4 Gene

Sources for HOXC4 Gene