GenomeNet

Database: UniProt
Entry: Q8LMR2
LinkDB: Q8LMR2
Original site: Q8LMR2 
ID   DCL1_ORYSJ              Reviewed;        1883 AA.
AC   Q8LMR2; A3ADL0;
DT   07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2002, sequence version 1.
DT   16-OCT-2019, entry version 131.
DE   RecName: Full=Endoribonuclease Dicer homolog 1;
DE   AltName: Full=Dicer-like protein 1;
DE            Short=OsDCL1;
DE            EC=3.1.26.-;
GN   Name=DCL1; OrderedLocusNames=Os03g0121800, LOC_Os03g02970;
GN   ORFNames=OJ1705B08.11, OsJ_09217;
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=16109971; DOI=10.1101/gr.3869505;
RG   The rice chromosome 3 sequencing consortium;
RA   Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R.,
RA   Haas B., Wortman J., Pertea M., Jones K.M., Kim M., Overton L.,
RA   Tsitrin T., Fadrosh D., Bera J., Weaver B., Jin S., Johri S.,
RA   Reardon M., Webb K., Hill J., Moffat K., Tallon L., Van Aken S.,
RA   Lewis M., Utterback T., Feldblyum T., Zismann V., Iobst S., Hsiao J.,
RA   de Vazeille A.R., Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H.,
RA   Rambo T., Currie J., Collura K., Kernodle-Thompson S., Wei F.,
RA   Kudrna K., Ammiraju J.S.S., Luo M., Goicoechea J.L., Wing R.A.,
RA   Henry D., Oates R., Palmer M., Pries G., Saski C., Simmons J.,
RA   Soderlund C., Nelson W., de la Bastide M., Spiegel L., Nascimento L.,
RA   Huang E., Preston R., Zutavern T., Palmer L., O'Shaughnessy A.,
RA   Dike S., McCombie W.R., Minx P., Cordum H., Wilson R., Jin W.,
RA   Lee H.R., Jiang J., Jackson S.;
RT   "Sequence, annotation, and analysis of synteny between rice chromosome
RT   3 and diverged grass species.";
RL   Genome Res. 15:1284-1291(2005).
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.,
RA   McCombie W.R., Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S.,
RA   Childs K.L., Davidson R.M., Lin H., Quesada-Ocampo L.,
RA   Vaillancourt B., Sakai H., Lee S.S., Kim J., Numa H., Itoh T.,
RA   Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using
RT   next 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.,
RA   Cong L., Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J.,
RA   Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X.,
RA   Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y.,
RA   Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J.,
RA   Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y.,
RA   Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y.,
RA   Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z.,
RA   Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T.,
RA   Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H.,
RA   Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W.,
RA   Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L.,
RA   Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J.,
RA   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   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=16126864; DOI=10.1104/pp.105.063420;
RA   Liu B., Li P., Li X., Liu C., Cao S., Chu C., Cao X.;
RT   "Loss of function of OsDCL1 affects microRNA accumulation and causes
RT   developmental defects in rice.";
RL   Plant Physiol. 139:296-305(2005).
RN   [7]
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
RT   and their expression analysis during reproductive development and
RT   stress in rice.";
RL   BMC Genomics 9:451-451(2008).
RN   [8]
RP   FUNCTION.
RX   PubMed=18353984; DOI=10.1073/pnas.0708743105;
RA   Lu C., Jeong D.-H., Kulkarni K., Pillay M., Nobuta K., German R.,
RA   Thatcher S.R., Maher C., Zhang L., Ware D., Liu B., Cao X.,
RA   Meyers B.C., Green P.J.;
RT   "Genome-wide analysis for discovery of rice microRNAs reveals natural
RT   antisense microRNAs (nat-miRNAs).";
RL   Proc. Natl. Acad. Sci. U.S.A. 105:4951-4956(2008).
CC   -!- FUNCTION: Involved in the RNA silencing pathway. Cleaves double-
CC       stranded RNA to produce microRNAs (miRNAs) of 21-24 nucleotides
CC       which target the selective destruction of complementary RNAs.
CC       Regulates by this way the development of the plant. May not be
CC       involved in small interfering RNAs (siRNAs) production.
CC       {ECO:0000269|PubMed:16126864, ECO:0000269|PubMed:18353984}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC   -!- SUBUNIT: May interact with ARGONAUTE1 or PINHEAD through their
CC       common PAZ domains. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC   -!- DISRUPTION PHENOTYPE: Severe dwarfism and dark green color.
CC       Seedling viability compromised. {ECO:0000269|PubMed:16126864}.
CC   -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC       {ECO:0000255|PROSITE-ProRule:PRU00657}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAF10710.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
DR   EMBL; AC105363; AAM52322.1; -; Genomic_DNA.
DR   EMBL; DP000009; ABF93701.1; -; Genomic_DNA.
DR   EMBL; AP008209; BAF10710.2; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014959; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CM000140; EAZ25399.1; -; Genomic_DNA.
DR   SMR; Q8LMR2; -.
DR   STRING; 4530.OS03T0121901-00; -.
DR   PaxDb; Q8LMR2; -.
DR   EnsemblPlants; Os03t0121800-01; Os03t0121800-01; Os03g0121800.
DR   Gramene; Os03t0121800-01; Os03t0121800-01; Os03g0121800.
DR   eggNOG; KOG0701; Eukaryota.
DR   eggNOG; COG0571; LUCA.
DR   HOGENOM; HOG000239675; -.
DR   InParanoid; Q8LMR2; -.
DR   Proteomes; UP000059680; Chromosome 3.
DR   GO; GO:0010445; C:nuclear dicing body; IEA:EnsemblPlants.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003725; F:double-stranded RNA binding; IEA:EnsemblPlants.
DR   GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0004525; F:ribonuclease III activity; IEA:InterPro.
DR   GO; GO:0000911; P:cytokinesis by cell plate formation; IEA:EnsemblPlants.
DR   GO; GO:0009880; P:embryonic pattern specification; IEA:EnsemblPlants.
DR   GO; GO:0035279; P:mRNA cleavage involved in gene silencing by miRNA; IEA:EnsemblPlants.
DR   GO; GO:0007275; P:multicellular organism development; IMP:UniProtKB.
DR   GO; GO:0010599; P:production of lsiRNA involved in RNA interference; IEA:EnsemblPlants.
DR   GO; GO:0035196; P:production of miRNAs involved in gene silencing by miRNA; IMP:UniProtKB.
DR   GO; GO:0010267; P:production of ta-siRNAs involved in RNA interference; IEA:EnsemblPlants.
DR   GO; GO:2000034; P:regulation of seed maturation; IEA:EnsemblPlants.
DR   GO; GO:0048317; P:seed morphogenesis; IEA:EnsemblPlants.
DR   GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IEA:EnsemblPlants.
DR   GO; GO:0009616; P:virus induced gene silencing; IEA:EnsemblPlants.
DR   CDD; cd00048; DSRM; 2.
DR   CDD; cd00593; RIBOc; 2.
DR   Gene3D; 1.10.1520.10; -; 1.
DR   Gene3D; 3.30.160.380; -; 1.
DR   InterPro; IPR038248; Dicer_dimer_sf.
DR   InterPro; IPR005034; Dicer_dimerisation_dom.
DR   InterPro; IPR014720; dsRBD_dom.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR001650; Helicase_C.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR003100; PAZ_dom.
DR   InterPro; IPR036085; PAZ_dom_sf.
DR   InterPro; IPR000999; RNase_III_dom.
DR   InterPro; IPR036389; RNase_III_sf.
DR   Pfam; PF03368; Dicer_dimer; 1.
DR   Pfam; PF00271; Helicase_C; 1.
DR   Pfam; PF02170; PAZ; 1.
DR   Pfam; PF00636; Ribonuclease_3; 2.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM00358; DSRM; 2.
DR   SMART; SM00490; HELICc; 1.
DR   SMART; SM00949; PAZ; 1.
DR   SMART; SM00535; RIBOc; 2.
DR   SUPFAM; SSF101690; SSF101690; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   SUPFAM; SSF69065; SSF69065; 2.
DR   PROSITE; PS51327; DICER_DSRBF; 1.
DR   PROSITE; PS50137; DS_RBD; 2.
DR   PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS51194; HELICASE_CTER; 1.
DR   PROSITE; PS50821; PAZ; 1.
DR   PROSITE; PS00517; RNASE_3_1; 1.
DR   PROSITE; PS50142; RNASE_3_2; 2.
PE   3: Inferred from homology;
KW   ATP-binding; Complete proteome; Endonuclease; Helicase; Hydrolase;
KW   Magnesium; Manganese; Metal-binding; Nuclease; Nucleotide-binding;
KW   Nucleus; Reference proteome; Repeat; RNA-binding;
KW   RNA-mediated gene silencing.
FT   CHAIN         1   1883       Endoribonuclease Dicer homolog 1.
FT                                /FTId=PRO_0000378416.
FT   DOMAIN      274    413       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   DOMAIN      629    789       Helicase C-terminal.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00542}.
FT   DOMAIN      817    912       Dicer dsRNA-binding fold.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00657}.
FT   DOMAIN     1156   1296       PAZ. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00142}.
FT   DOMAIN     1320   1498       RNase III 1. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00177}.
FT   DOMAIN     1538   1686       RNase III 2. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00177}.
FT   DOMAIN     1712   1775       DRBM 1. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00266}.
FT   DOMAIN     1797   1872       DRBM 2. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00266}.
FT   NP_BIND     287    294       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   MOTIF       358    361       DECH box. {ECO:0000250}.
FT   COMPBIAS      3     12       Poly-Gly.
FT   COMPBIAS     75     84       Poly-Pro.
FT   METAL      1576   1576       Magnesium or manganese. {ECO:0000250}.
FT   METAL      1672   1672       Magnesium or manganese. {ECO:0000250}.
FT   METAL      1675   1675       Magnesium or manganese. {ECO:0000250}.
FT   SITE       1668   1668       Important for activity. {ECO:0000250}.
FT   CONFLICT     79     79       P -> T (in Ref. 5; EAZ25399).
FT                                {ECO:0000305}.
SQ   SEQUENCE   1883 AA;  210203 MW;  0566ADA02CA424CF CRC64;
     MAGGGGVGGG AGEHAAAAYW YDACEDGASL LCGIDFAASA DFDPGLIPAM DTGADDGFVA
     EIDRILESIN AESSPAPPPP PPPPLPEPVP VAPPELPIQE KQLQVASAPV ANNAVAVVGV
     VQRSKGVVAR KEPRRESHGC AANGGGGGEW RDGKRPRLAS GGVGGPRQEW RRRPMLPPPP
     SRGWDDRRGR RDFDRVRKHE HHRREARGFW ERDRGGKMVF RSGTWEQESD REAKRARTQD
     GGSMEKKAEA DRMGAAQREK PVAEERARQY QLEVLEQAKS RNTIAFLETG AGKTLIAVLL
     IKSVCDKMLK ENKKMLAVFL VPKVPLVYQV LVMTAQILLN ILRHSIIKMD AIHLLILDEC
     HHAVKKHPYS LVMSEFYHTT PKEKRPAVFG MTASPVNLKG VTSQEDCAIK IRNLESKLDS
     VVCTIKDRKE LEKHVPMPLE VVVQYDKAAT LWSLHEQIKQ MESTVEEAAL SSSKRTKWQF
     MGARDAGSRD ELRLVYGVSE RTESDGAANL IQKLRAINYA LGELGQWCAY KVAQSFLTAL
     QNDERANYQV DVKFQESYLK KVVDLLHCQL TEGAAMKSET SDVEMQNTEK HNTNDLEEGE
     LPDSHGEHVD EVIGAAVADG KVTPRVQALI KILLKYQHTE DFRAIIFVER VVTALVLPKV
     LAELPSLSFI RCASLIGHNN NQEMRACQMQ DTISKFRDGR VTLLVATSVA EEGLDIRQCN
     VVIRFDLAKT VLAYIQSRGR ARKPGSDYIL MLERGNISHE TFLRNARNSE ETLRKEAMER
     TDLSHLDGTS VLSPVDTSPG SMYQVESTGA VVSLNSAVGL IHFYCSQLPS DRYSILHPEF
     IMQKYEKPGG SVEYSCKLQL PCNAPFEKLE GPICSSIRLA QQAVCLAACK KLHEMGAFTD
     TLLPDRGSGE GEKTEQNDEG EPLPGTARHR EFYPEGVADI LRGEWILSGR DGYQNSQFIK
     LYMYSVNCVN VGTSKDPFVT QLSNFAIIFG NELDAEVLST TMDLFVARTM ITKASLVFRG
     RIEITESQLV LLKSFHVRLM SIVLDVDVDP STTPWDPAKA YLFVPVGAEK CTDPLREIDW
     TLVNNIVNTD AWNNPLQRAR PDVYLGTNER TLGGDRREYG FGKLRHGTAF GQKAHPTYGI
     RGAIAEFDIV KASGLVPARD RGHFSDYQNQ GKLFMADSCW NAKDLAGMVV TAAHSGKRFY
     VDCICYNMNA ENSFPRKEGY LGPLEYSSYA DYYKQKYGVE LIYRKQPLIR ARGVSYCKNL
     LSPRFEHSDA REGDFSENLD KTYYVYLPPE LCLVHPLPGS LVRGAQRLPS IMRRVESMLL
     AVQLKDIIDY PVPATKILEA LTAASCQETL CYERAELLGD AYLKWVVSRF LFLKYPQKHE
     GQLTRMRQQM VSNMVLYQYA LNKTLQSYIQ ADRFAPSRWA APGVLPVFDE ESREYEPSIF
     DEESTGCELQ KESYDDYADN MQEDGEIEGD SSCYRVLSSK TLADVVEALI GVYYVAGGKI
     AANHLMKWIG IHAELDPEEI PPPKPYDIPE SIMRSINFDT LKGVLGIEFQ NKGLLVEAIT
     HASRPSSGVS CYQRLEFVGD AVLDHLITRH LFFTYTDLPP GRLTDLRAAA VNNENFARVA
     VKHKLHVHLR HGSSALETQI REFVKDVQEE LLKPGFNSFG LGDCKAPKVL GDIVESIAGA
     IFLDSGYDTS VVWKVFQPLL HPMVTPETLP MHPVRELQER CQQQAEGLEY KASRAGNIAT
     VEVFVDGVQI GVAQNPQKKM AQKLAARNAL VVLKEKETAT KKEDERDGEK KNGAQMFTRQ
     TLNDICLRRQ WPMPQYRCVN EGGPAHAKRF VYSVRVNTSD RGWTDECIGE PMPSVKKAKD
     SAAVLLLELL NRDFPDKPDG KQP
//
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