Human Gene HOXD13 (ENST00000392539.4) from GENCODE V44
  Description: Homo sapiens homeobox D13 (HOXD13), mRNA. (from RefSeq NM_000523)
RefSeq Summary (NM_000523): 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].
Gencode Transcript: ENST00000392539.4
Gencode Gene: ENSG00000128714.6
Transcript (Including UTRs)
   Position: hg38 chr2:176,092,721-176,095,944 Size: 3,224 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg38 chr2:176,092,891-176,094,730 Size: 1,840 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:176,092,721-176,095,944)mRNA (may differ from genome)Protein (343 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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neXtProtOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Homeobox protein Hox-D13; AltName: Full=Homeobox protein Hox-4I;
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.
POLYMORPHISM: 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.
DISEASE: Defects in HOXD13 are the cause of synpolydactyly 1 (SPD1) [MIM:186000]; also known as syndactyly type 2 (SDTY2). SPD1 is a limb malformation that shows a characteristic manifestation in both hands and feet. This condition is inherited as an autosomal dominant trait with reduced penetrance.
DISEASE: Defects in HOXD13 are the cause of brachydactyly type D (BDD) [MIM:113200]. BDD is characterized by short and broad terminal phalanges of the thumbs and big toes. Inheritance is autosomal dominant.
DISEASE: Defects in HOXD13 are the cause of syndactyly type 5 (SDTY5) [MIM:186300]; also known as syndactyly with 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. Inheritance is autosomal dominant.
DISEASE: Defects in HOXD13 are the cause of brachydactyly- syndactyly syndrome (BDSD) [MIM:610713]. Most of affected individuals exhibit 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.
DISEASE: Defects in HOXD13 are the cause of brachydactyly type E (BDE1) [MIM:113300]. BDE is characterized by shortening of the fingers mainly in the metacarpals and metatarsals. Inheritance is autosomal dominant.
DISEASE: Defects in HOXD13 are a cause of VACTERL association (VACTERL) [MIM:192350]; which includes also VATER association. VACTERL is an acronym for vertebral anomalies, anal atresia, congenital cardiac disease, tracheoesophageal fistula, renal anomalies, radial dysplasia, and other limb defects.
SIMILARITY: Belongs to the Abd-B homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
CAUTION: It is uncertain whether Met-1 or Met-9 is the initiator.
SEQUENCE CAUTION: Sequence=AAC51635.1; Type=Erroneous initiation; Sequence=BAA95352.1; Type=Erroneous initiation;
WEB RESOURCE: Name=GeneReviews; URL="";

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: HOXD13
Diseases sorted by gene-association score: brachydactyly, type e* (1669), syndactyly, type v* (1668), brachydactyly-syndactyly syndrome* (1635), synpolydactyly 1* (1589), brachydactyly, type d* (1330), synpolydactyly* (572), zygodactyly type 3* (350), hoxd13-related brachydactyly* (100), chromosome 2q35 duplication syndrome (29), vater/vacterl association* (25), brachydactyly (25), hand-foot-uterus syndrome (21), 2q31.1 microdeletion syndrome (18), vacterl association (18), triphalangeal thumb (10), hypospadias (9), tracheoesophageal fistula (8), clubfoot (7), talipes equinovarus (7), scarlet fever (6), split-hand/foot malformation 5 (5), bone development disease (4), leukemia, acute myeloid (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.30 RPKM in Vagina
Total median expression: 56.55 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -60.80170-0.358 Picture PostScript Text
3' UTR -319.601214-0.263 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR022067 - HoxA13_N

Pfam Domains:
PF00046 - Homeobox domain
PF12284 - Hox protein A13 N terminal

ModBase Predicted Comparative 3D Structure on P35453
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001158 enhancer sequence-specific DNA binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding
GO:1990837 sequence-specific double-stranded DNA binding

Biological Process:
GO:0001501 skeletal system development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007389 pattern specification process
GO:0009952 anterior/posterior pattern specification
GO:0022612 gland morphogenesis
GO:0030326 embryonic limb morphogenesis
GO:0030539 male genitalia development
GO:0030850 prostate gland development
GO:0033574 response to testosterone
GO:0035108 limb morphogenesis
GO:0042127 regulation of cell proliferation
GO:0042733 embryonic digit morphogenesis
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048619 embryonic hindgut morphogenesis
GO:0060527 prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis
GO:0060571 morphogenesis of an epithelial fold
GO:0060602 branch elongation of an epithelium
GO:0060687 regulation of branching involved in prostate gland morphogenesis

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  JD065640 - Sequence 46664 from Patent EP1572962.
BC148863 - Synthetic construct Homo sapiens clone IMAGE:100015923, MGC:183217 homeobox D13 (HOXD13) mRNA, encodes complete protein.
BC152760 - Synthetic construct Homo sapiens clone IMAGE:100015990, MGC:184156 homeobox D13 (HOXD13) mRNA, encodes complete protein.
AB463753 - Synthetic construct DNA, clone: pF1KB9705, Homo sapiens HOXD13 gene for homeobox D13, without stop codon, in Flexi system.
JD380770 - Sequence 361794 from Patent EP1572962.
JD231728 - Sequence 212752 from Patent EP1572962.
JD092856 - Sequence 73880 from Patent EP1572962.
JD091096 - Sequence 72120 from Patent EP1572962.
MK290762 - Homo sapiens homeobox protein Hox-D13 (HOXD13) mRNA, partial cds.
MK290763 - Homo sapiens homeobox protein Hox-D13 (HOXD13) mRNA, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000392539.1, ENST00000392539.2, ENST00000392539.3, HOX4I, HXD13_HUMAN, NM_000523, P35453, uc002ukf.1, uc002ukf.2, uc002ukf.3
UCSC ID: ENST00000392539.4
RefSeq Accession: NM_000523
Protein: P35453 (aka HXD13_HUMAN or HXDD_HUMAN)
CCDS: CCDS2264.2

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.