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Protein

Homeobox protein Hox-D13

Gene

HOXD13

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

Functioni

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).By similarity1 Publication

Caution

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

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi276 – 335HomeoboxPROSITE-ProRule annotationAdd BLAST60

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein, DNA-binding
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

SIGNORiP35453

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
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000128714.5
HGNCiHGNC:5136 HOXD13
MIMi142989 gene
neXtProtiNX_P35453

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Synpolydactyly 1 (SPD1)5 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionLimb malformation that shows a characteristic manifestation in both hands and feet. This condition is inherited as an autosomal dominant trait with reduced penetrance.
See also OMIM:186000
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00381857A → AAAAAAAAAA in SPD1. 2 Publications1
Natural variantiVAR_076833306R → G in SPD1; decreases the transcriptional activator activity. 1 PublicationCorresponds to variant dbSNP:rs28933082EnsemblClinVar.1
Natural variantiVAR_076834306R → Q in SPD1; decreases the transcriptional activator activity. 1 PublicationCorresponds to variant dbSNP:rs879255265EnsemblClinVar.1
Natural variantiVAR_031651306R → W in SPD1. 1 PublicationCorresponds to variant dbSNP:rs28933082EnsemblClinVar.1
Natural variantiVAR_075400313T → R in SPD1; disrupts interaction with DNA. 1 Publication1
Brachydactyly D (BDD)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:113200
Syndactyly 5 (SDTY5)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:186300
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_031652325Q → R in SDTY5; impairs capacity to transactivate EPHA7 promoter. 2 PublicationsCorresponds to variant dbSNP:rs104893635EnsemblClinVar.1
Brachydactyly-syndactyly syndrome (BDSD)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:610713
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03164957 – 63Missing in BDSD; does not affect capacity to transactivate EPHA7 promoter. 7
Brachydactyly E1 (BDE1)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:113300
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_015953322I → L in BDE1; decreases the transcriptional activator activity. 2 PublicationsCorresponds to variant dbSNP:rs28928891EnsemblClinVar.1
VACTERL association (VACTERL)1 Publication
The gene represented in this entry may be involved in disease pathogenesis.
Disease descriptionVACTERL is an acronym for vertebral anomalies, anal atresia, congenital cardiac disease, tracheoesophageal fistula, renal anomalies, radial dysplasia, and other limb defects.
See also OMIM:192350
Brachydactyly-syndactyly-oligodactyly syndrome (BDSDO)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:610713
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_076835325Q → K in BDSDO. 1 PublicationCorresponds to variant dbSNP:rs875989842EnsemblClinVar.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi3239
MalaCardsiHOXD13
MIMi113200 phenotype
113300 phenotype
186000 phenotype
186300 phenotype
192350 phenotype
610713 phenotype
OpenTargetsiENSG00000128714
Orphaneti93387 Brachydactyly type E
93409 Brachydactyly-syndactyly, Zhao type
93385 NON RARE IN EUROPE: Brachydactyly type D
93406 Syndactyly type 5
295195 Synpolydactyly type 1
887 VACTERL/VATER association
295191 Zygodactyly type 3
PharmGKBiPA29410

Polymorphism and mutation databases

BioMutaiHOXD13
DMDMi223590221

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002002441 – 343Homeobox protein Hox-D13Add BLAST343

Proteomic databases

EPDiP35453
MaxQBiP35453
PaxDbiP35453
PeptideAtlasiP35453
PRIDEiP35453
ProteomicsDBi55065

PTM databases

iPTMnetiP35453
PhosphoSitePlusiP35453

Expressioni

Gene expression databases

BgeeiENSG00000128714 Expressed in 36 organ(s), highest expression level in ectocervix
CleanExiHS_HOXD13
GenevisibleiP35453 HS

Organism-specific databases

HPAiHPA064064

Interactioni

Protein-protein interaction databases

BioGridi109479, 54 interactors
IntActiP35453, 17 interactors
MINTiP35453
STRINGi9606.ENSP00000376322

Structurei

3D structure databases

ProteinModelPortaliP35453
SMRiP35453
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi25 – 30Poly-Ser6
Compositional biasi32 – 36Poly-Ala5
Compositional biasi57 – 71Poly-AlaAdd BLAST15
Compositional biasi85 – 92Poly-Ser8
Compositional biasi113 – 118Poly-Ala6

Sequence similaritiesi

Belongs to the Abd-B homeobox family.Curated

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiKOG0487 Eukaryota
ENOG4111FJP LUCA
GeneTreeiENSGT00910000143984
HOGENOMiHOG000231176
HOVERGENiHBG106958
InParanoidiP35453
KOiK09298
OMAiFAYPGTS
OrthoDBiEOG091G0E5Q
PhylomeDBiP35453
TreeFamiTF330813

Family and domain databases

CDDicd00086 homeodomain, 1 hit
InterProiView protein in InterPro
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR022067 HoxA13_N
PfamiView protein in Pfam
PF00046 Homeobox, 1 hit
PF12284 HoxA13_N, 1 hit
SMARTiView protein in SMART
SM00389 HOX, 1 hit
SUPFAMiSSF46689 SSF46689, 1 hit
PROSITEiView protein in PROSITE
PS00027 HOMEOBOX_1, 1 hit
PS50071 HOMEOBOX_2, 1 hit

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 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAA95352 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAA95352 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)DescriptionActionsGraphical viewLength
Natural variantiVAR_03164957 – 63Missing in BDSD; does not affect capacity to transactivate EPHA7 promoter. 7
Natural variantiVAR_03164857 – 58Missing 1 Publication2
Natural variantiVAR_00381857A → AAAAAAAAAA in SPD1. 2 Publications1
Natural variantiVAR_031650252S → A. Corresponds to variant dbSNP:rs35290213Ensembl.1
Natural variantiVAR_076833306R → G in SPD1; decreases the transcriptional activator activity. 1 PublicationCorresponds to variant dbSNP:rs28933082EnsemblClinVar.1
Natural variantiVAR_076834306R → Q in SPD1; decreases the transcriptional activator activity. 1 PublicationCorresponds to variant dbSNP:rs879255265EnsemblClinVar.1
Natural variantiVAR_031651306R → W in SPD1. 1 PublicationCorresponds to variant dbSNP:rs28933082EnsemblClinVar.1
Natural variantiVAR_075400313T → R in SPD1; disrupts interaction with DNA. 1 Publication1
Natural variantiVAR_015952316S → C in BDE1 and BDD. 1 PublicationCorresponds to variant dbSNP:rs28928892EnsemblClinVar.1
Natural variantiVAR_015953322I → L in BDE1; decreases the transcriptional activator activity. 2 PublicationsCorresponds to variant dbSNP:rs28928891EnsemblClinVar.1
Natural variantiVAR_076835325Q → K in BDSDO. 1 PublicationCorresponds to variant dbSNP:rs875989842EnsemblClinVar.1
Natural variantiVAR_031652325Q → R in SDTY5; impairs capacity to transactivate EPHA7 promoter. 2 PublicationsCorresponds to variant dbSNP:rs104893635EnsemblClinVar.1

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.2 human

Keywords - Coding sequence diversityi

Polymorphism, Triplet repeat expansion

Similar proteinsi

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.
CCDSiCCDS2264.2
PIRiB39065
RefSeqiNP_000514.2, NM_000523.3
UniGeneiHs.152414

3D structure databases

ProteinModelPortaliP35453
SMRiP35453
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109479, 54 interactors
IntActiP35453, 17 interactors
MINTiP35453
STRINGi9606.ENSP00000376322

PTM databases

iPTMnetiP35453
PhosphoSitePlusiP35453

Polymorphism and mutation databases

BioMutaiHOXD13
DMDMi223590221

Proteomic databases

EPDiP35453
MaxQBiP35453
PaxDbiP35453
PeptideAtlasiP35453
PRIDEiP35453
ProteomicsDBi55065

Protocols and materials databases

DNASUi3239
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000392539; ENSP00000376322; ENSG00000128714
GeneIDi3239
KEGGihsa:3239
UCSCiuc002ukf.2 human

Organism-specific databases

CTDi3239
DisGeNETi3239
EuPathDBiHostDB:ENSG00000128714.5
GeneCardsiHOXD13
HGNCiHGNC:5136 HOXD13
HPAiHPA064064
MalaCardsiHOXD13
MIMi113200 phenotype
113300 phenotype
142989 gene
186000 phenotype
186300 phenotype
192350 phenotype
610713 phenotype
neXtProtiNX_P35453
OpenTargetsiENSG00000128714
Orphaneti93387 Brachydactyly type E
93409 Brachydactyly-syndactyly, Zhao type
93385 NON RARE IN EUROPE: Brachydactyly type D
93406 Syndactyly type 5
295195 Synpolydactyly type 1
887 VACTERL/VATER association
295191 Zygodactyly type 3
PharmGKBiPA29410
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0487 Eukaryota
ENOG4111FJP LUCA
GeneTreeiENSGT00910000143984
HOGENOMiHOG000231176
HOVERGENiHBG106958
InParanoidiP35453
KOiK09298
OMAiFAYPGTS
OrthoDBiEOG091G0E5Q
PhylomeDBiP35453
TreeFamiTF330813

Enzyme and pathway databases

SIGNORiP35453

Miscellaneous databases

ChiTaRSiHOXD13 human
GeneWikiiHOXD13
GenomeRNAii3239
PROiPR:P35453
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000128714 Expressed in 36 organ(s), highest expression level in ectocervix
CleanExiHS_HOXD13
GenevisibleiP35453 HS

Family and domain databases

CDDicd00086 homeodomain, 1 hit
InterProiView protein in InterPro
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR022067 HoxA13_N
PfamiView protein in Pfam
PF00046 Homeobox, 1 hit
PF12284 HoxA13_N, 1 hit
SMARTiView protein in SMART
SM00389 HOX, 1 hit
SUPFAMiSSF46689 SSF46689, 1 hit
PROSITEiView protein in PROSITE
PS00027 HOMEOBOX_1, 1 hit
PS50071 HOMEOBOX_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiHXD13_HUMAN
AccessioniPrimary (citable) accession number: P35453
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: February 10, 2009
Last modified: November 7, 2018
This is version 172 of the entry and version 3 of the sequence. See 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  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. Vertebrate homeotic Hox proteins
    Nomenclature of vertebrate homeotic Hox proteins and list of entries
  5. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  6. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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