Typing tool
|
Complete norovirus genomes
KY887600 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5099 ORF2: 5080..6702 ORF3: 6702..7508LOCUS KY887600 7562 bp RNA linear VRL 15-JUL-2017 DEFINITION Norovirus GII isolate Hu/UK/2016/GII.P16_GII.4_Sydney2012/NOR-2558, partial genome. ACCESSION KY887600 VERSION KY887600.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7562) AUTHORS Ruis,C., Roy,S., Brown,J.R., Allen,D.J., Goldstein,R.A. and Breuer,J. TITLE The emerging GII.P16-GII.4 Sydney 2012 norovirus lineage is circulating worldwide, arose by late-2014 and contains polymerase changes that may increase virus transmission JOURNAL PLoS ONE 12 (6), E0179572 (2017) PUBMED 28662035 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 7562) AUTHORS Ruis,C., Roy,S., Brown,J.R., Allen,D.J., Goldstein,R.A. and Breuer,J. TITLE Direct Submission JOURNAL Submitted (03-APR-2017) Infection and Immunity, University College London, Gower Street, London WC1E6BT, United Kingdom COMMENT ##Assembly-Data-START## Assembly Method :: CLC Genomics Workbench v. 8.5 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7562 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/UK/2016/GII.P16_GII.4_Sydney2012/NOR-2558" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom: London" /collection_date="06-Jan-2016" /note="genotype: GII.P16_GII.4_Sydney2012" CDS <1..5099 /codon_start=3 /product="non-structural polyprotein" /protein_id="ASK12140.1" /translation="KMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPK QPASRDESQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQP DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI SMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT MEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEA PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS LFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGT VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLS TMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEP MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE" CDS 5080..6702 /codon_start=1 /product="VP1" /protein_id="ASK12141.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" CDS 6702..7508 /codon_start=1 /product="VP2" /protein_id="ASK12142.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 tgaagatggc gtctaacgac gctaccgttg ccgttgcttg caacaacaac aacgacaagg 61 aaaaatcttc aggtgaaggc ttattcacaa atatgtcttc caccttaaag aaagccctcg 121 gggctaggcc caaacagcct gcctcgagag acgaatcaca aaagccccca agaccaccaa 181 ctcccgagtt ggtcaagagg ataccccctc ctccacctaa tggcgaagaa gaagaagaac 241 cagtcattag gtatgaggtt aagagtggga tctctggcct gcccgagctc acaacagtcc 301 cccaaccgga cgtggccaac acagcattca gtgttccacc actgagcttg agagaaaaca 361 gggaggccaa ggaaccgcta acaggggcaa tattagagat gtgggatgga gagatatacc 421 actatggcct gtacgtggag aaaggcttag tgttgggtgt gcacaaacca cctgcagcca 481 taagcatggc aagagtggag ctgacgccgc tgtcattgta ctggcgtgtg gtgtacactc 541 cccaatacct catctcccct gaaactctca ggaggctcaa cggagaggcg ttcccttaca 601 ccgccttcga caacaactgc tatgcctttt gctgctgggt gttagacctc aatgactcat 661 ggcttagcag gaggatggtg caaagaacaa cgggcttctt cagaccttac caagagtgga 721 acagaaaacc cctgcctacc atggatgact ccaaaattaa gaaggtagca aatatattcc 781 tatgttcatt gtccacatta ttcaccagac ccataaaaga cctcatagga aaaattaaac 841 cattaaacat attgaacatc ctggcaacgt gtgactggac gtttgccgga atagtggagt 901 ctctgatatt acttgctgaa ctcttcggag ttttctggac acccccagat gtgtctgcta 961 tgatcgctcc cttactcggg gactacgagt tgcaagggcc agaagacctc gccgttgaac 1021 tcgtacctgt ggtaatggga gggattggtt tggtgttggg attcaccaaa gagaaaattg 1081 gcaaaatgtt gtcctcagca gcatcaacac tcagggcttg caaagatctt ggtgcctatg 1141 gcttagagat actcaaattg gtcatgaagt ggttcttccc aaagaaagag gaggccaacg 1201 agctagccat ggtgagggcc atagaggatg ccgtactaga tcttgaggca atagaaaata 1261 accacatgac aaccctgttg aaagacaaag acagcttagc aacatacatg aaaacactgg 1321 acatggagga ggagaaagcc agaagattgt ccacaaaatc tgcatcccct gacatagttg 1381 ggacaatcaa cgccctgctg gctcgaatag cagcggccag gtcattagtc cacagggcca 1441 aggaagagct atctagcagg ataagaccag tagttgttat gatatctggc aaaccaggaa 1501 taggcaaaac tcatctggcc agggaggtgg caagaaaggt ggcatccact ctcacagggg 1561 atcaaagagt cggactcata ccaagaaacg gtgtggacca ttgggatgca tacaaaggtg 1621 agagagtcgt gctgtgggac gactatggca tgagtaaccc cattcatgat gctcttcgca 1681 tacaagaatt ggctgatacg tgtcccctta ccttaaattg tgacagaatt gaaaataagg 1741 gaaaagtttt tgacagtgaa gtcataataa ttacaacaaa ccttgccaat ccagccccac 1801 ttgattatgt caactttgag gcctgttcca ggagaattga tttcctggtg tacgctgagg 1861 caccagaagt agaaaaggca aaacgggact ttcctggtca gccagatatg tggaaggacg 1921 ccttcaagcc ggacttttca cacatcaagc tacagcttgc acctcagggc ggctttgaca 1981 agaatggcaa caccccacac gggaaaggag tgatgaagac cctcactacc ggttctctga 2041 ttgcccgtgc atcaggccta ctgcatgaga ggatggatga atttgaactc caaggtccca 2101 caatcaccac cttcaatttc gaccggaaca gaatcacagc attcaggcaa ttggctgcag 2161 aaaacaagta tggattggtg gataccatga aagttggcaa tcaactaaaa ggagtgaaaa 2221 ccatggaaga actcaaacaa gcaattagga atgtgaccat caagaggtgc cggatcatct 2281 acggtggctc cacgtatgac cttgaatctg atggcaaggg caaagttttg gtggaaaagg 2341 tcaagaacac ctctgtgcag accaacaacg agttggccgg ggccctgcac catctcaaac 2401 acgcccgaat caggtactat gtcaaatgtg tgcaagaagc agtctattcc atcatacaaa 2461 tcgccggcgc tgcgtttgtc accacgcgca ttgcacgccg catgaacata caagaactct 2521 ggtcgaagcc acaattagat caaaatgaat cagagactaa ggaagaggcc cccaagtcag 2581 aagatgacga gttcatcata tcttctaagg acatcaagga ggaaggaaag aagggcaaaa 2641 acaaaactgg ccgtggcaag aaacacactg cattctccag caagggtttg agcgatgagg 2701 agtatgacga gtacaagagg ataagagaag agagaaatgg gaagtactct atagaggagt 2761 atcttcaaga cagagacagg tactatgagg agctcgccat tgccaaggcc acggaagagg 2821 atttctgtga agaggaggag atcaaaatcc gccagagaat tttccgtccc accaggaaac 2881 aaagaaagga agagagggcc acattagggc tagtaacagg ttcggaaatc agaaaaagaa 2941 accctgatga cttcaaaccc aaagggaagc tgtgggccga tgacaacaga agtgttgact 3001 acaatgagaa actggacttt gaggcccccc caagcatatg gtctaggatt gtgagctttg 3061 gttctggctg gggcttctgg gtatcaccaa gcctgttcat aacatcaact catgtaatcc 3121 ccgcaggcat aacagaagcg tttggagtcc ccatcaaaca aattcagatc cacaaatcag 3181 gtgaattttg ccgattcaga ttcccaaaac caattagacc agatgtgaca ggaatgatct 3241 tggaagaagg tgcgcctgaa ggcaccgtgg caactgtgct catcaaacgc cccaccggag 3301 agctcatgcc tcttgcagcc agaatgggaa cacacgcaac catgaaaatt caaggccgca 3361 tggttggcgg acagatgggt atgttgctca ctggatcaaa tgctaaagga atggacttgg 3421 gaacaactcc tggtgactgt ggctgtcctt acatctataa aaggggcaat gactatatag 3481 tcattggggt gcacactgca gcagcccgtg gtggaaacac cgtcatttgt gccacacagg 3541 gaagtgaggg tgaggcaact cttgagggtg gagatgacaa aggaacatac tgtggggcac 3601 ccattctagg ccctgggggt gcaccaaaat tgagcaccaa aaccaaattt tggaggtcat 3661 cgaacacgcc ccttccacca gggacatatg agcctgccta cctcggtggc cgtgacccgc 3721 gtgttaaggg tgggccctcc ttgcagcagg taatgagaga ccagttgaag ccattcactg 3781 aacccagggg caaacctcca agaccaagtg tattggaagc agccaaacaa accattatca 3841 atgtcctcga acaaaccctg gaccctccac aaaaatggac atacgcacag gcgtgtgcct 3901 cacttgacaa aaccacctcc agcgggcatc cccatcacgt ccgaaagaat gaattctgga 3961 atggtgagac cttcactggt aaattggcag accaagcatc aaaagcaaac ctaatgtttg 4021 aggaagggaa acacatgaca ccagtgtata cagcagcact caaggacgag ctagtcaaga 4081 ctgagaaaat ctatggaaag atcaagaaga gactgctctg gggctctgac ttgtccacca 4141 tgatccggtg cgctaggtca tttggtggac tcatggacga gatgaaggca cactgcatat 4201 cactcccagt acgagttggc atgaatatga atgaagatgg cccaataata tttgagaaac 4261 attccagata caaataccac tatgatgcag actactctcg ttgggattca acacaacaga 4321 gggcagtgct agcagcagcc ttggaaatca tggtcagatt ctctgcagaa ccacaattgg 4381 cacaaatagt cgctgaggat ctgctggccc ctagtgtagt agatgtagga gactttaaaa 4441 tcacaataaa tgaagggctc ccatctggtg tgccatgcac ttctcaatgg aactccatcg 4501 cacactggct gctaactctc tgtgccttgt ctgaagtcac caaactgtcc cctgacatta 4561 tacaagcaaa ttccatgttc tcattttacg gtgatgacga gattgtcagc accgacataa 4621 aattggaccc tgaacagtta accgccaagt tgaaggagta cggcctgaaa ccaacccgcc 4681 cagacaagac cgagggaccc ctgatcatca gtgaagattt gaacggactc actttcctcc 4741 gaaggacggt gactcgtgac ccagctggct ggtttggaaa actggaccaa agctcgattt 4801 tgaggcagat gtactggact agaggaccaa atcatgaaga ccccaatgag acaatgatac 4861 cccattctca aagacccata cagctcatgg cactgcttgg tgaagcctct cttcacggac 4921 cctctttcta cagtaagatc agtaaattgg tcataactga actcaaagaa ggtgggatgg 4981 acttttacgt gccaaggcag gaacccatgt tcaggtggat gaggttttct gacttgagca 5041 cgtgggaggg cgatcgcaat ctggctccca atttcgtgaa tgaagatggc gtcgagtgac 5101 gccaacccat ctgatgggtc cgcagccaac ctcgtaccag aggtcaacaa tgaggttatg 5161 gctttggagc ccgttgttgg tgccgctatt gcggcacctg tagcgggcca acaaaatgta 5221 attgacccct ggattagaaa taattttgta caagcccctg gtggggagtt tacagtatcc 5281 cctagaaacg ctccaggtga aatactatgg agcgcgcccc taggccctga cctaaatccc 5341 tacctatccc atttggccag aatgtacaat ggttatgcag gtggttttga agtgcaagta 5401 attctcgcgg ggaacgcgtt caccgccggg aagatcatat ttgcagcagt cccaccaaat 5461 tttccaactg aaggcttaag tcctagccag gtcactatgt tcccccatat aatagtagat 5521 gttagacaat tagaacctgt gctgattccc ttacccgatg ttaggaataa tttctatcat 5581 tataatcagt caaatgactc cactattaag ttgatagcaa tgttgtatac accacttagg 5641 gctaataatg ctggggatga tgttttcaca gtttcgtgcc gagttctcac gagaccatcc 5701 cccgattttg atttcatatt tttagtgcca cctacagttg agtcaagaac taaaccattc 5761 tctgtcccag ttttaactgt tgaggagatg accaattcaa gattccccat tcctttggaa 5821 aagttgttca cgggccccag cagtgccttt gttgttcaac cacaaaacgg caggtgcaca 5881 actgatggcg tgctcctagg caccacccaa ctgtctcctg tcaacatctg caccttcaga 5941 ggggatgtca cccacatcac aggtagtcgc aactacacaa tgaatttggc ttctcaaaat 6001 tggaacaact atgacccaac agaagaaatc ccagcccctc taggaactcc agattttgtg 6061 ggaaagattc aaggcatgct cacccaaacc acaaggacag atggttcaac acgcggccac 6121 aaagctacag tgtacactgg gagcgccgac tttgctccaa aactgggtag agttcaattt 6181 gaaactgaca cagaccatga ttttgaagct aatcaaaaca caaagttcac cccagtcggt 6241 gtcatccaag atggtagcac cacccaccga aacgaacccc aacagtgggt gctcccaagt 6301 tactcaggca gaaatactca caatgtacat ctggcccccg ctgtagcccc cacctttccg 6361 ggtgagcaac ttctcttctt cagatccacc atgcccggat gcagcgggta ccccaacatg 6421 gatttggact gtctgctccc ccaggaatgg gtgcagtact tctaccaaga ggcagcccca 6481 gcacaatctg atgtggctct gctaagattt gtgaatccag acacaggtag ggttttgttt 6541 gagtgcaagc ttcacaaatc aggctatgtc acagtggctc acactggcca acatgatttg 6601 gttatccccc ccaatggtta ctttaggttt gattcctggg tcaaccagtt ctacacgctt 6661 gcccccatgg gaaatggaac ggggcgtaga cgtgtagtat aatggctgga gctttctttg 6721 ctggattggc atctgatgtc cttggctctg gacttggttc ccttatcaat gctggggctg 6781 gggccatcaa ccaaaaagtt gagtttgaaa ataacagaaa attgcaacaa gcatccttcc 6841 aatttagcag caatctgcaa caggcttcct ttcaacatga taaagagatg ctccaagcac 6901 aaattgaggc caccaaaaag ctacaacagg aaatgatgaa agttaagcag gcaatgctcc 6961 tagagggtgg gttctctgag acagatgcag cccgcggggc aattaacgcc cccatgacaa 7021 aagctttgga ctggagcggg acaaggtatt gggctcccga tgctaggact acaacataca 7081 atgcaggccg cttttccacc cctcaaccat cgggggcact gccaggaaga gctaatctta 7141 gggatgctgt ccctgctcgg ggaccctcca ataaatcttc taactcttct actgccacct 7201 ctgtgtactc aaatcaaact atttcaacga gacttggttc tacagctggt tctggaacca 7261 gtgtctcgag cctcccgtca actgcaagga ctaggagctg ggttgaggac caaagtagga 7321 atctgtcacc tttcatgagg ggggcccaca acatatcatt tgtcacccca ccatctagca 7381 gatcctctag ccaaggcaca gtctcaaccg tgcctaaaga gattttggac tcctggactg 7441 gcgctttcaa cacgcgcagg cagcctctct tcgctcacat tcgtaagcga ggggagtcac 7501 gggcgtaatg tgaaaagaca aaactgatta tctttctttt tctttagtgt cttttaaaaa 7561 aa //