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Q98SI1

- HXA1A_DANRE

UniProt

Q98SI1 - HXA1A_DANRE

Protein

Homeobox protein Hox-A1a

Gene

hoxa1a

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 87 (01 Oct 2014)
      Sequence version 1 (01 Jun 2001)
      Previous versions | rss
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    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 bindingi225 – 28460HomeoboxPROSITE-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

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Homeobox protein Hox-A1a
    Short name:
    Hox-A1
    Gene namesi
    Name:hoxa1a
    Synonyms:hoxa1
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Chromosome 19

    Organism-specific databases

    ZFINiZDB-GENE-000823-5. hoxa1a.

    Subcellular locationi

    Nucleus PROSITE-ProRule annotation

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 329329Homeobox protein Hox-A1aPRO_0000200033Add
    BLAST

    Expressioni

    Gene expression databases

    BgeeiQ98SI1.

    Structurei

    3D structure databases

    ProteinModelPortaliQ98SI1.
    SMRiQ98SI1. Positions 198-286.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi200 – 2056Antp-type hexapeptide

    Sequence similaritiesi

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

    Keywords - Domaini

    Homeobox

    Phylogenomic databases

    eggNOGiNOG236971.
    GeneTreeiENSGT00750000117389.
    HOGENOMiHOG000247020.
    HOVERGENiHBG006089.
    InParanoidiQ98SI1.
    KOiK09301.
    OMAiCAVSANS.
    OrthoDBiEOG7PK91P.
    PhylomeDBiQ98SI1.
    TreeFamiTF317730.

    Family and domain databases

    Gene3Di1.10.10.60. 1 hit.
    InterProiIPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR020479. Homeobox_metazoa.
    IPR009057. Homeodomain-like.
    [Graphical view]
    PfamiPF00046. Homeobox. 1 hit.
    [Graphical view]
    PRINTSiPR00024. HOMEOBOX.
    SMARTiSM00389. HOX. 1 hit.
    [Graphical view]
    SUPFAMiSSF46689. SSF46689. 1 hit.
    PROSITEiPS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q98SI1-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MSTFLDFSSI SGGGDGGSGG SCSVRAFHGD HGLSTFQSSC AVRLNSCSGD    50
    ERFMSNISSQ DVINSQPQQA GSYQSPGTLS ITYSAHPSYG TQSFCTGYNH 100
    YALNQDVESS VSFPQCGPLV YSGNISSTVV QHRHHRHGYS SGNVHLHGQF 150
    QYGSATYGNS SDQANLTFVA GCSNPLSPLH VPHHDACCSP LSDGVPTGQT 200
    FDWMKVKRNP PKTGKAGEYG FGGQPNTVRT NFSTKQLTEL EKEFHFNKYL 250
    TRARRVEIAA SLQLNETQVK IWFQNRRMKQ KKREKEGLLP KSLSEQKDGL 300
    EKTEDASEKS PSAPSTPSPS PTVEAYSSN 329
    Length:329
    Mass (Da):35,737
    Last modified:June 1, 2001 - v1
    Checksum:iCBF2C722F50A85D5
    GO
    Isoform 2 (identifier: Q98SI1-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         158-192: Missing.

    Show »
    Length:294
    Mass (Da):32,178
    Checksum:i8A603E507F410727
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti1 – 2828MSTFL…VRAFH → MEVAGARAQSGRSQ(PubMed:9831563)CuratedAdd
    BLAST
    Sequence conflicti296 – 2961Q → E in CAC34566. (PubMed:11493564)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei158 – 19235Missing in isoform 2. 1 PublicationVSP_012678Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ306430 mRNA. Translation: CAC34565.1.
    AJ306431 mRNA. Translation: CAC34566.1.
    AF071243 Genomic DNA. Translation: AAD15937.1.
    AL645756 Genomic DNA. Translation: CAD52136.1.
    AL645756 Genomic DNA. Translation: CAD52137.1.
    CR382300 Genomic DNA. Translation: CAK10852.1.
    DQ060531 mRNA. Translation: AAY67909.1.
    RefSeqiNP_571611.1. NM_131536.2. [Q98SI1-1]
    XP_005159579.1. XM_005159522.1. [Q98SI1-2]
    UniGeneiDr.83046.

    Genome annotation databases

    EnsembliENSDART00000080456; ENSDARP00000074905; ENSDARG00000057721. [Q98SI1-2]
    ENSDART00000080461; ENSDARP00000074910; ENSDARG00000057721. [Q98SI1-1]
    GeneIDi58051.
    KEGGidre:58051.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ306430 mRNA. Translation: CAC34565.1 .
    AJ306431 mRNA. Translation: CAC34566.1 .
    AF071243 Genomic DNA. Translation: AAD15937.1 .
    AL645756 Genomic DNA. Translation: CAD52136.1 .
    AL645756 Genomic DNA. Translation: CAD52137.1 .
    CR382300 Genomic DNA. Translation: CAK10852.1 .
    DQ060531 mRNA. Translation: AAY67909.1 .
    RefSeqi NP_571611.1. NM_131536.2. [Q98SI1-1 ]
    XP_005159579.1. XM_005159522.1. [Q98SI1-2 ]
    UniGenei Dr.83046.

    3D structure databases

    ProteinModelPortali Q98SI1.
    SMRi Q98SI1. Positions 198-286.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSDART00000080456 ; ENSDARP00000074905 ; ENSDARG00000057721 . [Q98SI1-2 ]
    ENSDART00000080461 ; ENSDARP00000074910 ; ENSDARG00000057721 . [Q98SI1-1 ]
    GeneIDi 58051.
    KEGGi dre:58051.

    Organism-specific databases

    CTDi 58051.
    ZFINi ZDB-GENE-000823-5. hoxa1a.

    Phylogenomic databases

    eggNOGi NOG236971.
    GeneTreei ENSGT00750000117389.
    HOGENOMi HOG000247020.
    HOVERGENi HBG006089.
    InParanoidi Q98SI1.
    KOi K09301.
    OMAi CAVSANS.
    OrthoDBi EOG7PK91P.
    PhylomeDBi Q98SI1.
    TreeFami TF317730.

    Miscellaneous databases

    NextBioi 20892315.
    PROi Q98SI1.

    Gene expression databases

    Bgeei Q98SI1.

    Family and domain databases

    Gene3Di 1.10.10.60. 1 hit.
    InterProi IPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR020479. Homeobox_metazoa.
    IPR009057. Homeodomain-like.
    [Graphical view ]
    Pfami PF00046. Homeobox. 1 hit.
    [Graphical view ]
    PRINTSi PR00024. HOMEOBOX.
    SMARTi SM00389. HOX. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46689. SSF46689. 1 hit.
    PROSITEi PS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish Hox paralogue group 1 genes."
      McClintock J.M., Carlson R., Mann D.M., Prince V.E.
      Development 128:2471-2484(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
    2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "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(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Tuebingen.
    4. "Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hoxb13a."
      Corredor-Adamez M., Welten M.C.M., Spaink H.P., Jeffery J.E., Schoon R.T., de Bakker M.A.G., Bagowski C.P., Meijer A.H., Verbeek F.J., Richardson M.K.
      Evol. Dev. 7:362-375(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 136-224.
      Strain: Tuebingen.

    Entry informationi

    Entry nameiHXA1A_DANRE
    AccessioniPrimary (citable) accession number: Q98SI1
    Secondary accession number(s): Q1L968
    , Q4PRB2, Q8AWZ1, Q98SI0, Q9YGT8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 2005
    Last sequence update: June 1, 2001
    Last modified: October 1, 2014
    This is version 87 of the entry and version 1 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