LOCUS       XM_015765976            5452 bp    mRNA    linear   PLN 10-JUL-2024
DEFINITION  PREDICTED: Oryza sativa Japonica Group endoribonuclease Dicer
            homolog 3a-like (LOC4324864), transcript variant X1, mRNA.
ACCESSION   XM_015765976
VERSION     XM_015765976.3
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_089035) 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_015765976.2.
            
            ##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..5452
                     /organism="Oryza sativa Japonica Group"
                     /mol_type="mRNA"
                     /db_xref="taxon:39947"
                     /chromosome="1"
     gene            1..5452
                     /gene="LOC4324864"
                     /note="endoribonuclease Dicer homolog 3a-like; Derived by
                     automated computational analysis using gene prediction
                     method: Gnomon. Supporting evidence includes similarity
                     to: 3 ESTs, 395 long SRA reads, 1 Protein, and 100%
                     coverage of the annotated genomic feature by RNAseq
                     alignments, including 58 samples with support for all
                     annotated introns"
                     /db_xref="GeneID:4324864"
     misc_feature    1
                     /gene="LOC4324864"
                     /experiment="COORDINATES: cap analysis [ECO:0007248]"
                     /note="transcription start site"
     CDS             169..5124
                     /gene="LOC4324864"
                     /codon_start=1
                     /product="endoribonuclease Dicer homolog 3a isoform X1"
                     /protein_id="XP_015621462.1"
                     /db_xref="GeneID:4324864"
                     /translation="

MNPLKRSLESSSQEHEAGKQKLQKRECQDFTPRRYQLDVYEVAMRRNTIAMLDTGAGKTMIAVMLIKEFGKINRTKNAGKVIIFLAPTVQLVTQQCEVIEIHTDFEVEQYYGAKGVDQWTGPRWQEQISKYQVMVMTPQVFLQALRNAFLILDMVSLMIFDECHHATGNHPYTRIMKEFYHKSEHKPSVFGMTASPVIRKGISSHLDCEGQFCELENLLDAKIYTVSDREEIEFCVPSAKEMCRYYDSKPVCFEDLSEELGVLCSKYDALITELQNKRSDMYKDADDITKESKRRLSKSIAKICYCLDDVGLICASEATKICIERGQEKGWLKEVVDATDQQTDANGSRLFAENSALHMKFFEEALHLIDKRLQQGIDMLLNSESGCVEAAKTGYISPKLYELIQIFHSFSNSRHARCLIFVDRKITARVIDRMIKKIGHLAHFTVSFLTGGRSSVDALTPKMQKDTLDSFRSGKVNLLFTTDVAEEGIHVPECSCVIRFDLPRTTRSYVQSRGRARQEDSQYILMIERGNVKQNDLISAIVRSETSMVKIASSRESGNLSPGFVPNEEINEYHVGTTGAKVTADSSISIVYRYCEKLPQDKCYSPKPTFEFTHHDDGYVCTLALPPSAVLQILVGPKARNMHKAKQLVCLDACKKLHELGALDDHLCLSVEDPVPEIVSKNKGTGIGTTKRKELHGTTRIHAWSGNWVSKKTALKLQSYKMNFVCDQAGQIYSEFVLLIDATLPDEVATLEIDLYLHDKMVKTSVSSCGLLELDAQQMEQAKLFQGLLFNGLFGKLFTRSKVPNAPREFILNKEDTFVWNTASVYLLLPTNPSFDSNVCINWSVIDAAATAVKLMRRIYSENKRELLGIFDSDQNVGDLIHLANKSCKANSLKDMVVLAVHTGKIYTALDITELSGDSAFDGASDKKECKFRTFAEYFKKKYGIVLRHPSQPLLVLKPSHNPHNLLSSKFRDEGNVVENMSNGTPVVNKTSNRVHMPPELLIPLDLPVEILRSFYLFPALMYRIESLTLASQLRSEIGYSDSNISSFLILEAITTLRCSEDFSMERLELLGDSVLKYAVSCHLFLKFPNKDEGQLSSIRCHMICNATLYKLGIERNVQGYVRDAAFDPRRWLAPGQLSIRPSPCECPVKSEVVTDDIHIIDDKAIVLGKACDKGHRWMCSKTIADCVEAIIGAYYAGGGLRAAMAVLKWLGIGAEIEEDLIVQAILSASVQTYLPKDNVFEMLEAKLGYSFSVKGLLVEALTHPSQQELGAKYCYERLEFLGDAVLDILLTRYLFNSHKDTNEGELTDLRSASVNNENFAQVAVKHNFHHFLQHSSGLLLDQITEYVNRLEGSSMDKVELLSDGLPKGPKVLGDIVESIAGAILLDTKLDLDVVWGIFEPLLSPIVTPENLELPPYRELIEWCGKHGYFVGINCRDQGDTVVATLDVQLKEVLLVRQGFSKKRKDAKAHASSLLLKDLEEKGLIIPKNASKTEQFEKHCGSTNPFNNLHVDAMDTQTPKPTKEKNAADSRNISDPLLGKPLHVIVKTSKGGPRIALYELCKKLQWPMPTMESEKVQPSFSSVCSSPGGSSQKATPQAFAFASTITLHIPNADVISLTGDGRADKKSSQDSAALFLLYELQRRGTLQLQEV"

     misc_feature    256..852
                     /gene="LOC4324864"
                     /note="DEXH-box helicase domain of endoribonuclease Dicer;
                     Region: DEXHc_dicer; cd18034"
                     /db_xref="CDD:350792"
     misc_feature    order(256..267,274..276,325..348,463..465,652..654,
                     748..750)
                     /gene="LOC4324864"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350792"
     misc_feature    order(427..432,499..504,577..579,583..588,595..597,
                     670..678)
                     /gene="LOC4324864"
                     /note="nucleic acid binding site [nucleotide binding];
                     other site"
                     /db_xref="CDD:350792"
     misc_feature    1351..1749
                     /gene="LOC4324864"
                     /note="C-terminal helicase domain of the endoribonuclease
                     Dicer; Region: SF2_C_dicer; cd18802"
                     /db_xref="CDD:350189"
     misc_feature    order(1435..1443,1618..1620,1675..1677,1681..1683)
                     /gene="LOC4324864"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:350189"
     misc_feature    order(1630..1632,1636..1638,1711..1713,1717..1719)
                     /gene="LOC4324864"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350189"
     misc_feature    1927..2169
                     /gene="LOC4324864"
                     /note="Dicer dimerization domain; Region: Dicer_dimer;
                     pfam03368"
                     /db_xref="CDD:460900"
     misc_feature    2719..3192
                     /gene="LOC4324864"
                     /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(2887..2889,2971..2973,2983..2985,3037..3039,
                     3151..3153,3157..3159)
                     /gene="LOC4324864"
                     /note="nucleic acid-binding interface [nucleotide
                     binding]; other site"
                     /db_xref="CDD:239210"
     misc_feature    3313..3831
                     /gene="LOC4324864"
                     /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(3364..3369,3376..3381,3388..3390,3397..3402,
                     3409..3414,3418..3426,3454..3456,3754..3756,3781..3783)
                     /gene="LOC4324864"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    order(3364..3366,3373..3375,3385..3387,3724..3726,
                     3733..3735)
                     /gene="LOC4324864"
                     /note="active site"
                     /db_xref="CDD:238333"
     misc_feature    order(3373..3375,3724..3726,3733..3735)
                     /gene="LOC4324864"
                     /note="metal binding site [ion binding]; metal-binding
                     site"
                     /db_xref="CDD:238333"
     misc_feature    3937..4404
                     /gene="LOC4324864"
                     /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(3997..4002,4009..4014,4021..4023,4030..4035,
                     4042..4047,4051..4059,4087..4089,4321..4323,4354..4356)
                     /gene="LOC4324864"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    order(3997..3999,4006..4008,4018..4020,4291..4293,
                     4300..4302)
                     /gene="LOC4324864"
                     /note="active site"
                     /db_xref="CDD:238333"
     misc_feature    order(4006..4008,4291..4293,4300..4302)
                     /gene="LOC4324864"
                     /note="metal binding site [ion binding]; metal-binding
                     site"
                     /db_xref="CDD:238333"
     misc_feature    4843..5094
                     /gene="LOC4324864"
                     /note="double-stranded RNA binding motif (DSRM)
                     superfamily; Region: DSRM_SF; cl00054"
                     /db_xref="CDD:444671"
     misc_feature    order(4843..4845,4849..4851,4969..4971,5038..5046,
                     5053..5055)
                     /gene="LOC4324864"
                     /note="RNA binding site [nucleotide binding]; other site"
                     /db_xref="CDD:380679"
     polyA_site      5452
                     /gene="LOC4324864"
                     /experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN      

accctcgccattttgacgtagtggcctctgtcgtccgtgagttaccctgacccctcctcgtcagtttgcccgccgcggcgccgccgccgccgccgccgatccccatccatcccgcgagcgagcagggcgccgtcgttcgtcctgctgcatccgccgcatcctgtaaacatgaaccctttaaagaggtcattggaatcatcttctcaggaacatgaagcaggcaaacagaaactgcagaagagagagtgtcaagatttcactcccagaagatatcagcttgatgtctatgaggttgcaatgcggagaaacacgattgcgatgcttgacacaggagccgggaagacaatgattgctgtgatgcttatcaaggagttcggaaagataaacagaacaaagaatgctggaaaagtcatcatatttcttgcaccaacagttcaacttgttacacagcaatgcgaggtgattgaaatccacacagattttgaggtagaacaatactatggtgcaaagggggttgatcaatggacaggtcctagatggcaagagcaaatctcaaaataccaggtcatggtcatgacaccacaggtgttcctacaagctttacgcaatgctttcttaatcttggacatggttagtctcatgatatttgatgaatgccatcatgcaactggaaaccacccttatacaagaataatgaaggagttctatcacaaatcagaacataagccaagtgtgtttggtatgacagcatcacctgttataagaaaaggtatctcttctcatttggattgtgaaggtcagttctgtgaattggagaacctgttagatgctaagatctacacagtttcagatagagaagagatagagttttgtgttccttctgcaaaagaaatgtgcaggtactatgactcgaaaccagtttgttttgaagatttgagtgaagaattgggagttttatgttccaagtatgatgcattgataacagagttgcagaataagcgaagcgacatgtataaagatgctgatgatataacaaaagaatcaaagagacgcctttctaaatctatagcaaaaatttgctactgccttgatgatgttggtcttatttgtgcaagtgaggccacaaaaatctgcattgaaaggggccaggagaaaggttggctgaaggaagtagttgatgccacagatcagcaaactgatgcaaatggatcacgcctatttgcagaaaattcagcgcttcatatgaagttctttgaggaagccttgcatttaattgacaaacgcctccaacaaggtatcgacatgcttctaaactcagaaagtggatgtgttgaagcagcaaagacgggctatatttccccaaagctctatgaactcatccagatctttcactcttttagtaactctcgtcatgctcgatgcctcatttttgttgatcgaaagatcactgctagagtcattgaccggatgattaagaaaattggccaccttgcacatttcacagtttcttttcttactggagggagatcttcggtggatgctctgacacccaaaatgcagaaggatacattggattcatttcgctctggaaaggtgaacttactatttactacagatgttgctgaagagggtatccatgtcccagaatgctcttgtgtaatacgatttgatttgccaaggacaacacgtagctatgtgcagtcacgtggacgagcacgccaggaagactctcagtacattctcatgattgaacgggggaacgtgaagcaaaatgatttgatatctgcaattgtgagaagtgagacttcaatggttaagattgcttcaagcagagagtctggaaatctgtcgcctggttttgttcccaatgaagaaataaacgaataccatgtaggcacaacaggagcgaaagtaactgctgattcaagcatcagtattgtctaccgatactgtgagaagcttccgcaggataagtgctactccccaaaacctacatttgagttcactcatcatgatgatggatatgtgtgtacattagcattaccaccaagtgctgtgcttcaaattctggtgggcccaaaagcaagaaacatgcacaaagcaaaacagctcgtttgccttgatgcatgtaagaagttgcatgagctaggagcacttgatgaccacctttgtctatctgttgaagatccagttccagaaattgtaagcaaaaataagggtactggtataggtacaaccaaacggaaggagctacatggtacaacaagaattcatgcttggtctggcaattgggtgtcaaagaaaactgcactcaagcttcaaagctacaaaatgaattttgtttgtgaccaagctggtcagatttactctgaatttgttctgttaattgatgcaactttaccggatgaagtcgctactttggagattgacctatatttgcacgacaagatggtcaaaacttcagtttcttcttgtggacttcttgagttggatgctcaacagatggaacaagcaaagttgtttcaagggcttctcttcaatggtttgtttggaaagctgtttactagatcaaaagtacctaatgctccgagggaattcattcttaataaagaggatacatttgtgtggaacactgcgagtgtatatttgcttttaccaacaaatccttcttttgactccaacgtttgtattaattggagtgtcattgatgcggcagctacggcagttaaacttatgagaaggatttattctgagaataaaagagaattacttggaatatttgattctgaccaaaatgttggagatttaattcatttagctaacaagtcgtgtaaggctaacagcctcaaagatatggtagttctagcagttcacactgggaagatatatactgctcttgatattactgaattatctggcgatagcgcttttgatggtgcatctgataagaaagaatgtaaattccggacattcgcagaatatttcaaaaagaagtatggcatagtacttcgccacccctcacagccactactagttttgaagcctagtcataatcctcacaaccttctttcctcgaagttcagggatgaaggtaatgttgtggagaatatgagtaatggcacaccagttgtaaataaaacaagcaaccgtgtccacatgcctcctgagttgctgattccccttgatttacctgtggaaattttgagatcattctatttgtttccggctttgatgtatcggattgagtcattaacgttagctagtcaactaagaagtgaaattggatacagcgattctaatatatcaagtttcctgattctggaagctattacaacgcttaggtgctctgaggatttctctatggagcgtctagaattattgggagactctgtattgaagtatgcagtgagttgtcatcttttcctgaaatttcctaataaggatgaggggcagctatcatccataaggtgccatatgatttgtaatgccacactttataagcttggaattgaacgcaatgtacagggttacgtacgtgatgctgcatttgatcctcgtcgatggctagcaccaggacagctctctattcgtccatctccttgtgaatgccctgtaaaatctgaggttgtaactgacgatattcatatcattgatgacaaggctattgttctaggcaaggcgtgtgacaagggacacagatggatgtgttccaaaaccattgctgattgtgttgaggctattattggggcatattatgcagggggtggtttaagagcagccatggcagttctcaaatggttgggcatcggggctgaaattgaagaagacttgattgtgcaggccatattgagtgcttctgtgcagacttatcttccaaaagacaatgtatttgaaatgcttgaagcaaaactaggctattctttctcggtgaaaggtcttttggtagaggctctgactcacccatcacagcaggagttaggtgcaaaatactgctacgagcgcctagagttcctcggtgatgcggtcttagacattctgttaacaagatatcttttcaatagtcataaagacactaatgagggggagttgacagacttacgttctgcatcagtcaataatgaaaactttgcacaagttgcagtaaagcacaacttccatcactttctccagcattcttctgggcttctgttagaccaaattactgaatatgtgaataggttggaaggttcatccatggacaaagttgaactgttatcagatggactcccaaaagggcctaaagtccttggtgatattgtagaaagtattgcaggtgcaattcttttagacaccaaacttgatttggatgtagtctggggtatttttgaaccccttctttccccaattgtcacacctgagaatctggagttacctccatacagagagcttatcgaatggtgtggcaaacatgggtattttgtaggaattaactgtagagatcaaggagacacagtagtggctactcttgatgtacagctcaaagaggtgcttcttgtgaggcaaggttttagcaagaaaagaaaagatgcgaaagcgcatgcatcttccttactgctcaaagatctcgaggaaaaaggactaataatcccaaagaatgcaagcaagacagaacaatttgaaaagcattgtggcagcactaatcccttcaacaatttgcatgtcgatgcaatggatacacagactccaaaaccaaccaaggaaaaaaacgcagctgattcaaggaacatttctgatcccctgcttggtaaaccattgcacgtgattgtgaaaacgagtaaaggaggaccacgcattgcattatatgagttgtgtaaaaagttgcaatggccaatgcctacaatggaatctgagaaagtacaaccaagctttagcagcgtgtgctcctcccctggtggttcctctcagaaagctaccccccaagcgttcgctttcgcttcaaccattacattgcatataccaaatgctgatgtgatcagcctcacaggagatggccgtgcagataagaagagctcacaggattctgctgccctgttcttgctctatgagcttcagcggcgaggtactttgcaactccaggaggtgtgaaggaacgacaactgattgcttgccaaccagttgcttggaagttggaataatagaccaaccagttgcttgccaccactcagctttgtacatcttctccagtgttcaccttctgaattatgataagagggtacccaaagaatggagaacagctgacctggttctggtgtgtgtcagttgttatgtgtgtttgtccatatgttatctgcgtagaaactgaataagcccccaaagttgttgctgacgataaacacgcaaatatcatgcccctgtagcctgtaggtgttaaaccaattgttcaaggataaaaagagagaccattttcaaatca

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