Typing tool
|
Complete norovirus genomes
JX846928 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 1..5068 ORF2: 5049..6671 ORF3: 6671..7477LOCUS JX846928 7497 bp ss-RNA linear VRL 24-OCT-2013 DEFINITION Norovirus Hu/GII.4/NIHIC9/2011/USA, partial genome. ACCESSION JX846928 VERSION JX846928.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII.4/NIHIC9/2011/USA ORGANISM Norovirus Hu/GII.4/NIHIC9/2011/USA Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7497) AUTHORS Madupu,R., Halpin,R., Ransier,A., Fedorova,N., Stockwell,T., Amedeo,P., Bishop,B., Edworthy,P., Gupta,N., Katzel,D., Li,K., Schobel,S., Shrivastava,S., Thovarai,V., Wang,S., Kim,M., Bok,K., Sosnovtsev,S.V., Wentworth,D.E. and Green,K.Y. TITLE Direct Submission JOURNAL Submitted (31-JUL-2012) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA COMMENT ##Assembly-Data-START## Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Coverage :: 105.2x Sequencing Technology :: Sanger; Illumina; 454 ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7497 /organism="Norovirus Hu/GII.4/NIHIC9/2011/USA" /mol_type="genomic RNA" /strain="Hu/GII.4/NIHIC9/2011/USA" /host="Homo sapiens" /db_xref="taxon:1260942" /country="USA: Maryland" /collection_date="14-Jun-2011" /note="genotype: GII.4" gene <1..5068 /gene="POL" CDS <1..5068 /gene="POL" /note="genome polyprotein" /codon_start=2 /product="nonstructural polyprotein" /protein_id="AFX71667.1" /translation="AVANSNNDIAKSSSDGVLSSMAVTFKRALGARPKQPPPREKPQR PPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNTAFSVPPL NQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVSLAKVELAPLSL YWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTT GFFRPYQDWNRKPLPTGDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNILA SCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMG GIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEKNELAIV RSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTI NALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGD QRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIEN KGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDM WKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEF ELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELKQALKNVS IKKCQIVYSGCTYTLESDGKGNVKVDKIQSATVQINNELAGALHHLRSARIRYYVKCV QEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETVSKDGCPKPKDDEEFVI SSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDR DKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPD DFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIP QGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRPT GELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGN DYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTKT KFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLE AAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLAD QASKANLMFEEGKNMTPVYTAALKDELVKTDKIYSKIKKRLLWGSDLATMIRCARAFG GLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRAVLAAA LEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLL TLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKVDPEKLTAKLREYGLKPTRPDK TEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIP HSQRPIQLMSLLGEAALHGPAFYRKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDL STWEGDRNLAPSFVNEDGVE" mat_peptide <1..958 /gene="POL" /product="protein p48" mat_peptide 959..2056 /gene="POL" /product="NTPase" /note="p41" mat_peptide 2057..2593 /gene="POL" /product="protein p22" mat_peptide 2594..2992 /gene="POL" /product="viral genome-linked protein" /note="VPg" mat_peptide 2993..3535 /gene="POL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3536..5065 /gene="POL" /product="RNA-directed RNA polymerase" gene 5049..6671 /gene="VP1" CDS 5049..6671 /gene="VP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AFX71668.1" /translation="MKMASSDASPSDGSTANLVPEVNNEVMALEPVAGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQLNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHISGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG NTTPRNEPQQWVLPSYSGRNIQNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6671..7477 /gene="VP2" CDS 6671..7477 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AFX71669.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNRKLQQA SFQFSSNQQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGASPGRANLRATVPARGSSSTSS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTMSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 cgctgttgct aacagcaaca acgacatcgc aaaatcttca agtgacggag tgctttctag 61 catggctgtc acttttaaac gagccctcgg ggcgcggcct aaacagcctc ccccgaggga 121 aaaaccacaa agacccccac gaccacctac tccagaactg gtcaaaaata ttccccctcc 181 cccacccaac ggagaggatg aaatagtggt ctcttatagt gtcaaggatg gtgtttccgg 241 cttgcctgac ctttccaccg tcaggcaacc ggaagaatcc aacacggcct tcagtgtccc 301 tccactcaac cagagggaga atagagatgc taaggagcca cttactggaa caattctgga 361 aatgtgggac ggggaaatct accattatgg cctgtatgtg gagcgaggtc ttgtactagg 421 tgtgcacaaa ccaccagctg ccgtcagcct cgctaaggtt gagctagcac cactctcctt 481 gtactggaga cctgtgtaca ctcctcagta ccttatctct ccagacactc tcaagaaatt 541 atccggagaa acgttcccct acacagcctt tgacaacaac tgttatgcct tttgttgctg 601 ggtcctggac ctaaatgact cgtggctgag caggagaatg atccagagaa caactggttt 661 cttcaggccc taccaagact ggaataggaa accccttccc actggggatg attccaaaat 721 aaagaaggta gctaacatat tcctgtgtgc tctgtcctcg ctgttcacca gacccataaa 781 agatataata gggaagataa ggcctcttaa catcctcaac atcttagcct catgtgattg 841 gacttttgca ggcatagtgg agtccctgat actcttggca gaactctttg gagttttctg 901 gacaccccca gatgtgtctg cgatgattgc ccccttactc ggtgactacg agctacaagg 961 acctgaggac cttgcagtgg agctcgtccc cgtggtgatg gggggaattg gtttggtgct 1021 aggattcacc aaagagaaga ttgggaaaat gttgtcatct gctgcgtcca ccttgagagc 1081 ttgtaaagac cttggtgcat atgggctaga gatcctaaag ttggttatga agtggttctt 1141 cccgaagaag gaggagaaaa atgagctggc tatagtgagg tctatcgagg atgcagtcct 1201 agatctcgag gcaattgaaa acaaccatat gaccaccttg ctcaaagaca aagacagtct 1261 ggcaacctat atgagaacac ttgaccttga ggaggagaaa gccaggaaac tctcaaccaa 1321 gtctgcctca cccgacatcg taggcacaat caacgccctc ctggcgagaa tcgctgccgc 1381 acgttctctg gtgcatcgag cgaaggagga gctttccagc agaccaagac ctgtggtgct 1441 gatgatatca ggcaggccag gaatagggaa gacccacctc gctagggaag tggctaagag 1501 aatcgcagcc tcccttacag gagaccagcg tgtgggcctc atcccacgca atggcgtcga 1561 ccactgggat gcgtacaagg gggaaagggt cgtcctatgg gacgattatg gaatgagcaa 1621 ccctattcac gatgccctca ggctgcaaga actcgctgac acttgccccc tcactctaaa 1681 ctgtgacagg attgaaaata aaggaaaggt ctttgacagc gatgtcatca ttatcaccac 1741 caatctggcc aacccagcac cactggacta tgtcaacttt gaagcatgct cgagacgcat 1801 cgacttcctc gtgtatgcag aagcccctga agtcgaaaag gcgaaacgtg acttcccagg 1861 ccagcctgac atgtggaaga acgctttcag tcctgatttc tcacacataa aactagcact 1921 ggccccacag ggtggtttcg acaagaacgg gaacaccccg cacggaaagg gcgtcatgaa 1981 gactctcacc actggctccc ttattgcccg ggcatcaggg ctactccatg agaggttaga 2041 tgaatttgaa ctacagggcc cagctctcac caccttcaat ttcgatcgca ataaagtgct 2101 tgcctttaga cagcttgctg ctgaaaataa atatggactg atggacacaa tgagggttgg 2161 gaaacagctc aaggatgtca gaaccatgcc agaactcaaa caagcactca agaatgtctc 2221 aatcaagaag tgccaaatag tgtatagtgg ttgcacctac acacttgagt ctgatggcaa 2281 gggcaatgtg aaggttgaca aaatccaaag cgccaccgtg cagatcaaca atgagctggc 2341 tggtgcccta caccatttga ggagcgccag aatcagatac tatgtcaagt gtgtccagga 2401 ggccctgtat tccatcattc aaattgctgg ggctgcattt gtcaccacgc gcattgccaa 2461 gcgcatgaac atacaaaacc tatggtccaa gccacaagtg gaagacacag aggagactgt 2521 cagcaaggac gggtgcccaa aacctaagga tgatgaggag tttgtcattt catccgacga 2581 catcaaaact gagggtaaga aagggaagaa caagactggc cgcggcaaga agcacacagc 2641 attttcaagc aaaggcctca gtgatgaaga gtacgatgag tacaagagga ttagagaaga 2701 aaggaatggc aagtactcca tagaagagta ccttcaggac agggacaaat actatgagga 2761 ggtggccatt gccagggcga ctgaggaaga cttctgtgaa gaggaggagg ccaagatccg 2821 gcaaaggatc tttaggccaa caaggaaaca acgcaaggag gaaagagcct ctctcggtct 2881 ggtcacaggt tctgaaatta ggaaaagaaa cccagatgac ttcaaaccca aggggaaact 2941 gtgggctgac gatgacagga atgtggacta caatgagaaa ctcagttttg aggccccacc 3001 aagcatctgg tcgagaatag tcaactttgg ttcaggctgg ggattctggg tctcccccag 3061 tctgtttata acatcaaccc atgtcatacc ccagggcgca aaggagttct ttggagtccc 3121 catcaaacaa atacaggtac acaagtcagg cgagttctgt cgcttgagat tcccaaaacc 3181 aattaggact gatgtgacgg gcatgatctt agaagaaggc gcacctgagg gcaccgtggt 3241 cacactactc ataaaaaggc ccactgggga actcatgccc ctagcagcta ggatggggac 3301 ccatgcgacc atgaagatcc aagggcgcac tgttggaggc cagatgggca tgcttctgac 3361 aggatccaac gccaagagca tggacctggg tactacacca ggtgattgtg gctgccccta 3421 tatctacaag agaggtaatg actatgtggt cattggagtc cacacggctg ccgcgcgtgg 3481 ggggaacact gtcatatgtg ccacccaggg gagtgaggga gaggctacac ttgaaggtgg 3541 tgacaacaag gggacatact gtggtgcacc aatcctaggc ccagggagtg ccccaacact 3601 tagcaccaag accaaattct ggagatcgtc cacagcatca ctcccacctg gcacctatga 3661 accagcctac cttggtggca aggaccctag agtcaagggt ggcccttcac tgcagcaagt 3721 catgagggaa cagttgaagc cattcacaga gccaaggggc aagccaccaa aaccaagtgt 3781 gttagaagct gccaagaaga ccatcatcaa tgtccttgag caaacaattg atccacctga 3841 gaagtggtcg ttcgcacaag cttgcgcgtc ccttgacaag accacttcca gtggtcatcc 3901 gcaccacatg cggaaaaacg actgctggaa cggggagtcc ttcacaggca agttggcaga 3961 ccaggcttcc aaggccaacc tgatgtttga agaagggaag aacatgaccc cagtctacac 4021 ggctgcgctc aaggatgaat tagttaaaac tgacaaaatt tatagtaaga tcaagaagag 4081 gcttctctgg ggctcggact tggcgaccat gatccggtgt gcccgagcat tcggaggcct 4141 aatggatgaa ctcaaagcac actgtgtcac gcttcccatt agagttggca tgaatatgaa 4201 tgaggatggc cccatcatct tcgagaggca ttccaggtac acgtatcact atgatgctga 4261 ttactctcga tgggattcaa cacaacagag agctgtgttg gcagcagctc tcgaaatcat 4321 ggttaaattc tccccagaac cacatttggc tcaggtagtc gcggaagacc tcctttctcc 4381 tagcgtggtg gacgtgggcg acttcacaat atcaatcaac gagggtcttc cctctggggt 4441 gccctgcacc tcccagtgga actccatcgc ccactggctt ctcactctct gcgcgctctc 4501 cgaagtcaca aacctatccc ctgataccat acaggccaac tctctcttct ctttttatgg 4561 tgatgatgaa attgttagca cagacataaa agtggaccca gagaaattga cagcaaagct 4621 cagagaatat gggttaaaac caacccgccc tgacaaaact gaaggacccc ttgtcatctc 4681 tgaagacctg aatggcctaa ctttcctgcg gagaactgtg acccgtgacc cagctggttg 4741 gtttggaaaa ctggagcaga gttcaatact caggcaaatg tactggacta ggggtcccaa 4801 ccatgaagac ccatctgaaa caatgattcc acactcccaa agacccatac aattgatgtc 4861 cctactgggg gaggccgctc tccacggccc agccttttac agaaaaatca gcaagttggt 4921 cattgcagag ttaaaagaag gtggcatgga tttttacgtg cccagacaag agccaatgtt 4981 cagatggatg agattctcag atctgagcac gtgggagggc gatcgcaatc tggctcccag 5041 ttttgtgaat gaagatggcg tcgagtgacg ccagcccatc tgatgggtcc acagccaacc 5101 tcgtcccaga ggtcaacaat gaggttatgg ctttggagcc cgtagctggt gccgccattg 5161 cggcacctgt agcgggccaa caaaatgtaa ttgacccctg gattagaaac aattttgtac 5221 aagcccctgg tggagagttt acagtatccc ctagaaacgc tccaggtgaa atactatgga 5281 gcgcgccctt aggccctgat ctgaatccct acctttccca tttggccaga atgtacaatg 5341 gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg gaacgcgttc accgccggga 5401 aaatcatatt tgcagcagtc ccaccaaatt tcccaactga aggtttgagc cccagccagg 5461 tcactatgtt cccccatata atagtagatg ttaggcaatt ggaacctgtg ttgatcccct 5521 tacccgatgt taggaataac ttctaccatt acaatcaatt aaatgacccc accatcaaat 5581 tgatagcaat gttgtacaca ccacttaggg ctaataatgc tggggacgat gtcttcacag 5641 tttcttgtcg agttcttacg agaccatccc ccgattttga tttcatattt ttggtgccac 5701 ccacagttga atcaagaact aaaccattct ctgtcccagt tttaactgtt gaggaaatga 5761 ccaattcaag gttccccatt cctttggaaa agttgttcac gggccccagt agtgccttcg 5821 ttgttcaacc acaaaatggc aggtgcacga ctgatggcgt gctcctaggt actacccaac 5881 tgtcccctgt caacatctgc accttcagag gggatgtcac ccatatttca ggcagtcgta 5941 actacacaat gaatttggcc tcccaaaatt ggaatagtta cgatccaaca gaagaaatcc 6001 cagcccctct aggaactcca gatttcgtgg ggaagattca aggtgtgctc acccaaacca 6061 caaggacaaa tggctcgacc cgcggccaca aagctacagt ttacactggg agcgccgact 6121 tttctccaaa actgggtaga gttcaatttg ccactgacac agacaatgat tttgaaacta 6181 accaaaacac aaagttcacc ccagtcggtg ttatccaaga tggtaacacc accccccgaa 6241 atgaacccca acaatgggtg ctcccaagtt actcaggcag aaacattcaa aatgtgcacc 6301 tggcccccgc tgtagccccc actttcccgg gcgagcagct cctcttcttc agatctacta 6361 tgcccggatg cagcgggtac cccaacatgg acttggactg tctgctcccc caggaatggg 6421 tgcagtactt ctaccaggaa gcagccccag cacaatctga tgtggctctg ttaagatttg 6481 tgaatccaga cacaggtagg gttttgtttg agtgtaagct tcataaatca ggctatgtta 6541 cagtggctca cactggccaa catgatttgg ttatcccccc caatggttat tttagatttg 6601 attcctgggt caaccagttc tacacacttg cccccatggg aaatgggacg gggcgtagac 6661 gtgcattata atggctggag ctttctttgc tggattggca tctgacgtcc ttggctctgg 6721 acttggttcc ctaatcaatg ctggggctgg ggtcatcaac caaaaagttg attttgaaaa 6781 taacagaaaa ttgcaacaag cttccttcca gtttagcagc aatcaacaac aggcttcctt 6841 ccaacatgac aaagagatgc tccaagcaca aattgaggcc accaaaaagt tgcaacagga 6901 aatgatgaga gttaaacaag caatgctcct agagggtgga ttctctgaga cagatgcggc 6961 ccgtggggca atcaacgccc ccatgacaaa agctctggac tggagcggga caaggtactg 7021 ggctcccgat gctaggacta caacatacaa tgcaggccgc ttttccaccc ctcaaccctc 7081 gggggcatca ccaggaagag ctaatcttag ggctaccgtc cccgcccggg gttcctccag 7141 cacgtcttct aactcttcta ttgctacttc tgtgtattca aatcaaacca cctcaacgag 7201 acttggttct acagctggtt ctggtaccag tgtctcgagc ctcccgtcaa ctgcaaggac 7261 catgagctgg gttgaggatc aaaataggaa tttgtcacct ttcatgaggg gggcccacaa 7321 catctcgttt gtcaccccac catctagcag atcctctagc caaggcacag tctcaaccgt 7381 gcccaaagaa gttttggact cctggactgg cgctttcaac acgcgcaggc agcctctctt 7441 cgctcacatt cgcaagcgag gggagtcacg ggtgtaatgt gaaaagacaa aattgat //