ID   RDR4_ORYSJ              Reviewed;        1183 AA.
AC   Q5QMN4;
DT   07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   07-JUL-2009, sequence version 2.
DT   03-AUG-2022, entry version 87.
DE   RecName: Full=Probable RNA-dependent RNA polymerase 4;
DE            Short=OsRDR4;
DE            EC=2.7.7.48;
GN   Name=RDR4; OrderedLocusNames=Os01g0198000, LOC_Os01g10140;
GN   ORFNames=B1046G12.14, P0419B01.26;
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 MRNA] OF 1-456 AND 588-1183.
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   [6]
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=BAD73222.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAD73329.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAF04218.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAG89036.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; AP003200; BAD73222.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP003244; BAD73329.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008207; BAF04218.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AK064209; BAG89036.1; ALT_INIT; mRNA.
DR   EMBL; AK119908; -; NOT_ANNOTATED_CDS; mRNA.
DR   RefSeq; XP_015624482.1; XM_015768996.1.
DR   AlphaFoldDB; Q5QMN4; -.
DR   STRING; 4530.OS01T0198000-01; -.
DR   PaxDb; Q5QMN4; -.
DR   PRIDE; Q5QMN4; -.
DR   GeneID; 4327336; -.
DR   KEGG; osa:4327336; -.
DR   eggNOG; KOG0988; Eukaryota.
DR   HOGENOM; CLU_008367_1_1_1; -.
DR   InParanoid; Q5QMN4; -.
DR   OrthoDB; 104603at2759; -.
DR   Proteomes; UP000000763; Chromosome 1.
DR   Proteomes; UP000059680; Chromosome 1.
DR   Genevisible; Q5QMN4; OS.
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; 1.
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..1183
FT                   /note="Probable RNA-dependent RNA polymerase 4"
FT                   /id="PRO_0000378448"
SQ   SEQUENCE   1183 AA;  132399 MW;  291AAA377BC1D134 CRC64;
     MNPHGGGNQM REPALPAAVG AELERLEARL GQLACAEARR QLAELGEPAA ARVLRAIGEA
     RQVRTLSGFI RHMANQERMK RNARGIPTAH SAACISGPCR EEESISTPLY YNEVQMDAQT
     PNDMVEVGSP NQQMPLRLHD NGGSVGHIAR VVPDLANPAV GSPYGRISSV LLQNQNCVEG
     YTPSRGMVSP ASNQVGSPGH RMPSGLQRHM EIDSPIQPIV STPERVSTPS PVRDLSRCVE
     NMAGPSGSPP CPIWVMPQIP PAICPDTTNV LREVVSPQML ALGELEFRKI FMIFAYLSWN
     KKGVKPPLST PKSSKIEDVL SVDSIRSLKS MSMAQFESRI WSTFGHDNIS SSDRAKNLDS
     GPGMSKVYHC NVEIRGGTVV KIFKGPYIEN RRTHLQKVLG DDNVLVVKFM EISSDTETDL
     STYLEHYHKV AEEGIVLGLR CYRFFLYKDG GKENKMKEEN REEENKKCTS SVRCYFVRTE
     SGWNMDEPYI LSGRTIGQAR DLFMHIRTVL TLAKYMLRFA LIVSKTITLD VDLSEVLVKL
     IDDEPCLDEH GKEVFRDGER LIHTDGTGLI SEDLAQKCTY SNSKGKLLEP QDIVDCAASK
     LMGSNNTTEY PLLIQLRLFY NGSAVKGTVL VDKRLPPRTI HIRPSMLKIK TYPELSGVQS
     VNSLDIVSAR NAKKSLSGVQ SVNSFEIVST SNRSGRTFTS NNLIALLHYG GVPEEFFMEL
     LQTAIEEADN ARFDYAGALN IAFNYADMED SMPARMILSG IPLEESYLQS RLDFLSLLER
     KGIKNGKIPI DDCYYLMGTA DPTGKLGPNE VCVILDYGQV SGDVLVYKYP GLHPGDIHVL
     KATYSSDIEK VVGNSKHAIL FPTTGQRSLA DEMANSDFDG DIYWVSLNPK LLEHFKPSKP
     WVPAITPNGT KQKGPEDFNE SELERVLFHE FLKTRFAPSY ARATAATNWL VYMDRLLTVS
     LDESEKKLIE KKMLKLVDLY YLALDAPKMG NKVNIPRDLM VKQYPHFMDR SPSYHSSSIL
     GKIYDKAGDP KPLRSDNVQP TSISSLPCFA ERDVPPAIKQ LWQHRYNEYL ADSSLLYAEE
     ADEEEKKIKF QELYEKYKHL LYGASEFEET PRDLDDVFSE ACAIYQIAYE KARSANNVAR
     CGFAWKVAGR ALCHFYTVKN EGNAVVCSLQ LLRNFRFTKK YRK