Typing tool
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Typing tool
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Complete norovirus genomes
| MT238672 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5096
ORF2: 5077..6699
ORF3: 6699..7505
LOCUS MT238672 7568 bp RNA linear VRL 01-MAY-2020
DEFINITION Norovirus GII isolate 259-3 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT238672
VERSION MT238672.1
DBLINK BioProject: PRJNA604000
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7568)
AUTHORS Yang,Z., Williams-Hill,D., Wolfe,J., Silva,A.J., Hirneisen,K.,
Ruelle,S., Kulka,M. and Hellberg,R.
TITLE Direct Submission
JOURNAL Submitted (24-MAR-2020) Molecular Virology Team/Devision of
Molecular Biology, OARSA/CFSAN/FDA, 8301 Muirkirk Rd., Laurel, MD
20708, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC Genomics Workbench v. 11
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7568
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="259-3"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="17-Dec-2018"
/note="genotype: GII.P16-GII.4"
gene <1..5096
/gene="ORF1"
CDS <1..5096
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QIQ09403.1"
/translation="MASNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPKQ
PAPRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPD
VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS
MARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGK
IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREV
ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC
PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTM
EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLK
HARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAP
KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG
SEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL
FITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGTV
ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG
CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGPG
GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRG
KPPRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNG
ETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLST
MIRCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDST
QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ
WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY
GLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH
EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM
FRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..992
/gene="ORF1"
/product="p48"
mat_peptide 993..2090
/gene="ORF1"
/product="NTPase"
mat_peptide 2091..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..6699
/gene="ORF2"
CDS 5077..6699
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QIQ09404.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6699..7505
/gene="ORF3"
CDS 6699..7505
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QIQ09405.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 agatggcgtc taacgacgct accgttgccg ttgcttgcaa caacaacaac gacaaggaaa
61 aatcttcagg tgaaggctta ttcacaaata tgtctttcac cttaaagaaa gccctcgggg
121 ctaggcccaa acagcctgcc ccgagagacg aaccacaaaa gcccccaaga ccaccaaccc
181 ccgagttggt caagaggata ccccctcctc cacctaatgg cgaaggagaa gaagaaccag
241 tcattaggta tgaggttaag agtgggatct ctggcctgcc cgagctcaca acagtccccc
301 aaccggacgt ggccaacaca gcattcagtg ttccaccact gagcttgaga gaaaacaggg
361 aggccaagga accgctaaca ggggcaatat tagagatgtg ggatggagag atataccact
421 atggcctgta cgtggagaaa ggcttagtgt tgggtgtgca caaaccacct gcagccataa
481 gcatggcaag agtggagctg acgccgctgt cattgtactg gcgtgtggtg tacactcccc
541 aatacctcat ctcccctgaa actctcagga ggctcaacgg agaggcgttc ccttacaccg
601 ccttcgacaa caactgctac gccttttgct gctgggtgtt agacctcaat gactcatggc
661 ttagcaggag gatggtgcaa agaacaacgg gcttcttcag accttaccaa gagtggaaca
721 gaaagcccct gcctaccatg gatgactcca aaattaagaa ggtagcaaat atattcctat
781 gttcattgtc cacattattc accagaccca taaaagacct catagggaaa attaaaccat
841 taaacatatt gaacatcctg gcaacgtgtg actggacgtt tgccggaata gtggagtctc
901 tgatattact tgctgaactc ttcggagttt tctggacgcc cccagatgtg tctgctatga
961 tcgctccctt actcggggac tacgagttgc aagggccaga agacctcgcc gttgaactcg
1021 tacctgtggt aatgggaggg attggtttgg tgttgggatt caccaaagag aaaattggca
1081 aaatgttgtc ctcagcagca tcaacactca gggcttgcaa agatcttggt gcctatggct
1141 tagagatact caagttggtc atgaagtggt tcttcccaaa gaaagaggag gccaatgagc
1201 tagccatggt gagggccata gaggatgccg tgctagatct tgaggcaata gaaaataacc
1261 acatgacaac cctgttgaaa gacaaagaca gcttagcaac atacatgaaa acactggaca
1321 tggaggagga gaaagccaga aggttgtcca caaaatctgc atcccctgac atagttggga
1381 caatcaacgc cctgctggct cgaatagcag cggccaggtc attagtccac agggccaagg
1441 aagagctatc tagcaggata aggccagtag ttgttatgat atctggcaaa ccaggaatag
1501 gcaaaactca tctggccagg gaggtggcaa gaaaggtggc atccactctc acaggggacc
1561 aaagagtcgg actcatacca agaaacggtg tggaccattg ggatgcatac aaaggtgaga
1621 gagtcgtgct gtgggacgac tatggcatga gtaaccccat ccatgatgct cttcgcatac
1681 aagaattggc tgatacgtgt ccccttacct taaattgtga cagaattgaa aataagggaa
1741 aagtttttga cagtgaagtc ataataatta caacaaacct tgccaatcca gccccacttg
1801 attatgtcaa ctttgaggcc tgttccagga gaattgattt cctggtgtac gctgaggcac
1861 cagaagtaga aaaggcaaaa cgggactttc ctggtcagcc agatatgtgg aaggacgcct
1921 tcaagccgga cttttcacac atcaagctac agcttgcacc tcagggcggc tttgacaaga
1981 atggcaacac cccacatggg aaaggagtga tgaagaccct cactaccggt tctctgattg
2041 cccgtgcatc aggcctacta catgagagga tggatgaatt tgaactccaa ggtcccacaa
2101 tcaccacctt caatttcgac cgaaacagaa tcacagcatt cagacaattg gctgcagaaa
2161 acaagtatgg attggtggat accatgaaag ttggcaatca attaaaagga gtgaaaacca
2221 tggaagaact caaacaagca atcagaaatg tgaccatcaa gaggtgccgg atcatctacg
2281 gtggctccac gtatgacctt gaatctgatg gcaagggcaa agttttggtg gaaaaggtca
2341 agaacacctc tgtacagacc aacaacgagt tggccggggc cctgcaccat ctcaaacacg
2401 cccgaatcag gtactatgtc aaatgtgtgc aagaagcagt ctattccatc atacaaattg
2461 ccggcgctgc gtttgtcacc acgcgcattg cacgccgcat gaacatacaa gaactctggt
2521 cgaagccaca attagatcaa aatgaatcag agactaagga agaggccccc aaatcagaag
2581 atgacgagtt catcatatct tctaaggaca tcaaggagga aggaaagaag ggcaaaaaca
2641 aaactggccg tggcaagaaa cacactgcat tctccagcaa gggcttgagc gatgaggagt
2701 atgacgagta caagaggata agagaagaga gaaatgggaa gtactctata gaggagtatc
2761 ttcaagacag agacaggtac tatgaggagc tcgccattgc caaggccacg gaagaagact
2821 tctgtgaaga ggaggagata aaaatccgtc agagaatttt ccgtcccacc aggaaacaaa
2881 gaaaggaaga gagggccaca ttaggactgg taacaggttc agaaatcaga aaaagaaacc
2941 ctgatgactt caaacccaaa gggaagctgt gggccgatga caacagaagt gttgactata
3001 atgagaaact ggactttgag gcccccccaa gcatatggtc taggattgtg agctttggtt
3061 ctggctgggg cttctgggta tcaccaagcc tgttcataac atcaactcat gtaatccccg
3121 caggcataac agaagcattt ggagtcccca tcaaacaaat tcagatccac aaatcaggtg
3181 aattttgccg attcagattc ccaagaccaa ttagaccaga cgtgacagga atgatcttgg
3241 aagaaggtgc gcctgaaggc accgtggcaa ctgtgctcat caaacgcccc accggagagc
3301 tcatgcctct tgcagccaga atgggaacac acgcaaccat gaaaattcaa ggccgcatgg
3361 ttggcggaca gatgggtatg ttgctcactg gatcaaatgc taaaggaatg gatttgggaa
3421 caactcctgg tgactgtggc tgtccttaca tctacaaaag gggcaatgac tatatagtca
3481 ttggggtgca cactgcagca gcccgtggtg gaaacaccgt catctgtgcc acacagggaa
3541 gtgagggtga ggcaactctt gagggtggat atgacaaagg aacatactgt ggggcaccca
3601 ttctaggccc tgggggtgca ccaaagttga gcaccaaaac caaattttgg aggtcatcga
3661 acacgcccct cccaccaggg acatatgagc ctgcctacct cggtggccgt gatccgcgtg
3721 ttaagggtgg gccctccttg cagcaggtaa tgagagacca gttgaagcca ttcactgaac
3781 ccaggggcaa acctccaaga ccaagtgtat tggaagcagc caaacaaacc gttatcaatg
3841 tcctcgaaca aaccctggat cctccacaaa aatggacata cgcacaggcg tgtgcctcac
3901 ttgacaaaac cacttccagc gggcatcctc atcacgtccg aaagaatgaa ttctggaatg
3961 gtgagacctt caccggcaaa ttggcagacc aagcatcaaa agcaaaccta atgtttgagg
4021 aagggaaaca catgacacca gtgtatacag cagcactcaa ggacgagcta gtcaagactg
4081 agaaaatcta tagaaagatc aagaagagac tgctctgggg ctctgacttg tccaccatga
4141 tccggtgcgc taggtcattt ggtgggctca tggacgagat gaaggcacac tgcatatcac
4201 tcccagtacg agttggcatg aatgtgaatg aagatggccc aataatattt gagaaacatt
4261 ccagatacaa ataccactat gacgcagact actctcgttg ggattcaaca caacagaggg
4321 cagtactagc agcagccttg gaaatcatgg tcagattctc tgcagaacca caattggcac
4381 aaatagtcgc tgaggatctt ctggccccta gcgtagtaga tgtaggagac tttaaaatca
4441 ctataaatga agggctccca tctggtgtgc catgcacctc ccaatggaac tccatcgcac
4501 actggctgct aactctctgt gccttgtctg aagtcaccaa actgtcccct gacattatac
4561 aagcaaattc catgttctca ttttacggtg atgacgagat tgtcagcacc gacataaaat
4621 tggaccctga acagttaacc gccaagttga aggagtatgg cctgaaacca acccgcccag
4681 acaagaccga gggacccctg atcatcagtg aagatttgaa cggactcact ttcctccgaa
4741 ggacggtgac tcgtgaccca gctggctggt ttggaaaact ggaccaaagt tcaattttga
4801 ggcagatgta ctggactaga ggaccaaatc acgaagatcc caatgagaca atgatacccc
4861 attctcaaag acccatacag ctcatggcac tgcttggtga agcctctctt cacggaccct
4921 ctttctacag tagaatcagt aaattggtca taactgaact caaagaaggt gggatggact
4981 tttacgtgcc aaggcaggaa cccatgttca ggtggatgag gttttctgac ttgagcacgt
5041 gggagggcga tcgcaatctg gctcccaatt ttgtgaatga agatggcgtc gagtgacgcc
5101 aacccatctg atgggtccgc agccaacctc gtaccagagg tcaacaatga ggttatggct
5161 ttggagcccg ttgtcggtgc cgctattgcg gcacctgtag cgggccaaca aaatgtaatt
5221 gacccctgga ttagaaataa ttttgtacaa gcccctggtg gggagtttac agtatccccc
5281 agaaacgctc caggtgaaat actatggagc gcgcccctag gccctgacct aaatccctac
5341 ctatcccatt tggccagaat gtacaatggt tatgcaggtg gttttgaagt gcaggtaatt
5401 ctcgcgggga acgcgttcac cgccgggaag atcatatttg cagcagtccc accaaatttt
5461 ccaactgaag gcttaagtcc tagccaggtc actatgttcc cccatataat agtagatgtt
5521 agacagttag aacctgtgct gattccttta cccgatgtta ggaataattt ctatcattac
5581 aatcagtcaa atgactccac tattaagttg atagcaatgt tgtacacacc acttagggct
5641 aataatgctg gggatgatgt tttcacagtt tcgtgccgag ttctcacgag accatccccc
5701 gattttgatt tcatattttt agtgccaccc acagttgagt caagaactaa accattctct
5761 gtcccagttt taactgttga ggagatgacc aattcaagat tccccatccc tttggaaaag
5821 ctgttcacag gccccagcag tgcctttgtt gttcaaccac aaaacggcag gtgcacaact
5881 gatggcgtgc tcctaggcac cacccaactt tctcctgtca acatctgcac cttcagaggg
5941 gatgtcaccc acatcacagg tagtcgcaac tacacaatga atttggcttc tcaaaattgg
6001 aacaactatg acccaacaga agaaatccca gcccctctag gaactccaga ttttgtgggg
6061 aagattcaag gcatgctcac ccaaaccaca aggacagatg gttcaacacg cggccacaaa
6121 gctacagtgt acactgggag cgccgacttt gctccaaaac tgggtagagt tcaatttgaa
6181 actgacacag accatgattt tgaagctaat caaaacacaa agttcacccc agtcggtgtc
6241 atccaagatg gtagcaccac ccatcgaaac gaaccccaac agtgggtgct cccaagttac
6301 tcaggcagaa atactcacaa tgtacatctg gcccccgctg tagcccccac ctttccgggt
6361 gagcaacttc tcttcttcag atccaccatg cccggatgca gcgggtaccc caacatggat
6421 ttggactgtc tgctccccca ggaatgggtg cagtacttct atcaagaggc agccccagca
6481 caatctgatg tggctctgct aagatttgtg aatccagaca caggtagggt tttgtttgag
6541 tgcaagcttc acaaatcagg ctatgttaca gtggctcaca ctggccaaca tgatttggtt
6601 atccccccca atggctactt tagatttgat tcctgggtca accagttcta tacgcttgcc
6661 cccatgggaa atggaacggg gcgtagacgt gtagtataat ggctggagct ttctttgctg
6721 gattggcatc tgatgtcctt ggctctggac ttggttccct catcaatgct ggggctgggg
6781 ccatcaacca aaaagttgag tttgaaaata acagaaaatt gcaacaagca tccttccaat
6841 ttagcagcaa tctgcaacag gcttcctttc aacatgataa agagatgctc caagcacaaa
6901 ttgaggccac taaaaagcta caacaggaaa tgatgaaagt taagcaggca atgctcctag
6961 agggtgggtt ctctgagaca gatgcagccc gcggggcaat taacgccccc atgacaaaag
7021 ctttggactg gagtgggaca aggtactggg ctcccgatgc taggactaca acatacaatg
7081 caggccgctt ttccacccct caaccatcgg gggcactgcc aggaagagct aatcttaggg
7141 atgctgtccc tgctcgggga ccctccaaca aatcttctaa ctcttctact gccacctctg
7201 tgtattcaaa tcaaactatt tcaacgagac ttggttctac agctggttct ggaaccagtg
7261 tctcgagcct cccgtcaact gcaaggacta ggagctgggt tgaggatcaa aataggaatt
7321 tgtcaccttt catgaggggg gcccacaaca tatcatttgt caccccacca tctagcagat
7381 cctctagcca aggcacagtc tcaaccgtgc ctaaagagat tttggactcc tggactggcg
7441 ctttcaacac gcgcaggcag cctctcttcg ctcacattcg taagcgaggg gagtcacggg
7501 tgtaatgtga aaagacaaaa ttgattattt ttctttttct ttagtgtctt ttaaaaaaaa
7561 aaaaaaaa
//