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Aliases for HOXD13 Gene

Aliases for HOXD13 Gene

  • Homeobox D13 2 3
  • HOX4I 3 4 6
  • Homeobox Protein Hox-4I 3 4
  • Homeo Box D13 2 3
  • BDSD 3 6
  • SPD 3 6
  • Homeobox Protein Hox-D13 3
  • Homeo Box 4I 3
  • BDE 3

External Ids for HOXD13 Gene

Previous HGNC Symbols for HOXD13 Gene

  • HOX4I
  • SPD

Previous GeneCards Identifiers for HOXD13 Gene

  • GC02P175010
  • GC02P175618
  • GC02P176921
  • GC02P177160
  • GC02P176783
  • GC02P176665
  • GC02P168835

Summaries for HOXD13 Gene

Entrez Gene Summary for HOXD13 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 in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. Mutations in this particular gene cause synpolydactyly. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXD13 Gene

HOXD13 (Homeobox D13) is a Protein Coding gene. Diseases associated with HOXD13 include brachydactyly, type d and syndactyly, type v. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and chromatin binding. An important paralog of this gene is HOXD10.

UniProtKB/Swiss-Prot for HOXD13 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 HOXD13 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD13 Gene

Genomics for HOXD13 Gene

Regulatory Elements for HOXD13 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for HOXD13 Gene

Start:
176,092,804 bp from pter
End:
176,095,938 bp from pter
Size:
3,135 bases
Orientation:
Plus strand

Genomic View for HOXD13 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HOXD13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXD13 Gene

Proteins for HOXD13 Gene

  • Protein details for HOXD13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P35453-HXD13_HUMAN
    Recommended name:
    Homeobox protein Hox-D13
    Protein Accession:
    P35453
    Secondary Accessions:

    Protein attributes for HOXD13 Gene

    Size:
    343 amino acids
    Molecular mass:
    36101 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC51635.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA95352.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for HOXD13 Gene

Proteomics data for HOXD13 Gene at MOPED

Post-translational modifications for HOXD13 Gene

  • Ubiquitination at Lys289
  • Modification sites at PhosphoSitePlus

Other Protein References for HOXD13 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXD13 Gene

Domains for HOXD13 Gene

Gene Families for HOXD13 Gene

HGNC:
  • HOXL :Homeoboxes / ANTP class : HOXL subclass

Protein Domains for HOXD13 Gene

Suggested Antigen Peptide Sequences for HOXD13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P35453

UniProtKB/Swiss-Prot:

HXD13_HUMAN :
  • P35453
Domain:
  • Contains 1 homeobox DNA-binding domain.
Family:
  • Belongs to the Abd-B homeobox family.
genes like me logo Genes that share domains with HOXD13: view

Function for HOXD13 Gene

Molecular function for HOXD13 Gene

GENATLAS Biochemistry: homeo box D13(4I),homologous to mouse Hox-4.8,involved in patterning and polarization of the mouse autopodium
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 HOXD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS 8614804
GO:0003682 chromatin binding IEA --
GO:0003700 sequence-specific DNA binding transcription factor activity IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXD13: view
genes like me logo Genes that share phenotypes with HOXD13: view

Animal Models for HOXD13 Gene

MGI Knock Outs for HOXD13:

Animal Model Products

CRISPR Products

Targeting motifs for HOXD13 Gene
HOMER Transcription Factor Regulatory Elements motif HOXD13
  • Consensus sequence: NCYAATAAAA Submotif: canonical Cell Type: Chicken GeoId: GSE38910

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targeting for HOXD13 Gene

Localization for HOXD13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXD13 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HOXD13 Gene COMPARTMENTS Subcellular localization image for HOXD13 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for HOXD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with HOXD13: view

Pathways for HOXD13 Gene

SuperPathways for HOXD13 Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for HOXD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IEA --
GO:0006355 regulation of transcription, DNA-templated TAS 9207113
GO:0006366 transcription from RNA polymerase II promoter TAS 8614804
GO:0007275 multicellular organismal development TAS 9207113
GO:0007389 pattern specification process --
genes like me logo Genes that share ontologies with HOXD13: view

No data available for Pathways by source for HOXD13 Gene

Compounds for HOXD13 Gene

(1) Novoseek inferred chemical compound relationships for HOXD13 Gene

Compound -log(P) Hits PubMed IDs
alanine 65.3 18
genes like me logo Genes that share compounds with HOXD13: view

Transcripts for HOXD13 Gene

mRNA/cDNA for HOXD13 Gene

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

Unigene Clusters for HOXD13 Gene

Homeobox D13:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HOXD13

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for HOXD13

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXD13 Gene

No ASD Table

Relevant External Links for HOXD13 Gene

GeneLoc Exon Structure for
HOXD13
ECgene alternative splicing isoforms for
HOXD13

Expression for HOXD13 Gene

mRNA expression in normal human tissues for HOXD13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXD13 Gene

This gene is overexpressed in Colon - Sigmoid (14.7), Vagina (13.5), Cervix - Ectocervix (11.5), Prostate (6.2), and Cervix - Endocervix (4.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for HOXD13 Gene

SOURCE GeneReport for Unigene cluster for HOXD13 Gene Hs.152414

genes like me logo Genes that share expressions with HOXD13: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for HOXD13 Gene

Orthologs for HOXD13 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXD13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HOXD13 35
  • 98.93 (n)
  • 99.13 (a)
HOXD13 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia EVX2 35
  • 90 (n)
  • 96.3 (a)
HOXD13 36
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hoxd13 35
  • 86.82 (n)
  • 94.69 (a)
Hoxd13 16
Hoxd13 36
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HOXD13 36
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HOXD13 36
  • 94 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hoxd13 35
  • 88.09 (n)
  • 96.72 (a)
chicken
(Gallus gallus)
Aves HOXD13 35
  • 77.19 (n)
  • 86.52 (a)
HOXD13 36
  • 94 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HOXD13 36
  • 83 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.21863 35
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxd13 35
  • 71.51 (n)
  • 78.38 (a)
zebrafish
(Danio rerio)
Actinopterygii hoxd13a 36
  • 38 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Abd-B 36
  • 15 (a)
OneToMany
Species with no ortholog for HOXD13:
  • 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)
  • dog (Canis familiaris)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 HOXD13 Gene

ENSEMBL:
Gene Tree for HOXD13 (if available)
TreeFam:
Gene Tree for HOXD13 (if available)

Paralogs for HOXD13 Gene

Selected SIMAP similar genes for HOXD13 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HOXD13: view

Variants for HOXD13 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for HOXD13 Gene

P35453-HXD13_HUMAN
The poly-Ala region is polymorphic (11 to 15 residues) in the normal population and is expanded to about 22-29 residues in SPD1 and syndactyly type 5 patients

Sequence variations from dbSNP and Humsavar for HOXD13 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs847192 -- 176,094,351(-) AAATG(C/T)CATGC intron-variant
rs847193 -- 176,094,280(-) TGCAC(C/T)TAACA intron-variant
rs847194 -- 176,093,973(-) AAAAG(G/T)TCTCT intron-variant
rs847195 -- 176,093,283(-) TTGCC(A/G)AAGTG reference, synonymous-codon
rs847196 -- 176,092,390(-) GAGGC(C/G)GGCGC upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HOXD13 Gene

Variant ID Type Subtype PubMed ID
nsv520227 CNV Loss 19592680
dgv676n67 CNV Gain 20364138
nsv875437 CNV Loss 21882294
nsv875438 CNV Loss 21882294
nsv527187 CNV Loss 19592680
nsv517968 CNV Loss 19592680
dgv4368n71 CNV Loss 21882294
nsv524250 CNV Loss 19592680
nsv875441 CNV Loss 21882294
nsv875442 CNV Loss 21882294
dgv4369n71 CNV Loss 21882294
nsv875446 CNV Loss 21882294

Relevant External Links for HOXD13 Gene

HapMap Linkage Disequilibrium report
HOXD13
Human Gene Mutation Database (HGMD)
HOXD13

Disorders for HOXD13 Gene

(6) OMIM Diseases for HOXD13 Gene (142989)

UniProtKB/Swiss-Prot

HXD13_HUMAN
  • Synpolydactyly 1 (SPD1) [MIM:186000]: Limb malformation that shows a characteristic manifestation in both hands and feet. This condition is inherited as an autosomal dominant trait with reduced penetrance. {ECO:0000269 PubMed:12414828, ECO:0000269 PubMed:8817328}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Brachydactyly D (BDD) [MIM:113200]: A form of brachydactyly. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. Brachydactyly type D is characterized by short and broad terminal phalanges of the thumbs and big toes. {ECO:0000269 PubMed:12649808}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Syndactyly 5 (SDTY5) [MIM:186300]: A form of syndactyly, a congenital anomaly of the hand or foot marked by persistence of the webbing between adjacent digits that are more or less completely attached. The characteristic finding in SDTY5 is the presence of an associated metacarpal and metatarsal fusion. The metacarpals and metatarsals most commonly fused are the 4th and 5th or the 3rd and 4th. Soft tissue syndactyly usually affects the 3rd and 4th fingers and the 2nd and 3rd toes. {ECO:0000269 PubMed:17236141}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Brachydactyly-syndactyly syndrome (BDSD) [MIM:610713]: A disease characterized by generalized shortening of the hands and feet, broad and short distal phalanges of the thumbs, and cutaneous syndactyly of toes 2 and 3. The limb phenotypes observed in this syndrome overlap those of brachydactyly types A4, D, E and syndactyly type 1. {ECO:0000269 PubMed:17236141}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Brachydactyly E1 (BDE1) [MIM:113300]: A form of brachydactyly. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. Brachydactyly type E is characterized by shortening of the fingers mainly in the metacarpals and metatarsals. Wide variability in the number of digits affected occurs from person to person, even in the same family. Some individuals are moderately short of stature. Brachydactyly type E1 is characterized by shortening limited to fourth metacarpals and/or metatarsals. {ECO:0000269 PubMed:12649808}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • VACTERL association (VACTERL) [MIM:192350]: VACTERL is an acronym for vertebral anomalies, anal atresia, congenital cardiac disease, tracheoesophageal fistula, renal anomalies, radial dysplasia, and other limb defects. {ECO:0000269 PubMed:19006232}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(5) University of Copenhagen DISEASES for HOXD13 Gene

(13) Novoseek inferred disease relationships for HOXD13 Gene

Disease -log(P) Hits PubMed IDs
synpolydactyly 99 25
limb malformation 94.2 11
hand-foot-genital syndrome 93.2 2
brachydactyly, type d 92.8 2
malformation foot 85.5 3

Relevant External Links for HOXD13

Genetic Association Database (GAD)
HOXD13
Human Genome Epidemiology (HuGE) Navigator
HOXD13
genes like me logo Genes that share disorders with HOXD13: view

Publications for HOXD13 Gene

  1. Altered growth and branching patterns in synpolydactyly caused by mutations in HOXD13. (PMID: 8614804) Muragaki Y. … Olsen B.R. (Science 1996) 3 4 23
  2. Genomic structure of HOXD13 gene: a nine polyalanine duplication causes synpolydactyly in two unrelated families. (PMID: 8817328) Akarsu A.N. … Sarfarazi M. (Hum. Mol. Genet. 1996) 3 4 23
  3. Missense mutations in the homeodomain of HOXD13 are associated with brachydactyly types D and E. (PMID: 12649808) Johnson D. … Wilkie A.O. (Am. J. Hum. Genet. 2003) 3 4 23
  4. Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. (PMID: 17236141) Zhao X. … Zhang X. (Am. J. Hum. Genet. 2007) 3 4 23
  5. Association of hypospadias with hypoplastic synpolydactyly and role of HOXD13 gene mutations. (PMID: 17656229) TA1zel E. … GA1ler C. (Urology 2007) 3 23

Products for HOXD13 Gene

Sources for HOXD13 Gene

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