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

Aliases for HOXD13 Gene

Aliases for HOXD13 Gene

  • Homeobox D13 2 3 5
  • Homeobox Protein Hox-4I 3 4
  • Homeo Box D13 2 3
  • HOX4I 3 4
  • Homeo Box 4I 3
  • BDSD 3
  • BDE 3
  • SPD 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 E and Syndactyly, Type V. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding 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

Enhancers for HOXD13 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 HOXD13 on UCSC Golden Path with GeneCards custom track

Genomic Location for HOXD13 Gene

Chromosome:
2
Start:
176,087,505 bp from pter
End:
176,095,938 bp from pter
Size:
8,434 bases
Orientation:
Plus strand

Genomic View for HOXD13 Gene

Genes around HOXD13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXD13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

    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; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA95352.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; 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 Lys 289
  • 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 & Families for HOXD13 Gene

Gene Families for HOXD13 Gene

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

Human Phenotype Ontology for HOXD13 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HOXD13 Gene

MGI Knock Outs for HOXD13:

Animal Model Products

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

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function and Transcription Factor Targets 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

No data available for Gene Ontology (GO) - Cellular Components for HOXD13 Gene

Pathways & Interactions for HOXD13 Gene

SuperPathways for HOXD13 Gene

No Data Available

SIGNOR curated interactions for HOXD13 Gene

Activates:

Gene Ontology (GO) - Biological Process for HOXD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0007275 multicellular organism development TAS 9207113
GO:0009952 anterior/posterior pattern specification IEA --
GO:0035108 limb morphogenesis IEA --
GO:0042733 embryonic digit morphogenesis IEA --
genes like me logo Genes that share ontologies with HOXD13: view

No data available for Pathways by source for HOXD13 Gene

Drugs & Compounds for HOXD13 Gene

(1) Drugs for HOXD13 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with HOXD13: view

Transcripts for HOXD13 Gene

mRNA/cDNA for HOXD13 Gene

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

Unigene Clusters for HOXD13 Gene

Homeobox D13:
Representative Sequences:

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 (x14.7), Vagina (x13.5), Cervix - Ectocervix (x11.5), Prostate (x6.2), and Cervix - Endocervix (x4.4).

Protein differential expression in normal tissues from HIPED for HOXD13 Gene

This gene is overexpressed in Pancreatic juice (52.0) and Heart (17.0).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with HOXD13: view

Protein tissue co-expression partners for HOXD13 Gene

Primer 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
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
chimpanzee
(Pan troglodytes)
Mammalia HOXD13 35
  • 98.93 (n)
  • 99.13 (a)
HOXD13 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hoxd13 35
  • 88.09 (n)
  • 96.72 (a)
oppossum
(Monodelphis domestica)
Mammalia HOXD13 36
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HOXD13 36
  • 94 (a)
OneToOne
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
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxd13 35
  • 71.51 (n)
  • 78.38 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.21863 35
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

(5) 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

HXD13_HUMAN-P35453
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
rs28928892 Brachydactyly D (BDD), Brachydactyly E1 (BDE1) 176,094,645(+) CCTAT(A/C/G)TGAGA reference, missense
rs28928891 Brachydactyly E1 (BDE1) 176,094,662(+) TGACC(A/C/G)TTTGG reference, missense
rs35290213 - 176,093,644(-) GTGGG(A/C)CCCCT intron-variant, reference, missense
rs28933082 Synpolydactyly 1 (SPD1) 176,094,614(+) ACAAG(C/T)GGCGG reference, missense
VAR_031652 Syndactyly 5 (SDTY5)

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

Variation tolerance for HOXD13 Gene

Residual Variation Intolerance Score: 56% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.11; 38.50% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HOXD13 Gene

Human Gene Mutation Database (HGMD)
HOXD13

Disorders for HOXD13 Gene

MalaCards: The human disease database

(21) MalaCards diseases for HOXD13 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
brachydactyly, type e
  • diamond-blackfan anemia 1
syndactyly, type v
  • syndactyly type 5
synpolydactyly, type ii
  • synpolydactyly with foot anomalies
brachydactyly, type d
  • brachydactyly type d
brachydactyly-syndactyly syndrome
  • bdsd
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

HXD13_HUMAN
  • 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.
  • 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.
  • 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.
  • 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.
  • 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:26581570, ECO:0000269 PubMed:8817328}. 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 gene represented in this entry may be involved in disease pathogenesis.

Relevant External Links for HOXD13

Genetic Association Database (GAD)
HOXD13
Human Genome Epidemiology (HuGE) Navigator
HOXD13
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HOXD13
genes like me logo Genes that share disorders with HOXD13: view

No data available for Genatlas for HOXD13 Gene

Publications for HOXD13 Gene

  1. 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 67
  2. A G220V substitution within the N-terminal transcription regulating domain of HOXD13 causes a variant synpolydactyly phenotype. (PMID: 19060004) Fantini S. … Zappavigna V. (Hum. Mol. Genet. 2009) 3 23
  3. HOX D13 expression across 79 tumor tissue types. (PMID: 19488988) Cantile M. … Cillo C. (Int. J. Cancer 2009) 3 23
  4. Polyalanine repeat expansion mutations in the HOXD13 gene in Pakistani families with synpolydactyly. (PMID: 19686284) Wajid M. … Christiano A.M. (Clin. Genet. 2009) 3 23
  5. HOXD13 binds DNA replication origins to promote origin licensing and is inhibited by geminin. (PMID: 19703996) Salsi V. … Zappavigna V. (Mol. Cell. Biol. 2009) 3 23

Products for HOXD13 Gene

Sources for HOXD13 Gene

Content