ID   SHL2_ORYSJ              Reviewed;        1218 AA.
AC   Q8LHH9; Q0JM85;
DT   07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2002, sequence version 1.
DT   03-AUG-2022, entry version 118.
DE   RecName: Full=Probable RNA-dependent RNA polymerase SHL2;
DE            EC=2.7.7.48;
DE   AltName: Full=Protein SHOOTLESS 2;
GN   Name=SHL2; OrderedLocusNames=Os01g0527600, LOC_Os01g34350;
GN   ORFNames=B1074C08.31;
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 [MRNA], FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=17804793; DOI=10.1073/pnas.0704339104;
RA   Nagasaki H., Itoh J., Hayashi K., Hibara K., Satoh-Nagasawa N., Nosaka M.,
RA   Mukouhata M., Ashikari M., Kitano H., Matsuoka M., Nagato Y., Sato Y.;
RT   "The small interfering RNA production pathway is required for shoot
RT   meristem initiation in rice.";
RL   Proc. Natl. Acad. Sci. U.S.A. 104:14867-14871(2007).
RN   [2]
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   [3]
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   [4]
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   [5]
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   [6]
RP   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: Involved in the RNA silencing pathway. Probably required for
CC       the generation of small interfering RNAs (siRNAs). Regulates shoot
CC       apical meristem (SAM) initiation and maintenance and leaf polarization
CC       through the trans-acting siRNAS (ta-siRNAs) pathway which probably
CC       modulates the expression of the ARF2, ARF3, ARF4, ARF14 and ARF15
CC       genes. {ECO:0000269|PubMed:17804793}.
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   -!- DISRUPTION PHENOTYPE: Lack of the shoot apical meristem (SAM) in the
CC       embryo, but formation of radicle and scutellum. In weak alleles,
CC       formation of an incomplete SAM and abnormal leaves production.
CC       {ECO:0000269|PubMed:17804793}.
CC   -!- SIMILARITY: Belongs to the RdRP family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAF05143.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; AB353923; BAF80151.1; -; mRNA.
DR   EMBL; AP004357; BAC00725.1; -; Genomic_DNA.
DR   EMBL; AP008207; BAF05143.1; ALT_INIT; Genomic_DNA.
DR   EMBL; AP014957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   RefSeq; XP_015622237.1; XM_015766751.1.
DR   AlphaFoldDB; Q8LHH9; -.
DR   SMR; Q8LHH9; -.
DR   STRING; 4530.OS01T0527600-01; -.
DR   PaxDb; Q8LHH9; -.
DR   PRIDE; Q8LHH9; -.
DR   EnsemblPlants; Os01t0527600-01; Os01t0527600-01; Os01g0527600.
DR   GeneID; 4323938; -.
DR   Gramene; Os01t0527600-01; Os01t0527600-01; Os01g0527600.
DR   KEGG; osa:4323938; -.
DR   eggNOG; KOG0988; Eukaryota.
DR   HOGENOM; CLU_001366_1_1_1; -.
DR   InParanoid; Q8LHH9; -.
DR   OrthoDB; 63910at2759; -.
DR   Proteomes; UP000000763; Chromosome 1.
DR   Proteomes; UP000059680; Chromosome 1.
DR   Genevisible; Q8LHH9; 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:0048467; P:gynoecium development; IEA:EnsemblPlants.
DR   GO; GO:0048366; P:leaf development; IEA:EnsemblPlants.
DR   GO; GO:0010492; P:maintenance of shoot apical meristem identity; IMP:UniProtKB.
DR   GO; GO:0035194; P:post-transcriptional gene silencing by RNA; IMP:UniProtKB.
DR   GO; GO:0048544; P:recognition of pollen; IEA:EnsemblPlants.
DR   GO; GO:0009616; P:RNAi-mediated antiviral immune response; IEA:EnsemblPlants.
DR   GO; GO:0030422; P:siRNA processing; IBA:GO_Central.
DR   GO; GO:0010267; P:ta-siRNA processing; IEA:EnsemblPlants.
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..1218
FT                   /note="Probable RNA-dependent RNA polymerase SHL2"
FT                   /id="PRO_0000378444"
SQ   SEQUENCE   1218 AA;  136534 MW;  984FD38DC5474482 CRC64;
     MRSPRGGAAA QPSGRRGDTT AAAAGDLVTT QVSLGGFDAG VAAGDLADFL EHEVGLVWRC
     RVKTSWTPPD SYPDFALPTA PASASAAAAP PRYDRVPPHA FVHFARPEGA RRAADLAGET
     RLILRGKPLR VASAPDSSLR VSRRSSIAPF RFPDVRLEVG ALPSPGAFLA AWRGPDAGLD
     LSVDPFDGCC RLVFTRDTAF TFPGFREVAA IRCDVKLEFP VRDVLEVRLY RLDCSLLLRL
     AAAPLVHYRT ADDDFHEPVP FDLLDDDDPW IRTTDITPSG AIGRCGVYRI SFSARFWPKM
     DRALDYMRER RVAIVDCGGG WGPRRGLTVR DELEFGEPMQ DVFFCLQHAE GLKFPLLFMV
     NALVHKGIIN QHQLTPEFFS LLGRSEENVN VAALRDFWGD KFPVFDACGR LKKALNRVAR
     NPKLLCSKVG DDHAEVRRLV ITPTRAYCLP PEVERSNRVL RHYHEVADRF LRVTFMDEGM
     QVLNNNVLNS FTAPIVKDLM SNFFQQKTTV YKRVRMLLTE GFHMCGRKYS FLAFSSNQLR
     DKSAWFFAED RKTTVEAIRK WMGRFTSKNV AKHAARMGQC FSSTYATVTM RPDEVDESFD
     DVVHNEYIFS DGIGKITPDL ALEVAERLQL TDNPPSAYQI RFAGFKGVIA VWQGHGDGTR
     LFLRPSMRKF ESNHLVLEVV SWTKFQPGFL NRQIIILLSS LNVPDSIFWQ MQETMLSNLN
     NILSDRDVAF EVLTTSCADD GNTAALMLSA GFEPRTEPHL KAMLLAIRSA QLQDLLEKAR
     IFVPKGRWLM GCLDELGVLE QGQCFIRATV PSLNSYFVKH GSRFSSTDKN TEVILGTVVI
     AKNPCLHPGD VRILEAVDVP ELHHLVDCLV FPQKGERPHA NEASGSDLDG DLYFVTWDEK
     LIPPGKKSWN PMDYSPPEAK QLPRQVSQHD IIDFFLKNMI SENLGRICNA HVVHADLSEY
     GAMDEKCIHL AELAATAVDF PKTGKLAIMP PHLKPKVYPD FMGKEDGQSY KSEKILGRLY
     RSIQEASNGD VVSQEVCTPN DLPYDIDLEV PGASDFLASA WQCKCSYDAQ LSALLSQYRV
     RTEAELVTGH ITFLVKNSSK KQGDIKDRLK TAYSALRKEF KSTFESIASD QCEIGDDEKN
     LLYEMKASAW YQVTYHPKWV EKSRGILGPD GEEIPASLSF AWIPVDYLAR IKLRCHGKVR
     VEGQKPVERL AAYISERI