Typing tool
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Typing tool
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Complete norovirus genomes
| MT409886 | GII.3 | |
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| GII.P12 |
ORF1: 1..5088
ORF2: 5069..6715
ORF3: 6715..7479
LOCUS MT409886 7488 bp RNA linear VRL 01-JUN-2020
DEFINITION Norovirus GII isolate 236-3 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT409886
VERSION MT409886.1
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 7488)
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..7488
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="236-3"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="03-Dec-2015"
/note="genotype: GII.P12-GII.3"
gene <1..5088
/gene="ORF1"
CDS <1..5088
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QJF54138.1"
/translation="SNDASAAAAANSNNDNAKSSSDGVLSSMAVTFKRALGARQKQPP
PREIPQRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVWQPDETNT
AFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV
ELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLCR
RMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKVRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLLDTMRVGKQLKDVKTMSELK
QALKNVAIKSCQIVYGGCTYRLESDGKGDVRVDRVQNATVQTNNELAGALHHLRCARI
RYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEEIASKDGCPKPQ
DGEEFVISSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNERLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSA
PKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGRP
PKPSVLEAAKKTIVNVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMEELKAHCVTLPVRVGMNMNEDGPIIFERHSRYKYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQKVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDIVQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGL
KPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHED
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..978
/gene="ORF1"
/product="p48"
mat_peptide 979..2076
/gene="ORF1"
/product="NTPase"
mat_peptide 2077..2613
/gene="ORF1"
/product="p22"
mat_peptide 2614..3012
/gene="ORF1"
/product="VPg"
mat_peptide 3013..3555
/gene="ORF1"
/product="Pro"
mat_peptide 3556..5085
/gene="ORF1"
/product="RdRp"
gene 5069..6715
/gene="ORF2"
CDS 5069..6715
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QJF54139.1"
/translation="MKMASNDATPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLVAMLYTPLRANNSGDDVFTVSCRVLTRPSPEFSFNFLVPP
TVESKTKPFTLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDSTTRAHEAKVDTTAGRFTPKLGSLEISTESDDFDQNQP
TRFTPVGIGVDNEADFQQWSLPDYSGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
GRSNGILDCLVPQEWVQHFYQESAPAQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRVQ"
gene 6715..7479
/gene="ORF3"
CDS 6715..7479
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QJF54140.1"
/translation="MAGAFIAGLAGDIFTNTVGSLVNAGANAINQKVDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPSATSTTSMSGGFTNQAVHRTTPNFKMNQAPRSTPSSGSSVRSLSTQVTSLSS
HSSGSSRSSGSTVASSLPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgctgct aatagcaaca acgacaacgc aaaatcttca
61 agtgacggag tgctctctag catggctgtc acttttaaac gagccctcgg ggcgcggcaa
121 aaacagcctc ccccgaggga aataccacaa aggcctccac ggccacccac cccagaactg
181 gtcaaaaaga tccctcctcc cccacccaat ggggaggatg agctagtggt ctcttatagc
241 gccaaagatg gcgtttctgg tttgcctgaa ctcaccactg tctggcaacc ggatgagacc
301 aacacggcat tcagtgttcc ccctctcaac caaagggaga acagggacgc caaggagccg
361 ctgaccggaa caatcctgga aatgtgggac ggggagatct atcattacgg tctgtatgtg
421 gagcgaggcc ttgtacttgg tgtgcacaaa ccaccagctg ccatcagcct cgccaaggtt
481 gaactagcac cactctctct attttggagg ccagtgtaca caccacagta tctcatctct
541 ccagacactc ttaggagact gcatggagag tcgttcccct acacagcctt tgacaacaac
601 tgctatgcct tctgttgttg ggttctggac ctaaacgact cgtggttgtg caggagaatg
661 atccagagaa caactggctt cttcagacct taccaagaat ggaacaggaa acccctccct
721 accatggatg actctaaatt gaaaaaggta gccaacatat tcttgtgtgc gctatcttcg
781 ctattcacta ggcccatcaa agacataata ggaaaggtaa gaccgctcaa catccttaac
841 atcctggcct catgtgattg gacttttgca ggcatagtgg aatctttgat cctcttggca
901 gagctctttg gagttttctg gacaccccca gatgtgtctg cgatgatcgc ccccttacta
961 ggtgactacg aactgcaggg gcctgaggac cttgcagtgg aactcgtacc agtagtgatg
1021 ggagggattg gtttggtgtt aggattcacc aaagagaaga tcggaaaaat gttgtcatcc
1081 gccgcttcca ccttaagagc ttgtaaagac cttggtgcat acggactgga aatcctaaaa
1141 ttggtcatga aatggttctt cccaaagaaa gaggaagcaa atgagctagc tatggtgagg
1201 tccatcgagg atgcggtgct ggacctcgaa gcaattgaga acaaccacat gactgccctc
1261 ctcaaagaca aagacagctt ggcaacctac atgaggaccc ttgacctcga ggaggagaaa
1321 gccaggaagc tttcaaccaa gtctgcttca cctgacatcg tgggcacaat caacgctctt
1381 ctggcgagaa tcgctgctgc acgttccctg gtgcatcggg cgaaagagga gctctccagc
1441 agaccaagac ctgttgttgt tatgatatca ggtaggccag ggatagggaa aactcacctt
1501 gccagggagc tagccaagaa gatcgcagct tcactcacag gggaccagcg cgtgggtctc
1561 atcccccgca atggcgttga ccactgggat gcatacaagg gagaaagagt cgtcctatgg
1621 gacgattatg gaatgagcaa tcccatccac gacgccctca ggctacagga acttgctgac
1681 acctgccccc ttacgctaaa ctgtgacagg attgagaaca aaggaaaggt ctttgacagt
1741 gatgccataa tcatcaccac taatctagcc aacccagcac cattggacta tgtcaacttt
1801 gaagcatgct cgaggcgcat tgacttcctc gtgtacgcag aagcccctga ggtcgagaaa
1861 gcaaagcgtg atttcccagg tcaacctgac atgtggaaga acgcatttag ctctgacttc
1921 tcgcacataa aactggcgct ggctccgcaa ggtggtttcg acaagaacgg aaacacccca
1981 cacgggaaag gcgtcatgaa aaccctcacc actggttccc tcatcgcccg agcatcaggg
2041 ctactccatg agaggttgga tgagtacgag ctgcagggcc caactcccac cacctttaat
2101 tttgaccgca acaaggtgct tgcgttcaga caacttgctg ccgaaaacaa gtatggattg
2161 ttggacacaa tgagagttgg aaaacagctc aaggatgtta agaccatgtc agagctcaaa
2221 caggcactca agaatgtcgc aatcaagagt tgtcagatag tgtatggtgg ctgcacctac
2281 aggcttgagt ctgatggcaa gggtgatgta agagttgaca gagttcagaa cgccactgta
2341 cagaccaaca atgagcttgc cggcgcacta caccatctta ggtgcgccag aatcagatat
2401 tatgtcaagt gtgttcagga ggccctgtat tccatcatcc aaatcgctgg ggctgcattt
2461 gttaccacgc gcattgtcaa gcgcatgaac atacaagatc tctggtccaa gccacaggtg
2521 gaggatacag aggaaatcgc tagcaaggat gggtgcccaa aaccccagga tggtgaagag
2581 tttgttatct catccgacga catcaaaacc gagggcaaga aagggaagaa caagtctggc
2641 cgtggcaaga aacacacagc attttcaagt aaaggtctca gtgatgaaga gtacgatgag
2701 tacaaaagaa ttagagaaga aagaaatggc aaatactcca tagaggaata cctccaggac
2761 agagacaggt attatgagga ggtggccatc gccagggcaa ccgaagagga cttctgtgaa
2821 gaagaagagg ccaagatccg acagaggatc ttcaggccaa caaggaaaca acgcaaagag
2881 gagagagcct ctctcggttt ggtcacaggt tctgaaatca ggaagaggaa cccagacgac
2941 ttcaagccta aaggaaagct gtgggctgat gatgacagga gtgttgacta caatgagaga
3001 ctcagttttg aagccccacc aagcatctgg tcgaggatag tcaactttgg ctcaggttgg
3061 ggtttttggg tttcccccag cctgttcata acatcaactc atgtcatacc ccagggcgca
3121 caggagttct ttggtgtacc catcaaacaa atccagatac acaaatcagg tgaattctgc
3181 cgcttgaggt ttccaaagcc gatcagaact gacgtgacag gcatgatctt agaagaaggt
3241 gcacccgaag ggaccgtggt cacattactc atcaaaagac caactggaga gctcatgccc
3301 ctggcagcca gaatgggaac ccacgcaacc atgaagatac aagggcgcac tgtcggaggt
3361 caaatgggca tgctcctaac agggtccaac gccaagagta tggacctggg caccacacca
3421 ggtgactgtg gctgccccta catttacaag agggggaatg actacgtggt cattggggtc
3481 catacagctg ccgcccgtgg aggaaacact gtcatttgtg ccacccaggg gagcgaggga
3541 gaagccacac ttgaaggcgg tgatagcaag gggacctact gcggtgcacc aatcttaggt
3601 ccaggaagtg ccccaaaact cagcaccaag accaagttct ggaggtcatc cacggcacca
3661 ctcccacctg gtacctatga accagcttac ctcggtggca aggaccccag agttaagggt
3721 ggcccttcac tgcaacaagt tatgagggat caactgaaac cattcactga gcctaggggt
3781 aggccaccaa aaccaagtgt gctagaagct gccaagaaaa ccatcgtcaa tgtcctagaa
3841 cagacaattg acccacctca aaagtggtcg tttgcgcagg catgcgcatc ccttgacaag
3901 accacttcta gcggtcatcc gcaccacatg cggaagaatg actgctggaa cggggagtcc
3961 ttcacaggaa aattggcaga ccaggcttcc aaggccaacc tgatgtttga ggagggaaag
4021 aacatgaccc cagtttacac gggtgcgctt aaggatgagc tggtcaagac tgacaagatt
4081 tatggtaaga tcaaaaagag gcttctctgg ggttctgacc tggcgaccat gattcggtgc
4141 gctcgagcat tcgggggtct gatggaggaa ctcaaagcac attgtgtcac actacctgtt
4201 agggtgggta tgaatatgaa tgaggatggc cctatcatct ttgagagaca ctccagatat
4261 aaatatcatt atgatgctga ttactcccgg tgggattcaa cacaacaaag agctgtgttg
4321 gcggcagcct tagaaatcat ggtcaagttt tccccagagc cgcacctggc ccaaaaggtt
4381 gcagaagacc ttctttctcc cagcgtgatg gacgtgggtg atttcaaaat atcaatcaat
4441 gagggtctcc cctccggagt gccctgcacc tcccaatgga attccatcgc ccactggctc
4501 ctcactctct gtgcactctc cgaggttaca aacctgtccc ctgacattgt tcaggctaac
4561 tctctctttt ctttctacgg tgatgatgaa attgtgagta cagacataaa attggaccca
4621 gaaaaactga cagcaaaact caaggaatac gggttgaaac cgacccgccc tgacaaaact
4681 gaagggcctc tcgtcatttc cgaagacctg aatggcctaa ccttcctgcg gaggaccgtg
4741 actcgcgacc cagcaggttg gtttggaaag ttggaacaga gctcaatact caggcaaatg
4801 tactggacta ggggccccaa ccatgaagat ccatctgaaa caatgatacc acactcccag
4861 aggcccatac aattgatgtc cttgctggga gaggcagcac tccacggccc agcattctac
4921 agcaaaatca gtaaactggt cattgcagag ttgaaggagg gtggcatgga tttttacgtg
4981 ccaagacaag agccaatgtt cagatggatg agattctcgg atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgaatgacg ccactccatc
5101 taatgatggt gccgccggcc tcgtcccaga gatcaacaat gaggcaatgg cgctagaacc
5161 agtggcgggt gcagcgatag cagcacccct caccggccag caaaatataa ttgatccctg
5221 gattatgaat aattttgtgc aagcacctgg tggtgagttc acagtgtctc ctaggaattc
5281 ccctggtgaa gtgctcctca atttggaatt gggcccagag ataaacccct atctggccca
5341 tcttgctaga atgtataatg gttatgcagg tgggtttgaa gtgcaggtgg tcctggctgg
5401 aaatgcgttt acagcaggaa agataatctt tgcagctata ccccctaact tcccaattga
5461 caatctaagt gcagcacaga tcacaatgtg tccacacgtg attgtggatg tcaggcagtt
5521 ggaaccggtc aacctcccga tgcctgacgt tcgtaacaac ttcttccact acaaccaagg
5581 gtctgattcg agattgcgct tggttgcaat gctgtataca cctcttaggg caaataactc
5641 tggggatgat gttttcactg tgtcttgtag agtgctgact agacctagtc ctgaattttc
5701 atttaacttc cttgtgcccc ccactgtgga atcaaagaca aaacccttta ccctcccaat
5761 tctgactatc tctgaaatgt ctaattctag gtttccagtg ccgattgatt ctctgcacac
5821 cagcccaact gagaatattg ttgtccagtg tcagaatgga cgcgtcactc ttgatggtga
5881 gttgatgggc accactcagc tcttacctag tcaaatctgt gctttcaggg gcgtgctcac
5941 tagatcaaca agcagggcta gtgaccaggc cgacacagca acccctagat tgtttaatta
6001 ttattggcac atacaattgg ataatctaaa tgggactcct tatgatcctg cagaagacat
6061 accaggcccc ctagggacac cagatttccg aggcaaagtc tttggcgtgg ccagccaaag
6121 aaaccccgac agtacaacta gagcacatga agcaaaggtg gacacaacag ctggtcgctt
6181 caccccaaaa ctaggctcat tagagatatc cactgaatct gatgactttg accaaaacca
6241 accaacaaga ttcaccccag ttggcattgg ggttgacaac gaggcagact tccaacaatg
6301 gtccttacca gactactctg gccagttcac tcacaacatg aacttagccc cagctgttgc
6361 tcccaatttc cctggtgagc agctcctttt cttccgctca cagttaccat cttctggtgg
6421 gcgatccaat gggattctag actgcctggt cccccaagaa tgggtccagc acttctacca
6481 agaatcagcc cccgcccaaa cccaggtggc tctggttaga tatgtcaacc ctgacactgg
6541 tagagtgttg tttgaggcca agctgcacaa attaggtttc atgactatag ctaagaatgg
6601 tgactctcca ataactgtcc ccccaaatgg atactttagg tttgaatctt gggtgaaccc
6661 attttataca cttgccccca tgggaactgg gaacgggcgt agaagagttc aataatggct
6721 ggtgctttta tagcaggatt agctggtgat atattcacaa acactgtagg gtctctagtt
6781 aatgcagggg ctaatgctat taatcaaaaa gttgattttg aaaataacaa atacttgcaa
6841 aatgcttcct tcaatcatga taaggaaatg ttaaatgcac agattgaggc aacaaagagg
6901 ttacaggctg acatgattgc tatcaaacag ggggttttga ccgctggcgg cttttccccc
6961 actgatgcag ctcgcggggc aattaacgcc cccatgacaa aagtcctaga ttggaatgga
7021 acaaggtact gggcaccaag tgccacctct acaacctcga tgtcgggtgg cttcacaaac
7081 caggctgtgc acagaaccac gccaaatttt aaaatgaacc aggcccccag atccacaccc
7141 agcagtgggt cttcagtgag gtcactctca acccaagtca ctagtctgag ctcacactcg
7201 tccgggtcgt ctcgatctag cgggtctaca gttgctagct cattaccatc ctctaacagg
7261 actagggact gggtcaatca gcaaaatttc aatttggaac cacacatgcc tgggtcgctt
7321 aggacggctt ttgtcactcc accatctagt acagcctcta gttcaggcac tgtctcaacc
7381 gtgcccaaaa atgttttgga ctcctggaca tctgcgttta acacgcgcag acagccgcta
7441 ttcgcacacc ttcgtagaag gggggagtca aatgtttagt gaaaaggt
//