Aliases for HOXD13 Gene
Aliases for HOXD13 Gene
External Ids for HOXD13 Gene
- HGNC: 5136
- Entrez Gene: 3239
- Ensembl: ENSG00000128714
- OMIM: 142989
- UniProtKB: P35453
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
-
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 Syndactyly, Type V and Brachydactyly, Type E. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and chromatin binding. An important paralog of this gene is HOXA13.
UniProtKB/Swiss-Prot for HOXD13 Gene
-
Sequence-specific transcription factor that binds gene promoters and activates their transcription (PubMed:24789103). Part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis (By similarity).
No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD13 Gene
Genomics for HOXD13 Gene
Regulatory Elements for HOXD13 Gene
- Transcription factor binding sites by QIAGEN in the HOXD13 gene promoter:
Regulatory Element Products
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
- Cytogenetic band:
-
- 2q31.1 by Ensembl
- 2q31.1 by Entrez Gene
- 2q31.1 by HGNC
Genomic Neighborhood
• Exon Structure
• Gene 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};
Protein Expression for HOXD13 Gene
Post-translational modifications for HOXD13 Gene
Other Protein References for HOXD13 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- EMD Millipore Complete listing of Mono and Polychlonal Antibodies for HOXD13
-
Custom Antibody ServicesOriGene Antibodies for HOXD13
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- antibodies-online Antibodies for HOXD13: See all 66
- GeneTex HOXD13 antibody for HOXD13
Protein Products
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OriGene Purified Proteins for HOXD13
- Search Origene for MassSpec and Protein Over-expression Lysates for HOXD13
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- antibodies-online Proteins for HOXD13: See all 5
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- Search GeneTex for Proteins for HOXD13
Assay Products
- antibodies-online Kits for HOXD13: See all 7
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
- InterPro:
- ProtoNet:
Suggested Antigen Peptide Sequences for HOXD13 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
P35453- Family:
-
- Belongs to the Abd-B homeobox family.
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 that binds gene promoters and activates their transcription (PubMed:24789103). Part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis (By similarity).
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000978 | RNA polymerase II core promoter proximal region sequence-specific DNA binding | IEA | -- |
| GO:0001077 | transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding | IEA | -- |
| GO:0001228 | transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding | IMP | 24789103 |
| GO:0003677 | DNA binding | TAS,IDA | 26581570 |
| GO:0003682 | chromatin binding | IEA | -- |
Phenotypes for HOXD13 Gene
- MGI mutant phenotypes for HOXD13:
-
inferred from 9 alleles
- mortality/aging
- growth/size/body region phenotype
- muscle phenotype
- digestive/alimentary phenotype
- reproductive system phenotype
- endocrine/exocrine gland phenotype
- vision/eye phenotype
- integument phenotype
- limbs/digits/tail phenotype
- skeleton phenotype
- embryo phenotype
- renal/urinary system phenotype
- no phenotypic analysis
- GenomeRNAi human phenotypes for HOXD13:
Animal Models for HOXD13 Gene
Animal Model Products
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ViGene Biosciences lentiviral particle packaged cDNA for HOXD13 gene
-
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CRISPR Products
-
OriGene CRISPR knockouts for HOXD13
-
Santa Cruz Biotechnology (SCBT) CRISPR for HOXD13
- GenScript: Design CRISPR guide RNA sequences for HOXD13
miRNA for HOXD13 Gene
- miRTarBase miRNAs that target HOXD13
-
- hsa-mir-103a-3p (MIRT027146)
- hsa-mir-423-3p (MIRT042641)
- hsa-mir-149-5p (MIRT045586)
- hsa-mir-10a-5p (MIRT047651)
- hsa-mir-16-5p (MIRT051222)
- hsa-mir-1260b (MIRT052694)
- hsa-mir-329-5p (MIRT086201)
- hsa-mir-488-5p (MIRT086202)
- hsa-mir-298 (MIRT086204)
- hsa-mir-922 (MIRT086205)
- hsa-mir-4271 (MIRT086207)
- hsa-mir-4725-3p (MIRT086209)
- hsa-mir-6077 (MIRT086211)
- hsa-mir-6783-5p (MIRT086212)
- hsa-mir-6780b-5p (MIRT086213)
- hsa-mir-92a-1-5p (MIRT299542)
- hsa-mir-3147 (MIRT299543)
- hsa-mir-1303 (MIRT557012)
- hsa-mir-6721-5p (MIRT557013)
- hsa-mir-3936 (MIRT557014)
Targeted motifs for HOXD13 Gene
- Consensus sequence: NCYAATAAAA Submotif: canonical Cell Type: Chicken GEO ID: GSE38910
miRNA Products
- Search ViGene Biosciences for HOXD13
Inhibitory RNA Products
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Horizon Cell Lines for HOXD13
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-
ViGene Biosciences lentiviral particle packaged cDNA for HOXD13 gene
-
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Flow Cytometry Products
No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for HOXD13 Gene
Localization for HOXD13 Gene
Subcellular locations from UniProtKB/Swiss-Prot for HOXD13 Gene
- Nucleus.
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IDA | -- |
Pathways & Interactions for HOXD13 Gene
Interacting Proteins for HOXD13 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0001501 | skeletal system development | IEA,TAS | -- |
| GO:0006351 | transcription, DNA-templated | IEA | -- |
| GO:0006355 | regulation of transcription, DNA-templated | TAS | 9207113 |
| GO:0006366 | transcription from RNA polymerase II promoter | TAS | 8614804 |
| GO:0007275 | multicellular organism development | TAS | 9207113 |
No data available for Pathways by source for HOXD13 Gene
Transcripts for HOXD13 Gene
mRNA/cDNA for HOXD13 Gene
- (3) REFSEQ mRNAs :
- (0) Additional mRNA sequences :
- -
- (11) Selected AceView cDNA sequences:
- (1) Ensembl transcripts including schematic representations, and UCSC links where relevant :
CRISPR Products
-
OriGene CRISPR knockouts for HOXD13
-
Santa Cruz Biotechnology (SCBT) CRISPR for HOXD13
- GenScript: Design CRISPR guide RNA sequences for HOXD13
miRNA Products
- Search ViGene Biosciences for HOXD13
Inhibitory RNA Products
- Origene shRNA, siRNA, and RNAi products in human, mouse, rat for HOXD13
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Flow Cytometry Products
Expression for HOXD13 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
-
Limb (Muscoskeletal System)
- Apical Ectodermal Ridge Cells Limb Ectoderm
- Zone Of Polarizing Activity Cells Limb Bud
- Limb Bud Mesenchyme Cells Limb Bud
- Limb Muscle Progenitor Cells Forelimb Myotome
- Prechondrocytic Mesenchymal Cells Autopod
-
Mesoderm (Gastrulation Derivatives)
- Zone Of Polarizing Activity Cells Limb Bud
- Limb Bud Mesenchyme Cells Limb Bud
-
Ectoderm (Gastrulation Derivatives)
- Apical Ectodermal Ridge Cells Limb Ectoderm
-
Skeletal Muscle (Muscoskeletal System)
- Limb Muscle Progenitor Cells Forelimb Myotome
- Bone (Muscoskeletal System)
- Cartilage (Muscoskeletal System)
- Intermediate Mesoderm (Gastrulation Derivatives)
-
Colon (Gastrointestinal Tract)
mRNA differential expression in normal tissues according to GTEx for HOXD13 Gene
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HOXD13 Gene
NURSA nuclear receptor signaling pathways regulating expression of HOXD13 Gene:
HOXD13SOURCE GeneReport for Unigene cluster for HOXD13 Gene:
Hs.152414Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXD13 Gene
- ectoderm
- endoderm
- mesoderm
- cardiovascular
- digestive
- integumentary
- nervous
- reproductive
- respiratory
- skeletal muscle
- skeleton
- urinary
- brain
- cheek
- chin
- ear
- epiglottis
- face
- head
- jaw
- larynx
- mandible
- maxilla
- mouth
- neck
- nose
- pharynx
- skull
- tooth
- vocal cord
- bronchus
- chest wall
- clavicle
- diaphragm
- esophagus
- heart
- heart valve
- lung
- rib
- rib cage
- sternum
- trachea
- intestine
- kidney
- large intestine
- liver
- small intestine
- stomach
- anus
- pelvis
- penis
- placenta
- rectum
- ureter
- urethra
- urinary bladder
- uterus
- vagina
- ankle
- arm
- digit
- elbow
- finger
- foot
- forearm
- hand
- hip
- knee
- lower limb
- nail
- radius
- shoulder
- toe
- ulna
- upper limb
- wrist
- blood
- blood vessel
- skin
- spinal column
- spinal cord
- vertebrae
Primer Products
-
OriGene qPCR primer pairs for HOXD13
No data available for mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for HOXD13 Gene
Orthologs for HOXD13 Gene
This gene was present in the common ancestor of animals.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | HOXD13 34 35 |
|
||
| cow (Bos Taurus) |
Mammalia | HOXD13 35 |
|
OneToOne | |
| EVX2 34 |
|
||||
| platypus (Ornithorhynchus anatinus) |
Mammalia | HOXD13 35 |
|
OneToOne | |
| rat (Rattus norvegicus) |
Mammalia | Hoxd13 34 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | HOXD13 35 |
|
OneToOne | |
| mouse (Mus musculus) |
Mammalia | Hoxd13 34 16 35 |
|
||
| chicken (Gallus gallus) |
Aves | HOXD13 34 35 |
|
||
| lizard (Anolis carolinensis) |
Reptilia | HOXD13 35 |
|
OneToOne | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | hoxd13 34 |
|
||
| African clawed frog (Xenopus laevis) |
Amphibia | Xl.21863 34 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | hoxd13a 35 |
|
OneToOne | |
| fruit fly (Drosophila melanogaster) |
Insecta | Abd-B 35 |
|
OneToMany |
- Species where no ortholog for HOXD13 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)
- 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)
Paralogs for HOXD13 Gene
Paralogs for HOXD13 Gene
(5) SIMAP similar genes for HOXD13 Gene using alignment to 1 proteins:
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.
| SNP ID | Clin | Chr 02 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs104893635 | Pathogenic, Syndactyly 5 (SDTY5) [MIM:186300] | 176,094,672(+) | GTTTC(A/G)GAACC | reference, missense | |
| rs28928891 | Pathogenic, Brachydactyly E1 (BDE1) [MIM:113300] | 176,094,662(+) | TGACC(A/C/G)TTTGG | reference, missense | |
| rs28928892 | Pathogenic, Brachydactyly D (BDD) [MIM:113200], Brachydactyly E1 (BDE1) [MIM:113300] | 176,094,645(+) | CCTAT(A/C/G)TGAGA | reference, missense | |
| rs28933082 | Pathogenic, Synpolydactyly 1 (SPD1) [MIM:186000] | 176,094,614(+) | ACAAG(C/G/T)GGCGG | reference, missense | |
| VAR_075400 | Synpolydactyly 1 (SPD1) [MIM:186000] |
Relevant External Links for HOXD13 Gene
Disorders for HOXD13 Gene
(21) MalaCards diseases for HOXD13 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| syndactyly, type v |
|
|
| brachydactyly, type e |
|
|
| brachydactyly-syndactyly syndrome |
|
|
| synpolydactyly, type ii |
|
|
| brachydactyly, type d |
|
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, ECO:0000269 PubMed:24789103}. 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-syndactyly-oligodactyly syndrome (BDSDO) [MIM:610713]: A syndrome characterized by a complex brachydactyly-syndactyly-oligodactyly phenotype. Limb anomalies include reduced number of digits that are severely shortened, camptodactyly, syndactyly, absence of terminal phalanges of the thumbs, and absence of nails of the thumbs and toes. {ECO:0000269 PubMed:23995701}. 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:16222680, ECO:0000269 PubMed:24789103, 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
No data available for Genatlas for HOXD13 Gene
Publications for HOXD13 Gene
- 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 22 64
- 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 22 64
- 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 22 64
- Altered growth and branching patterns in synpolydactyly caused by mutations in HOXD13. (PMID: 8614804) Muragaki Y. … Olsen B.R. (Science 1996) 3 4 22 64
- A homozygous HOXD13 missense mutation causes a severe form of synpolydactyly with metacarpal to carpal transformation. (PMID: 26581570) Ibrahim D.M. … Spielmann M. (Am. J. Med. Genet. A 2015) 3 4 64
Products for HOXD13 Gene
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- antibodies-online Antibodies for HOXD13: See all 66
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- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for HOXD13 Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
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