LOCUS       XM_015780808            4685 bp    mRNA    linear   PLN 10-JUL-2024
DEFINITION  PREDICTED: Oryza sativa Japonica Group endoribonuclease Dicer
            homolog 4-like (LOC4336362), transcript variant X1, mRNA.
ACCESSION   XM_015780808
VERSION     XM_015780808.3
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_089038) annotated using gene prediction method: Gnomon,
            supported by mRNA and EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Jul 10, 2024 this sequence version replaced XM_015780808.2.
            
            ##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..4685
                     /organism="Oryza sativa Japonica Group"
                     /mol_type="mRNA"
                     /db_xref="taxon:39947"
                     /chromosome="4"
     gene            1..4685
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="endoribonuclease Dicer homolog 4-like; Derived by
                     automated computational analysis using gene prediction
                     method: Gnomon. Supporting evidence includes similarity
                     to: 1 mRNA, 15 ESTs, 388 long SRA reads, 3 Proteins, and
                     100% coverage of the annotated genomic feature by RNAseq
                     alignments, including 34 samples with support for all
                     annotated introns"
                     /db_xref="GeneID:4336362"
     CDS             118..4440
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /codon_start=1
                     /product="endoribonuclease Dicer homolog 4 isoform X1"
                     /protein_id="XP_015636294.1"
                     /db_xref="GeneID:4336362"
                     /translation="

MTASPIIGKGGSNKLNYTKCINSLEELLHAKVCSVDNEELESVVASPDMEVYFYGPVNHSNLTTICIKELDSLKLQSERMLRASLCDFKDSQKKLKSLWRLHENIIFCLQELGSFGALQAARTFLSFDGDKLDRREVDLNGSTSSFAHHYLNGATSILSRNKTDGSHAGSFDLEKLEEPFFSNKFSVLINVLSRYGLQENMKCIVFVKRITVARAISNILQNLKCLEFWKCEFLVGCHSGSKNMSRNKMDAIVQRFSSGEVNLLVATSVGEEGLDIQTCCLVVRFDLPETVASFIQSRGRARMTKSKYVVLLERENQSHEKLLNGYIAGESIMNEEIDSRTSNDMFDCLEENIYQVDNTGASISTACSVSLLHCYCDNLPRDMFFTPSPVFFYIDGIEGIICRLILPPNAAFRQADGQPCLSKDEAKRDACLKACVKLHKLGALTDFLLPGPGSRKNKVSVTNNSSNNKVEDDSLREELHEMLIPAVLKPSGLKLDSLSNLHFYYVKFIPIPEDRRYQMFGLFVINPLPVEAETLQVDLHLARGRIVKAGIKHLGKIAFEKEKMMLAHKFQEMCLKILLDRSEFTSPHVKLGNDVTLEINSTFYLLLPIKQKCYGDRFMIDWPAVERCLSSPIFKDPIDVSVHASYSSNESLRLLDGIFSKTDVVGSVVFSPHNNIFFFVDGILDEINAWSEHSGATYAEHFKERFRIELSHPEQPLLKAKQIFNLRNLLHNRLPETTESEGRELLEHFVELPPELCSLKVIGFSKDMGSSLSLLPSLMYRLENLLVAIELKDVMLSSFPEASQISASGILEALTTEKCLERISLERFEVLGDAFLKYVVGRHKFITYEGLDEGQLTRRRSDVVNNSHLYELSIRKKLQVYIRDQQFEPTQFFAPGRPCKVVCNTDVEVRLHQMDIHPDNRENCNLRCTRSHHWLHRKVIADVVESLIGAFLVEGGFKAAFAFLHWIGIDVDFNNPALYRVLDSSSINLSLMDYTDIAGLEELIGYKFKHKGLLLQAFVHPSFSQHSGGCYQRLEFLGDAVLEYVITSYLYSTYPDIKPGQITDLRSLAVGNDSLAYAAVEKSIHKHLIKDSNHLTSAISKFEMYVKLSNSEKDLLEEPACPKALGDIVESCIGAVLLDSGFNLNYVWKVMLMLLKPVLTFANMHTNPMRELRELCQCHGFELGLPKPMKADGEYHVKVEVNIKSKIIICTAANRNSKAARKFAAQETLSKLKNYGYKHRNKSLEEILIVARKRESELIGYNEDPIDVEADISVKMKSPHIHEENIPFQNTETSFTRSSKFHNQIIAGSGKHDVNNGRNNQPKLATQSGRLPSEATEKSNKKVYHGDMVHKTARSFLFELCAANYWKPPEFKLCKEEGPSHLRKFTYKVVVEIKGASATLLECHSDGKLQKKAAQEHAAQGALWCLKQLGHLPKEEDVRV"

     misc_feature    646..1053
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="Members of the P-loop NTPase domain superfamily are
                     characterized by a conserved nucleotide phosphate-binding
                     motif, also referred to as the Walker A motif
                     (GxxxxGK[S/T], where x is any residue), and the Walker B
                     motif (hhhh[D/E], where h is a...; Region: P-loop
                     containing Nucleoside Triphosphate Hydrolases; cl38936"
                     /db_xref="CDD:476819"
     misc_feature    1015..1017
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350171"
     misc_feature    1219..1467
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="Dicer dimerization domain; Region: Dicer_dimer;
                     pfam03368"
                     /db_xref="CDD:460900"
     misc_feature    2026..2406
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="PAZ domain, named PAZ after the proteins Piwi
                     Argonaut and Zwille. PAZ is found in two families of
                     proteins that are essential components of RNA-mediated
                     gene-silencing pathways, including RNA interference, the
                     piwi and Dicer families. PAZ functions as a...; Region:
                     PAZ; cl00301"
                     /db_xref="CDD:469713"
     misc_feature    order(2149..2151,2209..2211,2221..2223,2275..2277,
                     2365..2367,2371..2373)
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="nucleic acid-binding interface [nucleotide
                     binding]; other site"
                     /db_xref="CDD:239207"
     misc_feature    2545..3045
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /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(2593..2598,2605..2610,2617..2619,2626..2631,
                     2638..2643,2647..2655,2683..2685,2971..2973,2998..3000)
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    order(2593..2595,2602..2604,2614..2616,2941..2943,
                     2950..2952)
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="active site"
                     /db_xref="CDD:238333"
     misc_feature    order(2602..2604,2941..2943,2950..2952)
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="metal binding site [ion binding]; metal-binding
                     site"
                     /db_xref="CDD:238333"
     misc_feature    3154..3609
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /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(3211..3216,3223..3228,3235..3237,3244..3249,
                     3256..3261,3265..3273,3301..3303,3526..3528,3559..3561)
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    order(3211..3213,3220..3222,3232..3234,3496..3498,
                     3505..3507)
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="active site"
                     /db_xref="CDD:238333"
     misc_feature    order(3220..3222,3496..3498,3505..3507)
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="metal binding site [ion binding]; metal-binding
                     site"
                     /db_xref="CDD:238333"
     misc_feature    4192..4401
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="double-stranded RNA binding motif (DSRM)
                     superfamily; Region: DSRM_SF; cl00054"
                     /db_xref="CDD:444671"
     misc_feature    order(4192..4194,4198..4200,4270..4272,4345..4353,
                     4360..4362)
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /note="RNA binding site [nucleotide binding]; other site"
                     /db_xref="CDD:380679"
     polyA_site      4685
                     /gene="LOC4336362"
                     /gene_synonym="DCL4; OsDCL4; SHO1"
                     /experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN      

ccatatgcgcaaattatgaaggagtaggcttttgggtccagttgcttgttgctcctgttgtatcaataggaattctataatagtaacagtgttgagaaattccctcgggtttttggcatgactgcttcaccaattattgggaaaggtgggtctaataaacttaactacacgaaatgtatcaacagtcttgaggaattacttcatgcaaaggtttgttcagttgataatgaagaacttgaaagtgtggttgcatctcctgatatggaggtgtacttttatggcccagttaatcactctaaccttaccacaatatgcatcaaagagcttgatagcttaaagcttcagagcgagcgcatgctaagagcgagcctatgcgatttcaaggattctcagaagaaactgaagtccttatggaggttgcatgaaaatattattttctgtttgcaagaacttggttctttcggagctctgcaagctgcgaggacctttttgtcctttgatggtgataagctagatagaagggaggtcgatcttaacggcagtacttccagcttcgcacatcactacctgaacggagcaacttctattcttagtcgcaacaaaacagatggttcccacgctggttcatttgaccttgagaagcttgaagaacctttcttctcaaataaattttctgttcttatcaatgttctttcgagatacgggttgcaggaaaacatgaaatgcattgtttttgtgaaaagaataactgttgcaagagcaatatcaaacattctccaaaacttgaagtgtcttgaattttggaaatgtgagtttcttgtgggctgccactcaggatcaaagaacatgtcaaggaataagatggatgctattgttcaaaggttttcttctggtgaggtgaatcttttggttgctacaagcgtaggtgaagagggacttgatattcagacgtgttgtcttgttgtgcgatttgatcttccagaaactgttgctagttttatccaatcaagggggcgtgcccggatgactaaatctaaatacgttgttctcctagagagagaaaatcagtctcatgaaaagttgcttaatggttatattgctggtgaaagcattatgaatgaagagatagactcaagaacttcaaatgatatgtttgattgcctcgaggagaacatttatcaagtggataacaccggtgcttccattagcactgcttgtagtgtatctctactacattgctactgcgacaaccttcctagggatatgttttttactccttccccagtgttcttctacattgatggcatcgagggaataatctgcagactaattcttccaccaaatgctgctttccgtcaagcagatggtcaaccatgtctgtcaaaagatgaagctaagagagatgcatgcttaaaggcatgcgtaaaacttcataaattgggtgctttgacagattttcttctgccgggtccaggttcaagaaagaataaagtatcagtaacaaataattcatcaaacaacaaagttgaagatgatagtctaagagaagagcttcatgagatgttaattcctgcagttctcaaaccttcgggattaaagttggattctttatcgaacttgcatttctactatgttaaatttattcccataccagaagataggcgatatcagatgtttggtctctttgtgatcaatccccttcctgtggaagctgaaacattgcaagttgatttgcatcttgctcgtggcaggattgtgaaagcaggaattaagcatttggggaaaatagcatttgagaaagagaagatgatgcttgcacacaagtttcaagagatgtgtctgaagattctcctggacagatctgagtttacttcaccccatgttaaattgggcaatgatgttacattagaaatcaattcaacattttaccttctgcttcccatcaagcaaaagtgttatggtgatagatttatgattgactggccagcagttgagcgctgtttatcatcaccgatttttaaagaccctatagatgtgtctgtgcatgcctcatattcatcaaatgagtctctgagacttcttgatggaatcttcagtaaaaccgatgtagttggcagtgtagtctttagtccccacaacaatatctttttctttgttgatggcattctggacgaaataaatgcttggagcgagcacagtggtgcaacttatgcagaacacttcaaggaaaggtttcgtattgagctatcacatcctgaacagccacttttgaaggctaaacagatcttcaacctgcgaaatttgcttcataatcggttaccggagaccacagaatcggagggccgtgaattactagagcacttcgtggagttacctccagaattatgctctttgaaggtcattgggttttcaaaagatatgggcagttccctgtccttgttaccttctttaatgtatcgtttggagaatttgctggtggctattgagttgaaggatgtgatgttatcttcttttccagaggcatctcaaattagtgcttctggtatacttgaagcgcttactactgagaaatgtttggagaggatatctttggagcgatttgaagtcctaggcgatgctttcttgaagtacgtagttggacgtcacaagtttattacatatgaaggacttgatgaagggcaattgaccaggagacgttctgatgtagtgaacaattcacatttatatgagttatcgatcagaaaaaaattgcaggtatacatacgggatcaacagtttgaaccgactcagttctttgctccaggaaggccttgtaaagttgtttgcaatactgacgtggaagtgagactacaccagatggatattcatccagataacagagaaaactgtaacctgagatgtacaaggtcacatcattggctgcataggaaagtgattgcagatgttgtcgaatcgcttattggagcatttcttgttgagggtggattcaaagctgcatttgctttcctgcattggattggaatagacgttgattttaataatccagctctctatagggtattagattcaagctccatcaatttatctcttatggactacactgacattgccgggcttgaagaattgataggttacaagttcaaacataagggtctacttctccaagcattcgtacacccttcatttagtcaacattctggaggctgctaccagagactggagtttcttggagacgctgttttggagtatgtgataacttcgtacctctactctacttatccggatataaaacctggtcaaataacagatctaagatcgttagctgttggtaatgattcgcttgcttatgcggcggttgagaaatctatccataagcatcttataaaggattcaaaccatctcacgtcagcaataagtaaatttgagatgtatgtgaagctctccaattcagagaaagacttgcttgaagaaccagcatgtcccaaggctcttggtgatattgttgaatcttgtattggcgcagtgcttttagattcaggcttcaacctgaactatgtttggaaggtaatgcttatgcttctaaagccagtattgaccttcgccaacatgcacactaatccgatgagagaacttcgagagctttgtcagtgtcatggatttgagttaggccttccgaaacctatgaaagctgatggagagtaccatgtcaaagtagaagttaacataaagagcaaaattatcatttgtactgcagcaaatcggaattcaaaagccgctagaaagtttgctgcacaagaaacactttctaaactgaagaattacggttataagcacagaaacaagtcccttgaggagattttgattgttgccaggaagagggaatcagaactgataggatataatgaagatccaatcgatgttgaggctgacatatctgtaaaaatgaagagtccacatatacatgaagagaacataccttttcaaaatacagaaacatctttcactaggagttctaaattccacaatcaaattatagcagggtctggcaaacatgatgtcaataatggaaggaacaatcaacccaagttggcaacacagagtggtcgtctgcctagtgaagcaacagagaaaagcaataaaaaggtgtatcatggtgacatggtacacaaaacagcaagatcattcctttttgaactatgtgctgcaaattattggaaacctcctgaattcaagttatgtaaagaggaagggccaagccaccttcggaagttcacttacaaggtggttgttgagatcaagggtgcttcggcgacccttttggagtgtcatagcgatggtaagcttcagaagaaggctgcacaagagcatgcggcacaaggggcgctctggtgtctcaagcaacttgggcacctaccaaaagaagaggacgttcgtgtatagcaacattgtcatgttttgggggtcacagtgcgaaagtacagtgatatttgtttgtccagagataaacgtgcctttctctcttttgctctgatgtccaacctcccttattaagggacgtgtataaattttcacttctccagtgccctttgaatggctagagttgtatagctagtccattattttccatgagacgtatattggtatatagttttattcttcaatagacgcatatagtattctttcaa

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