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P31249 (HXD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 146. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Homeobox protein Hox-D3
Alternative name(s):
Homeobox protein Hox-4A
Gene names
Name:HOXD3
Synonyms:HOX1D, HOX4A
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length432 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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.

Subcellular location

Nucleus.

Sequence similarities

Belongs to the Antp homeobox family.

Contains 1 homeobox DNA-binding domain.

Caution

It is uncertain whether Met-1 or Met-17 is the initiator.

Sequence caution

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

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityPolymorphism
   DomainHomeobox
   LigandDNA-binding
   Molecular functionDevelopmental protein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processNotch signaling pathway

Inferred from mutant phenotype PubMed 12836255. Source: UniProtKB

anterior/posterior pattern specification

Inferred from sequence or structural similarity. Source: UniProtKB

cartilage development

Inferred from sequence or structural similarity. Source: UniProtKB

cell-matrix adhesion

Inferred from direct assay PubMed 7742539. Source: UniProtKB

embryonic skeletal system morphogenesis

Inferred from sequence or structural similarity. Source: UniProtKB

glossopharyngeal nerve morphogenesis

Inferred from electronic annotation. Source: Ensembl

positive regulation of gene expression

Inferred from mutant phenotype PubMed 12836255. Source: UniProtKB

positive regulation of neuron differentiation

Inferred from sequence or structural similarity. Source: UniProtKB

thyroid gland development

Inferred from sequence or structural similarity. Source: UniProtKB

transcription, DNA-templated

Inferred from mutant phenotype PubMed 12836255. Source: UniProtKB

   Cellular_componentnucleus

Inferred by curator PubMed 12836255. Source: UniProtKB

   Molecular_functionprotein binding

Inferred from physical interaction PubMed 23088713. Source: IntAct

sequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Hoxa1P090223EBI-3957655,EBI-3957603From a different organism.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 432432Homeobox protein Hox-D3
PRO_0000200204

Regions

DNA binding194 – 25360Homeobox
Motif160 – 1656Antp-type hexapeptide
Compositional bias100 – 1045Poly-Gly
Compositional bias116 – 1249Poly-Pro
Compositional bias150 – 1534Poly-Ser

Natural variations

Natural variant1291S → C.
Corresponds to variant rs1051932 [ dbSNP | Ensembl ].
VAR_011881

Experimental info

Sequence conflict2571G → A Ref.5

Sequences

Sequence LengthMass (Da)Tools
P31249 [UniParc].

Last modified March 3, 2009. Version 3.
Checksum: BC962D2AA076B87B

FASTA43245,730
        10         20         30         40         50         60 
MLFEQGQQAL ELPECTMQKA AYYENPGLFG GYGYSKTTDT YGYSTPHQPY PPPAAASSLD 

        70         80         90        100        110        120 
TDYPGSACSI QSSAPLRAPA HKGAELNGSC MRPGTGNSQG GGGGSQPPGL NSEQQPPQPP 

       130        140        150        160        170        180 
PPPPTLPPSS PTNPGGGVPA KKPKGGPNAS SSSATISKQI FPWMKESRQN SKQKNSCATA 

       190        200        210        220        230        240 
GESCEDKSPP GPASKRVRTA YTSAQLVELE KEFHFNRYLC RPRRVEMANL LNLTERQIKI 

       250        260        270        280        290        300 
WFQNRRMKYK KDQKAKGILH SPASQSPERS PPLGGAAGHV AYSGQLPPVP GLAYDAPSPP 

       310        320        330        340        350        360 
AFAKSQPNMY GLAAYTAPLS SCLPQQKRYA APEFEPHPMA SNGGGFASAN LQGSPVYVGG 

       370        380        390        400        410        420 
NFVESMAPAS GPVFNLGHLS HPSSASVDYS CAAQIPGNHH HGPCDPHPTY TDLSAHHSSQ 

       430 
GRLPEAPKLT HL 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS2270.1.
PIRS15548.
S27198.
RefSeqNP_008829.3. NM_006898.4.
XP_005246566.1. XM_005246509.1.
XP_005246567.1. XM_005246510.2.
XP_005246568.1. XM_005246511.1.
XP_005246569.1. XM_005246512.1.
XP_005246570.1. XM_005246513.2.
XP_006712540.1. XM_006712477.1.
UniGeneHs.93574.

3D structure databases

ProteinModelPortalP31249.
SMRP31249. Positions 196-253.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid109472. 5 interactions.
IntActP31249. 1 interaction.
STRING9606.ENSP00000249440.

PTM databases

PhosphoSiteP31249.

Polymorphism databases

DMDM224471887.

Proteomic databases

PaxDbP31249.
PRIDEP31249.

Protocols and materials databases

DNASU3232.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000249440; ENSP00000249440; ENSG00000128652.
ENST00000410016; ENSP00000386498; ENSG00000128652.
ENST00000468418; ENSP00000424734; ENSG00000128652.
GeneID3232.
KEGGhsa:3232.
UCSCuc002ukt.1. human.

Organism-specific databases

CTD3232.
GeneCardsGC02P177001.
HGNCHGNC:5137. HOXD3.
HPAHPA051831.
MIM142980. gene.
neXtProtNX_P31249.
PharmGKBPA29411.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG284589.
HOGENOMHOG000252944.
HOVERGENHBG107984.
InParanoidP31249.
KOK09303.
OMAPSFAKPQ.
PhylomeDBP31249.
TreeFamTF315938.

Gene expression databases

ArrayExpressP31249.
BgeeP31249.
CleanExHS_HOXD3.
GenevestigatorP31249.

Family and domain databases

Gene3D1.10.10.60. 1 hit.
InterProIPR025281. DUF4074.
IPR001827. Homeobox_Antennapedia_CS.
IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamPF13293. DUF4074. 1 hit.
PF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSPR00024. HOMEOBOX.
SMARTSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
PROSITEPS00032. ANTENNAPEDIA. 1 hit.
PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiHOXD3.
GenomeRNAi3232.
NextBio12861.
PROP31249.
SOURCESearch...

Entry information

Entry nameHXD3_HUMAN
AccessionPrimary (citable) accession number: P31249
Secondary accession number(s): Q99955, Q9BSC5
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: March 3, 2009
Last modified: July 9, 2014
This is version 146 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM

Vertebrate homeotic Hox proteins

Nomenclature of vertebrate homeotic Hox proteins and list of entries