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2024-03-29 14:05:47, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       XM_026020835            4938 bp    mRNA    linear   PLN 07-AUG-2018
DEFINITION  PREDICTED: Oryza sativa Japonica Group endoribonuclease Dicer
            homolog 3b (LOC4348944), transcript variant X4, mRNA.
ACCESSION   XM_026020835
VERSION     XM_026020835.1
DBLINK      BioProject: PRJNA122
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_029265.1) annotated using gene prediction method: Gnomon,
            supported by EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI
            Annotation Status           :: Full annotation
            Annotation Name             :: Oryza sativa Japonica Group
                                           Annotation Release 102
            Annotation Version          :: 102
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 8.1
            Annotation Method           :: Best-placed RefSeq; Gnomon
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..4938
                     /organism="Oryza sativa Japonica Group"
                     /mol_type="mRNA"
                     /cultivar="Nipponbare"
                     /db_xref="taxon:39947"
                     /chromosome="10"
     gene            1..4938
                     /gene="LOC4348944"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Gnomon. Supporting evidence
                     includes similarity to: 1 EST, 3 Proteins, and 100%
                     coverage of the annotated genomic feature by RNAseq
                     alignments, including 1 sample with support for all
                     annotated introns"
                     /db_xref="GeneID:4348944"
     CDS             182..4525
                     /gene="LOC4348944"
                     /codon_start=1
                     /product="endoribonuclease Dicer homolog 3b isoform X4"
                     /protein_id="XP_025876620.1"
                     /db_xref="GeneID:4348944"
                     /translation="
MYLSAFAFFITRQYISGSASTLHNCEAHISQLELTLDAKIYIVEDRNELESFSPPTTIVNKYYDAYMVDFDNLKSKLQIFSDEFDSLLVGLQESPSNKFKDTDNILETSRKSLSRYHGKILYSLNDLGPIITSEVVKIHIESVKPLCDSEDCIFSKASLCLHMSYFKEALSLIEEILPQGYGELMKSESGSEELTKRGYISSKVNTLINIFKSFGSSNEVLCLIFVDRIITAKAVERFMRGIVNFSCFSISYLTGGSTSKDALSPAVQRFTLDLFRAGKVNLLFTTDVTEEGVDVPNCSCVIRFDLPRTVCSYVQSRGRARRNNSEFILMIERGNLQQQEHIFRMIQTGYYVKNCALYRHPNALSYDLSIQGMYTYQVQSTGATITADCCVNLIRKYCEKLPKDRYFMPKPSFEVTIEDGLFKCTLTLPRNAAFQSIVGPLSSSSNLSKQLVSLEACKKLHQLGELNDHLVPLTEEPMDTDFTTADEKCISGPGTTKRKELHGTTCVLALSGTWIHDSENITLNTYRIDFLCDQEGENYAGFVLLMEPELDDDVAPSKMDLFLIPNKMVYTTVTPRGKVQLNKKQLGKGKLFQEFFFNGIFGRLFHGSRKSGAQRDFIFKKGHEIQWNTESMYLLLPLRDSSYIQDDLSIHWEAIESCAGAVEQLWSSYQGDENVIPVNCIPQKRRGGQEEIIHLANKSLHCSSIKDSVVLSLHTGRIYTVLDLILDTTAEDSFDEMCKGKASPFTSFVDYYHQKYGIIIQHPEQPLLLLKQSHNAHNLLFSKLKYLDGSTGKPLLMEKEQIHARVPPELLIHLDVTTDILKSFYLLPSVIHRLQSLMLASQLRREIGYNQHIPVTLILEAITTLRCCETFSLERLELLGDSVLKYVVGCDLFLRYPMKHEGQLSDMRSKAVCNATLHKHGIWRSLQGYVRDNAFDPRRWVAPGQISLRPFPCNCGIETAFVPSHRRYIRDDPSFFVGKPCDRGHRWMCSKTISDCVEALVGAYYVGGGIAAALWVMRWFGIDIKCDMKLLQEVKFNASHLCSLSKINDIEELEAKLKYNFSVKGLLLEAITHPSLQELGVDYCYQRLEFLGDSVLDLLLTRHLYATHTDVDPGELTDLRSALVSNENFAQAVVRNNIHSHLQHGSGILLEQITEYVRSNLECQGKESEFLQHTTCKVPKVLGDIMESIAGAVFIDTDFNVDMVWEIFEPLLSPLITPDKLALPPYRELLELCSHIGCFLNSKCTSKGEEVIIEMSLQLRDELLVAQGHDRNKKRAKAKAASRILADLKQQQGLSIKQCLSKAKQLDIVTSDLQFDLTSSGTQLSYSDLNDYHILEGLSSVKKEVVLPLKMEKGGPRSALFKLCKILQWPMPEFEFVEQRFRTPIVMDGATTTNFNSFVSTITLHIPDATTITFQGERRTDKKSAQDSASLMMLHKLQELKICICKT"
     misc_feature    776..1174
                     /gene="LOC4348944"
                     /note="C-terminal helicase domain of the DEAD-like
                     helicases; Region: DEAD-like_helicase_C; cl38915"
                     /db_xref="CDD:365791"
     misc_feature    1136..1138
                     /gene="LOC4348944"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350171"
     misc_feature    1352..1612
                     /gene="LOC4348944"
                     /note="Dicer dimerization domain; Region: Dicer_dimer;
                     pfam03368"
                     /db_xref="CDD:427264"
     misc_feature    2198..2629
                     /gene="LOC4348944"
                     /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:444818"
     misc_feature    order(2336..2338,2423..2425,2435..2437,2489..2491,
                     2591..2593,2597..2599)
                     /gene="LOC4348944"
                     /note="nucleic acid-binding interface [nucleotide
                     binding]; other site"
                     /db_xref="CDD:239207"
     misc_feature    2747..3256
                     /gene="LOC4348944"
                     /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(2801..2806,2813..2818,2825..2827,2834..2839,
                     2846..2851,2855..2863,2891..2893,3194..3196,3221..3223)
                     /gene="LOC4348944"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    order(2801..2803,2810..2812,2822..2824,3164..3166,
                     3173..3175)
                     /gene="LOC4348944"
                     /note="active site"
                     /db_xref="CDD:238333"
     misc_feature    order(2810..2812,3164..3166,3173..3175)
                     /gene="LOC4348944"
                     /note="metal binding site [ion binding]; metal-binding
                     site"
                     /db_xref="CDD:238333"
     misc_feature    3377..3838
                     /gene="LOC4348944"
                     /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(3437..3442,3449..3454,3461..3463,3470..3475,
                     3482..3487,3491..3499,3527..3529,3761..3763,3794..3796)
                     /gene="LOC4348944"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    order(3437..3439,3446..3448,3458..3460,3731..3733,
                     3740..3742)
                     /gene="LOC4348944"
                     /note="active site"
                     /db_xref="CDD:238333"
     misc_feature    order(3446..3448,3731..3733,3740..3742)
                     /gene="LOC4348944"
                     /note="metal binding site [ion binding]; metal-binding
                     site"
                     /db_xref="CDD:238333"
     misc_feature    4268..4498
                     /gene="LOC4348944"
                     /note="double-stranded RNA binding motif (DSRM)
                     superfamily; Region: DSRM_SF; cl00054"
                     /db_xref="CDD:444671"
ORIGIN      
atcatgtgcttttttgtaacgaaaatagtcacgtgcttttaaccctgtgtatatttcattgatcaatagtttcagaaaatgtgttttagctttgttattaaaataagcatgtcgtgtgactgttattatcttcctttttgaagaatgccccaactgccatgtactgtcaaaaactcatgtgatgtatttgagtgcttttgccttcttcataacaagacaatacatttctggaagtgcttccacactacacaattgtgaagcacacatttctcaactagaactaaccttggatgccaagatatacatcgtagaagatcgaaatgagcttgagagcttttcccctcctacaacaattgtgaacaaatactatgatgcttacatggttgattttgataatctgaaatcaaagcttcagatattttctgatgagtttgattctttgttggttggtcttcaagaatcgccatctaataaatttaaagacaccgataatatcctagagacttcaagaaagagcttgtccagataccatgggaaaatattgtacagcctaaacgatcttggtccaattatcacctctgaggtagtcaaaatacatattgaaagcgttaagccattatgtgattctgaagactgcattttttctaaagctagcttgtgcttacatatgtcttattttaaagaagctttaagtctaatagaggaaattcttccacaaggatatggtgaactaatgaaatcagaatctggttctgaggaattaactaaaaggggatacatttcttcaaaagtgaatacgctaatcaacatcttcaaatcgtttgggtcatcaaatgaagtgctttgcctaattttcgtagacagaattataacagctaaagccgtcgaaaggtttatgagaggaattgttaacttctcttgtttttcaatttcttacttgactggagggagtacatcaaaagatgctctgagtccagcagttcagagatttactttggatttgttccgagctggaaaggtgaacttgctttttacaacagatgtgactgaagagggcgtcgatgtacctaactgttcttgtgtgatacgcttcgacctacccagaactgtttgtagctatgtccaatctcgtggtcgtgctagaaggaacaactcggaatttattcttatgattgagaggggaaacttgcagcagcaagaacacatatttcgtatgatacagactggttactatgttaaaaactgtgcactctatagacaccccaatgctttatcctatgacttgtctatccaagggatgtacacctaccaagttcagtcaactggagcaactataaccgcagattgctgtgtcaacctaattcgtaaatactgtgagaagcttcctaaagataggtatttcatgccaaagccttcctttgaggtgaccattgaagatggattattcaaatgcacattgacgctacctcgaaatgcagcatttcaaagtatagttggccctttaagcagttcaagtaatttatccaagcagcttgtatccctagaggcctgcaagaaattgcatcaactgggagaacttaatgatcatcttgtacctttgactgaagaacctatggatacagatttcactacagcagatgaaaaatgcatatctggaccaggaacaactaaaaggaaggagcttcatggtactacatgtgttcttgctttatcaggaacttggattcatgacagtgaaaatattacactgaatacttacagaattgattttctttgtgaccaagagggtgaaaactatgctgggtttgttctcttaatggaaccagaacttgatgatgatgtggcaccctcaaaaatggatctgttcctgatccctaataaaatggtctacaccactgtaactcctcgcggaaaagttcaactaaacaaaaagcagttaggtaaagggaaattgttccaagaattctttttcaatggaatctttggtagattatttcatggttctcgaaaaagtggagcacaaagggattttattttcaaaaagggtcatgaaatacagtggaacacggaaagcatgtacttgcttttacctttgagggattcttcatatatccaggatgacctaagcatacactgggaagcaattgaatcttgtgctggtgcagttgagcagttgtggagttcgtatcaaggagatgaaaatgtcattcctgtaaattgtattccacaaaaaagaagagggggccaagaagaaattattcatctggccaataagtctcttcattgttccagcatcaaagattcagtcgtgctatcactgcatacaggaaggatatacactgttcttgatttgatcttagacacaactgcagaggactcgtttgatgagatgtgtaaggggaaagcctcaccttttacttcatttgtggactattaccatcaaaagtatggtattattattcaacatccagaacaaccactattgctgttaaagcaaagccacaatgcacacaatcttctcttttcaaaattgaagtatctagatggctccactggcaaacctctgctcatggaaaaagaacaaattcatgctcgggttccacctgaactacttatccatctcgatgtaacaactgatattctgaagtcattttatttactcccttctgtaatacatcggcttcagtcacttatgctagccagccagcttcgcagagaaattggttacaatcaacacataccagtcactttgattttggaagctataacaactttaagatgctgtgagacattttctctggagcgtttagagctgttaggagactccgtgctaaagtatgtggtaggatgtgaccttttcctaaggtatcctatgaaacatgaaggtcagctctctgatatgagatccaaggctgtctgcaatgctacacttcataaacatggaatatggcggtcgttgcagggttatgtacgtgataatgcttttgacccacggcgttgggttgctcctggacagatatcgttgcgcccttttccttgtaactgtggaatcgagactgcatttgttccttctcatagaaggtatatccgagatgacccatctttttttgtgggaaaaccatgtgacagaggtcataggtggatgtgctcaaaaacaatatctgattgtgttgaagcactggttggagcatattatgttggtggtggcattgctgctgcactttgggttatgaggtggtttggaatcgatatcaaatgtgatatgaagctattgcaggaagtgaagttcaatgcatctcatttatgctccttatcaaaaataaatgacattgaggaactggaagcaaaactgaagtacaacttctcagtcaagggccttcttttggaagccataactcatccatctctgcaggaattaggtgttgattactgttaccagcgtcttgaatttcttggtgattctgtgctggatctacttcttacacgtcatctctatgctactcatactgatgttgatcctggagaattaacggatttacgctccgctttggttagtaatgagaattttgcacaagcagttgtaagaaacaacattcacagtcatctacaacatggatccggaatacttttggagcaaattactgaatatgtcaggtcaaatttggagtgtcaagggaaagagagtgaattccttcaacatactacatgtaaagtacctaaggttcttggtgacattatggaaagcatcgctggtgcagtatttatagacaccgattttaatgttgacatggtttgggagattttcgagccattgctttctccactgattacacctgataagcttgcattgccaccttaccgtgagttgctggagctatgcagtcacattggttgcttcttaaattcaaaatgcaccagtaaaggagaagaagtaattatagagatgtcactgcaactacgagatgagctgctggtagcacaagggcatgacagaaacaaaaagagggcaaaggcaaaagcagcatctcgtattttggcagatcttaagcagcaacagggtctttcaattaaacaatgtttgtccaaggctaaacagctggatatcgtgacttcagatcttcagtttgacttgacaagttcaggaacacaactcagttattctgatttgaatgactatcatatcctagaaggtctttcctcagtaaagaaagaagttgtgcttccactcaaaatggagaaaggtggacctcgaagtgcgcttttcaagctatgcaagattttgcagtggccaatgccagaattcgaatttgtggaacaaaggttcaggactcctattgttatggatggggcgacaacaacaaacttcaatagctttgtttcgacaatcaccttgcacatacctgacgcaacaaccattacatttcaaggtgagcgacgtactgacaaaaagagtgctcaggattcagcatccttgatgatgcttcacaagcttcaagaactcaagatctgtatatgcaagacttagcaaagcatcattgagacatgggccaatatgccagttaacgattgcgactagctaatgcgagctacttccctcccaaagtgagatgcgacgaaaatatttctgaaaagctcgatgctccagactgtcactgatcctatgttattttggggaagaagatccctatggtatactaccttgcattacctggatacattgttgtcgagtttccaatattccacgatgtatcgccccaagattcagggacatacctggctacttttctcttatccaacttcaaggtttccgaggtgctctctctatatatgttttattgtgcttcagtgtttggagagattaaagatacgtcttagagaaagcacttggtagtctaaatagtacacttaatggatatgaagataaaatgttctgcaaaa
//

by @meso_cacase at DBCLS
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If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596. [Full Text]