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2024-03-29 01:08:22, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       XM_039113365            6047 bp    mRNA    linear   ROD 11-JUN-2023
DEFINITION  PREDICTED: Rattus norvegicus dicer 1 ribonuclease III (Dicer1),
            transcript variant X9, mRNA.
ACCESSION   XM_039113365
VERSION     XM_039113365.1
DBLINK      BioProject: PRJNA677964
KEYWORDS    RefSeq.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
COMMENT     MODEL REFSEQ:  This record is predicted by automated computational
            analysis. This record is derived from a genomic sequence
            (NC_051341.1) 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 RefSeq
            Annotation Status           :: Updated annotation
            Annotation Name             :: GCF_015227675.2-RS_2023_06
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.1
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 06/06/2023
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..6047
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN/NHsdMcwi"
                     /db_xref="taxon:10116"
                     /chromosome="6"
                     /sex="male"
                     /tissue_type="kidney"
                     /country="USA: Wisconsin, Milwaukee, Medical College of
                     Wisconsin"
                     /collection_date="2019-03-08"
                     /collected_by="Rebecca Schilling"
     gene            1..6047
                     /gene="Dicer1"
                     /note="dicer 1 ribonuclease III; Derived by automated
                     computational analysis using gene prediction method:
                     Gnomon. Supporting evidence includes similarity to: 11
                     ESTs, 1 long SRA read, 2 Proteins, and 100% coverage of
                     the annotated genomic feature by RNAseq alignments,
                     including 37 samples with support for all annotated
                     introns"
                     /db_xref="GeneID:299284"
                     /db_xref="RGD:1309381"
     CDS             477..5864
                     /gene="Dicer1"
                     /codon_start=1
                     /product="endoribonuclease Dicer isoform X3"
                     /protein_id="XP_038969293.1"
                     /db_xref="GeneID:299284"
                     /db_xref="RGD:1309381"
                     /translation="
MKSPALQPLSMAGLQLMTPASSPMGPFFGLPWQQEAIHDNIYTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGDLSPHAKRTVFLVNSANQVAQQVSAVRTHSDLKVGEYSNLEVNASWTKERWSQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSCPSCPRILGLTASILNGKCDPDELEEKIQKLEKILKSGAETATDLVVLDRYTSQPCEIVVDCGPFTDRSGLYERLLMELEEALDFINDCNVSVHSKERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELHRKFLLFTDTLLRKIHALCEEYFSPASLDLKYVTPKVMKLLEILRKYKPYERQQFESVEWYNNRNQDNYVSWSDSEDDDDDEEIEEKEKPETNFPSPFTNILCGIIFVERRYTAVVLNRLIKEAGKQDPELAYISSNFITGHGIGKNQPRSKQMEAEFRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRARAPISNYVMLADTDKIKSFEEDLKTYKAIEKILRNKCSKSVDGAEADVHAVVDDDDVFPPYVLRPDDGGPRVTINTAIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRASIVGPPMGCVRLAERVVALICCEKLHKIGELDEHLMPVGKETVKYEEELDLHDEEETSVPGRPGSTKRRQCYPKAIPECLRESYPKPDQPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFTLSQQMLELVTRLHQYIFSHILRLEKPALEFQPAGAESAYCVLPLNVVNDSSTLDIDFKFMEDIEKSEARIGIPSTKYSKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQKGKALPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTAEELRAQTASDAGVGVRSLPADFRYPNLDFGWKKSIDSKSFISTCNSSLAESDNYCKHSTTVVPENAAHQGATRPSLENHDQMSVNCKRLPAESPAKLQSEVSVDLTAINGLSYNKSLANGSYDLVNRDFCQGNQLTYFKQEIPVQPTTSYPIQNLYNYENQPTPSNECPLLSNKYLDGNANTSTSDGSPAGSPRPAMMTAVEALEGRTDSEQSPSVGHSSRTLGPNPGLILQALTLSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRMVVSIFDPPVNWLPPGYVVNQDKSNSEKWEKDEMTKDCLLANGKLGEDCEEEEEEELAWRAPKEEAEYEDDLLEYDQEHIQFIDSMLMGSGAFVKKIPLSPFSTSDSAYEWKMPKKASLGSVPFSSDLEDFDYSSWDAMCYLDPSKAVEEDDFVVGFWNPSEENCGVDTGKQSISYDLHTEQCIADKSIADCVEALLGCYLTSCGERAAQLFLCSLGLKVLPVIKRTSRDKASYPAQENSSSQQKSPSGSCAAAVSPRSSAGKDLEYGCLKIPPRCMFDHPDAEKTLNHLISGFENFEKKINYIFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDSEKSFLQMCLVLR"
     misc_feature    600..1193
                     /gene="Dicer1"
                     /note="DEXH-box helicase domain of endoribonuclease Dicer;
                     Region: DEXHc_dicer; cd18034"
                     /db_xref="CDD:350792"
     misc_feature    order(600..611,618..620,669..692,813..815,1002..1004,
                     1095..1097)
                     /gene="Dicer1"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350792"
     misc_feature    order(777..782,849..854,927..929,933..938,945..947,
                     1020..1028)
                     /gene="Dicer1"
                     /note="nucleic acid binding site [nucleotide binding];
                     other site"
                     /db_xref="CDD:350792"
     misc_feature    999..1010
                     /gene="Dicer1"
                     /note="DEAD box helicase motif; other site"
                     /db_xref="CDD:350792"
     misc_feature    1287..1571
                     /gene="Dicer1"
                     /note="Partner-binding domain of the endoribonuclease
                     Dicer; Region: Dicer_PBD; cd15903"
                     /db_xref="CDD:277191"
     misc_feature    order(1302..1307,1314..1316,1320..1325,1500..1505,
                     1512..1517,1524..1526,1533..1538,1545..1547)
                     /gene="Dicer1"
                     /note="Trbp binding interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:277191"
     misc_feature    1590..2168
                     /gene="Dicer1"
                     /note="C-terminal helicase domain of the endoribonuclease
                     Dicer; Region: SF2_C_dicer; cd18802"
                     /db_xref="CDD:350189"
     misc_feature    order(1821..1829,2037..2039,2094..2096,2100..2102)
                     /gene="Dicer1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:350189"
     misc_feature    order(2049..2051,2055..2057,2130..2132,2136..2138)
                     /gene="Dicer1"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350189"
     misc_feature    2364..2630
                     /gene="Dicer1"
                     /note="Dicer dimerization domain; Region: Dicer_dimer;
                     pfam03368"
                     /db_xref="CDD:427264"
     misc_feature    3132..3500
                     /gene="Dicer1"
                     /note="PAZ domain, dicer_like subfamily. Dicer is an RNAse
                     involved in cleaving dsRNA in the RNA interference
                     pathway. It generates dsRNAs which are approximately 20 bp
                     long (siRNAs), which in turn target hydrolysis of
                     homologous RNAs. PAZ domains are named...; Region:
                     PAZ_dicer_like; cd02843"
                     /db_xref="CDD:239209"
     misc_feature    order(3321..3323,3360..3362,3378..3380,3390..3392,
                     3444..3446,3468..3470,3474..3476)
                     /gene="Dicer1"
                     /note="nucleic acid-binding interface [nucleotide
                     binding]; other site"
                     /db_xref="CDD:239209"
     misc_feature    4362..>4637
                     /gene="Dicer1"
                     /note="Ribonuclease III family; Region: RIBOc; smart00535"
                     /db_xref="CDD:197778"
     misc_feature    order(4413..4418,4425..4430,4437..4439,4446..4451,
                     4458..4463,4467..4475,4503..4505)
                     /gene="Dicer1"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    5508..>5765
                     /gene="Dicer1"
                     /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(5568..5573,5580..5585,5592..5594,5601..5606,
                     5613..5618,5622..5630,5658..5660)
                     /gene="Dicer1"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
ORIGIN      
cgggaacgaggcgacggcgagcggcaggaaatggcggcggcggcggcggcgccgggcggcaccgggaggcctgggctgtgacgcgcgcgccggagcggggtccgatggttctggaaggcccgcggcgcccagtgctgcagagatcgtgcttggagctctggaggaaaccttctgtagttagtgcactggaggctcaaggttccacacactgcagcaggagaagggaattctgaaacacaaaggaaaagggatttcttctgatttcaacaggttacctagggtatgcataaatacagacttggaaactgaaagaacttagagtcagcatttcgagagctgaagcttgggcatgctgtgattttccaataagctatcacaatgtcagaatgcagttcagacagcagcaacacagcgctcgcagacattaaaacgtaagctgtgctagaacaaaatgcaatgaaagaaacactggatgaatgaaaagccctgctttgcagcccctcagcatggcaggcctgcagctcatgacccctgcttcctcaccaatgggtcctttctttggactgccatggcaacaagaagcaattcatgataacatttatacgccaagaaaataccaggttgagctgctggaagcagctctggaccacaacaccattgtgtgcttgaacactggctcagggaagacgttcatcgccgtcctgctcaccaaagagctggcccaccagatcaggggcgacctcagtccgcatgcaaaaaggactgtgttcctcgtcaactctgcaaaccaggttgctcaacaagtgtcagctgtcagaactcactcagatctcaaggttggggagtactcaaacctcgaagtgaatgcatcttggacaaaagagagatggagccaagagtttactaagcaccaggttctcattatgacttgctatgtcgccttgaatgttttgaaaaatggttacttatcactgtcagacattaaccttttggtgtttgatgagtgtcatcttgcaattctagaccacccctatcgtgaaattatgaagctctgtgacagttgtccatcatgccctcgaattttgggactaactgcttccattttaaatgggaaatgtgacccagacgaattggaagaaaagattcagaaactggaaaagattctcaagagtggcgctgagaccgcaactgacctggtggtcctggacagatacacttctcagccttgtgagattgtggtggattgcggaccatttactgacagaagtgggctttatgaaagactgctgatggagttagaagaagcacttgactttatcaatgactgtaatgtatctgtacattcaaaggaaagagattctactttgatttccaaacaaatcctctcagactgccgtgcagtgctggtcgtcctgggaccctggtgtgcagataaagtagcggggatgatggtaagagaacttcagaagtacatcaaacatgagcaagaggagctacacaggaagttcttattgtttacagacactctgctaaggaaaatacatgcactgtgtgaagagtacttctcccctgcctcacttgacctgaagtatgtaactcccaaagtcatgaaactgctcgagatcctgcgcaaatacaagccctatgagcgacagcagttcgaaagtgttgagtggtacaataacaggaatcaggataattatgtgtcctggagtgattctgaggacgatgacgatgatgaagaaattgaagaaaaagaaaagccagagacaaattttccttctccatttaccaatattttatgtggaattatttttgtggaaagaagatacacagcagttgtcctaaacagattgataaaggaagctggcaaacaagatccagagctggcttatatcagcagcaactttataactgggcatggcattggaaagaaccagcctcgcagcaagcagatggaggcggagttcagaaagcaagaggaggtacttaggaaatttcgagcacatgagaccaacctgctcattgcaacaagtgttgtagaagagggtgtggacattcccaagtgcaatttggtggttcgttttgatttgcccacagagtatcgttcttacgttcagtctaaaggacgggcacgagcaccgatctctaattatgtaatgttagcagacacagacaaaataaagagctttgaagaagacctcaagacctacaaagctatagaaaagatcttaagaaacaagtgttcaaagtcagtggatggtgctgaggctgacgtccatgctgttgtagatgatgatgatgttttcccgccatatgtactgaggcctgatgatgggggtcctcgagtcacaatcaacactgccattggacacatcaacagatattgtgctcgattaccaagtgatccgtttacgcatctagctcccaaatgtagaacccgagaattgcctgatggtacattttattcaactctttatcttccgattaactcacctcttcgagcctccattgttggtccaccgatgggctgtgtacggctggctgagagagtggtagctctcatctgctgtgaaaaactgcacaaaattggtgaactggatgaacatttgatgccagttgggaaagagactgttaagtatgaagaagaacttgacttacatgatgaagaggagaccagcgttccagggagaccaggatccacaaaacgaaggcagtgctaccccaaagcaattccagagtgcttgagggagagttaccccaaacccgatcaaccctgttacctgtatgtgataggaatggtcttaaccaccccccttcctgatgagctcaacttcaggcggcggaagctctaccctcctgaggacaccaccagatgctttgggatcctgacagccaaacccatacctcagatccctcactttcctgtgtatactcgctctggagaggtcaccatatccatcgagctgaagaagtctggtttcacactgtctcaacaaatgcttgagctggttacgagactgcaccagtacatattctcacacattctccggctcgagaagcctgccctggagtttcaacccgcgggcgctgagtcagcgtactgtgttctacctcttaacgtcgttaatgactccagcactttggacattgactttaaattcatggaggatattgagaagtctgaagctcgtataggcattcccagcactaagtattcaaaggaaacaccgtttgtttttaagttagaagattaccaagatgcagttatcattccaagataccgcaattttgatcagcctcatcgattttatgtagctgatgtgtatactgatcttaccccactcagtaaatttccttcccctgaatatgaaacttttgcagaatattataaaacaaagtataaccttgacctgaccaatctcaaccagccactgctggatgttgaccacacatcttccagactgaaccttctaacccctcggcatttgaatcagaaggggaaagcacttcctctaagcagtgctgaaaagaggaaagccaaatgggaaagtctgcagaacaaacagatactggttccggaactctgtgctatacatccaatcccagcatcactgtggagaaaagcagtttgtctccccagcatactgtatcgccttcactgccttctgactgcggaggagctcagagctcagacagccagcgatgctggcgtaggagtcagatcacttccggccgattttagataccctaacttagacttcgggtggaaaaagtctattgatagcaagtctttcatctcaacctgtaactcctcgttggctgagagtgataattactgtaagcacagcacaactgtagtccctgaaaatgctgcacatcaaggtgctactagaccctccttagaaaaccatgaccaaatgtctgtgaactgcaaaaggttgcccgccgagtcacctgctaagctccaaagtgaggtttcagtggatcttacagcaatcaatggtctttcttacaataaaagccttgccaatggcagttatgatttagttaacagagacttttgccaaggaaatcagctgacttacttcaagcaggaaatacctgtacaaccaactacctcatatcccattcagaatttatacaattatgagaaccagcccacgcccagcaatgaatgtcctctactgagtaataagtaccttgatgggaacgctaacacatctacctcagacggaagccccgcagggtccccaaggcctgccatgatgactgctgttgaagcactggagggcaggacagactctgagcagagcccttctgtggggcactcctcaaggactctcggccccaacccaggactgattcttcaggctttgacactgtcgaacgctagcgatgggtttaacctagagcggcttgagatgcttggcgactccttcttaaagcacgctatcaccacgtatctgttttgcacataccctgatgctcatgagggccgcctttcatatatgagaagcaaaaaggtcagcaactgtaacctgtaccgccttggcaagaagcagggactgcccagccgcatggtggtgtcgatatttgatcctcctgtgaattggcttcctcctggttatgtggtaaaccaagacaaaagtaactcagagaaatgggaaaaggatgaaatgacaaaagactgcttgctggctaatggcaaactgggtgaggactgtgaggaggaggaggaggaggagctggcgtggagggctcccaaggaggaggctgagtatgaagacgacctcctggagtatgaccaggagcacattcagtttatagacagcatgctaatgggctcaggggcctttgtgaagaaaatccctctttcccccttttccacctctgattctgcatatgaatggaaaatgcccaaaaaggcctccctgggcagtgtgccgttttcctcagaccttgaggattttgattacagctcttgggatgcaatgtgctatctggatcctagcaaagccgttgaagaggatgactttgtggtaggtttctggaatccatcagaagaaaactgtggcgtggacacagggaagcagtccatttcttacgacttgcacactgagcagtgcatcgcggacaagagcatagcggactgcgtggaggccctgctgggctgttacttaaccagctgtggtgagagggctgctcagctcttcctctgctcgctggggctgaaggtgctcccagtcatcaaaaggaccagccgggacaaggcctcgtaccctgctcaggagaactcaagcagccaacagaagagcccttcagggagctgtgctgctgcagtcagtccccgctcctctgcagggaaagacttggagtatggctgcttgaagatcccgccaaggtgtatgtttgaccatccagatgcagagaaaaccctgaaccacctcatatctgggtttgaaaattttgaaaagaaaatcaactacatattcaagaataaggcttaccttctgcaggcttttacacatgcctcctaccactacaacactattactgattgttaccagcgcttagaattcctgggagatgcgattttggactacctcataaccaagcacctttatgaagacccacggcagcattctccaggggtcctgactgacctgcgctctgccctggtcaataacaccatctttgcgtcgctggctgtgaagtatgactaccacaagtactttaaagccgtctctcctgagctcttccacgtcattgatgacttcgtgcagtttcagctggagaagaacgagatgcaaggaatggactctgagaaaagttttctgcaaatgtgcctcgttctccggtaagagaattgcttgagatggaaccagaaactgccaagtttagcccagcggagagaacttacgatgggaaggtcagagtcaccgtggaagtggtgggaaaggggaagtttaaaggtgtcggccggagctacaggatcgcaaagtctgctgcagcacgaagagccctccgcagcctcaaagctaacc
//

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]