ID   HXD3A_DANRE             Reviewed;         396 AA.
AC   O42370; B0S5Y4;
DT   15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
DT   10-FEB-2009, sequence version 2.
DT   03-AUG-2022, entry version 147.
DE   RecName: Full=Homeobox protein Hox-D3a;
DE            Short=Hox-D3;
GN   Name=hoxd3a; Synonyms=hoxd3; ORFNames=si:rp71-78h1.2;
OS   Danio rerio (Zebrafish) (Brachydanio rerio).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC   Danionidae; Danioninae; Danio.
OX   NCBI_TaxID=7955;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Tuebingen;
RX   PubMed=23594743; DOI=10.1038/nature12111;
RA   Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA   Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA   Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA   White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA   Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA   Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA   Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA   Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA   Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA   Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA   Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA   Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA   Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA   Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA   Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA   McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA   Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA   Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA   Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA   Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA   Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA   Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA   Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA   Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA   Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA   Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA   Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA   Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA   de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA   Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT   "The zebrafish reference genome sequence and its relationship to the human
RT   genome.";
RL   Nature 496:498-503(2013).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA] OF 189-354.
RC   TISSUE=Embryo;
RX   PubMed=9425135; DOI=10.1242/dev.125.3.393;
RA   Prince V.E., Moens C.B., Kimmel C.B., Ho R.K.;
RT   "Zebrafish hox genes: expression in the hindbrain region of wild-type and
RT   mutants of the segmentation gene, valentino.";
RL   Development 125:393-406(1998).
CC   -!- FUNCTION: Sequence-specific transcription factor which is part of a
CC       developmental regulatory system that provides cells with specific
CC       positional identities on the anterior-posterior axis. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus.
CC   -!- DEVELOPMENTAL STAGE: First expressed at the 1-2 somite stage. By the 3-
CC       4 somite stage, the anterior expression limit in the developing
CC       hindbrain is at the rhombomere 5/6 boundary, and this is maintained
CC       until the 20 somite stage. By 30 hours post-fertilization, there is
CC       also limited expression within rhombomere 5.
CC   -!- SIMILARITY: Belongs to the Antp homeobox family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=CAA74286.1; Type=Frameshift; Evidence={ECO:0000305};
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DR   EMBL; BX322661; CAQ15516.1; -; Genomic_DNA.
DR   EMBL; Y13948; CAA74286.1; ALT_FRAME; mRNA.
DR   RefSeq; NP_571200.1; NM_131125.1.
DR   AlphaFoldDB; O42370; -.
DR   SMR; O42370; -.
DR   STRING; 7955.ENSDARP00000093704; -.
DR   PaxDb; O42370; -.
DR   Ensembl; ENSDART00000082359; ENSDARP00000093704; ENSDARG00000059280.
DR   Ensembl; ENSDART00000146131; ENSDARP00000120633; ENSDARG00000059280.
DR   Ensembl; ENSDART00000190712; ENSDARP00000156094; ENSDARG00000059280.
DR   GeneID; 30349; -.
DR   KEGG; dre:30349; -.
DR   CTD; 30349; -.
DR   ZFIN; ZDB-GENE-990415-120; hoxd3a.
DR   eggNOG; KOG0489; Eukaryota.
DR   GeneTree; ENSGT00940000160027; -.
DR   HOGENOM; CLU_051508_1_0_1; -.
DR   InParanoid; O42370; -.
DR   OMA; KTAYYDN; -.
DR   OrthoDB; 934469at2759; -.
DR   PhylomeDB; O42370; -.
DR   PRO; PR:O42370; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 9.
DR   Bgee; ENSDARG00000059280; Expressed in rhombomere 8 and 18 other tissues.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR   GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR   GO; GO:0009952; P:anterior/posterior pattern specification; IBA:GO_Central.
DR   GO; GO:0048704; P:embryonic skeletal system morphogenesis; IBA:GO_Central.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR   CDD; cd00086; homeodomain; 1.
DR   InterPro; IPR025281; DUF4074.
DR   InterPro; IPR009057; Homeobox-like_sf.
DR   InterPro; IPR001827; Homeobox_Antennapedia_CS.
DR   InterPro; IPR017970; Homeobox_CS.
DR   InterPro; IPR001356; Homeobox_dom.
DR   InterPro; IPR020479; Homeobox_metazoa.
DR   Pfam; PF13293; DUF4074; 1.
DR   Pfam; PF00046; Homeodomain; 1.
DR   PRINTS; PR00024; HOMEOBOX.
DR   SMART; SM00389; HOX; 1.
DR   SUPFAM; SSF46689; SSF46689; 1.
DR   PROSITE; PS00032; ANTENNAPEDIA; 1.
DR   PROSITE; PS00027; HOMEOBOX_1; 1.
DR   PROSITE; PS50071; HOMEOBOX_2; 1.
PE   2: Evidence at transcript level;
KW   Developmental protein; DNA-binding; Homeobox; Nucleus; Reference proteome;
KW   Transcription; Transcription regulation.
FT   CHAIN           1..396
FT                   /note="Homeobox protein Hox-D3a"
FT                   /id="PRO_0000200209"
FT   DNA_BIND        161..220
FT                   /note="Homeobox"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT   REGION          18..163
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          219..246
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          364..396
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           126..131
FT                   /note="Antp-type hexapeptide"
FT   COMPBIAS        22..148
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   396 AA;  43102 MW;  A608A1E60C315786 CRC64;
     MQKATYYDNA GLFGGYSYPK SDSYTYGPTH QGFSSSSIEN DYQSPICPIQ TTSVRQATHK
     NGDINGSCMR PSASQGNSQP ESISEQQQAA PLAASSPSPS TNSTQKKKSP SSNGSSTATP
     VISKQIFPWM KETRQNAKQK STNCPAAGET CDDKSPPGPA SKRVRTAYTS AQLVELEKEF
     HFNRYLCRPR RVEMANLLNL TERQIKIWFQ NRRMKYKKDQ KSKGIMHSPL GHSPDRSPPL
     SGSNHIGYSG QLPNVNSLSY DAPSPPSFAK PQQNIYGLAA YTAPLGGCIP QQKRYPGTEY
     DHHSMQGNGS FANANLQSSP VYVGGNFVDS MPASGPMFNL GHLPHPSSAS VDYSCAAQIP
     GNHHHGPCDP HPTYTDLSSH HASQGRLQDA PKLTHL