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P35453

- HXD13_HUMAN

UniProt

P35453 - HXD13_HUMAN

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Protein

Homeobox protein Hox-D13

Gene

HOXD13

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi276 – 33560HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. chromatin binding Source: Ensembl
  2. DNA binding Source: ProtInc
  3. sequence-specific DNA binding Source: InterPro
  4. sequence-specific DNA binding transcription factor activity Source: Ensembl

GO - Biological processi

  1. anterior/posterior pattern specification Source: Ensembl
  2. branch elongation of an epithelium Source: Ensembl
  3. embryonic digit morphogenesis Source: Ensembl
  4. embryonic hindgut morphogenesis Source: Ensembl
  5. male genitalia development Source: Ensembl
  6. morphogenesis of an epithelial fold Source: Ensembl
  7. multicellular organismal development Source: ProtInc
  8. positive regulation of transcription from RNA polymerase II promoter Source: Ensembl
  9. prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis Source: Ensembl
  10. regulation of branching involved in prostate gland morphogenesis Source: Ensembl
  11. regulation of cell proliferation Source: Ensembl
  12. regulation of transcription, DNA-templated Source: ProtInc
  13. skeletal system development Source: ProtInc
  14. transcription from RNA polymerase II promoter Source: ProtInc
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Homeobox protein Hox-D13
Alternative name(s):
Homeobox protein Hox-4I
Gene namesi
Name:HOXD13
Synonyms:HOX4I
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 2

Organism-specific databases

HGNCiHGNC:5136. HOXD13.

Subcellular locationi

GO - Cellular componenti

  1. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

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.2 Publications
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti57 – 571A → AAAAAAAAAA in SPD1 and in syndactyly type 5. 2 Publications
VAR_003818
Natural varianti306 – 3061R → W in SPD1. 1 Publication
Corresponds to variant rs28933082 [ dbSNP | Ensembl ].
VAR_031651
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.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti316 – 3161S → C in BDE1 and BDD. 1 Publication
Corresponds to variant rs28928892 [ dbSNP | Ensembl ].
VAR_015952
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.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti325 – 3251Q → R in SDTY5; impairs capacity to transactivate EPHA7 promoter. 1 Publication
VAR_031652
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 1.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti57 – 637Missing in BDSD; does not affect capacity to transactivate EPHA7 promoter.
VAR_031649
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.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti316 – 3161S → C in BDE1 and BDD. 1 Publication
Corresponds to variant rs28928892 [ dbSNP | Ensembl ].
VAR_015952
Natural varianti322 – 3221I → L in BDE1. 1 Publication
Corresponds to variant rs28928891 [ dbSNP | Ensembl ].
VAR_015953
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.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.

Keywords - Diseasei

Disease mutation

Organism-specific databases

MIMi113200. phenotype.
113300. phenotype.
186000. phenotype.
186300. phenotype.
192350. phenotype.
610713. phenotype.
Orphaneti93385. Brachydactyly type D.
93387. Brachydactyly type E.
93409. Brachydactyly-syndactyly, Zhao type.
93406. Syndactyly type 5.
295195. Synpolydactyly type 1.
887. VACTERL/VATER association.
295191. Zygodactyly type 3.
PharmGKBiPA29410.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 343343Homeobox protein Hox-D13PRO_0000200244Add
BLAST

Proteomic databases

MaxQBiP35453.
PaxDbiP35453.
PRIDEiP35453.

PTM databases

PhosphoSiteiP35453.

Expressioni

Gene expression databases

BgeeiP35453.
CleanExiHS_HOXD13.
GenevestigatoriP35453.

Interactioni

Protein-protein interaction databases

BioGridi109479. 10 interactions.
STRINGi9606.ENSP00000376322.

Structurei

3D structure databases

ProteinModelPortaliP35453.
SMRiP35453. Positions 276-341.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi25 – 306Poly-Ser
Compositional biasi32 – 365Poly-Ala
Compositional biasi57 – 7115Poly-AlaAdd
BLAST
Compositional biasi85 – 928Poly-Ser
Compositional biasi113 – 1186Poly-Ala

Sequence similaritiesi

Belongs to the Abd-B homeobox family.Curated
Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiNOG251666.
GeneTreeiENSGT00760000118834.
HOGENOMiHOG000231176.
HOVERGENiHBG106958.
InParanoidiP35453.
KOiK09298.
OMAiAKECPAP.
OrthoDBiEOG7SJD53.
PhylomeDBiP35453.
TreeFamiTF330813.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR022067. HoxA13_N.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF12284. HoxA13_N. 1 hit.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P35453-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSRAGSWDMD GLRADGGGAG GAPASSSSSS VAAAAASGQC RGFLSAPVFA
60 70 80 90 100
GTHSGRAAAA AAAAAAAAAA ASGFAYPGTS ERTGSSSSSS SSAVVAARPE
110 120 130 140 150
APPAKECPAP TPAAAAAAPP SAPALGYGYH FGNGYYSCRM SHGVGLQQNA
160 170 180 190 200
LKSSPHASLG GFPVEKYMDV SGLASSSVPA NEVPARAKEV SFYQGYTSPY
210 220 230 240 250
QHVPGYIDMV STFGSGEPRH EAYISMEGYQ SWTLANGWNS QVYCTKDQPQ
260 270 280 290 300
GSHFWKSSFP GDVALNQPDM CVYRRGRKKR VPYTKLQLKE LENEYAINKF
310 320 330 340
INKDKRRRIS AATNLSERQV TIWFQNRRVK DKKIVSKLKD TVS
Length:343
Mass (Da):36,101
Last modified:February 10, 2009 - v3
Checksum:iCF34D0319021430A
GO

Sequence cautioni

The sequence AAC51635.1 differs from that shown. Reason: Erroneous initiation. Curated
The sequence BAA95352.1 differs from that shown. Reason: Erroneous initiation. Curated

Polymorphismi

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.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti57 – 637Missing in BDSD; does not affect capacity to transactivate EPHA7 promoter.
VAR_031649
Natural varianti57 – 582Missing.1 Publication
VAR_031648
Natural varianti57 – 571A → AAAAAAAAAA in SPD1 and in syndactyly type 5. 2 Publications
VAR_003818
Natural varianti252 – 2521S → A.
Corresponds to variant rs35290213 [ dbSNP | Ensembl ].
VAR_031650
Natural varianti306 – 3061R → W in SPD1. 1 Publication
Corresponds to variant rs28933082 [ dbSNP | Ensembl ].
VAR_031651
Natural varianti316 – 3161S → C in BDE1 and BDD. 1 Publication
Corresponds to variant rs28928892 [ dbSNP | Ensembl ].
VAR_015952
Natural varianti322 – 3221I → L in BDE1. 1 Publication
Corresponds to variant rs28928891 [ dbSNP | Ensembl ].
VAR_015953
Natural varianti325 – 3251Q → R in SDTY5; impairs capacity to transactivate EPHA7 promoter. 1 Publication
VAR_031652

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF005220, AF005219 Genomic DNA. Translation: AAC51635.1. Different initiation.
AB032481 Genomic DNA. Translation: BAA95352.1. Different initiation.
AC009336 Genomic DNA. No translation available.
CCDSiCCDS2264.2.
PIRiB39065.
RefSeqiNP_000514.2. NM_000523.3.
UniGeneiHs.152414.

Genome annotation databases

EnsembliENST00000392539; ENSP00000376322; ENSG00000128714.
GeneIDi3239.
KEGGihsa:3239.
UCSCiuc002ukf.1. human.

Polymorphism databases

DMDMi223590221.

Keywords - Coding sequence diversityi

Polymorphism, Triplet repeat expansion

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF005220 , AF005219 Genomic DNA. Translation: AAC51635.1 . Different initiation.
AB032481 Genomic DNA. Translation: BAA95352.1 . Different initiation.
AC009336 Genomic DNA. No translation available.
CCDSi CCDS2264.2.
PIRi B39065.
RefSeqi NP_000514.2. NM_000523.3.
UniGenei Hs.152414.

3D structure databases

ProteinModelPortali P35453.
SMRi P35453. Positions 276-341.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 109479. 10 interactions.
STRINGi 9606.ENSP00000376322.

PTM databases

PhosphoSitei P35453.

Polymorphism databases

DMDMi 223590221.

Proteomic databases

MaxQBi P35453.
PaxDbi P35453.
PRIDEi P35453.

Protocols and materials databases

DNASUi 3239.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000392539 ; ENSP00000376322 ; ENSG00000128714 .
GeneIDi 3239.
KEGGi hsa:3239.
UCSCi uc002ukf.1. human.

Organism-specific databases

CTDi 3239.
GeneCardsi GC02P176921.
HGNCi HGNC:5136. HOXD13.
MIMi 113200. phenotype.
113300. phenotype.
142989. gene.
186000. phenotype.
186300. phenotype.
192350. phenotype.
610713. phenotype.
neXtProti NX_P35453.
Orphaneti 93385. Brachydactyly type D.
93387. Brachydactyly type E.
93409. Brachydactyly-syndactyly, Zhao type.
93406. Syndactyly type 5.
295195. Synpolydactyly type 1.
887. VACTERL/VATER association.
295191. Zygodactyly type 3.
PharmGKBi PA29410.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG251666.
GeneTreei ENSGT00760000118834.
HOGENOMi HOG000231176.
HOVERGENi HBG106958.
InParanoidi P35453.
KOi K09298.
OMAi AKECPAP.
OrthoDBi EOG7SJD53.
PhylomeDBi P35453.
TreeFami TF330813.

Miscellaneous databases

ChiTaRSi HOXD13. human.
GeneWikii HOXD13.
GenomeRNAii 3239.
NextBioi 12891.
PROi P35453.
SOURCEi Search...

Gene expression databases

Bgeei P35453.
CleanExi HS_HOXD13.
Genevestigatori P35453.

Family and domain databases

Gene3Di 1.10.10.60. 1 hit.
InterProi IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR022067. HoxA13_N.
[Graphical view ]
Pfami PF00046. Homeobox. 1 hit.
PF12284. HoxA13_N. 1 hit.
[Graphical view ]
SMARTi SM00389. HOX. 1 hit.
[Graphical view ]
SUPFAMi SSF46689. SSF46689. 1 hit.
PROSITEi PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Altered growth and branching patterns in synpolydactyly caused by mutations in HOXD13."
    Muragaki Y., Mundlos S., Upton J., Olsen B.R.
    Science 272:548-551(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The t(2:11)(q31:p15) translocation in acute myeloid leukemia fuses NUP98 nucleoporin gene to HOXD13 homeobox gene."
    Arai Y., Arai K., Kita K., Miwa H., Kamada N., Ohki M.
    Submitted (SEP-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "EVX2, a human homeobox gene homologous to the even-skipped segmentation gene, is localized at the 5' end of HOX4 locus on chromosome 2."
    D'Esposito M., Morelli F., Acampora D., Migliaccio E., Simeone A., Boncinelli E.
    Genomics 10:43-50(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 276-341.
  5. Cited for: INVOLVEMENT IN VACTERL.
  6. "Genomic structure of HOXD13 gene: a nine polyalanine duplication causes synpolydactyly in two unrelated families."
    Akarsu A.N., Stoilov I., Yilmaz E., Sayli B.S., Sarfarazi M.
    Hum. Mol. Genet. 5:945-952(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT SPD1 ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-57 INS.
  7. "Severe digital abnormalities in a patient heterozygous for both a novel missense mutation in HOXD13 and a polyalanine tract expansion in HOXA13."
    Debeer P., Bacchelli C., Scambler P.J., De Smet L., Fryns J.-P., Goodman F.R.
    J. Med. Genet. 39:852-856(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT SPD1 TRP-306.
  8. "Missense mutations in the homeodomain of HOXD13 are associated with brachydactyly types D and E."
    Johnson D., Kan S.H., Oldridge M., Trembath R.C., Roche P., Esnouf R.M., Giele H., Wilkie A.O.
    Am. J. Hum. Genet. 72:984-997(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS BDE1 CYS-316 AND LEU-322, VARIANT BDD CYS-316.
  9. "A 72-year-old Danish puzzle resolved -- comparative analysis of phenotypes in families with different-sized HOXD13 polyalanine expansions."
    Kjaer K.W., Hansen L., Eiberg H., Utkus A., Skovgaard L.T., Leicht P., Opitz J.M., Tommerup N.
    Am. J. Med. Genet. A 138:328-339(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-57 INS, VARIANT 57-ALA-ALA-58 DEL.
  10. "Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome."
    Zhao X., Sun M., Zhao J., Leyva J.A., Zhu H., Yang W., Zeng X., Ao Y., Liu Q., Liu G., Lo W.H.Y., Jabs E.W., Amzel L.M., Shan X., Zhang X.
    Am. J. Hum. Genet. 80:361-371(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT BDSD 57-ALA--ALA-62 DEL, VARIANT SDTY5 ARG-325, CHARACTERIZATION OF VARIANT BDSD 57-ALA--ALA-62 DEL, CHARACTERIZATION OF VARIANT SDTY5 ARG-325.

Entry informationi

Entry nameiHXD13_HUMAN
AccessioniPrimary (citable) accession number: P35453
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: February 10, 2009
Last modified: October 29, 2014
This is version 140 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Caution

It is uncertain whether Met-1 or Met-9 is the initiator.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Vertebrate homeotic Hox proteins
    Nomenclature of vertebrate homeotic Hox proteins and list of entries
  2. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3