2024-05-04 21:28:56, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS XM_039113362 6202 bp mRNA linear ROD 11-JUN-2023 DEFINITION PREDICTED: Rattus norvegicus dicer 1 ribonuclease III (Dicer1), transcript variant X6, mRNA. ACCESSION XM_039113362 VERSION XM_039113362.1 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 mRNA and 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..6202 /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..6202 /gene="Dicer1" /note="dicer 1 ribonuclease III; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 mRNA, 21 ESTs, 4 long SRA reads, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 11 samples with support for all annotated introns" /db_xref="GeneID:299284" /db_xref="RGD:1309381" CDS 379..6045 /gene="Dicer1" /codon_start=1 /product="endoribonuclease Dicer isoform X2" /protein_id="XP_038969290.1" /db_xref="GeneID:299284" /db_xref="RGD:1309381" /translation="
MSECSSDSSNTALADIKTVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGDLSPHAKRTVFLVNSANQVAQQVSAVRTHSDLKVGEYSNLEVNASWTKERWSQEFTKHQVLIMTCYVALNVLKNGYLSLSDINLLVFDECHLAILDHPYREIMKLCDSCPSCPRILGLTASILNGKCDPDELEEKIQKLEKILKSGAETATDLVVLDRYTSQPCEIVVDCGPFTDRSGLYERLLMELEEALDFINDCNVSVHSKERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYIKHEQEELHRKFLLFTDTLLRKIHALCEEYFSPASLDLKYVTPKVMKLLEILRKYKPYERQQFESVEWYNNRNQDNYVSWSDSEDDDDDEEIEEKEKPETNFPSPFTNILCGIIFVERRYTAVVLNRLIKEAGKQDPELAYISSNFITGHGIGKNQPRSKQMEAEFRKQEEVLRKFRAHETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRARAPISNYVMLADTDKIKSFEEDLKTYKAIEKILRNKCSKSVDGAEADVHAVVDDDDVFPPYVLRPDDGGPRVTINTAIGHINRYCARLPSDPFTHLAPKCRTRELPDGTFYSTLYLPINSPLRASIVGPPMGCVRLAERVVALICCEKLHKIGELDEHLMPVGKETVKYEEELDLHDEEETSVPGRPGSTKRRQCYPKAIPECLRESYPKPDQPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFTLSQQMLELVTRLHQYIFSHILRLEKPALEFQPAGAESAYCVLPLNVVNDSSTLDIDFKFMEDIEKSEARIGIPSTKYSKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQKGKALPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTAEELRAQTASDAGVGVRSLPADFRYPNLDFGWKKSIDSKSFISTCNSSLAESDNYCKHSTTVVPENAAHQGATRPSLENHDQMSVNCKRLPAESPAKLQSEVSVDLTAINGLSYNKSLANGSYDLVNRDFCQGNQLTYFKQEIPVQPTTSYPIQNLYNYENQPTPSNECPLLSNKYLDGNANTSTSDGSPAGSPRPAMMTAVEALEGRTDSEQSPSVGHSSRTLGPNPGLILQALTLSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKQGLPSRMVVSIFDPPVNWLPPGYVVNQDKSNSEKWEKDEMTKDCLLANGKLGEDCEEEEEEELAWRAPKEEAEYEDDLLEYDQEHIQFIDSMLMGSGAFVKKIPLSPFSTSDSAYEWKMPKKASLGSVPFSSDLEDFDYSSWDAMCYLDPSKAVEEDDFVVGFWNPSEENCGVDTGKQSISYDLHTEQCIADKSIADCVEALLGCYLTSCGERAAQLFLCSLGLKVLPVIKRTSRDKASYPAQENSSSQQKSPSGSCAAAVSPRSSAGKDLEYGCLKIPPRCMFDHPDAEKTLNHLISGFENFEKKINYIFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMRPLIEKFSANVPRSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLKANQPLVPNS"
misc_feature 433..1005 /gene="Dicer1" /note="DEXH-box helicase domain of endoribonuclease Dicer; Region: DEXHc_dicer; cd18034" /db_xref="CDD:350792" misc_feature order(589..594,661..666,739..741,745..750,757..759, 832..840) /gene="Dicer1" /note="nucleic acid binding site [nucleotide binding]; other site" /db_xref="CDD:350792" misc_feature 811..822 /gene="Dicer1" /note="DEAD box helicase motif; other site" /db_xref="CDD:350792" misc_feature 1099..1383 /gene="Dicer1" /note="Partner-binding domain of the endoribonuclease Dicer; Region: Dicer_PBD; cd15903" /db_xref="CDD:277191" misc_feature order(1114..1119,1126..1128,1132..1137,1312..1317, 1324..1329,1336..1338,1345..1350,1357..1359) /gene="Dicer1" /note="Trbp binding interface [polypeptide binding]; other site" /db_xref="CDD:277191" misc_feature 1402..1980 /gene="Dicer1" /note="C-terminal helicase domain of the endoribonuclease Dicer; Region: SF2_C_dicer; cd18802" /db_xref="CDD:350189" misc_feature order(1633..1641,1849..1851,1906..1908,1912..1914) /gene="Dicer1" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:350189" misc_feature order(1861..1863,1867..1869,1942..1944,1948..1950) /gene="Dicer1" /note="ATP binding site [chemical binding]; other site" /db_xref="CDD:350189" misc_feature 2176..2442 /gene="Dicer1" /note="Dicer dimerization domain; Region: Dicer_dimer; pfam03368" /db_xref="CDD:427264" misc_feature 2944..3312 /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(3133..3135,3172..3174,3190..3192,3202..3204, 3256..3258,3280..3282,3286..3288) /gene="Dicer1" /note="nucleic acid-binding interface [nucleotide binding]; other site" /db_xref="CDD:239209" misc_feature 4174..>4449 /gene="Dicer1" /note="Ribonuclease III family; Region: RIBOc; smart00535" /db_xref="CDD:197778" misc_feature order(4225..4230,4237..4242,4249..4251,4258..4263, 4270..4275,4279..4287,4315..4317) /gene="Dicer1" /note="dimerization interface [polypeptide binding]; other site" /db_xref="CDD:238333" misc_feature 5320..5814 /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(5380..5385,5392..5397,5404..5406,5413..5418, 5425..5430,5434..5442,5470..5472,5734..5736,5767..5769) /gene="Dicer1" /note="dimerization interface [polypeptide binding]; other site" /db_xref="CDD:238333" misc_feature order(5380..5382,5389..5391,5401..5403,5704..5706, 5713..5715) /gene="Dicer1" /note="active site" /db_xref="CDD:238333" misc_feature order(5389..5391,5704..5706,5713..5715) /gene="Dicer1" /note="metal binding site [ion binding]; metal-binding site" /db_xref="CDD:238333" misc_feature 5827..6015 /gene="Dicer1" /note="double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins; Region: DSRM_DICER; cd10843" /db_xref="CDD:380680" misc_feature order(5827..5832,5836..5841,5848..5853,5860..5865, 5875..5877,5890..5898,5902..5904,5908..5910,5959..5970, 5977..5979) /gene="Dicer1" /note="putative RNA binding site [nucleotide binding]; other site" /db_xref="CDD:380680" ORIGIN
cgggaacgaggcgacggcgagcggcaggaaatggcggcggcggcggcggcgccgggcggcaccgggaggcctgggctgtgacgcgcgcgccggagcggggtccgatggttctggaaggcccgcggcgcccagtgctgcagagatcgtgcttggagctctggaggaaaccttctgtagttagtgcactggaggctcaaggttccacacactgcagcaggagaagggaattctgaaacacaaaggaaaagggatttcttctgatttcaacaggttacctagggtatgcataaatacagacttggaaactgaaagaacttagagtcagcatttcgagagctgaagcttgggcatgctgtgattttccaataagctatcacaatgtcagaatgcagttcagacagcagcaacacagcgctcgcagacattaaaacggttgagctgctggaagcagctctggaccacaacaccattgtgtgcttgaacactggctcagggaagacgttcatcgccgtcctgctcaccaaagagctggcccaccagatcaggggcgacctcagtccgcatgcaaaaaggactgtgttcctcgtcaactctgcaaaccaggttgctcaacaagtgtcagctgtcagaactcactcagatctcaaggttggggagtactcaaacctcgaagtgaatgcatcttggacaaaagagagatggagccaagagtttactaagcaccaggttctcattatgacttgctatgtcgccttgaatgttttgaaaaatggttacttatcactgtcagacattaaccttttggtgtttgatgagtgtcatcttgcaattctagaccacccctatcgtgaaattatgaagctctgtgacagttgtccatcatgccctcgaattttgggactaactgcttccattttaaatgggaaatgtgacccagacgaattggaagaaaagattcagaaactggaaaagattctcaagagtggcgctgagaccgcaactgacctggtggtcctggacagatacacttctcagccttgtgagattgtggtggattgcggaccatttactgacagaagtgggctttatgaaagactgctgatggagttagaagaagcacttgactttatcaatgactgtaatgtatctgtacattcaaaggaaagagattctactttgatttccaaacaaatcctctcagactgccgtgcagtgctggtcgtcctgggaccctggtgtgcagataaagtagcggggatgatggtaagagaacttcagaagtacatcaaacatgagcaagaggagctacacaggaagttcttattgtttacagacactctgctaaggaaaatacatgcactgtgtgaagagtacttctcccctgcctcacttgacctgaagtatgtaactcccaaagtcatgaaactgctcgagatcctgcgcaaatacaagccctatgagcgacagcagttcgaaagtgttgagtggtacaataacaggaatcaggataattatgtgtcctggagtgattctgaggacgatgacgatgatgaagaaattgaagaaaaagaaaagccagagacaaattttccttctccatttaccaatattttatgtggaattatttttgtggaaagaagatacacagcagttgtcctaaacagattgataaaggaagctggcaaacaagatccagagctggcttatatcagcagcaactttataactgggcatggcattggaaagaaccagcctcgcagcaagcagatggaggcggagttcagaaagcaagaggaggtacttaggaaatttcgagcacatgagaccaacctgctcattgcaacaagtgttgtagaagagggtgtggacattcccaagtgcaatttggtggttcgttttgatttgcccacagagtatcgttcttacgttcagtctaaaggacgggcacgagcaccgatctctaattatgtaatgttagcagacacagacaaaataaagagctttgaagaagacctcaagacctacaaagctatagaaaagatcttaagaaacaagtgttcaaagtcagtggatggtgctgaggctgacgtccatgctgttgtagatgatgatgatgttttcccgccatatgtactgaggcctgatgatgggggtcctcgagtcacaatcaacactgccattggacacatcaacagatattgtgctcgattaccaagtgatccgtttacgcatctagctcccaaatgtagaacccgagaattgcctgatggtacattttattcaactctttatcttccgattaactcacctcttcgagcctccattgttggtccaccgatgggctgtgtacggctggctgagagagtggtagctctcatctgctgtgaaaaactgcacaaaattggtgaactggatgaacatttgatgccagttgggaaagagactgttaagtatgaagaagaacttgacttacatgatgaagaggagaccagcgttccagggagaccaggatccacaaaacgaaggcagtgctaccccaaagcaattccagagtgcttgagggagagttaccccaaacccgatcaaccctgttacctgtatgtgataggaatggtcttaaccaccccccttcctgatgagctcaacttcaggcggcggaagctctaccctcctgaggacaccaccagatgctttgggatcctgacagccaaacccatacctcagatccctcactttcctgtgtatactcgctctggagaggtcaccatatccatcgagctgaagaagtctggtttcacactgtctcaacaaatgcttgagctggttacgagactgcaccagtacatattctcacacattctccggctcgagaagcctgccctggagtttcaacccgcgggcgctgagtcagcgtactgtgttctacctcttaacgtcgttaatgactccagcactttggacattgactttaaattcatggaggatattgagaagtctgaagctcgtataggcattcccagcactaagtattcaaaggaaacaccgtttgtttttaagttagaagattaccaagatgcagttatcattccaagataccgcaattttgatcagcctcatcgattttatgtagctgatgtgtatactgatcttaccccactcagtaaatttccttcccctgaatatgaaacttttgcagaatattataaaacaaagtataaccttgacctgaccaatctcaaccagccactgctggatgttgaccacacatcttccagactgaaccttctaacccctcggcatttgaatcagaaggggaaagcacttcctctaagcagtgctgaaaagaggaaagccaaatgggaaagtctgcagaacaaacagatactggttccggaactctgtgctatacatccaatcccagcatcactgtggagaaaagcagtttgtctccccagcatactgtatcgccttcactgccttctgactgcggaggagctcagagctcagacagccagcgatgctggcgtaggagtcagatcacttccggccgattttagataccctaacttagacttcgggtggaaaaagtctattgatagcaagtctttcatctcaacctgtaactcctcgttggctgagagtgataattactgtaagcacagcacaactgtagtccctgaaaatgctgcacatcaaggtgctactagaccctccttagaaaaccatgaccaaatgtctgtgaactgcaaaaggttgcccgccgagtcacctgctaagctccaaagtgaggtttcagtggatcttacagcaatcaatggtctttcttacaataaaagccttgccaatggcagttatgatttagttaacagagacttttgccaaggaaatcagctgacttacttcaagcaggaaatacctgtacaaccaactacctcatatcccattcagaatttatacaattatgagaaccagcccacgcccagcaatgaatgtcctctactgagtaataagtaccttgatgggaacgctaacacatctacctcagacggaagccccgcagggtccccaaggcctgccatgatgactgctgttgaagcactggagggcaggacagactctgagcagagcccttctgtggggcactcctcaaggactctcggccccaacccaggactgattcttcaggctttgacactgtcgaacgctagcgatgggtttaacctagagcggcttgagatgcttggcgactccttcttaaagcacgctatcaccacgtatctgttttgcacataccctgatgctcatgagggccgcctttcatatatgagaagcaaaaaggtcagcaactgtaacctgtaccgccttggcaagaagcagggactgcccagccgcatggtggtgtcgatatttgatcctcctgtgaattggcttcctcctggttatgtggtaaaccaagacaaaagtaactcagagaaatgggaaaaggatgaaatgacaaaagactgcttgctggctaatggcaaactgggtgaggactgtgaggaggaggaggaggaggagctggcgtggagggctcccaaggaggaggctgagtatgaagacgacctcctggagtatgaccaggagcacattcagtttatagacagcatgctaatgggctcaggggcctttgtgaagaaaatccctctttcccccttttccacctctgattctgcatatgaatggaaaatgcccaaaaaggcctccctgggcagtgtgccgttttcctcagaccttgaggattttgattacagctcttgggatgcaatgtgctatctggatcctagcaaagccgttgaagaggatgactttgtggtaggtttctggaatccatcagaagaaaactgtggcgtggacacagggaagcagtccatttcttacgacttgcacactgagcagtgcatcgcggacaagagcatagcggactgcgtggaggccctgctgggctgttacttaaccagctgtggtgagagggctgctcagctcttcctctgctcgctggggctgaaggtgctcccagtcatcaaaaggaccagccgggacaaggcctcgtaccctgctcaggagaactcaagcagccaacagaagagcccttcagggagctgtgctgctgcagtcagtccccgctcctctgcagggaaagacttggagtatggctgcttgaagatcccgccaaggtgtatgtttgaccatccagatgcagagaaaaccctgaaccacctcatatctgggtttgaaaattttgaaaagaaaatcaactacatattcaagaataaggcttaccttctgcaggcttttacacatgcctcctaccactacaacactattactgattgttaccagcgcttagaattcctgggagatgcgattttggactacctcataaccaagcacctttatgaagacccacggcagcattctccaggggtcctgactgacctgcgctctgccctggtcaataacaccatctttgcgtcgctggctgtgaagtatgactaccacaagtactttaaagccgtctctcctgagctcttccacgtcattgatgacttcgtgcagtttcagctggagaagaacgagatgcaaggaatggactctgagcttaggagatccgaggaggatgaggagaaagaagaggatattgaagtccccaaggccatgggagacatttttgagtctcttgctggtgccatttatatggacagtgggatgtccctggaggtggtctggcaggtgtactatccgatgatgcggcctctaatagaaaagttttctgcaaatgtgcctcgttctccggtaagagaattgcttgagatggaaccagaaactgccaagtttagcccagcggagagaacttacgatgggaaggtcagagtcaccgtggaagtggtgggaaaggggaagtttaaaggtgtcggccggagctacaggatcgcaaagtctgctgcagcacgaagagccctccgcagcctcaaagctaaccagcctctggttcctaacagctgaagcttccagactcacaggcggcaaggcagtgaccagaaccatagcagcacaccacaaaggatgactcaagccgacacagagcagaaagattgacggcagaacttaaagtttgataatgagatagataacagaataaaacctttaatatgtgtataaa
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DBCLS
This page is licensed under a
Creative Commons Attribution 4.0 International License (CC BY 4.0).
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.
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