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Entry: Q12149
LinkDB: Q12149
Original site: Q12149 
ID   RRP6_YEAST              Reviewed;         733 AA.
AC   Q12149; D6W267; Q6B280;
DT   01-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   09-JUL-2014, entry version 130.
DE   RecName: Full=Exosome complex exonuclease RRP6;
DE            EC=3.1.13.-;
DE   AltName: Full=Ribosomal RNA-processing protein 6;
GN   Name=RRP6; Synonyms=UNC733; OrderedLocusNames=YOR001W;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
OC   Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=8896276;
RX   DOI=10.1002/(SICI)1097-0061(199609)12:10B<1091::AID-YEA22>3.3.CO;2-9;
RA   Sterky F., Holmberg A., Pettersson B., Uhlen M.;
RT   "The sequence of a 30 kb fragment on the left arm of chromosome XV
RT   from Saccharomyces cerevisiae reveals 15 open reading frames, five of
RT   which correspond to previously identified genes.";
RL   Yeast 12:1091-1095(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169874;
RA   Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W.,
RA   Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R.,
RA   Boyer J., Camasses A., Casamayor A., Casas C., Cheret G.,
RA   Cziepluch C., Daignan-Fornier B., Dang V.-D., de Haan M., Delius H.,
RA   Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F.,
RA   Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A.,
RA   Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA   Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA   Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA   Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J.,
RA   Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P.,
RA   Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M.,
RA   Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R.,
RA   Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S.,
RA   Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A.,
RA   Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M.,
RA   Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C.,
RA   Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S.,
RA   Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL   Nature 387:98-102(1997).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
RA   Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and
RT   now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=17322287; DOI=10.1101/gr.6037607;
RA   Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA   Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
RA   Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
RA   Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
RA   Kolodner R.D., LaBaer J.;
RT   "Approaching a complete repository of sequence-verified protein-
RT   encoding clones for Saccharomyces cerevisiae.";
RL   Genome Res. 17:536-543(2007).
RN   [5]
RP   FUNCTION.
RX   PubMed=9582370; DOI=10.1074/jbc.273.21.13255;
RA   Briggs M.W., Burkard K.T.D., Butler J.S.;
RT   "Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen,
RT   is essential for efficient 5.8 S rRNA 3' end formation.";
RL   J. Biol. Chem. 273:13255-13263(1998).
RN   [6]
RP   FUNCTION, IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS
RP   SPECTROMETRY, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX   PubMed=10465791; DOI=10.1101/gad.13.16.2148;
RA   Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D.,
RA   Mitchell P.;
RT   "The yeast exosome and human PM-Scl are related complexes of 3'-->5'
RT   exonucleases.";
RL   Genes Dev. 13:2148-2158(1999).
RN   [7]
RP   CATALYTIC ACTIVITY, FUNCTION, INTERACTION WITH NPL3 AND PAP1,
RP   SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX   PubMed=10611239; DOI=10.1128/MCB.20.2.604-616.2000;
RA   Burkard K.T.D., Butler J.S.;
RT   "A nuclear 3'-5' exonuclease involved in mRNA degradation interacts
RT   with Poly(A) polymerase and the hnRNA protein Npl3p.";
RL   Mol. Cell. Biol. 20:604-616(2000).
RN   [8]
RP   INTERACTION WITH LRP1.
RX   PubMed=12972615; DOI=10.1128/MCB.23.19.6982-6992.2003;
RA   Mitchell P., Petfalski E., Houalla R., Podtelejnikov A., Mann M.,
RA   Tollervey D.;
RT   "Rrp47p is an exosome-associated protein required for the 3'
RT   processing of stable RNAs.";
RL   Mol. Cell. Biol. 23:6982-6992(2003).
RN   [9]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=14562095; DOI=10.1038/nature02026;
RA   Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA   Weissman J.S., O'Shea E.K.;
RT   "Global analysis of protein localization in budding yeast.";
RL   Nature 425:686-691(2003).
RN   [10]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
RA   Dephoure N., O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
RN   [11]
RP   FUNCTION, INTERACTION WITH LRP1, AND SUBCELLULAR LOCATION.
RX   PubMed=15489286; DOI=10.1101/gad.1241204;
RA   Hieronymus H., Yu M.C., Silver P.A.;
RT   "Genome-wide mRNA surveillance is coupled to mRNA export.";
RL   Genes Dev. 18:2652-2662(2004).
RN   [12]
RP   RECONSTITUTION OF THE RNA EXOSOME COMPLEX, AND EXONUCLEASE ACTIVITY.
RX   PubMed=17174896; DOI=10.1016/j.cell.2006.10.037;
RA   Liu Q., Greimann J.C., Lima C.D.;
RT   "Reconstitution, activities, and structure of the eukaryotic RNA
RT   exosome.";
RL   Cell 127:1223-1237(2006).
RN   [13]
RP   ERRATUM.
RA   Liu Q., Greimann J.C., Lima C.D.;
RL   Cell 131:188-189(2007).
RN   [14]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138 AND SER-645, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=ADR376;
RX   PubMed=17330950; DOI=10.1021/pr060559j;
RA   Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA   Elias J.E., Gygi S.P.;
RT   "Large-scale phosphorylation analysis of alpha-factor-arrested
RT   Saccharomyces cerevisiae.";
RL   J. Proteome Res. 6:1190-1197(2007).
RN   [15]
RP   IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH THE RNA EXOSOME,
RP   SUBUNIT, AND DISRUPTION PHENOTYPE.
RX   PubMed=17173052; DOI=10.1038/nsmb1184;
RA   Dziembowski A., Lorentzen E., Conti E., Seraphin B.;
RT   "A single subunit, Dis3, is essentially responsible for yeast exosome
RT   core activity.";
RL   Nat. Struct. Mol. Biol. 14:15-22(2007).
RN   [16]
RP   INTERACTION WITH NOP53.
RX   PubMed=18631361; DOI=10.1111/j.1742-4658.2008.06565.x;
RA   Granato D.C., Machado-Santelli G.M., Oliveira C.C.;
RT   "Nop53p interacts with 5.8S rRNA co-transcriptionally, and regulates
RT   processing of pre-rRNA by the exosome.";
RL   FEBS J. 275:4164-4178(2008).
RN   [17]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-520 AND SER-645, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
RA   Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT   "A multidimensional chromatography technology for in-depth
RT   phosphoproteome analysis.";
RL   Mol. Cell. Proteomics 7:1389-1396(2008).
RN   [18]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-640 AND SER-645, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19779198; DOI=10.1126/science.1172867;
RA   Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT   "Global analysis of Cdk1 substrate phosphorylation sites provides
RT   insights into evolution.";
RL   Science 325:1682-1686(2009).
RN   [19]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA   Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA   Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
RA   Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
RA   Aldabe R.;
RT   "N-terminal acetylome analyses and functional insights of the N-
RT   terminal acetyltransferase NatB.";
RL   Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC   -!- FUNCTION: Nuclear-specific catalytic component of the RNA exosome
CC       complex which has 3'->5' exoribonuclease activity and participates
CC       in a multitude of cellular RNA processing and degradation events.
CC       In the nucleus, the RNA exosome complex is involved in proper
CC       maturation of stable RNA species such as rRNA, snRNA and snoRNA,
CC       in the elimination of RNA processing by-products and non-coding
CC       'pervasive' transcripts, such as antisense RNA species and cryptic
CC       unstable transcripts (CUTs), and of mRNAs with processing defects,
CC       thereby limiting or excluding their export to the cytoplasm. The
CC       catalytic inactive RNA exosome core complex of 9 subunits (Exo-9)
CC       is proposed to play a pivotal role in the binding and presentation
CC       of RNA for ribonucleolysis, and to serve as a scaffold for the
CC       association with catalytic subunits and accessory proteins or
CC       complexes. RRP6 has 3'-5' exonuclease activity which is not
CC       modulated upon association with Exo-9 suggesting that the complex
CC       inner RNA-binding path is not used to access its active site.
CC   -!- SUBUNIT: Component of the RNA exosome complex. The catalytically
CC       inactive RNA exosome core (Exo-9) complex associates with
CC       catalytic subunits DIS3 and RRP6 in cytoplasmic- and nuclear-
CC       specific RNA exosome complex forms. Exo-9 is formed by a hexameric
CC       ring of RNase PH domain-containing subunits and peripheral S1
CC       domain-containing components CSL4, RRP4 and RRP40 located on the
CC       top of the ring structure. RRP6 specifically is part of the
CC       nuclear form of the RNA exosome complex; the association appears
CC       to be mediated by Exo-9 and not by DIS3. Interacts with LRP1.
CC       Interacts with NPL3, NOP53 and PAP1.
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleolus.
CC   -!- DISRUPTION PHENOTYPE: Deletion mutant is impaired in growth at all
CC       temperatures and is nonviable at 37 degrees Celsius. It is
CC       defective in the 3' processing of the 5.8S rRNA and accumulates a
CC       discrete species, 5.8S + 30, that is 3' extended by about 30
CC       nucleotides. Deletion also causes an accumulation of 7S RNA and 5'
CC       ETS and increases the level of poly(A)+ mRNA.
CC   -!- MISCELLANEOUS: Present with 2160 molecules/cell in log phase SD
CC       medium.
CC   -!- SIMILARITY: Belongs to the exosome component 10/RRP6 family.
CC   -!- SIMILARITY: Contains 1 HRDC domain.
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DR   EMBL; Z74909; CAA99189.1; -; Genomic_DNA.
DR   EMBL; U43491; AAC49480.1; -; Genomic_DNA.
DR   EMBL; AY692850; AAT92869.1; -; Genomic_DNA.
DR   EMBL; BK006948; DAA10783.1; -; Genomic_DNA.
DR   PIR; S61984; S61984.
DR   RefSeq; NP_014643.1; NM_001183420.1.
DR   PDB; 1M0Y; Model; -; A=207-382.
DR   PDB; 2HBJ; X-ray; 2.10 A; A=129-536.
DR   PDB; 2HBK; X-ray; 2.25 A; A=129-536.
DR   PDB; 2HBL; X-ray; 2.30 A; A=129-536.
DR   PDB; 2HBM; X-ray; 2.70 A; A=129-536.
DR   PDB; 4IFD; X-ray; 2.80 A; K=518-693.
DR   PDBsum; 1M0Y; -.
DR   PDBsum; 2HBJ; -.
DR   PDBsum; 2HBK; -.
DR   PDBsum; 2HBL; -.
DR   PDBsum; 2HBM; -.
DR   PDBsum; 4IFD; -.
DR   ProteinModelPortal; Q12149; -.
DR   SMR; Q12149; 129-516, 532-619.
DR   BioGrid; 34404; 301.
DR   DIP; DIP-4560N; -.
DR   IntAct; Q12149; 27.
DR   MINT; MINT-534618; -.
DR   STRING; 4932.YOR001W; -.
DR   MaxQB; Q12149; -.
DR   PaxDb; Q12149; -.
DR   EnsemblFungi; YOR001W; YOR001W; YOR001W.
DR   GeneID; 854162; -.
DR   KEGG; sce:YOR001W; -.
DR   CYGD; YOR001w; -.
DR   SGD; S000005527; RRP6.
DR   eggNOG; COG0349; -.
DR   GeneTree; ENSGT00390000015408; -.
DR   HOGENOM; HOG000196525; -.
DR   KO; K12591; -.
DR   OMA; EYKFLHA; -.
DR   OrthoDB; EOG7WT49D; -.
DR   BioCyc; YEAST:G3O-33552-MONOMER; -.
DR   EvolutionaryTrace; Q12149; -.
DR   NextBio; 975938; -.
DR   PRO; PR:Q12149; -.
DR   Genevestigator; Q12149; -.
DR   GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD.
DR   GO; GO:0005730; C:nucleolus; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; IDA:SGD.
DR   GO; GO:0000175; F:3'-5'-exoribonuclease activity; IDA:SGD.
DR   GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
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); IMP:SGD.
DR   GO; GO:0071044; P:histone mRNA catabolic process; IMP:SGD.
DR   GO; GO:0071040; P:nuclear polyadenylation-dependent antisense transcript catabolic process; IMP:SGD.
DR   GO; GO:0071039; P:nuclear polyadenylation-dependent CUT catabolic process; IMP:SGD.
DR   GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IMP:SGD.
DR   GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
DR   GO; GO:0071036; P:nuclear polyadenylation-dependent snoRNA catabolic process; IMP:SGD.
DR   GO; GO:0071037; P:nuclear polyadenylation-dependent snRNA catabolic process; IMP:SGD.
DR   GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
DR   GO; GO:0071033; P:nuclear retention of pre-mRNA at the site of transcription; IGI:SGD.
DR   GO; GO:0071049; P:nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription; IGI:SGD.
DR   GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IMP:SGD.
DR   GO; GO:0000973; P:posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery; IMP:SGD.
DR   GO; GO:0034473; P:U1 snRNA 3'-end processing; IMP:SGD.
DR   GO; GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD.
DR   GO; GO:0034476; P:U5 snRNA 3'-end processing; IMP:SGD.
DR   Gene3D; 3.30.420.10; -; 1.
DR   InterPro; IPR002562; 3'-5'_exonuclease_dom.
DR   InterPro; IPR012588; Exosome-assoc_fac_Rrp6_N.
DR   InterPro; IPR010997; HRDC-like.
DR   InterPro; IPR002121; HRDC_dom.
DR   InterPro; IPR012337; RNaseH-like_dom.
DR   Pfam; PF01612; DNA_pol_A_exo1; 1.
DR   Pfam; PF00570; HRDC; 1.
DR   Pfam; PF08066; PMC2NT; 1.
DR   SMART; SM00474; 35EXOc; 1.
DR   SMART; SM00341; HRDC; 1.
DR   SUPFAM; SSF47819; SSF47819; 1.
DR   SUPFAM; SSF53098; SSF53098; 1.
DR   PROSITE; PS50967; HRDC; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Complete proteome; Exonuclease; Exosome; Hydrolase;
KW   Nuclease; Nucleus; Phosphoprotein; Reference proteome; RNA-binding;
KW   rRNA processing.
FT   CHAIN         1    733       Exosome complex exonuclease RRP6.
FT                                /FTId=PRO_0000097456.
FT   DOMAIN      435    515       HRDC.
FT   MOD_RES     138    138       Phosphoserine.
FT   MOD_RES     520    520       Phosphothreonine.
FT   MOD_RES     640    640       Phosphoserine.
FT   MOD_RES     645    645       Phosphoserine.
FT   CONFLICT    402    402       E -> G (in Ref. 4; AAT92869).
FT   HELIX       132    135
FT   HELIX       162    165
FT   STRAND      173    175
FT   HELIX       184    189
FT   HELIX       194    196
FT   HELIX       208    210
FT   STRAND      214    216
FT   HELIX       219    229
FT   STRAND      233    242
FT   STRAND      244    248
FT   STRAND      250    257
FT   STRAND      262    266
FT   TURN        267    273
FT   HELIX       274    277
FT   HELIX       278    281
FT   STRAND      286    292
FT   HELIX       294    304
FT   STRAND      309    313
FT   HELIX       314    321
FT   HELIX       328    335
FT   TURN        343    346
FT   HELIX       356    367
FT   HELIX       369    382
FT   HELIX       386    398
FT   HELIX       404    406
FT   STRAND      413    416
FT   STRAND      421    427
FT   HELIX       436    438
FT   HELIX       439    456
FT   HELIX       460    463
FT   HELIX       466    475
FT   HELIX       480    484
FT   HELIX       492    496
FT   HELIX       498    515
FT   TURN        534    536
FT   HELIX       539    553
FT   STRAND      570    572
FT   TURN        573    577
FT   STRAND      582    585
FT   STRAND      591    594
FT   HELIX       596    611
FT   HELIX       612    614
FT   STRAND      617    619
SQ   SEQUENCE   733 AA;  84039 MW;  B19A0B2ED74C6DA7 CRC64;
     MTSENPDVLL SRVINVVRAA SSLASQDVDF YKNLDRGFSK DLKSKADKLA DMANEIILSI
     DEHHESFELK EEDISDLWNN FGNIMDNLLE MSDHSLDKLN CAINSKSRGS DLQYLGEFSG
     KNFSPTKRVE KPQLKFKSPI DNSESHPFIP LLKEKPNALK PLSESLRLVD DDENNPSHYP
     HPYEYEIDHQ EYSPEILQIR EEIPSKSWDD SVPIWVDTST ELESMLEDLK NTKEIAVDLE
     HHDYRSYYGI VCLMQISTRE RDYLVDTLKL RENLHILNEV FTNPSIVKVF HGAFMDIIWL
     QRDLGLYVVG LFDTYHASKA IGLPRHSLAY LLENFANFKT SKKYQLADWR IRPLSKPMTA
     YARADTHFLL NIYDQLRNKL IESNKLAGVL YESRNVAKRR FEYSKYRPLT PSSEVYSPIE
     KESPWKILMY QYNIPPEREV LVRELYQWRD LIARRDDESP RFVMPNQLLA ALVAYTPTDV
     IGVVSLTNGV TEHVRQNAKL LANLIRDALR NIKNTNEEAT PIPSSETKAD GILLETISVP
     QIRDVMERFS VLCNSNISKS RAKPVTNSSI LLGKILPREE HDIAYSKDGL PNKVKTEDIR
     IRAQNFKSAL ANLEDIIFEI EKPLVVPVKL EEIKTVDPAS APNHSPEIDN LDDLVVLKKK
     NIQKKQPAKE KGVTEKDAVD YSKIPNILSN KPGQNNRQQK KRRFDPSSSD SNGPRAAKKR
     RPAAKGKNLS FKR
//
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