ID   EXOS9_DANRE             Reviewed;         393 AA.
AC   Q5XJQ5;
DT   05-DEC-2018, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   03-AUG-2022, entry version 118.
DE   RecName: Full=Exosome complex component RRP45;
DE   AltName: Full=Exosome component 9;
GN   Name=exosc9 {ECO:0000312|ZFIN:ZDB-GENE-041010-180};
OS   Danio rerio (Zebrafish) (Brachydanio rerio).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC   Danionidae; Danioninae; Danio.
OX   NCBI_TaxID=7955;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Tuebingen;
RX   PubMed=23594743; DOI=10.1038/nature12111;
RA   Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA   Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA   Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA   White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA   Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA   Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA   Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA   Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA   Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA   Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA   Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA   Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA   Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA   Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA   Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA   McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA   Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA   Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA   Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA   Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA   Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA   Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA   Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA   Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA   Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA   Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA   Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA   Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA   de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA   Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT   "The zebrafish reference genome sequence and its relationship to the human
RT   genome.";
RL   Nature 496:498-503(2013).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Olfactory epithelium;
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   DISRUPTION PHENOTYPE.
RX   PubMed=29727687; DOI=10.1016/j.ajhg.2018.03.011;
RA   Burns D.T., Donkervoort S., Mueller J.S., Knierim E., Bharucha-Goebel D.,
RA   Faqeih E.A., Bell S.K., Alfaifi A.Y., Monies D., Millan F., Retterer K.,
RA   Dyack S., MacKay S., Morales-Gonzalez S., Giunta M., Munro B., Hudson G.,
RA   Scavina M., Baker L., Massini T.C., Lek M., Hu Y., Ezzo D., Alkuraya F.S.,
RA   Kang P.B., Griffin H., Foley A.R., Schuelke M., Horvath R.,
RA   Boennemann C.G.;
RT   "Variants in EXOSC9 disrupt the RNA exosome and result in cerebellar
RT   atrophy with spinal motor neuronopathy.";
RL   Am. J. Hum. Genet. 102:858-873(2018).
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. 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. {ECO:0000250|UniProtKB:Q06265}.
CC   -!- SUBUNIT: Component of the RNA exosome complex.
CC       {ECO:0000250|UniProtKB:Q06265}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q06265}. Nucleus
CC       {ECO:0000250|UniProtKB:Q06265}. Nucleus, nucleolus
CC       {ECO:0000250|UniProtKB:Q06265}. Nucleus, nucleoplasm
CC       {ECO:0000250|UniProtKB:Q06265}.
CC   -!- DISRUPTION PHENOTYPE: Morpholino knockdown of the protein affects brain
CC       and neuromuscular development. Morphant embryos have small heads, small
CC       or absent eyes, truncated bodies, and reduced and damaged myofibers.
CC       Motor axons fail to migrate properly to the neuromuscular junctions.
CC       The brain has abnormal morphology, the cerebellum and hindbrain are
CC       absent. {ECO:0000269|PubMed:29727687}.
CC   -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
CC   -!- CAUTION: The six exosome core subunits containing a RNase PH-domain are
CC       not phosphorolytically active. {ECO:0000305}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; BX323984; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; BC083243; AAH83243.1; -; mRNA.
DR   EMBL; BC164713; AAI64713.1; -; mRNA.
DR   RefSeq; NP_001006077.1; NM_001006077.1.
DR   AlphaFoldDB; Q5XJQ5; -.
DR   SMR; Q5XJQ5; -.
DR   STRING; 7955.ENSDARP00000005262; -.
DR   PaxDb; Q5XJQ5; -.
DR   Ensembl; ENSDART00000002886; ENSDARP00000005262; ENSDARG00000006392.
DR   GeneID; 450057; -.
DR   KEGG; dre:450057; -.
DR   CTD; 5393; -.
DR   ZFIN; ZDB-GENE-041010-180; exosc9.
DR   eggNOG; KOG1614; Eukaryota.
DR   GeneTree; ENSGT00950000183130; -.
DR   HOGENOM; CLU_038194_7_0_1; -.
DR   InParanoid; Q5XJQ5; -.
DR   OMA; CQIAKYG; -.
DR   OrthoDB; 996662at2759; -.
DR   PhylomeDB; Q5XJQ5; -.
DR   TreeFam; TF300092; -.
DR   Reactome; R-DRE-429958; mRNA decay by 3' to 5' exoribonuclease.
DR   Reactome; R-DRE-450385; Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
DR   Reactome; R-DRE-450513; Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
DR   Reactome; R-DRE-450604; KSRP (KHSRP) binds and destabilizes mRNA.
DR   Reactome; R-DRE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR   PRO; PR:Q5XJQ5; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 1.
DR   Bgee; ENSDARG00000006392; Expressed in blastula and 28 other tissues.
DR   ExpressionAtlas; Q5XJQ5; baseline and differential.
DR   GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IBA:GO_Central.
DR   GO; GO:0000176; C:nuclear exosome (RNase complex); IBA:GO_Central.
DR   GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR   GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0043928; P:exonucleolytic catabolism of deadenylated mRNA; IBA:GO_Central.
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:0071028; P:nuclear mRNA surveillance; IBA:GO_Central.
DR   GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IBA:GO_Central.
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:0016075; P:rRNA catabolic process; IBA:GO_Central.
DR   GO; GO:0034473; P:U1 snRNA 3'-end processing; IBA:GO_Central.
DR   GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
DR   GO; GO:0034476; P:U5 snRNA 3'-end processing; IBA:GO_Central.
DR   CDD; cd11368; RNase_PH_RRP45; 1.
DR   Gene3D; 3.30.230.70; -; 1.
DR   InterPro; IPR001247; ExoRNase_PH_dom1.
DR   InterPro; IPR015847; ExoRNase_PH_dom2.
DR   InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR   InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR   InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR   InterPro; IPR033100; Rrp45.
DR   Pfam; PF01138; RNase_PH; 1.
DR   Pfam; PF03725; RNase_PH_C; 1.
DR   SUPFAM; SSF54211; SSF54211; 1.
DR   SUPFAM; SSF55666; SSF55666; 1.
PE   2: Evidence at transcript level;
KW   Cytoplasm; Exosome; Nucleus; Reference proteome; RNA-binding;
KW   rRNA processing.
FT   CHAIN           1..393
FT                   /note="Exosome complex component RRP45"
FT                   /id="PRO_0000445730"
FT   REGION          1..268
FT                   /note="ARE binding"
FT                   /evidence="ECO:0000250|UniProtKB:Q06265"
SQ   SEQUENCE   393 AA;  44135 MW;  CAFA889928212B63 CRC64;
     MRDTPLSNCE RLFLLKAIKE KKRLDGRQTY DYRNIKISFG TDYGCCVVEL GKTRVLSQVS
     CELVPPKDSR PTEGIVFFNL ELSPMASPAF EPNRQSELLV TLNRQLERCL RNSKCIDTES
     LCVVSGEKVW QIRVDVHVLN HDGNLMDAAS IAAISALSHF RRPDVAIQGR DVTVFGPEER
     DPIPLSIYHM PICVSFAFFL QGSFLLVDPC EREERVKDGL LVIAMNKHRE ICSIQSSGGI
     MLLKEQVLRC SKIASVKVSE ITELINKALE NDKKVRKEGG KFGFAESMPK ERITTLKRDE
     APVEMTDVKE TADDIVQRTE TTTETVPSPI LVATGTAQIG EGIVNSWGLD EDEDDELQTE
     DRKTDEVVVI TDSEEEEVVI LNDQKSKKTS KQK