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Protein

Homeobox protein Hox-D3

Gene

HOXD3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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 bindingi194 – 25360HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. sequence-specific DNA binding Source: InterPro
  2. sequence-specific DNA binding transcription factor activity Source: InterPro

GO - Biological processi

  1. anterior/posterior pattern specification Source: UniProtKB
  2. cartilage development Source: UniProtKB
  3. cell-matrix adhesion Source: UniProtKB
  4. embryonic skeletal system morphogenesis Source: UniProtKB
  5. Notch signaling pathway Source: UniProtKB
  6. positive regulation of gene expression Source: UniProtKB
  7. positive regulation of neuron differentiation Source: UniProtKB
  8. thyroid gland development Source: UniProtKB
  9. transcription, DNA-templated Source: UniProtKB
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-D3
Alternative name(s):
Homeobox protein Hox-4A
Gene namesi
Name:HOXD3
Synonyms:HOX1D, HOX4A
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:5137. HOXD3.

Subcellular locationi

GO - Cellular componenti

  1. nucleoplasm Source: HPA
  2. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA29411.

Polymorphism and mutation databases

BioMutaiHOXD3.
DMDMi224471887.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 432432Homeobox protein Hox-D3PRO_0000200204Add
BLAST

Proteomic databases

PaxDbiP31249.
PRIDEiP31249.

PTM databases

PhosphoSiteiP31249.

Expressioni

Gene expression databases

BgeeiP31249.
CleanExiHS_HOXD3.
ExpressionAtlasiP31249. baseline.
GenevestigatoriP31249.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
Hoxa1P090223EBI-3957655,EBI-3957603From a different organism.

Protein-protein interaction databases

BioGridi109472. 5 interactions.
IntActiP31249. 2 interactions.
STRINGi9606.ENSP00000249440.

Structurei

3D structure databases

ProteinModelPortaliP31249.
SMRiP31249. Positions 196-253.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi160 – 1656Antp-type hexapeptide

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi100 – 1045Poly-Gly
Compositional biasi116 – 1249Poly-Pro
Compositional biasi150 – 1534Poly-Ser

Sequence similaritiesi

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

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiNOG284589.
GeneTreeiENSGT00760000118940.
HOGENOMiHOG000252944.
HOVERGENiHBG107984.
InParanoidiP31249.
KOiK09303.
OMAiYSKAADT.
PhylomeDBiP31249.
TreeFamiTF315938.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR025281. DUF4074.
IPR001827. Homeobox_Antennapedia_CS.
IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF13293. DUF4074. 1 hit.
PF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSiPR00024. HOMEOBOX.
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00032. ANTENNAPEDIA. 1 hit.
PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P31249-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLFEQGQQAL ELPECTMQKA AYYENPGLFG GYGYSKTTDT YGYSTPHQPY
60 70 80 90 100
PPPAAASSLD TDYPGSACSI QSSAPLRAPA HKGAELNGSC MRPGTGNSQG
110 120 130 140 150
GGGGSQPPGL NSEQQPPQPP PPPPTLPPSS PTNPGGGVPA KKPKGGPNAS
160 170 180 190 200
SSSATISKQI FPWMKESRQN SKQKNSCATA GESCEDKSPP GPASKRVRTA
210 220 230 240 250
YTSAQLVELE KEFHFNRYLC RPRRVEMANL LNLTERQIKI WFQNRRMKYK
260 270 280 290 300
KDQKAKGILH SPASQSPERS PPLGGAAGHV AYSGQLPPVP GLAYDAPSPP
310 320 330 340 350
AFAKSQPNMY GLAAYTAPLS SCLPQQKRYA APEFEPHPMA SNGGGFASAN
360 370 380 390 400
LQGSPVYVGG NFVESMAPAS GPVFNLGHLS HPSSASVDYS CAAQIPGNHH
410 420 430
HGPCDPHPTY TDLSAHHSSQ GRLPEAPKLT HL
Length:432
Mass (Da):45,730
Last modified:March 3, 2009 - v3
Checksum:iBC962D2AA076B87B
GO

Sequence cautioni

The sequence BAA01891.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti257 – 2571G → A (PubMed:2576652).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti129 – 1291S → C.
Corresponds to variant rs1051932 [ dbSNP | Ensembl ].
VAR_011881

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D11117 Genomic DNA. Translation: BAA01891.1. Different initiation.
Y09980 Genomic DNA. Translation: CAA71102.1.
AC009336 Genomic DNA. No translation available.
BC005124 mRNA. Translation: AAH05124.1.
BC008789 mRNA. Translation: AAH08789.1.
CCDSiCCDS2270.1.
PIRiS15548.
S27198.
RefSeqiNP_008829.3. NM_006898.4.
XP_005246566.1. XM_005246509.2.
XP_005246567.1. XM_005246510.3.
XP_005246568.1. XM_005246511.2.
XP_005246570.1. XM_005246513.3.
XP_006712540.1. XM_006712477.2.
UniGeneiHs.93574.

Genome annotation databases

EnsembliENST00000249440; ENSP00000249440; ENSG00000128652.
ENST00000410016; ENSP00000386498; ENSG00000128652.
GeneIDi3232.
KEGGihsa:3232.
UCSCiuc002ukt.1. human.

Polymorphism and mutation databases

BioMutaiHOXD3.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D11117 Genomic DNA. Translation: BAA01891.1. Different initiation.
Y09980 Genomic DNA. Translation: CAA71102.1.
AC009336 Genomic DNA. No translation available.
BC005124 mRNA. Translation: AAH05124.1.
BC008789 mRNA. Translation: AAH08789.1.
CCDSiCCDS2270.1.
PIRiS15548.
S27198.
RefSeqiNP_008829.3. NM_006898.4.
XP_005246566.1. XM_005246509.2.
XP_005246567.1. XM_005246510.3.
XP_005246568.1. XM_005246511.2.
XP_005246570.1. XM_005246513.3.
XP_006712540.1. XM_006712477.2.
UniGeneiHs.93574.

3D structure databases

ProteinModelPortaliP31249.
SMRiP31249. Positions 196-253.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109472. 5 interactions.
IntActiP31249. 2 interactions.
STRINGi9606.ENSP00000249440.

PTM databases

PhosphoSiteiP31249.

Polymorphism and mutation databases

BioMutaiHOXD3.
DMDMi224471887.

Proteomic databases

PaxDbiP31249.
PRIDEiP31249.

Protocols and materials databases

DNASUi3232.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000249440; ENSP00000249440; ENSG00000128652.
ENST00000410016; ENSP00000386498; ENSG00000128652.
GeneIDi3232.
KEGGihsa:3232.
UCSCiuc002ukt.1. human.

Organism-specific databases

CTDi3232.
GeneCardsiGC02P177001.
HGNCiHGNC:5137. HOXD3.
MIMi142980. gene.
neXtProtiNX_P31249.
PharmGKBiPA29411.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG284589.
GeneTreeiENSGT00760000118940.
HOGENOMiHOG000252944.
HOVERGENiHBG107984.
InParanoidiP31249.
KOiK09303.
OMAiYSKAADT.
PhylomeDBiP31249.
TreeFamiTF315938.

Miscellaneous databases

GeneWikiiHOXD3.
GenomeRNAii3232.
NextBioi12861.
PROiP31249.
SOURCEiSearch...

Gene expression databases

BgeeiP31249.
CleanExiHS_HOXD3.
ExpressionAtlasiP31249. baseline.
GenevestigatoriP31249.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR025281. DUF4074.
IPR001827. Homeobox_Antennapedia_CS.
IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF13293. DUF4074. 1 hit.
PF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSiPR00024. HOMEOBOX.
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00032. ANTENNAPEDIA. 1 hit.
PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of the human homeobox gene HOX4A."
    Taniguchi Y., Fujii A., Moriuchi T.
    Biochim. Biophys. Acta 1132:332-334(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cianetti L.
    Submitted (DEC-1996) 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. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain and Lung.
  5. "Organization of human class I homeobox genes."
    Boncinelli E., Acampora D., Pannese M., D'Esposito M., Somma R., Gaudino G., Stornaiuolo A., Cafiero M., Faiella A., Simeone A.
    Genome 31:745-756(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 194-259.

Entry informationi

Entry nameiHXD3_HUMAN
AccessioniPrimary (citable) accession number: P31249
Secondary accession number(s): Q99955, Q9BSC5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: March 3, 2009
Last modified: April 29, 2015
This is version 152 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-17 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

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 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.