Typing tool
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Typing tool
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Complete norovirus genomes
| MT409885 | GII.3 | |
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| GII.P12 |
ORF1: 1..5096
ORF2: 5077..6723
ORF3: 6723..7487
LOCUS MT409885 7525 bp RNA linear VRL 01-JUN-2020
DEFINITION Norovirus GII isolate 236-2 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT409885
VERSION MT409885.1
DBLINK BioProject: PRJNA604000
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7525)
AUTHORS Ruelle,S.B., Hirneisen,K.A. and Silva,A.J.
TITLE Direct Submission
JOURNAL Submitted (29-APR-2020) Microbiology, FDA/ORA/PSFFL, 19701
Fairchild, Irvine, CA 92612, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC Genomics Workbench v. 12
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7525
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="236-2"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="04-Dec-2015"
/note="genotype: GII.P12-GII.3"
gene <1..5096
/gene="ORF1"
CDS <1..5096
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QJF54135.1"
/translation="MASNDASAAAAANSNNDNAKSSSDGVLSSMAVTFKRALGARQKQ
PPPREIPQRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVWQPDET
NTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLA
KVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWL
CRRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKVR
PLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLA
VELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKK
EEANELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLSTKS
ASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAK
KIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPL
TLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAK
RDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASG
LLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLLDTMRVGKQLKDVKTMSE
LKQALKNVAIKSCQIVYGGCTYRLESDGKGDVRVDRVQNATVQTNNELAGALHHLRCA
RIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEEIASKDGCPK
PQDGEEFVISSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
SIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTG
SEIRKRNPDDFKPKGKLWADDDRSVDYNERLSFEAPPSIWSRIVNFGSGWGFWVSPSL
FITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTV
VTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCG
CPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPG
SAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRG
RPPKPSVLEAAKKTIVNVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNG
ESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLAT
MIRCARAFGGLMEELKAHCVTLPVRVGMNMNEDGPIIFERHSRYKYHYDADYSRWDST
QQRAVLAAALEIMVKFSPEPHLAQKVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQ
WNSIAHWLLTLCALSEVTNLSPDIVQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEY
GLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNH
EDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPM
FRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..986
/gene="ORF1"
/product="p48"
mat_peptide 987..2084
/gene="ORF1"
/product="NTPase"
mat_peptide 2085..2621
/gene="ORF1"
/product="p22"
mat_peptide 2622..3020
/gene="ORF1"
/product="VPg"
mat_peptide 3021..3563
/gene="ORF1"
/product="Pro"
mat_peptide 3564..5093
/gene="ORF1"
/product="RdRp"
gene 5077..6723
/gene="ORF2"
CDS 5077..6723
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QJF54136.1"
/translation="MKMASNDATPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLVAMLYTPLRANNSGDDVFTVSCRVLTRPSPEFSFNFLVPP
TVESKTKPFTLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDSTTRAHEAKVDTTAGRFTPKLGSLEISTESDDFDQNQP
TRFTPVGIGVDNEADFQQWSLPDYSGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
GRSNGILDCLVPQEWVQHFYQESAPAQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRVQ"
gene 6723..7487
/gene="ORF3"
CDS 6723..7487
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QJF54137.1"
/translation="MAGAFIAGLAGDIFTNTVGSLVNAGANAINQKVDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPSATSTTSMSGGFTNQAVHRTTPNFKMNQAPRSTPSSGSSVRSLSTQVTSLSS
HSSGSSRSSGSTVASSLPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 agatggcgtc taacgacgct tccgctgccg ctgctgctaa tagcaacaac gacaacgcaa
61 aatcttcaag tgacggagtg ctctctagca tggctgtcac ttttaaacga gccctcgggg
121 cgcggcaaaa acagcctccc ccgagggaaa taccacaaag gcctccacgg ccacccaccc
181 cagaactggt caaaaagatc cctcctcccc cacccaatgg ggaggatgag ctagtggtct
241 cttatagcgc caaagatggc gtttctggtt tgcctgaact caccactgtc tggcaaccgg
301 atgagaccaa cacggcattc agtgttcccc ctctcaacca aagggagaac agggacgcca
361 aggagccgct gaccggaaca atcctggaaa tgtgggacgg ggagatctat cattacggtc
421 tgtatgtgga gcgaggcctt gtacttggtg tgcacaaacc accagctgcc atcagcctcg
481 ccaaggttga actagcacca ctctctctat tttggaggcc agtgtacaca ccacagtatc
541 tcatctctcc agacactctt aggagactgc atggagagtc gttcccctac acagcctttg
601 acaacaactg ctatgccttc tgttgttggg ttctggacct aaacgactcg tggttgtgca
661 ggagaatgat ccagagaaca actggcttct tcagacctta ccaagaatgg aacaggaaac
721 ccctccccac catggatgac tctaaattga aaaaggtagc caacatattc ttgtgtgcgc
781 tatcttcgct attcactagg cccatcaaag acataatagg aaaggtaaga ccgctcaaca
841 tccttaacat cctggcctca tgtgattgga cttttgcagg catagtggaa tctttgatcc
901 tcttggcaga gctctttgga gttttctgga cacccccaga tgtgtctgcg atgatcgccc
961 ccttactagg tgactacgaa ctgcaggggc ctgaggacct tgcagtggaa ctcgtaccag
1021 tagtgatggg agggattggt ttggtgttag gattcaccaa agagaagatc ggaaaaatgt
1081 tgtcatccgc cgcttccacc ttaagagctt gtaaagacct tggtgcatac ggactggaaa
1141 tcctaaaatt ggtcatgaaa tggttcttcc caaagaaaga ggaagcaaat gagctagcta
1201 tggtgaggtc catcgaggat gcggtgctgg acctcgaagc aattgagaac aaccacatga
1261 ctgccctcct caaagacaaa gacagcttgg caacctacat gaggaccctt gacctcgagg
1321 aggagaaagc caggaagctt tcaaccaagt ctgcttcacc tgacatcgtg ggcacaatca
1381 acgctcttct ggcgagaatc gctgctgcac gttccctggt gcatcgggcg aaagaggagc
1441 tctccagcag accaagacct gttgttgtta tgatatcagg taggccaggg atagggaaaa
1501 ctcaccttgc cagggagcta gccaagaaga tcgcagcttc actcacaggg gaccagcgcg
1561 tgggtctcat cccccgcaat ggcgttgacc actgggatgc atacaaggga gaaagagtcg
1621 tcctatggga cgattatgga atgagcaatc ccatccacga cgccctcagg ctacaggaac
1681 ttgctgacac ctgccccctt acgctaaact gtgacaggat tgagaacaaa ggaaaggtct
1741 ttgacagtga tgccataatc atcaccacta atctagccaa cccagcacca ttggactatg
1801 tcaactttga agcatgctcg aggcgcattg acttcctcgt gtacgcagaa gcccctgagg
1861 tcgagaaagc aaagcgtgat ttcccaggtc aacctgacat gtggaagaac gcatttagct
1921 ctgacttctc gcacataaaa ctggcgctgg ctccgcaagg tggtttcgac aagaacggaa
1981 acaccccaca cgggaaaggc gtcatgaaaa ccctcaccac tggttccctc atcgcccgag
2041 catcagggct actccatgag aggttggatg agtacgagct gcagggccca actcccacca
2101 cctttaattt tgaccgcaac aaggtgcttg cgttcagaca acttgctgcc gaaaacaagt
2161 atggattgtt ggacacaatg agagttggaa aacagctcaa ggatgttaag accatgtcag
2221 agctcaaaca ggcactcaag aatgtcgcaa tcaagagttg tcagatagtg tatggtggct
2281 gcacctacag gcttgagtct gatggcaagg gtgatgtaag agttgacaga gttcagaacg
2341 ccactgtaca gaccaacaat gagcttgccg gcgcactaca ccatcttagg tgcgccagaa
2401 tcagatatta tgtcaagtgt gttcaggagg ccctgtattc catcatccaa atcgctgggg
2461 ctgcatttgt taccacgcgc attgtcaagc gcatgaacat acaagatctc tggtccaaac
2521 cacaggtgga ggatacagag gaaatcgcta gcaaggatgg gtgcccaaaa ccccaggatg
2581 gtgaagagtt tgttatctca tccgacgaca tcaaaaccga gggcaagaaa gggaagaaca
2641 agtctggccg tggcaagaaa cacacagcat tttcaagtaa aggtctcagt gatgaagagt
2701 acgatgagta caaaagaatt agagaagaaa gaaatggcaa atactccata gaggaatacc
2761 tccaggacag agacaggtat tatgaggagg tggccatcgc cagggcaacc gaagaggact
2821 tctgtgaaga agaagaggcc aagatccgac agaggatctt caggccaaca aggaaacaac
2881 gcaaagagga gagagcctct ctcggtttgg tcacaggttc tgaaatcagg aagaggaacc
2941 cagacgactt caagcctaaa ggaaagctgt gggctgatga tgacaggagt gttgactaca
3001 atgagagact cagttttgaa gccccaccaa gcatctggtc gaggatagtc aactttggct
3061 caggttgggg tttttgggtt tcccccagcc tgttcataac atcaactcat gtcatacccc
3121 agggcgcaca ggagttcttt ggtgtaccca tcaaacaaat ccagatacac aaatcaggtg
3181 aattctgccg cttgaggttt ccaaagccga tcagaactga cgtgacaggc atgatcttag
3241 aagaaggtgc acccgaaggg accgtggtca cattactcat caaaagacca actggagagc
3301 tcatgcccct ggcagccaga atgggaaccc acgcaaccat gaagatacaa gggcgcactg
3361 tcggaggtca aatgggcatg ctcctaacag ggtccaacgc caagagtatg gacctgggca
3421 ccacaccagg tgactgtggc tgcccctaca tttacaagag ggggaatgac tacgtggtca
3481 ttggggtcca tacagctgcc gcccgtggag gaaacactgt catttgtgcc acccagggga
3541 gcgagggaga agccacactt gaaggcggtg atagcaaggg gacctactgc ggtgcaccaa
3601 tcttaggtcc aggaagtgcc ccaaaactca gcaccaagac caagttctgg aggtcatcca
3661 cggcaccact cccacctggt acctatgaac cagcttacct cggtggcaag gaccccagag
3721 ttaagggtgg cccttcactg caacaagtta tgagggatca actgaaacca ttcactgagc
3781 ctaggggtag gccaccaaaa ccaagtgtgc tagaagctgc caagaaaacc atcgtcaatg
3841 tcctagaaca gacaattgac ccacctcaaa agtggtcgtt tgcgcaggca tgcgcatccc
3901 ttgacaagac cacttctagc ggtcatccgc accacatgcg gaagaatgac tgctggaacg
3961 gggagtcctt cacaggaaaa ttggcagacc aggcttccaa ggccaacctg atgtttgagg
4021 agggaaagaa catgacccca gtttacacgg gtgcgcttaa ggatgagctg gtcaagactg
4081 acaagattta tggtaagatc aaaaagaggc ttctctgggg ttctgacctg gcgaccatga
4141 ttcggtgcgc tcgagcattc gggggtctga tggaggaact caaagcacat tgtgtcacac
4201 tacctgttag ggtgggtatg aatatgaatg aggatggccc tatcatcttt gagagacact
4261 ccagatataa atatcattat gatgctgatt actcccggtg ggattcaaca caacaaagag
4321 ctgtgttggc ggcagcctta gaaatcatgg tcaagttttc cccagagccg cacctggccc
4381 aaaaggttgc agaagacctt ctttctccca gcgtgatgga cgtgggtgat ttcaaaatat
4441 caatcaatga gggtctcccc tccggagtgc cctgcacctc ccaatggaat tccatcgccc
4501 actggctcct cactctctgt gcactctccg aggttacaaa cctgtcccct gacattgttc
4561 aggctaactc tctcttttct ttctacggtg atgatgaaat tgtgagtaca gacataaaat
4621 tggacccaga aaaactgaca gcaaaactca aggaatacgg gttgaaaccg acccgccctg
4681 acaaaactga agggcctctc gtcatttccg aagacctgaa tggcctaacc ttcctgcgga
4741 ggaccgtgac tcgcgaccca gcaggttggt ttggaaagtt ggaacagagc tcaatactca
4801 ggcaaatgta ctggactagg ggccccaacc atgaagatcc atctgaaaca atgataccac
4861 actcccagag gcccatacaa ttgatgtcct tgctgggaga ggcagcactc cacggcccag
4921 cattctacag caaaatcagt aaactggtca ttgcagagtt gaaggagggt ggcatggatt
4981 tttacgtgcc aagacaagag ccaatgttca gatggatgag attctcggat ctgagcacgt
5041 gggagggcga tcgcaatctg gctcccagtt ttgtgaatga agatggcgtc gaatgacgcc
5101 actccatcta atgatggtgc cgccggcctc gtcccagaga tcaacaatga ggcaatggcg
5161 ctagaaccag tggcgggtgc agcgatagca gcacccctca ccggccagca aaatataatt
5221 gatccctgga ttatgaataa ttttgtgcaa gcacctggtg gtgagttcac agtgtctcct
5281 aggaattccc ctggtgaagt gctcctcaat ttggaattgg gcccagagat aaacccctat
5341 ctggcccatc ttgctagaat gtataatggt tatgcaggtg ggtttgaagt gcaggtggtc
5401 ctggctggaa atgcgtttac agcaggaaag ataatctttg cagctatacc ccctaacttc
5461 ccaattgaca atctaagtgc agcacagatc acaatgtgtc cacacgtgat tgtggatgtc
5521 aggcagttgg aaccggtcaa cctcccgatg cctgacgttc gtaacaactt cttccactac
5581 aaccaagggt ctgattcgag attgcgcttg gttgcaatgc tgtatacacc tcttagggca
5641 aataactctg gggatgatgt tttcactgtg tcttgtagag tgctgactag acctagtcct
5701 gaattttcat ttaacttcct tgtgcccccc actgtggaat caaagacaaa accctttacc
5761 ctcccaattc tgactatctc tgaaatgtct aattctaggt ttccagtgcc gattgattct
5821 ctgcacacca gcccaactga gaatattgtt gtccagtgtc agaatggacg cgtcactctt
5881 gatggtgagt tgatgggcac cactcagctc ttacctagtc aaatctgtgc tttcaggggc
5941 gtgctcacta gatcaacaag cagggctagt gaccaggccg acacagcaac ccctagattg
6001 tttaattatt attggcacat acaattggat aatctaaatg ggactcctta tgatcctgca
6061 gaagacatac caggccccct agggacacca gatttccgag gcaaagtctt tggcgtggcc
6121 agccaaagaa accccgacag tacaactaga gcacatgaag caaaggtgga cacaacagct
6181 ggtcgcttca ccccaaaact aggctcatta gagatatcca ctgaatctga tgactttgac
6241 caaaaccaac caacaagatt caccccagtt ggcattgggg ttgacaacga ggcagacttc
6301 caacaatggt ccttaccaga ctactctggc cagttcactc acaacatgaa cttagcccca
6361 gctgttgctc ccaatttccc tggtgagcag ctccttttct tccgctcaca gttaccatct
6421 tctggtgggc gatccaatgg gattctagac tgcctggtcc cccaagaatg ggtccagcac
6481 ttctaccaag aatcagcccc cgcccaaacc caggtggctc tggttagata tgtcaaccct
6541 gacactggta gagtgttgtt tgaggccaag ctgcacaaat taggtttcat gactatagct
6601 aagaatggtg actctccaat aactgtcccc ccaaatggat actttaggtt tgaatcttgg
6661 gtgaacccat tttatacact tgcccccatg ggaactggga acgggcgtag aagagttcaa
6721 taatggctgg tgcttttata gcaggattag ctggtgatat attcacaaac actgtagggt
6781 ctctagttaa tgcaggggct aatgctatta atcaaaaagt tgattttgaa aataacaaat
6841 acttgcaaaa tgcttccttc aatcatgata aggaaatgtt aaatgcacag attgaggcaa
6901 caaagaggtt acaggctgac atgattgcta tcaaacaggg ggttttgacc gctggcggct
6961 tttcccccac tgatgcagct cgcggggcaa ttaacgcccc catgacaaaa gtcctagatt
7021 ggaatggaac aaggtactgg gcaccaagtg ccacctctac aacctcgatg tcgggtggct
7081 tcacaaacca ggctgtgcac agaaccacgc caaattttaa aatgaaccag gcccccagat
7141 ccacacccag cagtgggtct tcagtgaggt cactctcaac ccaagtcact agtctgagct
7201 cacactcgtc cgggtcgtct cgatctagcg ggtctacagt tgctagctca ttaccatcct
7261 ctaacaggac tagggactgg gtcaatcagc aaaatttcaa tttggaacca cacatgcctg
7321 ggtcgcttag gacggctttt gtcactccac catctagtac agcctctagt tcaggcactg
7381 tctcaaccgt gcccaaaaat gttttggact cctggacatc tgcgtttaac acgcgcagac
7441 agccgctatt cgcacacctt cgtagaaggg gggagtcaaa tgtttagtga aaaggttatt
7501 ttaaatttga tttaaatttg atttg
//