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Protein

Homeobox protein Hox-D13

Gene

HOXD13

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Regions

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

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000128714-MONOMER.
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

HGNCiHGNC:5136. HOXD13.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Synpolydactyly 1 (SPD1)4 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 and in syndactyly type 5. 2 Publications1
Natural variantiVAR_076833306R → G in SPD1; decreases the transcriptional activator activity. 1 Publication1
Natural variantiVAR_076834306R → Q in SPD1; decreases the transcriptional activator activity. 1 Publication1
Natural variantiVAR_031651306R → W in SPD1. 1 PublicationCorresponds to variant rs28933082dbSNPEnsembl.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
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_015952316S → C in BDE1 and BDD. 1 PublicationCorresponds to variant rs28928892dbSNPEnsembl.1
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 rs104893635dbSNPEnsembl.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
Natural variantiVAR_076835325Q → K in BDSDO. 1 Publication1
Brachydactyly E1 (BDE1)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 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_015952316S → C in BDE1 and BDD. 1 PublicationCorresponds to variant rs28928892dbSNPEnsembl.1
Natural variantiVAR_015953322I → L in BDE1; decreases the transcriptional activator activity. 2 PublicationsCorresponds to variant rs28928891dbSNPEnsembl.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 Publication1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi3239.
MalaCardsiHOXD13.
MIMi113200. phenotype.
113300. phenotype.
186000. phenotype.
186300. phenotype.
192350. phenotype.
610713. phenotype.
OpenTargetsiENSG00000128714.
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.

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.

PTM databases

iPTMnetiP35453.
PhosphoSitePlusiP35453.

Expressioni

Gene expression databases

BgeeiENSG00000128714.
CleanExiHS_HOXD13.
GenevisibleiP35453. HS.

Organism-specific databases

HPAiHPA064064.

Interactioni

Protein-protein interaction databases

BioGridi109479. 38 interactors.
IntActiP35453. 16 interactors.
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
Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiKOG0487. Eukaryota.
ENOG4111FJP. LUCA.
GeneTreeiENSGT00760000118834.
HOGENOMiHOG000231176.
HOVERGENiHBG106958.
InParanoidiP35453.
KOiK09298.
OMAiAKECPAP.
OrthoDBiEOG091G0E5Q.
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 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 and in syndactyly type 5. 2 Publications1
Natural variantiVAR_031650252S → A.Corresponds to variant rs35290213dbSNPEnsembl.1
Natural variantiVAR_076833306R → G in SPD1; decreases the transcriptional activator activity. 1 Publication1
Natural variantiVAR_076834306R → Q in SPD1; decreases the transcriptional activator activity. 1 Publication1
Natural variantiVAR_031651306R → W in SPD1. 1 PublicationCorresponds to variant rs28933082dbSNPEnsembl.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 rs28928892dbSNPEnsembl.1
Natural variantiVAR_015953322I → L in BDE1; decreases the transcriptional activator activity. 2 PublicationsCorresponds to variant rs28928891dbSNPEnsembl.1
Natural variantiVAR_076835325Q → K in BDSDO. 1 Publication1
Natural variantiVAR_031652325Q → R in SDTY5; impairs capacity to transactivate EPHA7 promoter. 2 PublicationsCorresponds to variant rs104893635dbSNPEnsembl.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

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. 38 interactors.
IntActiP35453. 16 interactors.
STRINGi9606.ENSP00000376322.

PTM databases

iPTMnetiP35453.
PhosphoSitePlusiP35453.

Polymorphism and mutation databases

BioMutaiHOXD13.
DMDMi223590221.

Proteomic databases

EPDiP35453.
MaxQBiP35453.
PaxDbiP35453.
PeptideAtlasiP35453.
PRIDEiP35453.

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.
GeneCardsiHOXD13.
HGNCiHGNC:5136. HOXD13.
HPAiHPA064064.
MalaCardsiHOXD13.
MIMi113200. phenotype.
113300. phenotype.
142989. gene.
186000. phenotype.
186300. phenotype.
192350. phenotype.
610713. phenotype.
neXtProtiNX_P35453.
OpenTargetsiENSG00000128714.
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.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0487. Eukaryota.
ENOG4111FJP. LUCA.
GeneTreeiENSGT00760000118834.
HOGENOMiHOG000231176.
HOVERGENiHBG106958.
InParanoidiP35453.
KOiK09298.
OMAiAKECPAP.
OrthoDBiEOG091G0E5Q.
PhylomeDBiP35453.
TreeFamiTF330813.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000128714-MONOMER.
SIGNORiP35453.

Miscellaneous databases

ChiTaRSiHOXD13. human.
GeneWikiiHOXD13.
GenomeRNAii3239.
PROiP35453.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000128714.
CleanExiHS_HOXD13.
GenevisibleiP35453. HS.

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]
ProtoNetiSearch...

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: November 2, 2016
This is version 156 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.