ID   EXOS3_MOUSE             Reviewed;         274 AA.
AC   Q7TQK4; Q9CV81; Q9CVW2;
DT   26-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 3.
DT   27-MAR-2024, entry version 145.
DE   RecName: Full=Exosome complex component RRP40;
DE            EC=3.1.13.-;
DE   AltName: Full=Exosome component 3;
DE   AltName: Full=Ribosomal RNA-processing protein 40;
GN   Name=Exosc3; Synonyms=Rrp40;
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC   Murinae; Mus; Mus.
OX   NCBI_TaxID=10090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Mammary gland;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 32-274.
RC   STRAIN=C57BL/6J; TISSUE=Testis, and Tongue;
RX   PubMed=16141072; DOI=10.1126/science.1112014;
RA   Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA   Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA   Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA   Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA   Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA   Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA   Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA   Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA   Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA   Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA   Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA   Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA   Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA   Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA   Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA   Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA   Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA   Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA   Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA   Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA   Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA   Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA   Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA   Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA   Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA   van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA   Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA   Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA   Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA   Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA   Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA   Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA   Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA   Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT   "The transcriptional landscape of the mammalian genome.";
RL   Science 309:1559-1563(2005).
RN   [3]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Brain, Liver, Lung, Spleen, and Testis;
RX   PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA   Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA   Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT   "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL   Cell 143:1174-1189(2010).
RN   [4]
RP   FUNCTION IN IG CLASS-SWITCH.
RX   PubMed=21255825; DOI=10.1016/j.cell.2011.01.001;
RA   Basu U., Meng F.L., Keim C., Grinstein V., Pefanis E., Eccleston J.,
RA   Zhang T., Myers D., Wasserman C.R., Wesemann D.R., Januszyk K.,
RA   Gregory R.I., Deng H., Lima C.D., Alt F.W.;
RT   "The RNA exosome targets the AID cytidine deaminase to both strands of
RT   transcribed duplex DNA substrates.";
RL   Cell 144:353-363(2011).
CC   -!- FUNCTION: Non-catalytic component of the RNA exosome complex which has
CC       3'->5' exoribonuclease activity and participates in a multitude of
CC       cellular RNA processing and degradation events. In the nucleus, the RNA
CC       exosome complex is involved in proper maturation of stable RNA species
CC       such as rRNA, snRNA and snoRNA, in the elimination of RNA processing
CC       by-products and non-coding 'pervasive' transcripts, such as antisense
CC       RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs
CC       with processing defects, thereby limiting or excluding their export to
CC       the cytoplasm. The RNA exosome may be involved in Ig class switch
CC       recombination (CSR) and/or Ig variable region somatic hypermutation
CC       (SHM) by targeting AICDA deamination activity to transcribed dsDNA
CC       substrates. In the cytoplasm, the RNA exosome complex is involved in
CC       general mRNA turnover and specifically degrades inherently unstable
CC       mRNAs containing AU-rich elements (AREs) within their 3' untranslated
CC       regions, and in RNA surveillance pathways, preventing translation of
CC       aberrant mRNAs. It seems to be involved in degradation of histone mRNA.
CC       The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9)
CC       is proposed to play a pivotal role in the binding and presentation of
CC       RNA for ribonucleolysis, and to serve as a scaffold for the association
CC       with catalytic subunits and accessory proteins or complexes. EXOSC3 as
CC       peripheral part of the Exo-9 complex stabilizes the hexameric ring of
CC       RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5 (By
CC       similarity). {ECO:0000250, ECO:0000269|PubMed:21255825}.
CC   -!- SUBUNIT: Component of the RNA exosome complex. Specifically part of the
CC       catalytically inactive RNA exosome core (Exo-9) complex which is
CC       believed to associate with catalytic subunits EXOSC10, and DIS3 or
CC       DIS3L in cytoplasmic- and nuclear-specific RNA exosome complex forms.
CC       Exo-9 is formed by a hexameric ring of RNase PH domain-containing
CC       subunits specifically containing the heterodimers EXOSC4-EXOSC9,
CC       EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and peripheral S1 domain-containing
CC       components EXOSC1, EXOSC2 and EXOSC3 located on the top of the ring
CC       structure. Interacts with GTPBP1 (By similarity). Interacts with
CC       ZC3HAV1 (By similarity). Interacts with DDX17 only in the presence of
CC       ZC3HAV1 in an RNA-independent manner (By similarity). Interacts with
CC       DHX36; this interaction occurs in a RNase-insensitive manner (By
CC       similarity). {ECO:0000250, ECO:0000250|UniProtKB:Q9NQT5}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Nucleus, nucleolus
CC       {ECO:0000250}. Nucleus {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the RRP40 family. {ECO:0000305}.
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DR   EMBL; BC023669; AAH23669.1; -; mRNA.
DR   EMBL; BC054085; AAH54085.1; -; mRNA.
DR   EMBL; AK006281; BAB24501.1; -; mRNA.
DR   EMBL; AK009165; BAB26116.1; -; mRNA.
DR   CCDS; CCDS18136.1; -.
DR   RefSeq; NP_079789.1; NM_025513.3.
DR   AlphaFoldDB; Q7TQK4; -.
DR   SMR; Q7TQK4; -.
DR   BioGRID; 211414; 3.
DR   ComplexPortal; CPX-594; Nuclear exosome complex, Dis3-Exosc10 variant.
DR   ComplexPortal; CPX-595; Nucleolar exosome complex, Exosc10 variant.
DR   ComplexPortal; CPX-596; Cytoplasmic exosome complex, Dis3l variant.
DR   ComplexPortal; CPX-598; Exosome complex, Dis3 variant.
DR   ComplexPortal; CPX-601; Cytoplasmic exosome complex, Dis3l-Exosc10 variant.
DR   IntAct; Q7TQK4; 1.
DR   STRING; 10090.ENSMUSP00000030003; -.
DR   GlyGen; Q7TQK4; 1 site, 1 O-linked glycan (1 site).
DR   iPTMnet; Q7TQK4; -.
DR   PhosphoSitePlus; Q7TQK4; -.
DR   EPD; Q7TQK4; -.
DR   MaxQB; Q7TQK4; -.
DR   PaxDb; 10090-ENSMUSP00000030003; -.
DR   PeptideAtlas; Q7TQK4; -.
DR   ProteomicsDB; 275705; -.
DR   Pumba; Q7TQK4; -.
DR   Antibodypedia; 12051; 332 antibodies from 28 providers.
DR   DNASU; 66362; -.
DR   Ensembl; ENSMUST00000030003.10; ENSMUSP00000030003.4; ENSMUSG00000028322.12.
DR   GeneID; 66362; -.
DR   KEGG; mmu:66362; -.
DR   UCSC; uc008ssk.1; mouse.
DR   AGR; MGI:1913612; -.
DR   CTD; 51010; -.
DR   MGI; MGI:1913612; Exosc3.
DR   VEuPathDB; HostDB:ENSMUSG00000028322; -.
DR   eggNOG; KOG1004; Eukaryota.
DR   GeneTree; ENSGT00940000153596; -.
DR   HOGENOM; CLU_069847_5_1_1; -.
DR   InParanoid; Q7TQK4; -.
DR   OMA; SYMAFPN; -.
DR   OrthoDB; 1344899at2759; -.
DR   PhylomeDB; Q7TQK4; -.
DR   TreeFam; TF314927; -.
DR   Reactome; R-MMU-429958; mRNA decay by 3' to 5' exoribonuclease.
DR   Reactome; R-MMU-450385; Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
DR   Reactome; R-MMU-450513; Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
DR   Reactome; R-MMU-450604; KSRP (KHSRP) binds and destabilizes mRNA.
DR   Reactome; R-MMU-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR   BioGRID-ORCS; 66362; 26 hits in 118 CRISPR screens.
DR   ChiTaRS; Exosc3; mouse.
DR   PRO; PR:Q7TQK4; -.
DR   Proteomes; UP000000589; Chromosome 4.
DR   RNAct; Q7TQK4; Protein.
DR   Bgee; ENSMUSG00000028322; Expressed in embryonic post-anal tail and 207 other cell types or tissues.
DR   ExpressionAtlas; Q7TQK4; baseline and differential.
DR   GO; GO:0005737; C:cytoplasm; ISO:MGI.
DR   GO; GO:0000177; C:cytoplasmic exosome (RNase complex); ISO:MGI.
DR   GO; GO:0005829; C:cytosol; ISO:MGI.
DR   GO; GO:0000791; C:euchromatin; ISO:MGI.
DR   GO; GO:0000178; C:exosome (RNase complex); ISS:UniProtKB.
DR   GO; GO:0000176; C:nuclear exosome (RNase complex); ISO:MGI.
DR   GO; GO:0101019; C:nucleolar exosome (RNase complex); NAS:ComplexPortal.
DR   GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
DR   GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR   GO; GO:0005634; C:nucleus; ISO:MGI.
DR   GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR   GO; GO:0071034; P:CUT catabolic process; ISO:MGI.
DR   GO; GO:0045006; P:DNA deamination; ISO:MGI.
DR   GO; GO:0043928; P:exonucleolytic catabolism of deadenylated mRNA; ISO:MGI.
DR   GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IBA:GO_Central.
DR   GO; GO:0045190; P:isotype switching; IMP:UniProtKB.
DR   GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IBA:GO_Central.
DR   GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IBA:GO_Central.
DR   GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IBA:GO_Central.
DR   GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IBA:GO_Central.
DR   GO; GO:0045830; P:positive regulation of isotype switching; IMP:MGI.
DR   GO; GO:0006401; P:RNA catabolic process; ISO:MGI.
DR   GO; GO:0006396; P:RNA processing; ISO:MGI.
DR   GO; GO:0006364; P:rRNA processing; ISO:MGI.
DR   GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
DR   CDD; cd22526; KH-I_Rrp40; 1.
DR   CDD; cd05790; S1_Rrp40; 1.
DR   Gene3D; 2.40.50.100; -; 1.
DR   Gene3D; 3.30.1370.10; K Homology domain, type 1; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR   InterPro; IPR026699; Exosome_RNA_bind1/RRP40/RRP4.
DR   InterPro; IPR004088; KH_dom_type_1.
DR   InterPro; IPR036612; KH_dom_type_1_sf.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR049469; RRP40_KH-I.
DR   InterPro; IPR048541; RRP40_N.
DR   InterPro; IPR037319; Rrp40_S1.
DR   PANTHER; PTHR21321:SF1; EXOSOME COMPLEX COMPONENT RRP40; 1.
DR   PANTHER; PTHR21321; PNAS-3 RELATED; 1.
DR   Pfam; PF15985; KH_6; 1.
DR   Pfam; PF21261; RRP40_N_mamm; 1.
DR   Pfam; PF21262; RRP40_S1; 1.
DR   SUPFAM; SSF54791; Eukaryotic type KH-domain (KH-domain type I); 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   SUPFAM; SSF110324; Ribosomal L27 protein-like; 1.
DR   Genevisible; Q7TQK4; MM.
PE   1: Evidence at protein level;
KW   Acetylation; Cytoplasm; Exonuclease; Exosome; Hydrolase; Isopeptide bond;
KW   Nuclease; Nucleus; Reference proteome; RNA-binding; rRNA processing;
KW   Ubl conjugation.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000250|UniProtKB:Q9NQT5"
FT   CHAIN           2..274
FT                   /note="Exosome complex component RRP40"
FT                   /id="PRO_0000087132"
FT   MOD_RES         2
FT                   /note="N-acetylalanine"
FT                   /evidence="ECO:0000250|UniProtKB:Q9NQT5"
FT   CROSSLNK        150
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q9NQT5"
FT   CONFLICT        32
FT                   /note="E -> P (in Ref. 2; BAB24501)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   274 AA;  29546 MW;  0932E5B03DD708D4 CRC64;
     MAEVLSAGPE SVAGCRARAV HKVLNQVVLP GEELVLPDHE DVDGLGGAGE QPLRLNAGAR
     PRLRVVCGPG LRRCGDRLLV TKCGRLRHKE PSGGGGGVYW VDSQQKRYVP VKGDHVIGIV
     IAKSGDIFKV DVGGSEPASL SYLAFEGATK RNRPNVQVGD LIYGQCVVAN KDMEPEMVCI
     DSCGRANGMG VIGQDGLLFK VTLGLIRKLL APDCEIVQEL GKLYPLEIVF GMNGRIWVKA
     KTIQQTLILA NVLEACEHMT TEQRKQIFAR LAES
//