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Q7TQK4

- EXOS3_MOUSE

UniProt

Q7TQK4 - EXOS3_MOUSE

Protein

Exosome complex component RRP40

Gene

Exosc3

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 89 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5 By similarity.By similarity

    GO - Molecular functioni

    1. exonuclease activity Source: UniProtKB-KW
    2. RNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. CUT catabolic process Source: Ensembl
    2. DNA deamination Source: Ensembl
    3. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: Ensembl
    4. isotype switching Source: UniProtKB
    5. positive regulation of isotype switching Source: MGI
    6. rRNA processing Source: UniProtKB-KW

    Keywords - Molecular functioni

    Exonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    ReactomeiREACT_198696. KSRP destabilizes mRNA.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exosome complex component RRP40 (EC:3.1.13.-)
    Alternative name(s):
    Exosome component 3
    Ribosomal RNA-processing protein 40
    Gene namesi
    Name:Exosc3
    Synonyms:Rrp40
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 4

    Organism-specific databases

    MGIiMGI:1913612. Exosc3.

    Subcellular locationi

    Cytoplasm By similarity. Nucleusnucleolus By similarity. Nucleus By similarity

    GO - Cellular componenti

    1. cytoplasmic exosome (RNase complex) Source: Ensembl
    2. exosome (RNase complex) Source: UniProtKB
    3. nuclear exosome (RNase complex) Source: Ensembl
    4. nucleolus Source: UniProtKB
    5. transcriptionally active chromatin Source: Ensembl

    Keywords - Cellular componenti

    Cytoplasm, Exosome, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 274273Exosome complex component RRP40PRO_0000087132Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanineBy similarity

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiQ7TQK4.
    PaxDbiQ7TQK4.
    PRIDEiQ7TQK4.

    PTM databases

    PhosphoSiteiQ7TQK4.

    Expressioni

    Gene expression databases

    BgeeiQ7TQK4.
    CleanExiMM_EXOSC3.
    GenevestigatoriQ7TQK4.

    Interactioni

    Subunit structurei

    Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which is believed to associate with catalytic subunits EXOSC10, and DIS3 or DIS3L in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits specifically containing the heterodimers EXOSC4-EXOSC9, EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and peripheral S1 domain-containing components EXOSC1, EXOSC2 and EXOSC3 located on the top of the ring structure. Interacts with GTPBP1 By similarity. Interacts with ZC3HAV1 By similarity. Interacts with DDX17 only in the presence of ZC3HAV1 in an RNA-independent manner By similarity.By similarity

    Protein-protein interaction databases

    IntActiQ7TQK4. 2 interactions.
    MINTiMINT-4094772.

    Structurei

    3D structure databases

    ProteinModelPortaliQ7TQK4.
    SMRiQ7TQK4. Positions 17-274.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the RRP40 family.Curated

    Phylogenomic databases

    eggNOGiCOG1097.
    GeneTreeiENSGT00390000012042.
    HOGENOMiHOG000184644.
    HOVERGENiHBG051518.
    InParanoidiQ7TQK4.
    KOiK03681.
    OMAiVNGRVWI.
    OrthoDBiEOG76HQ2F.
    PhylomeDBiQ7TQK4.
    TreeFamiTF314927.

    Family and domain databases

    InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    [Graphical view]
    PANTHERiPTHR21321. PTHR21321. 1 hit.
    SUPFAMiSSF50249. SSF50249. 1 hit.
    SSF54791. SSF54791. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    Q7TQK4-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAEVLSAGPE SVAGCRARAV HKVLNQVVLP GEELVLPDHE DVDGLGGAGE    50
    QPLRLNAGAR PRLRVVCGPG LRRCGDRLLV TKCGRLRHKE PSGGGGGVYW 100
    VDSQQKRYVP VKGDHVIGIV IAKSGDIFKV DVGGSEPASL SYLAFEGATK 150
    RNRPNVQVGD LIYGQCVVAN KDMEPEMVCI DSCGRANGMG VIGQDGLLFK 200
    VTLGLIRKLL APDCEIVQEL GKLYPLEIVF GMNGRIWVKA KTIQQTLILA 250
    NVLEACEHMT TEQRKQIFAR LAES 274
    Length:274
    Mass (Da):29,546
    Last modified:January 23, 2007 - v3
    Checksum:i0932E5B03DD708D4
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti32 – 321E → P in BAB24501. (PubMed:16141072)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BC023669 mRNA. Translation: AAH23669.1.
    BC054085 mRNA. Translation: AAH54085.1.
    AK006281 mRNA. Translation: BAB24501.1.
    AK009165 mRNA. Translation: BAB26116.1.
    CCDSiCCDS18136.1.
    RefSeqiNP_079789.1. NM_025513.3.
    UniGeneiMm.275788.

    Genome annotation databases

    EnsembliENSMUST00000030003; ENSMUSP00000030003; ENSMUSG00000028322.
    GeneIDi66362.
    KEGGimmu:66362.
    UCSCiuc008ssk.1. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BC023669 mRNA. Translation: AAH23669.1 .
    BC054085 mRNA. Translation: AAH54085.1 .
    AK006281 mRNA. Translation: BAB24501.1 .
    AK009165 mRNA. Translation: BAB26116.1 .
    CCDSi CCDS18136.1.
    RefSeqi NP_079789.1. NM_025513.3.
    UniGenei Mm.275788.

    3D structure databases

    ProteinModelPortali Q7TQK4.
    SMRi Q7TQK4. Positions 17-274.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q7TQK4. 2 interactions.
    MINTi MINT-4094772.

    PTM databases

    PhosphoSitei Q7TQK4.

    Proteomic databases

    MaxQBi Q7TQK4.
    PaxDbi Q7TQK4.
    PRIDEi Q7TQK4.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000030003 ; ENSMUSP00000030003 ; ENSMUSG00000028322 .
    GeneIDi 66362.
    KEGGi mmu:66362.
    UCSCi uc008ssk.1. mouse.

    Organism-specific databases

    CTDi 51010.
    MGIi MGI:1913612. Exosc3.

    Phylogenomic databases

    eggNOGi COG1097.
    GeneTreei ENSGT00390000012042.
    HOGENOMi HOG000184644.
    HOVERGENi HBG051518.
    InParanoidi Q7TQK4.
    KOi K03681.
    OMAi VNGRVWI.
    OrthoDBi EOG76HQ2F.
    PhylomeDBi Q7TQK4.
    TreeFami TF314927.

    Enzyme and pathway databases

    Reactomei REACT_198696. KSRP destabilizes mRNA.

    Miscellaneous databases

    ChiTaRSi EXOSC3. mouse.
    NextBioi 321447.
    PROi Q7TQK4.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q7TQK4.
    CleanExi MM_EXOSC3.
    Genevestigatori Q7TQK4.

    Family and domain databases

    InterProi IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    [Graphical view ]
    PANTHERi PTHR21321. PTHR21321. 1 hit.
    SUPFAMi SSF50249. SSF50249. 1 hit.
    SSF54791. SSF54791. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "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].
      Tissue: Mammary gland.
    2. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 32-274.
      Strain: C57BL/6J.
      Tissue: Testis and Tongue.
    3. "The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates."
      Basu U., Meng F.L., Keim C., Grinstein V., Pefanis E., Eccleston J., Zhang T., Myers D., Wasserman C.R., Wesemann D.R., Januszyk K., Gregory R.I., Deng H., Lima C.D., Alt F.W.
      Cell 144:353-363(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN IG CLASS-SWITCH.

    Entry informationi

    Entry nameiEXOS3_MOUSE
    AccessioniPrimary (citable) accession number: Q7TQK4
    Secondary accession number(s): Q9CV81, Q9CVW2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 26, 2004
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 89 of the entry and version 3 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. 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