Typing tool
|
Complete norovirus genomes
JQ911597 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 2..5101 ORF2: 5082..6704 ORF3: 6704..7510LOCUS JQ911597 7510 bp ss-RNA linear VRL 13-MAR-2013 DEFINITION Norovirus Hu/GII/10012/2009/VNM, complete genome. ACCESSION JQ911597 VERSION JQ911597.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII/10012/2009/VNM ORGANISM Norovirus Hu/GII/10012/2009/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7510) 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., My,P.V., Campbell,J., Farrar,J., Vinh,H., Hoang,N.V., Wentworth,D.E. and Baker,S. TITLE Direct Submission JOURNAL Submitted (05-APR-2012) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA COMMENT Genome sequence lacks part of non-coding region. ##Assembly-Data-START## Assembly Method :: clc_ref_assemble_long v. 3.20.50819 Coverage :: 296.20x Sequencing Technology :: Illumina; 454; Sanger ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7510 /organism="Norovirus Hu/GII/10012/2009/VNM" /mol_type="genomic RNA" /strain="Hu/GII/10012/2009/VNM" /host="Homo sapiens; sex: F" /db_xref="taxon:1175311" /country="Viet Nam: Ho Chi Minh City" /collection_date="05-Jul-2009" /note="genotype: II" gene 2..5101 /gene="POL" CDS 2..5101 /gene="POL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AFI08239.1" /translation="MKMASNDASAAAVANGNNDTVKSSSDKMFSNMAVTFKRALGARP KQPPPGEIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVKTM PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRVVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTSLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 2..991 /gene="POL" /product="protein p48" mat_peptide 992..2089 /gene="POL" /product="NTPase" /note="p41" mat_peptide 2090..2626 /gene="POL" /product="protein p22" mat_peptide 2627..3025 /gene="POL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3026..3568 /gene="POL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3569..5098 /gene="POL" /product="RNA-directed RNA polymerase" gene 5082..6704 /gene="VP1" CDS 5082..6704 /gene="VP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AFI08240.1" /translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6704..7510 /gene="VP2" CDS 6704..7510 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AFI08241.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRTNPRTPTPARGSSSASS NASTATSILSNQTASTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 aatgaagatg gcgtctaacg acgcttccgc tgccgctgtt gctaacggca acaacgacac 61 cgtaaaatct tcaagtgaca aaatgttttc taacatggct gtcactttta aacgagccct 121 cggggcgcgg cctaaacagc cccccccggg ggaaatacca caaagacccc cacgaccacc 181 tactccagaa ctggtcaaaa agatccctcc tcccccgccc aacggagagg atgaagtagt 241 ggtttcttat agtgccaaag atggcgtttc cggtttacct gagctttcca ccgtcaggca 301 accggaagaa accaatacgg ccttcagtgt ccctccactc aaccagaggg agaatagaga 361 tgctaaggaa ccactgactg gaacaattct ggaaatgtgg gatggagaaa tctaccatta 421 tggcctgtat gttgagcgag gtcttgtgct gggtgtgcac aaaccaccag ctgccataag 481 cctcgccaag gtcgaactaa caccactctc cttgttctgg agacctgtgt acactcccca 541 gtacctcatc tctccagaca ctctcaagaa attacacgga gaaacgtttc cctacacagc 601 ctttgacaac aattgctatg ccttttgttg ttgggtcctg gatctaaatg actcgtggct 661 gagtaggaga atgatccaga gaacaactgg cttcttcaga ccctaccaag actggaatag 721 gaaacccctc cccactatgg atgattccaa attaaagaag gtagctaaca tattcctgtg 781 cgccctgtct tcgctattca ccaggcccat aaaagacata ataggaaagc taagacctct 841 caacatcatc aacatcctgg cttcatgtga ttggactttc gcaggcatag tggagtcctt 901 gatactcttg gcagagctct ttggagtctt ctggacaccc ccagatgtgt ctgcgatgat 961 tgccccctta ctcggtgatt tcgagttaca aggacctgag gaccttgtag tggagctcgt 1021 ccctgtagta atggggggaa ttggtttggt gctgggattc accaaagaga agattgggaa 1081 aatgttgtca tctgctgcat ccaccttgag agcttgtaaa gatcttggtg catatgggct 1141 agagatccta aagttagtca tgaagtggtt cttcccgaag aaagaggagg caaatgaact 1201 ggctatggtg agatccatcg aggatgcagt actggacctt gaggcaattg aaaacaacca 1261 tatgaccacc ttgctcaaag acaaagacag cctggcaacc tacatgagaa cccttgacct 1321 cgaggaagag aaagccagaa aactctcaac caagtctgct tcacctgaca tcgtgggcac 1381 aatcaacgcc cttttggcga gaatcgccgc tgcgcgctcc ctggtgcacc gagcgaagga 1441 ggagctttcc agcagaccaa gacctgtagt cttgatgata tcaggcagac cagggatagg 1501 aaaaacccac cttgctaggg aagtggctaa gagaatcgca gcctccctca caggagacca 1561 gcgtgtaggc ctcatcccac gcaatggcgt cgatcactgg gatgcgtaca agggggagag 1621 ggtcgtccta tgggacgact atggaatgag caaccccatt cacgacgccc ttaggctgca 1681 agaactcgcc gacacttgcc cccttactct aaattgtgac aggattgaga ataaaggaaa 1741 ggtctttgac agcgatgtca tcattatcac cactaatctg gccaacccag caccactgga 1801 ctatgtcaac tttgaagcgt gctcgaggcg catcgatttc ctcgtgtatg cagaagcccc 1861 cgaggtcgaa aaggcgaagc gtgacttccc gggccaacct gacatgtgga aaaacgcttt 1921 tagttctgat ttctcacaca taaaattggc actggctcca caaggtggct ttgataagaa 1981 cgggaacacc ccacacggga agggcgtcat gaagactctc accactggct ccctcattgc 2041 ccgggcatca gggctgctcc atgagagatt ggatgagttt gaactacagg gcccagctct 2101 taccaccttc aactttgacc gcaacaaagt gcttgccttc agacagcttg ctgctgaaaa 2161 caaatatggg ttgatagaca caatgaaagt tgggaggcag ctcaaggatg tcaaaaccat 2221 gccagaactt aaacaagcac tcaagaacat ctcaatcaag aagtgccaga ttgtgtatag 2281 tggttgcacc tacacacttg aatctgatgg caagggcaat gtgaaagttg acagaatcca 2341 gagcacctcc gtacagacca acaatgagct ggctggcgcc ctgcatcatc tgaggtgcgc 2401 cagaatcagg tactatgtca agtgtgtcca ggaggccctg tattctatca tccagattgc 2461 tggggctgca tttgtcacca cgcgcatcat caagcgtgtg aacattcaag acttatggtc 2521 caagccacaa gtggaaaaca cagaggaggc taccaacaag gacgggtgcc caaaacccaa 2581 agatgatgag gagttcgtca tttcatctga cgacattaaa actgagggta agaaagggaa 2641 gaacaagact ggccgtggca agaagcatac agccttctca agtaaaggtc tcagtgatga 2701 agagtatgat gagtacaaga gaattagaga ggaaaggaat ggcaagtatt ccatagaaga 2761 gtaccttcag gacagggaca aatactatga ggaggtggcc attgccaggg cgaccgagga 2821 agacttctgt gaagaggagg aggccaagat ccggcaaagg atcttcagac caacaaggaa 2881 acaacgcaag gaagaaagag cttctctcgg tttagtcaca ggttctgaga ttaggaaaag 2941 aaacccagaa gatttcaagc ctaagggaaa actatgggct gacgatgaca gaagtgtgga 3001 ctacaatgag aaactcagtt ttgaggcccc accaagcatc tggtcaagga tagtcaactt 3061 tggttcaggt tggggcttct gggtctcccc tagcctgttc ataacatcaa cccacgtcat 3121 accccagggc gcaaaggagt tctttggagt ccccatcaaa caaattcagg tacacaagtc 3181 aggcgaattc tgtcgcttga ggttcccaaa accaatcagg actgacgtga ctggcatgat 3241 cttggaagaa ggtgcgcccg aaggcaccgt ggtcacacta ctcatcaaaa ggtctactgg 3301 agaactcatg cccctagcag ctagaatggg gacccatgca accatgaaaa ttcaagggcg 3361 caccgttgga ggtcagatgg gcatgcttct gacaggatcc aacgccaaaa gcatggatct 3421 aggcaccaca ccaggtgatt gcggctgtcc ctacatctac aagagaggaa atgactatgt 3481 ggtcattgga gtccacacgg ctgccgctcg tgggggaaac actgtcatat gtgccaccca 3541 ggggggcgag ggggaagcta cacttgaagg tggtgacagt aagggaacat actgtggtgc 3601 accaatccta ggcccaggga gtgccccaaa acttagcacc aaaaccaaat tctggagatc 3661 atccacagca ccactcccac ctggcaccta tgaaccagcc taccttggtg gcaaggaccc 3721 cagagtcaag ggtggccctt cgttgcagca agtcatgagg gaccagctga aaccatttac 3781 agagcccagg ggtaagccac caaagccaag tgtgttagaa gctgccaaga aaaccatcat 3841 caatgtcctt gaacaaacaa ttgacccacc tgagaagtgg tcgttcgcgc aagcttgcgc 3901 ctcccttgac aagaccactt ctagcggcca tccgcaccat atgcggaaaa acgactgctg 3961 gaatggggag tccttcacag gcaagctggc agaccaggct tccaaggcta acctgatgtt 4021 tgaagaaggg aagaacatga ccccagtcta cacaggtgca cttaaggatg aattagtcaa 4081 aactgacaaa atttatggta agatcaagaa gaggcttctc tggggctcgg atttagcaac 4141 catgatccgg tgtgctcgag cattcggagg cctaatggat gaactcaaag cacactgtgt 4201 cacacttcct attagagttg gtatgaatat gaatgaggat ggccccatca tcttcgagaa 4261 gcattccagg tacagatacc actacgatgc tgattactct cggtgggatt caacacaaca 4321 gagagtcgtg ctggcagctg ctctagaaat catggttaaa ttctcctcag aaccacattt 4381 ggctcaggta gtcgcagaag atcttctttc ccctagcgtg gtggatgtgg gtgacttcac 4441 aatatcaatc aacgagggcc ttccctctgg ggtgccctgc acctcccaat ggaactccat 4501 cgcccactgg cttctcactc tttgtgcact ctccgaagtc acaagtttgt ctccagatat 4561 catacaggct aattctctct tctccttcta tggtgatgat gaaattgtta gtacagacat 4621 aaaattggac ccagagaagt tgacagcaaa gctcaaggaa tatgggttga aaccaacccg 4681 ccccgacaaa actgaaggac ctctcgttat ctctgaagac ttagatggtt tgactttcct 4741 gcggagaact gtgacccgcg acccagctgg ttggtttgga aaactggagc agagctcaat 4801 actcaggcaa atgtactgga ctaggggccc caaccatgaa gatccatctg aatcaatgat 4861 tccacactct caaagaccca tacaattgat gtccttactg ggagaggccg cactccacgg 4921 cccaacattc tacagtaaaa tcagcaaact agtcattgca gagctaaaag aaggtggtat 4981 ggatttttac gtgcccaggc aagagccaat gttcagatgg atgagattct cagatctgag 5041 cacgtgggag ggcgatcgca atctggctcc cagttttgtg aatgaagatg gcgtcgaatg 5101 acgccaaccc atctgatggg tccgcagcca acctcgtccc agaggtcagc aatgaggtta 5161 tggctttgga gcccgttgtc ggtgccgcta ttgcggcgcc tgtagcgggc caacaaaatg 5221 taattgaccc ctggattaga aacaattttg tacaagcccc tggtggagag ttcacagtat 5281 cccctagaaa cgctccaggt gagatactat ggagcgcgcc cttaggccct gatctgaatc 5341 cctacctatc tcacttggcc agaatgtata atggttatgc aggtggtttt gaagtgcagg 5401 tgatcctcgc ggggaacgcg ttcaccgccg gaaaaattat atttgcagca gtcccaccaa 5461 attttccaac tgaaggcctg agtcccagcc aggtcactat gttcccccac ataatagtag 5521 atgttaggca attggaacct gtgttgatcc ccttacctga tgttaggaat aatttctatc 5581 attataatca gacaaatgat tctaccatta aattgatagc aatgctgtat acaccactta 5641 gggccaataa tgctggggaa gacgtcttca cagtctcttg tcgagtcctc actaggccgt 5701 cccctgattt tgattttata tttttggtgc cacccacagt tgagtcaaga actaaaccat 5761 ttactgtccc aatcttaacc gttgaagaaa tgaccaattc aagattcccc attcctttgg 5821 aaaagttgtt cacgggtccc agcggtgcct ttgttgtcca accacaaaat ggcaggtgca 5881 cgactgatgg cgtgctctta ggcaccaccc aactgtctcc tgtcaacatc tgtaccttca 5941 gaggggatgt cacccacatt gcaggttctc gtaattacac aatgaatttg gcatctctaa 6001 attggaacaa ttatgaccca acagaagaaa ttccagcccc tctaggaact ccagatttcg 6061 tgggaaagat ccaaggtgtg ctcactcaaa ccacaaaagg agatggctcg acccgtggcc 6121 ataaagctac agtttacact gggagtgccc cctttactcc aaagctgggc agtgttcaat 6181 tcagtactga cacagaaaat gattttgaaa ctcaccaaaa cacaaaattc accccagtcg 6241 gtgtcatcca ggatggtggc accacccacc gaaatgaacc ccaacaatgg gtgctcccaa 6301 gttattcagg tagagatgtt cataatgtac acctagcccc tgctgtagcc cccacttttc 6361 cgggtgaaca acttcttttc ttcaggtcca ctatgcccgg atgcagcggg tatcccaaca 6421 tggatttgga ttgcctactc ccccaggagt gggtgcagca cttctaccaa gaggcagctc 6481 cagcacaatc tgatgtggct ctattgagat ttgtgaatcc agacacgggt agggtcctgt 6541 ttgagtgcaa acttcataaa tcaggctatg tcacagtggc tcacaccggt cagcatgatt 6601 tggtcatccc ccccaatggc tattttaggt ttgattcctg ggttaatcag ttttacacac 6661 ttgcccccat gggaaacgga acggggcgta ggcgcgcttt ataatggctg gagctttctt 6721 tgctggattg gcatctgatg tccttggctc tggacttggt tccctaatca atgctggggc 6781 tggggctatc aaccaaaaga ttgattttga aaataataga aaattgcagc aagcttcctt 6841 ccagtttagc agtaatctac aacaggcttc ctttcaacac gataaagaga tgctccaagc 6901 acaaattgag gccactaaaa agttgcaaca ggaaatgatg aaagtcaaac aggcaatgct 6961 cctagaaggt ggattctctg aaacagatgc agcccgtggg gcaatcaacg cccccatgac 7021 aaaggttttg gactggagcg gaacaaggta ctgggcccct gatgctagga ctacaacata 7081 caatgcgggc cgcttttcca cccctcaacc ttcggggacg ctgccaggaa gaaccaatcc 7141 caggactcct acccccgctc ggggctcctc tagcgcatct tctaatgctt ctactgctac 7201 ttctatactt tcaaatcaaa ctgcttcaac gagacttggt tctacagctg gttctggtac 7261 caatgtctcg agtctcccgt caactgcaag gactaggagt tgggttgagg atcaaaacag 7321 aaatttgtca cctttcatga ggggggctca caacatatcg tttgtcaccc caccatctag 7381 cagatcctct agccaaggca cagtctcaac cgtgcctaaa gaagttttgg actcctggac 7441 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaggc gaggggagtc 7501 acgggtgtaa //