Typing tool
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Typing tool
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Complete norovirus genomes
| MK590972 | GII.2 | |
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| GII.P16 |
ORF1: 1..4952
ORF2: 4933..6561
ORF3: 6561..7340
LOCUS MK590972 7367 bp RNA linear VRL 11-MAR-2019
DEFINITION Norovirus GII isolate V17T03029_Noro_GII_P16_GII_2 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION MK590972
VERSION MK590972.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7367)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and
Wadford,D.A.
TITLE Norovirus GII.P16-GII.2 from School Outbreaks; California, 2017
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7367)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and
Wadford,D.A.
TITLE Direct Submission
JOURNAL Submitted (05-MAR-2019) Viral and Rickettsial Disease Laboratory,
California Department of Public Health, 850 Marina Bay Parkway,
Richmond, CA 94804, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. R10; SPAdes v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7367
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="RGDS-2017-1013"
/isolate="V17T03029_Noro_GII_P16_GII_2"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA: CA"
/collection_date="May-2017"
/note="genotype: GII.P16-GII.2"
gene <1..4952
/gene="ORF1"
CDS <1..4952
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QBJ03981.1"
/translation="DKPQMPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGL
PELTTVPQPDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVL
GVHKPPAAVSMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAF
CCWVLDLNDSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLF
TRPIKDLIGKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLL
GDYELQGPEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEI
LKLVMKWFFPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDM
EEEKARRLSTKSASPDIVGTINALLARIAAARSLVHRAKEELSSRMRPVVVMISGKPG
IGKTHLAREVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDA
LRIQELADTCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFL
VYADAPEVEKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKT
LTTGSLIARASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMRV
GNQLKGVKTMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNN
ELAGALHHLKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQ
NESETKEEAPKSGDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYK
RIREERNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKE
ERATLGLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGS
GWGFWVSPSLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMI
LEEGAPEGTVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGM
DLGTTPGDCGCPYIYKRGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGT
YCGAPILGPGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRD
QLKPFTEPRGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPY
HVRKNEFWNGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKK
RLLWGSDLSTMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHY
DADYSRWDSTQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEG
LPSGVPCTSQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDP
EQLTAKLKEYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILR
QMYWTRGPNHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGM
DFYVPRQEPMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..848
/gene="ORF1"
/product="p48"
mat_peptide 849..1946
/gene="ORF1"
/product="NTPase"
mat_peptide 1947..2477
/gene="ORF1"
/product="p22"
mat_peptide 2478..2876
/gene="ORF1"
/product="VPg"
mat_peptide 2877..3419
/gene="ORF1"
/product="Pro"
mat_peptide 3420..4949
/gene="ORF1"
/product="RdRp"
gene 4933..6561
/gene="ORF2"
CDS 4933..6561
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QBJ03982.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6561..7340
/gene="ORF3"
CDS 6561..7340
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QBJ03983.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
GSSHGTVSSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMRGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 gagacaaacc acaaatgccc ccaagaccac caactcccga gttggtcaag aggatacccc
61 ctcctccacc taatggcgaa gaagaagaag aaccagtcat taggtatgag gttaagagtg
121 ggatctctgg cctgcccgag cttacaacag tcccccaacc ggacgtggcc aacacagcat
181 tcagtgttcc accactgagc ttgagagaaa acagggaggc caaggaaccg ctaacagggg
241 caatattaga gatgtgggat ggagagatat accactatgg cctgtacgtg gagaaaggct
301 tagtgttggg tgtgcacaaa ccacctgcag ccgtaagcat ggcaagagtg gagctgacgc
361 cgctgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc cctgaaactc
421 tcaggagact caacggagag gcattccctt acaccgcctt cgacaataac tgctatgcct
481 tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg gtgcaaagaa
541 caacgggctt cttcagacct tatcaagagt ggaacagaaa acccctgccc accatggatg
601 actccaaaat taagaaggta gcaaatatat tcctatgttc attgtccaca ttattcacca
661 gacccataaa agacctcata ggaaaaatta aaccattaaa catattgaat atcctggcaa
721 cgtgtgactg gacttttgcc ggaatagtgg agtctctgat attacttgct gaactcttcg
781 gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc ggggactacg
841 agttgcaggg gccagaagac ctcgccgttg aactcgtacc tgtggtaatg ggggggattg
901 gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat gttgtcctca gcagcatcaa
961 cactcagggc ttgcaaagat cttggtgctt atggcttaga gatactcaaa ttggtcatga
1021 agtggttctt cccaaagaaa gaggaggcca atgagttggc catggtgagg gccatagagg
1081 atgctgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg ttgaaagaca
1141 aagacagctt ggcaacatac atgaaaacac tggacatgga ggaggagaaa gccaggaggt
1201 tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg ctggctcgaa
1261 tagcagcggc cagatcatta gtccacaggg ccaaggaaga gctatctagc aggatgagac
1321 cagtagttgt tatgatatct ggcaaaccag gaataggcaa aactcatctg gccagggagg
1381 tggcaagaaa ggtggcgtcc actctcacag gggaccaaag agtcggactc ataccaagaa
1441 acggtgtgga ccattgggat gcatacaaag gtgagagagt cgtgttgtgg gacgactatg
1501 gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgat acgtgtcccc
1561 ttaccttaaa ttgtgacaga attgaaaaca agggaaaagt ttttgacagt gaggtcataa
1621 taattacaac aaaccttgcc aatccagccc cacttgatta tgttaatttt gaggcctgtt
1681 ccaggagaat tgatttcctg gtgtacgctg atgcaccaga agtagaaaag gcaaaacggg
1741 actttcctgg tcagccagat atgtggaagg acgccttcaa gccggacttt tcacacatca
1801 agctacagct tgcaccccag ggcggctttg acaagaatgg caacacccca catgggaaag
1861 gagtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc ctactgcatg
1921 agaggatgga tgaatttgaa ctccaaggtc ccacaatcac caccttcaat ttcgaccgga
1981 acagaatcac agcattcaga caattggccg cagaaaataa gtatggattg gtagacacca
2041 tgagagttgg caatcaacta aaaggagtga aaaccatgga ggaacttaaa caagcaatca
2101 ggaatgtgac catcaagagg tgccggatca tctacggtgg ctccacgtat gaccttgaat
2161 ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa cacctctgta cagaccaaca
2221 acgagttggc tggggccctg caccatctca aacacgcccg aatcaggtac tatgtcaaat
2281 gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt gtcaccacgc
2341 gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaatta gatcaaaatg
2401 aatcagagac taaggaagag gcccccaagt caggagatga cgagttcatc atatcttcta
2461 aggacatcaa ggaggaagga aagaagggca aaaacaaaac tggccgtggc aagaaacaca
2521 ctgcattctc cagcaagggc ttgagcgatg aggagtatga cgagtacaag aggataagag
2581 aagagagaaa tgggaagtac tccatagagg agtatcttca agacagagac aggtactatg
2641 aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag gagatcaaaa
2701 tccgtcagag aatttttcgt cccaccagga aacaaagaaa ggaagagagg gccacattag
2761 ggctagtaac aggttcagaa atcagaaaaa ggaaccctga tgacttcaaa cccaaaggga
2821 agctgtgggc cgatgacaac aggagtgttg actacaatga gaaactggac tttgaggccc
2881 ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc tgggtgtcac
2941 caagcctttt cataacgtca actcatgtaa tccccgcagg cataacagaa gcatttggag
3001 tccccatcaa acaaatccag atccacaaat caggtgaatt ttgccgattc agattcccaa
3061 aaccaattag accagatgtg acagggatga tcttggaaga aggtgcgcct gagggcaccg
3121 tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca gccagaatgg
3181 gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg ggtatgttgc
3241 tcactggatc aaatgctaaa ggaatggatt tgggaacaac tcctggtgac tgtggctgtc
3301 cttacatcta taaaaggggc aatgactata tagccattgg ggtgcacact gcagcagccc
3361 gtggtggaaa caccgtcatc tgtgccacac agggaagtga gggtgaggca actcttgagg
3421 gtggagatga caaaggaaca tactgtgggg cgcccattct aggccctggg ggtgcaccaa
3481 aattgagcac caaaaccaaa ttttggaggt catcgaacac gccccttcca ccagggacat
3541 atgaacctgc ctacctcggt ggccgtgatc cgcgtgttaa gggtgggccc tccctgcagc
3601 aggtaatgag agaccagttg aagccattca ctgaacccag gggcaaacct ccaagaccaa
3661 gtgtactgga agcggccaaa caaaccatca tcaatgtcct cgaacaaacc ctggaccctc
3721 cacaaaaatg gacatacgca caggcgtgtg cctcacttga caaaaccacc tccagcgggc
3781 atccctatca cgtccggaag aatgaattct ggaatggtga gaccttcact ggtaaattgg
3841 cagaccaagc atcaaaagca aacctaatgt ttgaggaagg gaaacacatg acaccagtgt
3901 acacagcagc actcaaggac gagctagtca agactgagaa aatctatgga aagatcaaga
3961 agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg tcatttggtg
4021 ggctcatgga cgagatgaag gcacactgca tatcactccc agtccgagtt ggcatgaata
4081 tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatat cactatgatg
4141 cagactactc tcgttgggat tcaacacaac agagggcagt actagcagca gccttggaaa
4201 ttatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag gatctgctgg
4261 cccctagtgt agtagatgta ggagacttta aaattacaat aaatgaaggg ctcccctctg
4321 gtgtgccatg cacttctcaa tggaactcca tcgcacactg gctgctaact ctctgtgcct
4381 tgtctgaagt caccaaactg tcccctgaca ttatacaggc aaattccatg ttctcatttt
4441 acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag ttaaccgcca
4501 aattgaagga gtacggcctg aaaccaaccc gcccagacaa aaccgaggga cccctgatta
4561 tcagtgaaga tttgaacgga ctcactttcc tccgaaggac agtgactcgt gatccagctg
4621 gctggtttgg aaaactggat caaagctcaa ttttgaggca gatgtactgg actagaggac
4681 caaatcatga agaccccaat gagacaatga taccccattc tcaaagaccc atacagctca
4741 tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctacagtaaa atcagtaaat
4801 tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg caggaaccca
4861 tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc aatctggctc
4921 ccaattttgt gaatgaagat ggcgtcgaat gacgccgctc catctactga tggtgcagcc
4981 ggcctcgtgc cagaaagtaa caatgaggtc atggctcttg aacccgtggc tggtgccgcc
5041 ttggcagccc cggtcactgg tcaaacaaat attatagacc cttggattag agcaaatttt
5101 gtccaggccc ccaatggtga gtttacagtc tctccccgta atgcccctgg tgaagtgcta
5161 ctgaatctgg agttgggtcc agaattaaat ccttatctgg cacatttagc aagaatgtac
5221 aatgggtatg ccggtgggat ggaggtgcag gtcatgttgg ctgggaacgc gttcacagcc
5281 ggcaagttgg tcttcgccgc cgtgccacct cacttcccag ttgaaaacct tagcccacag
5341 caaatcacca tgttccctca tgtgatcata gatgtgagaa ccttggaacc tgttctgtta
5401 ccactccctg atgttaggaa taatttcttc cattataatc agaaagatga tcccaagatg
5461 agaattgtgg ctatgcttta tacccccctc aggtctaatg gttcaggtga tgatgtgttt
5521 acagtctcct gcagagtgtt gactagacct tcccctgact ttgacttcac atacctggtg
5581 ccaccaacag tggagtctaa aacaaaacca ttcaccctcc caatcctcac acttggggaa
5641 ctttccaatt ccaggttccc agtgtccata gaccagatgt ataccagccc taatgaagtt
5701 atatcagtgc agtgtcaaaa tggtaggtgc acactggacg gggagctcca ggggacaaca
5761 caactccaag tcagtggcat ttgtgctttt aaaggtgaag tgaccgccca cttgcatgac
5821 aatgatcacc tatataatgt taccatcaca aacttgaatg ggtccccttt tgatccctcc
5881 gaggatatcc ctgcccctct gggtgtgcct gacttccagg gaagggtttt tggtatcatc
5941 tcccaaaggg acaaacacaa tagtcctggg cataatgaac cagcaaacag gggacacgac
6001 gctgtggtcc ccacttacac agcacagtac actccaaaac tgggacaaat tcaaattggc
6061 acatggcaga ctgacgacct tacagtcaac caaccagtca aattcacccc agttggactc
6121 aatgacactg aacattttaa ccaatgggtg gtccccaggt atgctggtgc cctaaacctc
6181 aatacaaacc ttgccccttc tgttgctcca gtatttccag gagagcgcct gctcttcttc
6241 agatcataca ttcccctcaa gggcggttat ggaaacccag ccattgattg cctactacca
6301 caagagtggg tgcaacactt ctatcaggaa gcagcccctt caatgagtga ggtggccctc
6361 gtcagataca tcaacccgga cactggtcgg gcactgtttg aggccaagct ccacagagct
6421 ggtttcatga cagtctcgag caacaccagt gccccggtgg ttgtgcctgc caacggatac
6481 ttcagatttg attcttgggt gaaccaattc tattctctcg cccccatggg aactgggaat
6541 gggcgtagaa gggttcaata atggctggag cttttgtagc tggtcttgca ggggacgtgc
6601 tcagcaatgg gcttagttca ttaatcaatg caggtgctaa tgcaataaat cagagggcag
6661 aatttgattt taatcagaaa ttgcagcaaa attcttttaa tcatgataag gagatgttgc
6721 aggctcagat tcaggcaact aagcagctgc aggcagacat gatggctata aaacaagggg
6781 tcttgaccgc tggcggcttt tcccctgctg atgcagccag aggtgctgtg aacgcgccca
6841 tgacacaagc gctggattgg aatggtacaa ggtattgggc accaaactcc atgaggacca
6901 catcttattc tggaaaattc acatcaaccg ccccagtgag gcaggccgac ttccagcaca
6961 cccaaagccg gccttcgagt ggctcctctg tgtcttcctt tgccactcag tcttcaaggc
7021 caactctgac cacaaccact ggttcctcac atggcacagt ctcatcaaat tcaactcgca
7081 gcacaagcct ctcccaatca acggtctcca gagctacatc taggactggt gagtgggtta
7141 gagatcaaaa tagaaatttg gaaccctaca tgcgtggtgc cttacagaca gcctttgtca
7201 ccccaccttc cagcagggca tctgacggga cagtctcaac cgtcccgaaa ggtgttttgg
7261 actcctggac acctgcgttt aacacccgca ggcagccgct ttttgcacac ctccgtaaga
7321 ggggggagtc acaagcttag tgaaaaggtg aaaatttatt taggatg
//