LOCUS       XM_026023643            6666 bp    mRNA    linear   PLN 10-JUL-2024
DEFINITION  PREDICTED: Oryza sativa Japonica Group endoribonuclease Dicer
            homolog 1 (LOC4331440), mRNA.
ACCESSION   XM_026023643
VERSION     XM_026023643.2
DBLINK      BioProject: PRJNA1123306
KEYWORDS    RefSeq.
SOURCE      Oryza sativa Japonica Group (Japanese rice)
  ORGANISM  Oryza sativa Japonica Group
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP
            clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
COMMENT     MODEL REFSEQ:  This record is predicted by automated computational
            analysis. This record is derived from a genomic sequence
            (NC_089037) annotated using gene prediction method: Gnomon,
            supported by EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Jul 10, 2024 this sequence version replaced XM_026023643.1.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Full annotation
            Annotation Name             :: GCF_034140825.1-RS_2024_06
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.3
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 06/21/2024
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..6666
                     /organism="Oryza sativa Japonica Group"
                     /mol_type="mRNA"
                     /db_xref="taxon:39947"
                     /chromosome="3"
     gene            1..6666
                     /gene="LOC4331440"
                     /note="endoribonuclease Dicer homolog 1; Derived by
                     automated computational analysis using gene prediction
                     method: Gnomon. Supporting evidence includes similarity
                     to: 43 ESTs, 237 long SRA reads, 5 Proteins, and 100%
                     coverage of the annotated genomic feature by RNAseq
                     alignments, including 79 samples with support for all
                     annotated introns"
                     /db_xref="GeneID:4331440"
     misc_feature    1
                     /gene="LOC4331440"
                     /experiment="COORDINATES: cap analysis [ECO:0007248]"
                     /note="transcription start site"
     CDS             563..6340
                     /gene="LOC4331440"
                     /codon_start=1
                     /product="endoribonuclease Dicer homolog 1"
                     /protein_id="XP_025879428.1"
                     /db_xref="GeneID:4331440"
                     /translation="

MAGGGGVGGGAGEHAAAAYWYDACEDGASLLCGIDFAASADFDPGLIPAMDTGADDGFVAEIDRILESINAESSPAPPPPPPPPLPEPVPVAPPELPIQEKQLQVASAPVANNAVAVVGVVQRSKGVVARKEPRRESHGCAANGGGGGEWRDGKRPRLASGGVGGPRQEWRRRPMLPPPPSRGWDDRRGRRDFDRVRKHEHHRREARGFWERDRGGKMVFRSGTWEQESDREAKRARTQDGGSMEKKAEADRMGAAQREKPVAEERARQYQLEVLEQAKSRNTIAFLETGAGKTLIAVLLIKSVCDKMLKENKKMLAVFLVPKVPLVYQQAEVIRDRTGYRVGHYCGEMGQDFWDARKWQREFESKQVLVMTAQILLNILRHSIIKMDAIHLLILDECHHAVKKHPYSLVMSEFYHTTPKEKRPAVFGMTASPVNLKGVTSQEDCAIKIRNLESKLDSVVCTIKDRKELEKHVPMPLEVVVQYDKAATLWSLHEQIKQMESTVEEAALSSSKRTKWQFMGARDAGSRDELRLVYGVSERTESDGAANLIQKLRAINYALGELGQWCAYKVAQSFLTALQNDERANYQVDVKFQESYLKKVVDLLHCQLTEGAAMKSETSDVEMQNTEKHNTNDLEEGELPDSHAVSVGEHVDEVIGAAVADGKVTPRVQALIKILLKYQHTEDFRAIIFVERVVTALVLPKVLAELPSLSFIRCASLIGHNNNQEMRACQMQDTISKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSDYILMLERGNISHETFLRNARNSEETLRKEAMERTDLSHLDGTSVLSPVDTSPGSMYQVESTGAVVSLNSAVGLIHFYCSQLPSDRYSILHPEFIMQKYEKPGGSVEYSCKLQLPCNAPFEKLEGPICSSIRLAQQAVCLAACKKLHEMGAFTDTLLPDRGSGEGEKTEQNDEGEPLPGTARHREFYPEGVADILRGEWILSGRDGYQNSQFIKLYMYSVNCVNVGTSKDPFVTQLSNFAIIFGNELDAEVLSTTMDLFVARTMITKASLVFRGRIEITESQLVLLKSFHVRLMSIVLDVDVDPSTTPWDPAKAYLFVPVGAEKCTDPLREIDWTLVNNIVNTDAWNNPLQRARPDVYLGTNERTLGGDRREYGFGKLRHGTAFGQKAHPTYGIRGAIAEFDIVKASGLVPARDRGHFSDYQNQGKLFMADSCWNAKDLAGMVVTAAHSGKRFYVDCICYNMNAENSFPRKEGYLGPLEYSSYADYYKQKYGVELIYRKQPLIRARGVSYCKNLLSPRFEHSDAREGDFSENLDKTYYVYLPPELCLVHPLPGSLVRGAQRLPSIMRRVESMLLAVQLKDIIDYPVPATKILEALTAASCQETLCYERAELLGDAYLKWVVSRFLFLKYPQKHEGQLTRMRQQMVSNMVLYQYALNKTLQSYIQADRFAPSRWAAPGVLPVFDEESREYEPSIFDEESTGCELQKESYDDYADNMQEDGEIEGDSSCYRVLSSKTLADVVEALIGVYYVAGGKIAANHLMKWIGIHAELDPEEIPPPKPYDIPESIMRSINFDTLKGVLGIEFQNKGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITRHLFFTYTDLPPGRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALETQIREFVKDVQEELLKPGFNSFGLGDCKAPKVLGDIVESIAGAIFLDSGYDTSVVWKVFQPLLHPMVTPETLPMHPVRELQERCQQQAEGLEYKASRAGNIATVEVFVDGVQIGVAQNPQKKMAQKLAARNALVVLKEKETATKKEDERDGEKKNGAQMFTRQTLNDICLRRQWPMPQYRCVNEGGPAHAKRFVYSVRVNTSDRGWTDECIGEPMPSVKKAKDSAAVLLLELLNRDFPDKPDGKQP"

     misc_feature    1358..1957
                     /gene="LOC4331440"
                     /note="DEXH-box helicase domain of endoribonuclease Dicer;
                     Region: DEXHc_dicer; cd18034"
                     /db_xref="CDD:350792"
     misc_feature    order(1358..1366,1373..1375,1424..1447,1562..1564,
                     1751..1753,1853..1855)
                     /gene="LOC4331440"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350792"
     misc_feature    order(1526..1531,1598..1603,1676..1678,1682..1687,
                     1694..1696,1769..1777)
                     /gene="LOC4331440"
                     /note="nucleic acid binding site [nucleotide binding];
                     other site"
                     /db_xref="CDD:350792"
     misc_feature    2552..2944
                     /gene="LOC4331440"
                     /note="C-terminal helicase domain of the endoribonuclease
                     Dicer; Region: SF2_C_dicer; cd18802"
                     /db_xref="CDD:350189"
     misc_feature    order(2633..2641,2813..2815,2870..2872,2876..2878)
                     /gene="LOC4331440"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:350189"
     misc_feature    order(2825..2827,2831..2833,2906..2908,2912..2914)
                     /gene="LOC4331440"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350189"
     misc_feature    3137..3400
                     /gene="LOC4331440"
                     /note="Dicer dimerization domain; Region: Dicer_dimer;
                     pfam03368"
                     /db_xref="CDD:460900"
     misc_feature    4142..4582
                     /gene="LOC4331440"
                     /note="PAZ domain, CAF_like subfamily. CAF (for carpel
                     factory) is a plant homolog of Dicer. CAF has been
                     implicated in flower morphogenesis and in early
                     Arabidopsis development and might function through
                     posttranscriptional regulation of specific mRNA...;
                     Region: PAZ_CAF_like; cd02844"
                     /db_xref="CDD:239210"
     misc_feature    order(4286..4288,4373..4375,4385..4387,4439..4441,
                     4541..4543,4547..4549)
                     /gene="LOC4331440"
                     /note="nucleic acid-binding interface [nucleotide
                     binding]; other site"
                     /db_xref="CDD:239210"
     misc_feature    4697..5242
                     /gene="LOC4331440"
                     /note="Ribonuclease III C terminal domain. This group
                     consists of eukaryotic, bacterial and archeal ribonuclease
                     III (RNAse III) proteins. RNAse III is a double stranded
                     RNA-specific endonuclease. Prokaryotic RNAse III is
                     important in post-transcriptional...; Region: RIBOc;
                     cd00593"
                     /db_xref="CDD:238333"
     misc_feature    order(4745..4750,4757..4762,4769..4771,4778..4783,
                     4790..4795,4799..4807,4835..4837,5168..5170,5195..5197)
                     /gene="LOC4331440"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    order(4745..4747,4754..4756,4766..4768,5138..5140,
                     5147..5149)
                     /gene="LOC4331440"
                     /note="active site"
                     /db_xref="CDD:238333"
     misc_feature    order(4754..4756,5138..5140,5147..5149)
                     /gene="LOC4331440"
                     /note="metal binding site [ion binding]; metal-binding
                     site"
                     /db_xref="CDD:238333"
     misc_feature    5297..6019
                     /gene="LOC4331440"
                     /note="dsRNA-specific ribonuclease [Transcription];
                     Region: Rnc; COG0571"
                     /db_xref="CDD:440336"
     misc_feature    6095..6304
                     /gene="LOC4331440"
                     /note="double-stranded RNA binding motif of plant
                     Dicer-like proteins; Region: DSRM_DCL_plant; cd19869"
                     /db_xref="CDD:380698"
     misc_feature    order(6095..6100,6107..6112,6125..6130,6158..6172,
                     6176..6178,6245..6256,6263..6268)
                     /gene="LOC4331440"
                     /note="putative RNA binding site [nucleotide binding];
                     other site"
                     /db_xref="CDD:380698"
     polyA_site      6666
                     /gene="LOC4331440"
                     /experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN      

acgcgccgctgcgtcccttccccctcctctccttcctcctcctcgtccgccatctcaatcgagagagcgagcacacgagagagagagagagggaagcggaggagggagaagagatcagaggaaagaggaagagagagagagagagaagagagagagagtgaagagaaagagtagcgttgatacaccgtcgaatcgaatcgaatcgtgccggacccccaccatcgcctcccctctccccatatcggaatcggaatggggagcatcgcatcccttccctttcctttccctcttgcgtttgcgtgattcgtacggtttatcaccgcctctttctcttccactctccccgtcgcatcgtcgtcaccgccgcgcgcgccgcaacgcccacgcccaccggaagtagtagcagcagcagcagcagtagtagtaccaacattcgttttcccctcctcatctctcgtcttttgtattctgctgcttctgattaatggaggagtgaagtggtcgggtgttggtgtggtgctgtgtgactgcttgcttgcagctgctgttgacggcgggagcgatggcgggaggaggaggagttggaggaggcgctggcgagcacgcggcggcggcgtactggtacgacgcgtgcgaggacggcgcgtcgctgctgtgcggcatcgacttcgccgcgtccgcggacttcgaccccggcctcatacccgcgatggacaccggcgccgacgacggcttcgtcgccgagatcgacaggatactcgagagcatcaacgcggagagctcccctgcgcccccacccccgccgccgccgccgctacctgagcccgtgcctgtggctccgccggagctaccgattcaggaaaagcaattacaggtggcctctgcgcccgtggccaacaatgccgtggcggtggtgggcgttgtgcagagaagtaaaggcgtggtggcgaggaaggagccgaggagggagtcgcatggctgtgctgcaaatggcggcggcggtggggagtggagggacgggaagcgcccgcgcctcgcctccggtggtgtcgggggaccgcgtcaggagtggcggcggaggccgatgctgccaccaccgccctcgcgtgggtgggatgacaggcgtggaaggcgcgatttcgacagggtccgcaagcacgagcaccatcggcgcgaggcccggggtttctgggagcgtgaccgcggcggcaagatggtgttccgctcaggcacctgggagcaggagtctgaccgcgaggcaaagcgtgccaggacgcaagatggaggctccatggagaagaaggcagaggcagataggatgggggctgcgcagcgggagaagcctgtcgcggaggagcgtgcaaggcaataccagctagaggtgcttgagcaagctaagagcaggaacacaatagccttcctggagactggcgcagggaagactctcatcgccgtgcttctcatcaaaagtgtgtgcgataaaatgctcaaggagaacaagaagatgcttgctgtcttcttggttcccaaggtgcctcttgtgtatcagcaagctgaggtgattcgtgacagaaccggctatcgtgttgggcattattgtggagagatgggacaggatttctgggatgctagaaagtggcagcgcgaattcgagtcgaaacaggtactagttatgacagcccaaattttgttaaacatcctcaggcacagtattattaaaatggatgcgatacatcttttgattttagatgagtgccatcatgcagtgaaaaaacatccatattctctagtgatgtcagaattttatcacacgactccgaaggagaagaggccagcagttttcggtatgacggcttctcctgtcaatctaaaaggagtgacgagtcaagaggactgtgccatcaagataagaaatcttgagagcaaactagattcagtagtttgtaccatcaaagatcgtaaagagcttgagaagcatgtccccatgcctttggaagttgttgtccaatatgacaaagcagccactctttggtccttgcatgagcaaatcaaacaaatggaaagcacggttgaagaagctgcactctctagctctaagagaactaaatggcagttcatgggggctagggatgctgggtctagagatgagctgcgtcttgtctatggtgtttcagagcgtacagagagtgatggtgcggctaatttaatccagaagttgagagctataaattatgctttaggtgaacttggacaatggtgtgcatataaggttgcacagtcctttttgactgcattacaaaatgatgaaagggcaaactatcaggttgatgtcaagtttcaagagtcttatttaaaaaaggttgttgatctgttacactgccagttgactgaaggggctgcaatgaaaagtgagaccagtgatgttgaaatgcaaaatactgaaaaacacaacacaaatgaccttgaggagggggagctgcctgacagtcatgctgtttctgtaggtgagcatgtagatgaagttatcggtgctgccgtagcagatggtaaagttactcctagggtgcaggctttgatcaaaatacttctcaaatatcagcatactgaggattttcgtgccataatctttgtggagagagttgtgacagcattagttcttcctaaggtattggcagaacttccatctctaagttttattcgatgtgcaagcttgataggccataacaataatcaagagatgcgcgcgtgccagatgcaggatacaatttcaaaatttcgtgatggccgtgttacacttttagtcgcaacaagcgttgcagaggaagggcttgatattcgacagtgcaatgttgtcattcgatttgaccttgcaaagaccgtcttagcctacatacagtcacgtggtcgtgcaagaaagcctggatctgattatatattaatgcttgaaaggggcaatatatcacatgaaacttttttgaggaatgctcggaatagtgaggagacgttgagaaaggaagctatggaaagaaccgatcttagtcatttggatggtacttctgtgttgagtcctgttgatacatcacctggttcaatgtatcaggttgaatcaacaggtgctgttgtcagcttgaactcagcagttggactcatacatttttactgttcacagttgccaagtgacagatactcaattcttcatccggaattcattatgcaaaagtatgagaagccaggtggttcagtggaatattcttgcaagcttcagctcccttgtaatgccccgttcgaaaaacttgagggtcctatatgcagttcaatacgactggcacagcaggctgtttgtttggctgcttgtaagaagctgcatgagatgggtgccttcacagatacgctcttacctgacagaggaagcggggaaggggaaaaaactgagcagaatgatgaaggtgaaccacttcctggaacagctcgccatagagagttttatcctgaaggtgttgctgatattctacggggagaatggattttatctggcagagatggctaccaaaactctcaatttattaagttatatatgtattctgtgaactgtgtaaacgttgggacttctaaggaccctttcgttacacaactttcaaattttgcaattatttttggcaatgagctggatgcagaggttttatcgacgacgatggatctctttgttgcaaggacaatgataacaaaggcatctctcgtattccgtggacgaattgaaattacagaaagtcagctggtgttgctgaagagctttcatgttaggctcatgagcatagtacttgatgttgatgttgatccctcaactacaccttgggatcccgcaaaagcatacctctttgtccctgtaggagctgagaagtgtacagatcctttaagagagattgattggactttggttaacaacattgttaacactgatgcctggaacaatccacttcagagggcacgcccagatgtctatctaggcaccaatgaacgaacacttggtggggataggagggaatacgggtttgggaaattgcgccatgggactgcttttggacaaaaggcccatcctacttatggtattaggggagctattgctgaatttgacattgtgaaagcatctggattagttcctgctcgtgatagaggacattttagtgattatcagaaccaaggcaagttgttcatggcagattcatgttggaatgctaaagatcttgctggaatggttgtcactgctgcccactcagggaagaggttttatgtggactgcatttgctataacatgaatgcagaaaattcattccctaggaaagaaggctacctggggccattggagtatagttcatatgctgattactacaagcagaagtacggtgtggagttaatctataggaaacagcctcttatacgggcccgtggtgtttcatattgcaagaatcttctttctcctagatttgagcattctgacgctagagaaggtgacttctctgagaaccttgacaaaacatactacgtgtatttgccacctgagttgtgccttgtgcacccacttcctggatcactagttcgtggagctcagaggttgccctcaataatgagaagggtggagagcatgcttcttgcagttcaattgaaggacataattgattaccctgttcctgcaactaagatactagaagccttgactgctgcatcatgccaggagacattatgctatgaaagagcagagctgctgggtgatgcatacctgaaatgggtcgtgagtagattcctcttcctaaaatatcctcaaaagcatgagggacagcttacaaggatgcggcagcagatggttagtaacatggtcctgtaccaatatgctctgaataaaaccctccaatcatatattcaagcagaccggtttgctccatcaagatgggcagctccaggagtgctacctgtattcgatgaagagtctagagagtatgaaccttccatctttgacgaggaatcaactggttgcgagttacagaaggaatcctatgatgactatgcagataacatgcaagaagatggtgaaattgaaggagactctagctgctatcgggttctgtcgagcaaaactttagcggatgttgttgaggcacttattggggtgtattatgtagcaggagggaaaatcgctgcaaaccacctgatgaaatggattggaattcatgcagagttggatcctgaagagatcccacctccaaagccatatgacattcctgagagcataatgagaagcatcaactttgacacgttgaaaggtgtcttgggtatcgaattccagaataaaggtttacttgttgaggccataacacatgcatcgagaccatcttctggtgtttcctgttaccagcgtttggaatttgttggtgatgctgtgttggatcatctcataaccaggcatttgttttttacatatactgacctacctcctggccgcttgactgatttgagagctgcagctgttaataatgagaattttgcaagggttgcagttaagcataagctgcatgtacatcttcgccatggatcatctgcattagaaacacagattcgagagtttgtgaaagatgtccaagaggagcttttgaaaccaggtttcaattcttttgggcttggggattgtaaggctcctaaagttcttggtgacattgttgagtcgattgctggcgcgatattcctggatagtggatatgatacctcagttgtctggaaggtttttcagccactccttcatccaatggtgacgccagagacccttccgatgcatccagttagggagctccaagaacgctgccaacagcaggctgaaggcctggaatacaaagcatcccgagcaggcaacatagctactgttgaagtatttgttgatggtgttcagatcggtgtagctcagaaccctcagaagaagatggcacagaagttggcagcgaggaatgcacttgtggtcctgaaggagaaggaaaccgcaacaaagaaagaagatgaaagggatggcgagaagaaaaatggtgctcagatgttcaccaggcagaccctgaacgacatctgcttgagaaggcagtggccaatgcctcagtacaggtgcgtaaacgagggtggccctgcccatgctaaaagattcgtctattcggtgagggtgaacacttctgatcgtggatggacggatgaatgcattggagagccaatgcctagtgtgaagaaggctaaagactctgctgcagttcttctcctcgagcttctgaatagagatttccctgacaagcctgacggtaagcagccgtaggcactgtggttgttattggtggtggcattgtgggcatttgtggtgttaggcattcagcattcttacacaaacacaaaattaattacccattcagtgctcctcagctttggctaataaggacataaccagagctggtgagtgagagtagaggattatttttacctgcgctggcgattatagtggtgagatgtgataaataggagccgcgatagaaaaaggatagcttgatagcataggataggcgcggggcctcataattctgtcgtgcaatgtgtaaacaaaacaatgcattaatccaataaatttatattaccattgcgctggca

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