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Q9JKB3

- YBOX3_MOUSE

UniProt

Q9JKB3 - YBOX3_MOUSE

Protein

Y-box-binding protein 3

Gene

Ybx3

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 101 (01 Oct 2014)
      Sequence version 2 (15 Mar 2005)
      Previous versions | rss
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    Functioni

    Binds to the GM-CSF promoter. Seems to act as a repressor By similarity. Binds also to full length mRNA and to short RNA sequences containing the consensus site 5'-UCCAUCA-3'. May have a role in translation repression.By similarity1 Publication

    GO - Molecular functioni

    1. DNA binding Source: MGI
    2. mRNA 3'-UTR binding Source: MGI
    3. protein binding Source: MGI
    4. RNA polymerase II regulatory region sequence-specific DNA binding Source: NTNU_SB
    5. RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription Source: NTNU_SB
    6. single-stranded DNA binding Source: MGI

    GO - Biological processi

    1. cellular hyperosmotic response Source: Ensembl
    2. cellular response to tumor necrosis factor Source: Ensembl
    3. fertilization Source: MGI
    4. in utero embryonic development Source: MGI
    5. male gonad development Source: MGI
    6. negative regulation of apoptotic process Source: MGI
    7. negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress Source: Ensembl
    8. negative regulation of necrotic cell death Source: Ensembl
    9. negative regulation of skeletal muscle tissue development Source: MGI
    10. negative regulation of transcription from RNA polymerase II promoter Source: NTNU_SB
    11. positive regulation of organ growth Source: MGI
    12. spermatogenesis Source: MGI

    Keywords - Molecular functioni

    Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding, RNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Y-box-binding protein 3
    Alternative name(s):
    Cold shock domain-containing protein A
    DNA-binding protein A
    Y-box protein 3
    Gene namesi
    Name:Ybx3
    Synonyms:Csda, Msy4
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 6

    Organism-specific databases

    MGIiMGI:2137670. Ybx3.

    Subcellular locationi

    Cytoplasm 1 Publication. Nucleus By similarity

    GO - Cellular componenti

    1. cytoplasm Source: MGI
    2. gap junction Source: MGI
    3. nucleus Source: MGI

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 361360Y-box-binding protein 3PRO_0000100215Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserineBy similarity
    Modified residuei126 – 1261PhosphoserineBy similarity
    Modified residuei193 – 1931PhosphoserineBy similarity
    Modified residuei195 – 1951PhosphoserineBy similarity
    Modified residuei196 – 1961PhosphoserineBy similarity
    Modified residuei313 – 3131PhosphoserineBy similarity

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiQ9JKB3.
    PaxDbiQ9JKB3.
    PRIDEiQ9JKB3.

    PTM databases

    PhosphoSiteiQ9JKB3.

    Expressioni

    Tissue specificityi

    Expressed in oocytes, spermatocytes and spermatids (at protein level). Expressed in skeletal muscle, kidney, brain, spleen, liver, heart and spermatids. Isoform 2 is preferentially expressed in somatic tissues (PubMed:10956549).3 Publications

    Gene expression databases

    BgeeiQ9JKB3.
    CleanExiMM_CSDA.
    GenevestigatoriQ9JKB3.

    Interactioni

    Subunit structurei

    Found in a mRNP complex with YBX2.1 Publication

    Protein-protein interaction databases

    BioGridi207989. 10 interactions.
    DIPiDIP-42746N.
    IntActiQ9JKB3. 7 interactions.
    MINTiMINT-1891951.
    STRINGi10090.ENSMUSP00000032309.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9JKB3.
    SMRiQ9JKB3. Positions 76-152.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini82 – 15271CSDAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi17 – 6953Ala-richAdd
    BLAST
    Compositional biasi161 – 329169Arg-richAdd
    BLAST

    Sequence similaritiesi

    Contains 1 CSD (cold-shock) domain.Curated

    Phylogenomic databases

    eggNOGiCOG1278.
    GeneTreeiENSGT00390000009256.
    HOGENOMiHOG000116439.
    HOVERGENiHBG008757.
    InParanoidiQ9JKB3.
    KOiK06099.
    OMAiLSFNRND.
    OrthoDBiEOG7TBC44.
    PhylomeDBiQ9JKB3.
    TreeFamiTF317306.

    Family and domain databases

    Gene3Di2.40.50.140. 1 hit.
    InterProiIPR019844. Cold-shock_CS.
    IPR011129. Cold_shock_prot.
    IPR002059. CSP_DNA-bd.
    IPR012340. NA-bd_OB-fold.
    [Graphical view]
    PfamiPF00313. CSD. 1 hit.
    [Graphical view]
    PRINTSiPR00050. COLDSHOCK.
    SMARTiSM00357. CSP. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 1 hit.
    PROSITEiPS00352. COLD_SHOCK. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9JKB3-1) [UniParc]FASTAAdd to Basket

    Also known as: Msy3l

    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

    MSEAGEATTG GTTLPQAAAD APAAAPPDPA PKSPAASGAP QAPAPAALLA    50
    GSPGGDAAPG PAPASSAPAG GEDAEKKVLA TKVLGTVKWF NVRNGYGFIN 100
    RNDTKEDVFV HQTAIKKNNP RKYLRSVGDG ETVEFDVVEG EKGAEAANVT 150
    GPDGVPVEGS RYAADRRRYR RGYYGRRRGP PRNYAGEEEE EGSGSSEGFE 200
    PPAADGQFSG ARNQLRRPQY RPPYRQRRFP PYHVGQTFDR RSRVFPHPNR 250
    MQAGEIGEMK DGVPEGTQLQ AHRNPTYRPR FRRGPARPRP APAIGEAEDK 300
    ENQQAANGPN QPSARRGFRR PYNYRRRSRP LNAVSQDGKE TKAGEAPTEN 350
    PAPATEQSSA E 361
    Length:361
    Mass (Da):38,814
    Last modified:March 15, 2005 - v2
    Checksum:i5BAF6A144A127CEC
    GO
    Isoform 2 (identifier: Q9JKB3-2) [UniParc]FASTAAdd to Basket

    Also known as: Msy3s

    The sequence of this isoform differs from the canonical sequence as follows:
         184-252: Missing.

    Show »
    Length:292
    Mass (Da):30,765
    Checksum:i57B2898DF2D18155
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti237 – 2371T → N in AAG14418. (PubMed:10956549)Curated
    Sequence conflicti306 – 3061A → G in AAF61741. (PubMed:10772793)Curated
    Sequence conflicti349 – 3491E → A in AAF61741. (PubMed:10772793)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei184 – 25269Missing in isoform 2. 2 PublicationsVSP_013051Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF246224 mRNA. Translation: AAF61741.1.
    AF248546 mRNA. Translation: AAG14418.1.
    AF248547 mRNA. Translation: AAG14419.1.
    BC048242 mRNA. Translation: AAH48242.1.
    BC062377 mRNA. Translation: AAH62377.1.
    CCDSiCCDS20605.1. [Q9JKB3-2]
    CCDS20606.1. [Q9JKB3-1]
    RefSeqiNP_035863.1. NM_011733.2. [Q9JKB3-2]
    NP_620817.2. NM_139117.2. [Q9JKB3-1]
    UniGeneiMm.458000.

    Genome annotation databases

    EnsembliENSMUST00000032309; ENSMUSP00000032309; ENSMUSG00000030189. [Q9JKB3-1]
    ENSMUST00000087865; ENSMUSP00000085172; ENSMUSG00000030189. [Q9JKB3-2]
    GeneIDi56449.
    KEGGimmu:56449.
    UCSCiuc009eis.1. mouse. [Q9JKB3-1]
    uc009eit.1. mouse. [Q9JKB3-2]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF246224 mRNA. Translation: AAF61741.1 .
    AF248546 mRNA. Translation: AAG14418.1 .
    AF248547 mRNA. Translation: AAG14419.1 .
    BC048242 mRNA. Translation: AAH48242.1 .
    BC062377 mRNA. Translation: AAH62377.1 .
    CCDSi CCDS20605.1. [Q9JKB3-2 ]
    CCDS20606.1. [Q9JKB3-1 ]
    RefSeqi NP_035863.1. NM_011733.2. [Q9JKB3-2 ]
    NP_620817.2. NM_139117.2. [Q9JKB3-1 ]
    UniGenei Mm.458000.

    3D structure databases

    ProteinModelPortali Q9JKB3.
    SMRi Q9JKB3. Positions 76-152.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 207989. 10 interactions.
    DIPi DIP-42746N.
    IntActi Q9JKB3. 7 interactions.
    MINTi MINT-1891951.
    STRINGi 10090.ENSMUSP00000032309.

    PTM databases

    PhosphoSitei Q9JKB3.

    Proteomic databases

    MaxQBi Q9JKB3.
    PaxDbi Q9JKB3.
    PRIDEi Q9JKB3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000032309 ; ENSMUSP00000032309 ; ENSMUSG00000030189 . [Q9JKB3-1 ]
    ENSMUST00000087865 ; ENSMUSP00000085172 ; ENSMUSG00000030189 . [Q9JKB3-2 ]
    GeneIDi 56449.
    KEGGi mmu:56449.
    UCSCi uc009eis.1. mouse. [Q9JKB3-1 ]
    uc009eit.1. mouse. [Q9JKB3-2 ]

    Organism-specific databases

    CTDi 8531.
    MGIi MGI:2137670. Ybx3.

    Phylogenomic databases

    eggNOGi COG1278.
    GeneTreei ENSGT00390000009256.
    HOGENOMi HOG000116439.
    HOVERGENi HBG008757.
    InParanoidi Q9JKB3.
    KOi K06099.
    OMAi LSFNRND.
    OrthoDBi EOG7TBC44.
    PhylomeDBi Q9JKB3.
    TreeFami TF317306.

    Miscellaneous databases

    ChiTaRSi CSDA. mouse.
    NextBioi 312662.
    PROi Q9JKB3.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q9JKB3.
    CleanExi MM_CSDA.
    Genevestigatori Q9JKB3.

    Family and domain databases

    Gene3Di 2.40.50.140. 1 hit.
    InterProi IPR019844. Cold-shock_CS.
    IPR011129. Cold_shock_prot.
    IPR002059. CSP_DNA-bd.
    IPR012340. NA-bd_OB-fold.
    [Graphical view ]
    Pfami PF00313. CSD. 1 hit.
    [Graphical view ]
    PRINTSi PR00050. COLDSHOCK.
    SMARTi SM00357. CSP. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50249. SSF50249. 1 hit.
    PROSITEi PS00352. COLD_SHOCK. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A sequence-specific RNA binding complex expressed in murine germ cells contains MSY2 and MSY4."
      Davies H.G., Giorgini F., Fajardo M.A., Braun R.E.
      Dev. Biol. 221:87-100(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), IDENTIFICATION IN A MRNP COMPLEX WITH YBX2, RNA-BINDING, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
      Tissue: Testis.
    2. "Developmental expression of Y-box protein 1 mRNA and alternatively spliced Y-box protein 3 mRNAs in spermatogenic cells in mice."
      Mastrangelo M.-A., Kleene K.C.
      Mol. Hum. Reprod. 6:779-788(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY.
      Strain: CD-1.
      Tissue: Testis.
    3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
      Strain: FVB/N.
      Tissue: Colon and Eye.
    4. "MSY2 and MSY4 bind a conserved sequence in the 3' untranslated region of protamine 1 mRNA in vitro and in vivo."
      Giorgini F., Davies H.G., Braun R.E.
      Mol. Cell. Biol. 21:7010-7019(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: RNA-BINDING.
    5. "Translational repression by MSY4 inhibits spermatid differentiation in mice."
      Giorgini F., Davies H.G., Braun R.E.
      Development 129:3669-3679(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN TRANSLATIONAL REPRESSION, TISSUE SPECIFICITY.

    Entry informationi

    Entry nameiYBOX3_MOUSE
    AccessioniPrimary (citable) accession number: Q9JKB3
    Secondary accession number(s): Q80WG4, Q9EQF7, Q9EQF8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 15, 2005
    Last sequence update: March 15, 2005
    Last modified: October 1, 2014
    This is version 101 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Transgenic mice overexpressing Ybx3 exhibit disruption of the normal completion of spermatogenesis, dominant sterility and anormal translation activation of repressed mRNA.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3