Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P56224

- P3F3A_DANRE

UniProt

P56224 - P3F3A_DANRE

Protein

POU domain, class 3, transcription factor 3-A

Gene

pou3f3a

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 115 (01 Oct 2014)
      Sequence version 2 (24 Nov 2009)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    Transcription factor that may play important roles in patterning the embryonic brain.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi334 – 39360HomeoboxPROSITE-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:
    POU domain, class 3, transcription factor 3-A
    Alternative name(s):
    Brain-specific homeobox/POU domain protein 1.1
    Short name:
    Brain-1.1
    Short name:
    zfBrn-1.1
    Class III POU domain protein taichi
    POU domain protein 12
    Short name:
    ZP-12
    Gene namesi
    Name:pou3f3a
    Synonyms:brn-1.1, brn1.1, pou12, tai-ji, zp12, zp12pou
    ORF Names:si:dkeyp-118h3.2
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Chromosome 9

    Organism-specific databases

    ZFINiZDB-GENE-980526-220. pou3f3a.

    Subcellular locationi

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 438438POU domain, class 3, transcription factor 3-APRO_0000100731Add
    BLAST

    Proteomic databases

    PRIDEiP56224.

    Expressioni

    Tissue specificityi

    Predominantly expressed in the embryonic and adult central nervous system. In adults, isoform 2 is expressed in the brain, ovary, basal cells of the skin and muscle satellite cells.3 Publications

    Developmental stagei

    Isoform 2 is expressed both maternally and zygotically, and is the major isoform in adults. Isoform 1 and isoform 3 are expressed zygotically. Maximal expression is after 1 to 2 days of development and becomes down-regulated as cells differentiate.4 Publications

    Gene expression databases

    BgeeiP56224.

    Structurei

    3D structure databases

    ProteinModelPortaliP56224.
    SMRiP56224. Positions 248-394.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini242 – 31675POU-specificPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi85 – 10016Ala-richAdd
    BLAST
    Compositional biasi209 – 23931His-richAdd
    BLAST

    Sequence similaritiesi

    Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation
    Contains 1 POU-specific domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Homeobox

    Phylogenomic databases

    GeneTreeiENSGT00730000110809.
    HOVERGENiHBG053120.
    InParanoidiP56224.
    OrthoDBiEOG7DJSMG.
    PhylomeDBiP56224.
    TreeFamiTF316413.

    Family and domain databases

    Gene3Di1.10.10.60. 1 hit.
    1.10.260.40. 1 hit.
    InterProiIPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR009057. Homeodomain-like.
    IPR010982. Lambda_DNA-bd_dom.
    IPR013847. POU.
    IPR000327. POU_specific.
    IPR016362. Transcription_factor_POU.
    [Graphical view]
    PfamiPF00046. Homeobox. 1 hit.
    PF00157. Pou. 1 hit.
    [Graphical view]
    PIRSFiPIRSF002629. Transcription_factor_POU. 1 hit.
    PRINTSiPR00028. POUDOMAIN.
    SMARTiSM00389. HOX. 1 hit.
    SM00352. POU. 1 hit.
    [Graphical view]
    SUPFAMiSSF46689. SSF46689. 1 hit.
    SSF47413. SSF47413. 1 hit.
    PROSITEiPS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    PS00035. POU_1. 1 hit.
    PS00465. POU_2. 1 hit.
    PS51179. POU_3. 1 hit.
    [Graphical view]

    Sequences (4)i

    Sequence statusi: Complete.

    This entry describes 4 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: P56224-1) [UniParc]FASTAAdd to Basket

    Also known as: A

    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

    MATAASNPYL ASSTILSSAS LVHSESGGGG MQPGSGAVTS VSGGYRGDPT    50
    VKMVQSDFMQ GAMAASNGGH MLSHAHQWVT SLPHAAAAAA AAAAAAAAEA 100
    GSPWSSSPVG MAGSPQQQDV KSSSNREDLH SGTALHHRPS HLGAHQSHQS 150
    AWGGTTASHI STITGGQQQS QQSLIYSQPG GFTVNGMLNP PGSLVHPGLM 200
    RGESPEMDHH HHHHHHQQQH PHHHHHHQHH AGVNSHDSHS DEDTPTSDDL 250
    EQFAKQFKQR RIKLGFTQAD VGLALGTLYG NVFSQTTICR FEALQLSFKN 300
    MCKLKPLLNK WLEEADSTTG SPTSIDKIAA QGRKRKKRTS IEVSVKGALE 350
    SHFLKCPKPS AQEITSLADN LQLEKEVVRV WFCNRRQKEK RMTPPGVPQT 400
    PEDVYTHAGN VSADTPPPSM DCKREFCGRL LKRCKFER 438
    Length:438
    Mass (Da):47,216
    Last modified:November 24, 2009 - v2
    Checksum:iDFC0E59F41D3E0CA
    GO
    Isoform 2 (identifier: P56224-2) [UniParc]FASTAAdd to Basket

    Also known as: U

    The sequence of this isoform differs from the canonical sequence as follows:
         425-438: EFCGRLLKRCKFER → MFTET

    Show »
    Length:429
    Mass (Da):46,058
    Checksum:iD755C0B19A342CC7
    GO
    Isoform 3 (identifier: P56224-3) [UniParc]FASTAAdd to Basket

    Also known as: B

    The sequence of this isoform differs from the canonical sequence as follows:
         411-438: VSADTPPPSMDCKREFCGRLLKRCKFER → GSFVVDYLKGASLKDEPDSNHNVTTASSYGQEILVH

    Show »
    Length:446
    Mass (Da):47,824
    Checksum:iA192568963882A9D
    GO
    Isoform 4 (identifier: P56224-4) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         402-438: EDVYTHAGNVSADTPPPSMDCKREFCGRLLKRCKFER → KDMDQCRQTLNIKQWKNLPQDTYQFYAQELYYSF

    Note: No experimental confirmation available.

    Show »
    Length:435
    Mass (Da):47,266
    Checksum:i63CD45022F05E9B8
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti26 – 261S → F in AAH65961. 1 PublicationCurated
    Sequence conflicti222 – 2221Missing in CAA69212. (PubMed:9016656)Curated
    Sequence conflicti222 – 2221Missing in CAA69213. (PubMed:9016656)Curated
    Sequence conflicti222 – 2221Missing in AAC41300. (PubMed:9582430)Curated
    Sequence conflicti222 – 2221Missing in AAB84079. (PubMed:9507055)Curated
    Sequence conflicti222 – 2221Missing in AAH44354. 1 PublicationCurated
    Sequence conflicti222 – 2221Missing in AAH70001. 1 PublicationCurated
    Sequence conflicti222 – 2221Missing in AAI65334. 1 PublicationCurated
    Sequence conflicti222 – 2221Missing in AAB92590. 1 PublicationCurated
    Sequence conflicti301 – 3011M → I in AAH70001. 1 PublicationCurated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei402 – 43837EDVYT…CKFER → KDMDQCRQTLNIKQWKNLPQ DTYQFYAQELYYSF in isoform 4. 1 PublicationVSP_012010Add
    BLAST
    Alternative sequencei411 – 43828VSADT…CKFER → GSFVVDYLKGASLKDEPDSN HNVTTASSYGQEILVH in isoform 3. 3 PublicationsVSP_002339Add
    BLAST
    Alternative sequencei425 – 43814EFCGR…CKFER → MFTET in isoform 2. 1 PublicationVSP_002340Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y07906 mRNA. Translation: CAA69212.1.
    Y07906 mRNA. Translation: CAA69213.1.
    AF039952 mRNA. Translation: AAC41300.1.
    U77736 Genomic DNA. Translation: AAB84079.1.
    BX842683 Genomic DNA. Translation: CAQ14274.1.
    BX842683 Genomic DNA. Translation: CAQ14275.1.
    BX842683 Genomic DNA. Translation: CAQ14276.1.
    BC044354 mRNA. Translation: AAH44354.1.
    BC058318 mRNA. Translation: AAH58318.1.
    BC065961 mRNA. Translation: AAH65961.1.
    BC070001 mRNA. Translation: AAH70001.1.
    BC165334 mRNA. Translation: AAI65334.1.
    U43898 mRNA. Translation: AAB92590.2.
    U43656 Genomic DNA. Translation: AAB00433.1.
    RefSeqiNP_571225.1. NM_131150.1.
    XP_005167492.1. XM_005167435.1. [P56224-1]
    UniGeneiDr.75085.

    Genome annotation databases

    EnsembliENSDART00000061593; ENSDARP00000061592; ENSDARG00000042032. [P56224-3]
    ENSDART00000113914; ENSDARP00000103222; ENSDARG00000042032. [P56224-1]
    ENSDART00000133178; ENSDARP00000117406; ENSDARG00000042032. [P56224-2]
    GeneIDi30386.
    KEGGidre:30386.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y07906 mRNA. Translation: CAA69212.1 .
    Y07906 mRNA. Translation: CAA69213.1 .
    AF039952 mRNA. Translation: AAC41300.1 .
    U77736 Genomic DNA. Translation: AAB84079.1 .
    BX842683 Genomic DNA. Translation: CAQ14274.1 .
    BX842683 Genomic DNA. Translation: CAQ14275.1 .
    BX842683 Genomic DNA. Translation: CAQ14276.1 .
    BC044354 mRNA. Translation: AAH44354.1 .
    BC058318 mRNA. Translation: AAH58318.1 .
    BC065961 mRNA. Translation: AAH65961.1 .
    BC070001 mRNA. Translation: AAH70001.1 .
    BC165334 mRNA. Translation: AAI65334.1 .
    U43898 mRNA. Translation: AAB92590.2 .
    U43656 Genomic DNA. Translation: AAB00433.1 .
    RefSeqi NP_571225.1. NM_131150.1.
    XP_005167492.1. XM_005167435.1. [P56224-1 ]
    UniGenei Dr.75085.

    3D structure databases

    ProteinModelPortali P56224.
    SMRi P56224. Positions 248-394.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi P56224.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSDART00000061593 ; ENSDARP00000061592 ; ENSDARG00000042032 . [P56224-3 ]
    ENSDART00000113914 ; ENSDARP00000103222 ; ENSDARG00000042032 . [P56224-1 ]
    ENSDART00000133178 ; ENSDARP00000117406 ; ENSDARG00000042032 . [P56224-2 ]
    GeneIDi 30386.
    KEGGi dre:30386.

    Organism-specific databases

    CTDi 30386.
    ZFINi ZDB-GENE-980526-220. pou3f3a.

    Phylogenomic databases

    GeneTreei ENSGT00730000110809.
    HOVERGENi HBG053120.
    InParanoidi P56224.
    OrthoDBi EOG7DJSMG.
    PhylomeDBi P56224.
    TreeFami TF316413.

    Miscellaneous databases

    NextBioi 20806799.

    Gene expression databases

    Bgeei P56224.

    Family and domain databases

    Gene3Di 1.10.10.60. 1 hit.
    1.10.260.40. 1 hit.
    InterProi IPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR009057. Homeodomain-like.
    IPR010982. Lambda_DNA-bd_dom.
    IPR013847. POU.
    IPR000327. POU_specific.
    IPR016362. Transcription_factor_POU.
    [Graphical view ]
    Pfami PF00046. Homeobox. 1 hit.
    PF00157. Pou. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF002629. Transcription_factor_POU. 1 hit.
    PRINTSi PR00028. POUDOMAIN.
    SMARTi SM00389. HOX. 1 hit.
    SM00352. POU. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46689. SSF46689. 1 hit.
    SSF47413. SSF47413. 1 hit.
    PROSITEi PS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    PS00035. POU_1. 1 hit.
    PS00465. POU_2. 1 hit.
    PS51179. POU_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Class III POU genes of zebrafish are predominantly expressed in the central nervous system."
      Spaniol P., Bornmann C., Hauptmann G., Gerster T.
      Nucleic Acids Res. 24:4874-4881(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
      Tissue: Embryo.
    2. "A new splicing variant of a type III POU gene from zebrafish encodes a POU protein with a distinct C-terminal."
      Lim J.H., He J., Korzh V., Gong Z.
      Biochim. Biophys. Acta 1397:253-256(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), DEVELOPMENTAL STAGE.
      Tissue: Embryo.
    3. "Progenitor cells in the adult zebrafish nervous system express a Brn-1-related POU gene, tai-ji."
      Huang S., Sato S.
      Mech. Dev. 71:23-35(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 2), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    4. "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.
    5. NIH - Zebrafish Gene Collection (ZGC) project
      Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 3 AND 4).
      Strain: AB.
      Tissue: Embryo.
    6. "Brn-1.1: an alternatively spliced class III POU domain gene expressed in the nervous system of the zebrafish."
      Shah D., Sampath K., Stuart G.W.
      Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 5-438 (ISOFORM 3).
      Tissue: Embryo.
    7. "Developmental expression of class III and IV POU domain genes in the zebrafish."
      Sampath K., Stuart G.W.
      Biochem. Biophys. Res. Commun. 219:565-571(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 265-378, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
      Tissue: Embryo.

    Entry informationi

    Entry nameiP3F3A_DANRE
    AccessioniPrimary (citable) accession number: P56224
    Secondary accession number(s): B0S7I5
    , B0S7I6, B0S7I7, B5DDP9, O57514, Q6IS23, Q6NZU9, Q6PE22, Q7ZU57, Q90433, Q90436
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: November 24, 2009
    Last modified: October 1, 2014
    This is version 115 of the entry and version 2 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3