ID   RDR3_ORYSJ              Reviewed;        1153 AA.
AC   Q5QMN5; B9ETN1; Q5QMN6;
DT   07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   07-JUL-2009, sequence version 2.
DT   03-AUG-2022, entry version 72.
DE   RecName: Full=Probable RNA-dependent RNA polymerase 3;
DE            Short=OsRDR3;
DE            EC=2.7.7.48;
GN   Name=RDR3; OrderedLocusNames=Os01g0197900, LOC_Os01g10130;
GN   ORFNames=B1046G12.12, B1046G12.13, OsJ_00745, P0419B01.24, P0419B01.25;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12447438; DOI=10.1038/nature01184;
RA   Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA   Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA   Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA   Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA   Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA   Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA   Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA   Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA   Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA   Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA   Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA   Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA   Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT   "The genome sequence and structure of rice chromosome 1.";
RL   Nature 420:312-316(2002).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 776-1153.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
RN   [7]
RP   TISSUE SPECIFICITY, GENE FAMILY, AND NOMENCLATURE.
RX   PubMed=18826656; DOI=10.1186/1471-2164-9-451;
RA   Kapoor M., Arora R., Lama T., Nijhawan A., Khurana J.P., Tyagi A.K.,
RA   Kapoor S.;
RT   "Genome-wide identification, organization and phylogenetic analysis of
RT   dicer-like, argonaute and RNA-dependent RNA polymerase gene families and
RT   their expression analysis during reproductive development and stress in
RT   rice.";
RL   BMC Genomics 9:451-451(2008).
CC   -!- FUNCTION: Probably involved in the RNA silencing pathway and required
CC       for the generation of small interfering RNAs (siRNAs). {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC         RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC         COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC         EC=2.7.7.48;
CC   -!- TISSUE SPECIFICITY: Expressed in shoot apical meristem (SAM) and
CC       panicles. {ECO:0000269|PubMed:18826656}.
CC   -!- SIMILARITY: Belongs to the RdRP family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAD73220.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAD73221.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAD73327.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAD73328.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAF04217.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=EEE54052.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AP003200; BAD73220.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP003200; BAD73221.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP003244; BAD73327.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP003244; BAD73328.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008207; BAF04217.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CM000138; EEE54052.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AK105570; -; NOT_ANNOTATED_CDS; mRNA.
DR   RefSeq; XP_015628373.1; XM_015772887.1.
DR   AlphaFoldDB; Q5QMN5; -.
DR   SMR; Q5QMN5; -.
DR   STRING; 4530.OS01T0197900-01; -.
DR   PaxDb; Q5QMN5; -.
DR   PRIDE; Q5QMN5; -.
DR   KEGG; osa:107280216; -.
DR   eggNOG; KOG0988; Eukaryota.
DR   InParanoid; Q5QMN5; -.
DR   Proteomes; UP000000763; Chromosome 1.
DR   Proteomes; UP000007752; Chromosome 1.
DR   Proteomes; UP000059680; Chromosome 1.
DR   GO; GO:0031380; C:nuclear RNA-directed RNA polymerase complex; IBA:GO_Central.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IBA:GO_Central.
DR   GO; GO:0030422; P:siRNA processing; IBA:GO_Central.
DR   InterPro; IPR007855; RNA-dep_RNA_pol_euk-typ.
DR   PANTHER; PTHR23079; PTHR23079; 2.
DR   Pfam; PF05183; RdRP; 1.
PE   2: Evidence at transcript level;
KW   Nucleotidyltransferase; Reference proteome; RNA-binding;
KW   RNA-directed RNA polymerase; RNA-mediated gene silencing; Transferase.
FT   CHAIN           1..1153
FT                   /note="Probable RNA-dependent RNA polymerase 3"
FT                   /id="PRO_0000378447"
FT   CONFLICT        809
FT                   /note="P -> S (in Ref. 6; AK105570)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1153 AA;  129994 MW;  ADC8D8BC66104694 CRC64;
     MYNPIGSAEA REPAELPAAV AAELERLEGR LRQLAGAEAR RHLAVLGEAG AARVLRAVAE
     SRRVRTLPGF IKYLAKREAA ITRRDARGVP TALSAPAFIS GPSREEESVY TQLFDNEVQM
     YDQSPSNEMA TSLSNHGMVE VGSPNQQMPF HLHGNGGSVR QIARLVPQLA QLTVESPCGH
     TSSVSQNQGC IEVGTPTQAM VSPGLNQMAL PCRCMPSGLQ NYIEIDSPIQ PMISTPRRVS
     TPSSVQDISR LIENMAGPSV SPPSPITAMP QNPTTTCHTT DNALREAASP QMLALEELGF
     RKIFMVFAYL ASEKIENVLS VDYIRSLKFL SMAQFESQIW RTFGHKYIAA SDRAKNLDSD
     PGMTKVYHCN VAIRGDTVVK IFKGPYIENT RTHLQKVVGD DNVLVVKFMG KLSDTKTDFS
     TYCEHYHKVA EDGIVLGLRR YRFFVYKDGG KEEKLKQEKI EDKNKCTSPV MCYFVRTESG
     WNMDEPYILS GRTVGQAREL FMHISSAPTL AKYMARFALI LSKTITWDAD LSAVYVRRIK
     DEPCMDRHGN VVHKDQEPLI HTDGTGLVSV DLALNCPTSI FKGKFLKPQP LLMQFRLFYN
     GSAVKGTVLV DRRLPPATIL IRPSMVKIET HPELSGVRSV NSSEIVSARN AKKSLSGVQS
     VNSFEIVSTS NRPRRTLTSR FLITLLCYGG VPEEYFLELL QSAIEGAENA CYDYEDALRI
     AFSYADMEDS MSARMILSGI PLEESYLQHR LDFMAQQERK GIKQGKIPID ECYYLMDTTD
     PTGTLRPNEV CVILENGQFS GDVLVYKHPG LHFGDIHVLK ATYIRDLEKE YVGYAKYAIL
     FPISGPRSLA DEMANSDFDG DIYWVSKNPK LLEHFKPSEP WVQAIKPKKT KQKKPQDCNE
     SKLERLLFHE FLKTRFTPSF ALGTAADSWL AYMDRLLTDS LDEIEKKLIE EKMLKLVDLY
     YLALDAPKTG NKVNIPSDLM VKQYPHFMGR SFSYHSSSIL GQIYDKAEDV ESLRSCNVQP
     IGVSLLPCFM EREAPPAARH LWQHRYEEYL TDSTMLYRAM VDKEERNMKF QELYEKYKHM
     LYDASEFEQT QRDPDDVFSE ACVIYQIVYE KARWSNDASR CGFAWKVAGR ALCHFYALKN
     EGDTALCSLP LLR