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Protein

Homeobox protein Hox-B3a

Gene

hoxb3a

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at transcript 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.By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi180 – 23960HomeoboxPROSITE-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. multicellular organismal development Source: UniProtKB-KW
  2. transcription, DNA-templated Source: UniProtKB-KW
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-B3a
Short name:
Hox-B3
Gene namesi
Name:hoxb3a
Synonyms:hoxb3
ORF Names:zgc:111819
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437 Componenti: Chromosome 3

Organism-specific databases

ZFINiZDB-GENE-990415-104. hoxb3a.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 417417Homeobox protein Hox-B3aPRO_0000200120Add
BLAST

Expressioni

Developmental stagei

First expressed at the 1- to 2-somite stages posterior to rhombomere 5 (r5) of the developing hindbrain. By the 3- to 4-somite stages, the anterior expression limit is at the r4/r5 boundary. At 5- to 10-somite stages, expressed at high levels in r5 and r6. From the 20- to 30-somite stages, expressed weakly in r4.1 Publication

Gene expression databases

BgeeiO42368.

Structurei

3D structure databases

ProteinModelPortaliO42368.
SMRiO42368. Positions 180-239.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi140 – 1456Antp-type hexapeptide

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.
InParanoidiO42368.
KOiK09303.
OMAiEYEPHVL.
OrthoDBiEOG754HPS.
PhylomeDBiO42368.
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.

O42368-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQKTTYYDNS TLFGGYSYQG ANGFGYDAPA PAFQNSAHLE GDYQRSACSL
60 70 80 90 100
QSLGTSAPPQ PQHAKTKELN GSCMRPSLPP EHHPPPQVSP PQNTVNVAAT
110 120 130 140 150
NATQQPGGSG GGGGAGSGGT SKSSSKSSSM ATNPTLTKQI FPWMKESRQN
160 170 180 190 200
TKQKNSSPSA SSANAESSGG EKSPPGSAAS KRARTAYTSA QLVELEKEFH
210 220 230 240 250
FNRYLCRPRR VEMANLLNLS ERQIKIWFQN RRMKYKKDQK SKGIGSSSGG
260 270 280 290 300
PSPTGSPPLP MQSSAGFMNS MHSMGSYDAP SPPSFNKPHQ NAYAMSTAYQ
310 320 330 340 350
NPMKGCPPQQ KYGNTPPDYD PHGLQGNSGN YGTPNMQGSP VYVGGNYVDA
360 370 380 390 400
MPATGPSMYG LNHLPHHQSA SMDYNGATQM SANQHHGPCD PHPTYTDLSA
410
HHPSQGRIQE APKLTHL
Length:417
Mass (Da):44,580
Last modified:January 31, 2005 - v3
Checksum:i33A68839BE3CC35A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti114 – 1141G → V in AAH95559 (Ref. 3) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ537509 mRNA. Translation: CAD61096.1.
AL645782 Genomic DNA. Translation: CAD59116.1.
BC095559 mRNA. Translation: AAH95559.1.
Y13944 mRNA. Translation: CAA74282.2.
BK005081 mRNA. Translation: DAA05213.1.
BK005082 mRNA. Translation: DAA05214.1.
RefSeqiNP_571192.2. NM_131117.3.
XP_005171611.1. XM_005171554.2.
XP_005171619.1. XM_005171562.2.
UniGeneiDr.132502.

Genome annotation databases

EnsembliENSDART00000078466; ENSDARP00000072928; ENSDARG00000029263.
ENSDART00000153512; ENSDARP00000128207; ENSDARG00000029263.
GeneIDi30339.
KEGGidre:30339.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ537509 mRNA. Translation: CAD61096.1.
AL645782 Genomic DNA. Translation: CAD59116.1.
BC095559 mRNA. Translation: AAH95559.1.
Y13944 mRNA. Translation: CAA74282.2.
BK005081 mRNA. Translation: DAA05213.1.
BK005082 mRNA. Translation: DAA05214.1.
RefSeqiNP_571192.2. NM_131117.3.
XP_005171611.1. XM_005171554.2.
XP_005171619.1. XM_005171562.2.
UniGeneiDr.132502.

3D structure databases

ProteinModelPortaliO42368.
SMRiO42368. Positions 180-239.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000078466; ENSDARP00000072928; ENSDARG00000029263.
ENSDART00000153512; ENSDARP00000128207; ENSDARG00000029263.
GeneIDi30339.
KEGGidre:30339.

Organism-specific databases

CTDi30339.
ZFINiZDB-GENE-990415-104. hoxb3a.

Phylogenomic databases

eggNOGiNOG284589.
GeneTreeiENSGT00760000118940.
HOGENOMiHOG000252944.
HOVERGENiHBG107984.
InParanoidiO42368.
KOiK09303.
OMAiEYEPHVL.
OrthoDBiEOG754HPS.
PhylomeDBiO42368.
TreeFamiTF315938.

Miscellaneous databases

NextBioi20806770.
PROiO42368.

Gene expression databases

BgeeiO42368.

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. "Ectopic expression of Hox paralog group 3 genes disrupts zebrafish hindbrain organization and craniofacial development in the absence of homeotic transformations."
    Hunter M.P., Prince V.E.
    Submitted (DEC-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Embryo.
  2. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  3. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Larva.
  4. "Zebrafish hox genes: expression in the hindbrain region of wild-type and mutants of the segmentation gene, valentino."
    Prince V.E., Moens C.B., Kimmel C.B., Ho R.K.
    Development 125:393-406(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 208-417, DEVELOPMENTAL STAGE.
    Tissue: Embryo.
  5. Prince V.E.
    Submitted (JUN-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  6. "Comparative genomic analysis of vertebrate Hox3 and Hox4 genes."
    Hadrys T., Prince V.E., Hunter M.P., Baker R., Rinkwitz S.
    J. Exp. Zool. B Mol. Dev. Evol. 302:147-164(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE STRUCTURE.

Entry informationi

Entry nameiHXB3A_DANRE
AccessioniPrimary (citable) accession number: O42368
Secondary accession number(s): Q4VBK5, Q8AWY5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 14, 1999
Last sequence update: January 31, 2005
Last modified: January 6, 2015
This is version 113 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Vertebrate homeotic Hox proteins
    Nomenclature of vertebrate homeotic Hox proteins and list of entries
  2. 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.