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Aliases for HOXD4 Gene

Aliases for HOXD4 Gene

  • Homeobox D4 2 3 5
  • Homeobox Protein HHO.C13 3 4
  • Homeobox Protein Hox-5.1 3 4
  • Homeobox Protein Hox-4B 3 4
  • HOX4B 3 4
  • Hox-4.2, Mouse, Homolog Of Homeo Box X 3
  • Homeobox Protein Hox-D4 3
  • Homeo Box D4 2
  • HHO.C13 3
  • HOX-5.1 3
  • Hox-4.2 3
  • HOX4 3

External Ids for HOXD4 Gene

Previous HGNC Symbols for HOXD4 Gene

  • HOX4B
  • HOX4

Previous GeneCards Identifiers for HOXD4 Gene

  • GC02P175067
  • GC02P175677
  • GC02P176980
  • GC02P177218
  • GC02P176841
  • GC02P176724
  • GC02P177016
  • GC02P168892
  • GC02P177019
  • GC02P177022
  • GC02P177026
  • GC02P177030
  • GC02P177034
  • GC02P176152
  • GC02P176154
  • GC02P176156
  • GC02P176158
  • GC02P176160
  • GC02P176162
  • GC02P176164

Summaries for HOXD4 Gene

Entrez Gene Summary for HOXD4 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, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The protein encoded by this gene may play a role in determining positional values in developing limb buds. Alternatively spliced variants have been described but their full length nature has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXD4 Gene

HOXD4 (Homeobox D4) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Developmental Biology. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is HOXC4.

UniProtKB/Swiss-Prot for HOXD4 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 HOXD4 Gene

Additional gene information for HOXD4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD4 Gene

Genomics for HOXD4 Gene

GeneHancer (GH) Regulatory Elements for HOXD4 Gene

Promoters and enhancers for HOXD4 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
GH02I176151 Promoter 0.7 EPDnew 550.8 +0.9 880 0.1 SUZ12 EZH2 ENSG00000278500 GC02P176168 GC02P176169 HOXD4 MIR10B PIR51248 HOXD8 ENSG00000272729 HOXD3
GH02I176128 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 18.9 -15.6 -15604 13.3 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B ZNF213 E2F8 HOXD8 HOXD3 HOXD1 HAGLR ATF2 HOXD4 HOXD9 HAGLROS HOXD11 HOXD-AS2
GH02I175180 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.8 -969.1 -969147 2.2 FEZF1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC PPARGC1A MEF2D ATP5MC3 GC02P175182 HOXD9 CIR1 HOXD4 GC02M175181
GH02I176552 Enhancer 1.3 FANTOM5 Ensembl ENCODE 11.4 +403.3 403297 3 ARNT FEZF1 ZNF2 ZBTB7B YY1 ZNF280A E2F8 ZNF143 ATF7 RUNX3 HNRNPA3 HOXD4 HOXD3 HOXD-AS2 MIR10B HAGLR HOXD1 HOXD13 ENSG00000236231 GC02P176590
GH02I176177 Enhancer 0.9 Ensembl ENCODE 11.5 +28.0 28024 2.2 CTCF USF1 ZNF777 SUZ12 JUN MAX E2F1 ZFHX2 CTBP1 EGR2 HAGLROS HAGLR HOXD1 HOXD4 HOXD3 HOXD-AS2 MIR10B HOXD11 HOXD12 HOXD10
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HOXD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXD4 gene promoter:

Genomic Locations for HOXD4 Gene

Genomic Locations for HOXD4 Gene
2,833 bases
Plus strand

Genomic View for HOXD4 Gene

Genes around HOXD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXD4 Gene

Proteins for HOXD4 Gene

  • Protein details for HOXD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-D4
    Protein Accession:
    Secondary Accessions:
    • B2R9R3
    • Q96AU0

    Protein attributes for HOXD4 Gene

    255 amino acids
    Molecular mass:
    27885 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXD4 Gene

Post-translational modifications for HOXD4 Gene

No Post-translational modifications

Other Protein References for HOXD4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXD4 Gene

Domains & Families for HOXD4 Gene

Gene Families for HOXD4 Gene

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

Suggested Antigen Peptide Sequences for HOXD4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Antp homeobox family. Deformed subfamily.
  • Belongs to the Antp homeobox family. Deformed subfamily.
genes like me logo Genes that share domains with HOXD4: view

Function for HOXD4 Gene

Molecular function for HOXD4 Gene

GENATLAS Biochemistry:
homeo box D4(4B),homologous to mouse Hox-4.2,Drosophila Dfd
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.

Phenotypes From GWAS Catalog for HOXD4 Gene

Gene Ontology (GO) - Molecular Function for HOXD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IMP 1756725
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IMP 1756725
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXD4: view
genes like me logo Genes that share phenotypes with HOXD4: view

Animal Models for HOXD4 Gene

MGI Knock Outs for HOXD4:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXD4 Gene

Localization for HOXD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXD4 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 HOXD4 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (4)
  • Cell Junctions (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HOXD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0030054 cell junction IDA --
genes like me logo Genes that share ontologies with HOXD4: view

Pathways & Interactions for HOXD4 Gene

genes like me logo Genes that share pathways with HOXD4: view

Gene Ontology (GO) - Biological Process for HOXD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development NAS 2879245
GO:0009952 anterior/posterior pattern specification IEA --
genes like me logo Genes that share ontologies with HOXD4: view

No data available for SIGNOR curated interactions for HOXD4 Gene

Drugs & Compounds for HOXD4 Gene

(1) Additional Compounds for HOXD4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HOXD4: view

Transcripts for HOXD4 Gene

mRNA/cDNA for HOXD4 Gene

Unigene Clusters for HOXD4 Gene

Homeobox D4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXD4 Gene

No ASD Table

Relevant External Links for HOXD4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of HOXD4 Gene:


SOURCE GeneReport for Unigene cluster for HOXD4 Gene:


Evidence on tissue expression from TISSUES for HOXD4 Gene

  • Kidney(4.1)
genes like me logo Genes that share expression patterns with HOXD4: view

No data available for mRNA differential expression in normal tissues , 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 HOXD4 Gene

Orthologs for HOXD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXD4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXD4 33 34
  • 99.74 (n)
(Bos Taurus)
Mammalia HOXD4 33 34
  • 89.28 (n)
(Rattus norvegicus)
Mammalia Hoxd4 33
  • 87.92 (n)
(Mus musculus)
Mammalia Hoxd4 33 16
  • 87.6 (n)
(Canis familiaris)
Mammalia HOXD4 33 34
  • 81.48 (n)
(Ornithorhynchus anatinus)
Mammalia HOXD4 34
  • 80 (a)
(Monodelphis domestica)
Mammalia HOXD4 34
  • 79 (a)
(Gallus gallus)
Aves HOXD4 33 34
  • 75.95 (n)
(Anolis carolinensis)
Reptilia HOXD4 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxd4 33
  • 68.36 (n)
Str.15492 33
African clawed frog
(Xenopus laevis)
Amphibia LOC398744 33
(Danio rerio)
Actinopterygii hoxd4a 33 34
  • 67.23 (n)
fruit fly
(Drosophila melanogaster)
Insecta Scr 35
  • 71 (a)
Dfd 35 34
  • 70 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 27 (a)
Species where no ortholog for HOXD4 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)
  • 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)
  • 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 HOXD4 Gene

Gene Tree for HOXD4 (if available)
Gene Tree for HOXD4 (if available)

Paralogs for HOXD4 Gene

(10) SIMAP similar genes for HOXD4 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HOXD4: view

Variants for HOXD4 Gene

Sequence variations from dbSNP and Humsavar for HOXD4 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs104893636 uncertain-significance, Leukemia, acute lymphoblastic, susceptibility to 176,151,875(+) A/C/T coding_sequence_variant, missense_variant
rs1000334284 -- 176,150,841(+) T/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000430812 -- 176,150,499(+) A/T 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000476286 -- 176,152,468(+) G/C intron_variant
rs1000607670 -- 176,148,630(+) G/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXD4 Gene

Variant ID Type Subtype PubMed ID
dgv676n67 CNV gain 20364138

Variation tolerance for HOXD4 Gene

Residual Variation Intolerance Score: 38.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.30; 81.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXD4 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXD4 Gene

Disorders for HOXD4 Gene

Additional Disease Information for HOXD4

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HOXD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HOXD4 Gene

Publications for HOXD4 Gene

  1. Mutation analysis of the HOX paralogous 4-13 genes in children with acute lymphoid malignancies: identification of a novel germline mutation of HOXD4 leading to a partial loss-of-function. (PMID: 15776434) van Scherpenzeel Thim V … Verellen-Dumoulin C (Human mutation 2005) 3 22 44 58
  2. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges LM … MrOS Research Group (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009) 3 44 58
  3. Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. (PMID: 19938081) Ester AR … Hecht JT (American journal of medical genetics. Part A 2009) 3 44 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. PBX and MEIS as non-DNA-binding partners in trimeric complexes with HOX proteins. (PMID: 10523646) Shanmugam K … Featherstone MS (Molecular and cellular biology 1999) 3 22 58

Products for HOXD4 Gene

Sources for HOXD4 Gene

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