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Q9DE25

- FXC1A_DANRE

UniProt

Q9DE25 - FXC1A_DANRE

Protein

Forkhead box C1-A

Gene

foxc1a

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 108 (01 Oct 2014)
      Sequence version 1 (01 Mar 2001)
      Previous versions | rss
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    Functioni

    Transcriptional regulator. Required for cell viability and resistance to oxidative stress in the eye through regulation of FOXO1A.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi74 – 16895Fork-headPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. chromatin DNA binding Source: RefGenome
    2. DNA binding, bending Source: RefGenome
    3. double-stranded DNA binding Source: RefGenome
    4. RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity Source: RefGenome
    5. sequence-specific DNA binding Source: InterPro
    6. transcription factor binding Source: RefGenome

    GO - Biological processi

    1. adrenal gland development Source: ZFIN
    2. blood vessel development Source: ZFIN
    3. camera-type eye development Source: ZFIN
    4. closure of optic fissure Source: ZFIN
    5. glomerular visceral epithelial cell fate commitment Source: ZFIN
    6. negative regulation of apoptotic process Source: RefGenome
    7. negative regulation of transcription from RNA polymerase II promoter Source: RefGenome
    8. Notch signaling pathway Source: RefGenome
    9. positive regulation of transcription from RNA polymerase II promoter Source: RefGenome
    10. pronephric glomerulus development Source: ZFIN
    11. regulation of organ growth Source: RefGenome
    12. regulation of sequence-specific DNA binding transcription factor activity Source: RefGenome
    13. regulation of vascular permeability Source: ZFIN
    14. somitogenesis Source: ZFIN
    15. transcription from RNA polymerase II promoter Source: GOC
    16. vascular endothelial growth factor receptor signaling pathway Source: RefGenome
    17. vasculature development Source: ZFIN

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Forkhead box C1-A
    Gene namesi
    Name:foxc1a
    Synonyms:foxc1.1
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Chromosome 2

    Organism-specific databases

    ZFINiZDB-GENE-010302-1. foxc1a.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell
    2. transcription factor complex Source: RefGenome

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 476476Forkhead box C1-APRO_0000419248Add
    BLAST

    Proteomic databases

    PRIDEiQ9DE25.

    Expressioni

    Developmental stagei

    First detected at the shield stage of gastrulation in the involuting mesendoderm with levels being highest in the paraxial mesoderm and decline laterally to become undetectable in the ventral mesoderm. Expression spreads in the hypoblast towards the animal pole and converges dorsally. At the tail bud stage (9.5 hpf), transcripts are seen in adaxial cells flanking the future notochord and in the presomitic mesoderm (PSM). During early somitogenesis, expression also extends into the future head, in two stripes continuous with the adaxial cells. Expression continues around the developing eye, presomitic mesoderm (PSM), trunk adaxial cells and somites. In late somatogenesis, expression in the presumptive pronephric primodia lateral to the second and third somite. In the early pharyngula stage, expressed in the perioptic mesoderm. Expression continues in the PSM and adaxial cells in the tail.1 Publication

    Gene expression databases

    BgeeiQ9DE25.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9DE25.
    SMRiQ9DE25. Positions 72-164.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi239 – 33799Ser-richAdd
    BLAST
    Compositional biasi377 – 3804Poly-Thr

    Sequence similaritiesi

    Contains 1 fork-head DNA-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    GeneTreeiENSGT00740000114928.
    HOGENOMiHOG000007939.
    HOVERGENiHBG051640.
    KOiK09396.
    OMAiYSSPCSQ.
    OrthoDBiEOG7C8GHD.
    PhylomeDBiQ9DE25.
    TreeFamiTF316127.

    Family and domain databases

    Gene3Di1.10.10.10. 1 hit.
    InterProiIPR001766. TF_fork_head.
    IPR018122. TF_fork_head_CS.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view]
    PfamiPF00250. Fork_head. 1 hit.
    [Graphical view]
    PRINTSiPR00053. FORKHEAD.
    SMARTiSM00339. FH. 1 hit.
    [Graphical view]
    PROSITEiPS00657. FORK_HEAD_1. 1 hit.
    PS00658. FORK_HEAD_2. 1 hit.
    PS50039. FORK_HEAD_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9DE25-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQARYSVSSP NSLGVVPYIS SDQSYYRAAA GGGYTGMPAP MTMYSHAAHD    50
    QYPASMARAY GPYTPQPQPK DMVKPPYSYI ALITMAIQNS PDKKVTLNGI 100
    YQFIMERFPF YRDNKQGWQN SIRHNLSLNE CFVKVPRDDK KPGKGSYWTL 150
    DPDSYNMFEN GSFLRRRRRF KKKDAMKDKE DRGVKEAPSR QAQPQAREQE 200
    QSVPGSQPVR IQDIKTENGT STPPQAVSPT LSTVPKIESP DSSSSMSSGS 250
    PHSIPSTRSL SLDSAGEQHH QAPAQGFSVD NIMTSLRGSP HSSGELTPSL 300
    VAPSRTGITP TLSLNYSPNQ SSVYSSPCSQ NSISTTSNAT YHCNMQAMSL 350
    YAGGDRSGHL GTTATTVDET LPDYSITTTT SSLSHGNLSS AQEGHHPHQG 400
    RLASWYLNQA GDIGHLGATY PAQQQNFHSV REMFESQRIG LNNSPVNGNN 450
    SCQMSFPPSQ PIYRTSGAFV YDCSKF 476
    Length:476
    Mass (Da):52,173
    Last modified:March 1, 2001 - v1
    Checksum:iE79BD7030D20B2D0
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CU929125 Genomic DNA. No translation available.
    AF219949 Genomic DNA. Translation: AAG44241.1.
    BC053129 mRNA. Translation: AAH53129.1.
    RefSeqiNP_571803.1. NM_131728.3.
    UniGeneiDr.82483.

    Genome annotation databases

    EnsembliENSDART00000122732; ENSDARP00000105372; ENSDARG00000091481.
    GeneIDi100148408.
    KEGGidre:100148408.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CU929125 Genomic DNA. No translation available.
    AF219949 Genomic DNA. Translation: AAG44241.1 .
    BC053129 mRNA. Translation: AAH53129.1 .
    RefSeqi NP_571803.1. NM_131728.3.
    UniGenei Dr.82483.

    3D structure databases

    ProteinModelPortali Q9DE25.
    SMRi Q9DE25. Positions 72-164.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi Q9DE25.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSDART00000122732 ; ENSDARP00000105372 ; ENSDARG00000091481 .
    GeneIDi 100148408.
    KEGGi dre:100148408.

    Organism-specific databases

    CTDi 100148408.
    ZFINi ZDB-GENE-010302-1. foxc1a.

    Phylogenomic databases

    GeneTreei ENSGT00740000114928.
    HOGENOMi HOG000007939.
    HOVERGENi HBG051640.
    KOi K09396.
    OMAi YSSPCSQ.
    OrthoDBi EOG7C8GHD.
    PhylomeDBi Q9DE25.
    TreeFami TF316127.

    Miscellaneous databases

    NextBioi 20792036.

    Gene expression databases

    Bgeei Q9DE25.

    Family and domain databases

    Gene3Di 1.10.10.10. 1 hit.
    InterProi IPR001766. TF_fork_head.
    IPR018122. TF_fork_head_CS.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view ]
    Pfami PF00250. Fork_head. 1 hit.
    [Graphical view ]
    PRINTSi PR00053. FORKHEAD.
    SMARTi SM00339. FH. 1 hit.
    [Graphical view ]
    PROSITEi PS00657. FORK_HEAD_1. 1 hit.
    PS00658. FORK_HEAD_2. 1 hit.
    PS50039. FORK_HEAD_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and expression of zebrafish foxc1a and foxc1b, encoding conserved forkhead/winged helix transcription factors."
      Topczewska J.M., Topczewski J., Solnica-Krezel L., Hogan B.L.
      Mech. Dev. 100:343-347(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], DEVELOPMENTAL STAGE.
    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(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Tuebingen.
    3. NIH - Zebrafish Gene Collection (ZGC) project
      Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Embryo.

    Entry informationi

    Entry nameiFXC1A_DANRE
    AccessioniPrimary (citable) accession number: Q9DE25
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 3, 2012
    Last sequence update: March 1, 2001
    Last modified: October 1, 2014
    This is version 108 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3