Typing tool
|
Complete norovirus genomes
KJ685408 | GII.4 New Orleans | ||
---|---|---|---|
GII.P4 New Orleans |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7509LOCUS KJ685408 7509 bp ss-RNA linear VRL 28-JAN-2015 DEFINITION Norovirus Hu/GII/BG1C0066/2011/BGD, complete genome. ACCESSION KJ685408 VERSION KJ685408.1 DBLINK BioProject: PRJNA242747 KEYWORDS . SOURCE Norovirus Hu/GII/BG1C0066/2011/BGD ORGANISM Norovirus Hu/GII/BG1C0066/2011/BGD Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7509) AUTHORS Das,S.R., Halpin,R.A., Mohan,M., Fedorova,N., Tsitrin,T., Puri,V., Stockwell,T., Amedeo,P., Bishop,B., Gupta,N., Hoover,J., Katzel,D., Schobel,S., Shrivastava,S., Ahmed,T., Haque,R., Knobler,S., Miller,M., Wentworth,D.E. and Nelson,M. TITLE Direct Submission JOURNAL Submitted (03-APR-2014) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA COMMENT This work was supported by the National Institute of Allergy and Infectious Diseases (NIAID), Genome Sequencing Centers for Infectious Diseases (GSCID) program. The genome sequence was generated using overlapping PCR amplicons spanning the genome. The amplicons were pooled by sample and then barcoded and sequenced using Next Generation Sequencing platforms. The consensus sequences of the internal PCR primer hybridization sites were manually verified using reads from amplicons that spanned across the sites. Genome sequence lacks part of non-coding region. ##Genome-Assembly-Data-START## Current Finishing Status :: Finished Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Genome Coverage :: 178.3x Sequencing Technology :: Ion Torrent ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7509 /organism="Norovirus Hu/GII/BG1C0066/2011/BGD" /mol_type="genomic RNA" /strain="Hu/GII/BG1C0066/2011/BGD" /host="Homo sapiens; sex: M; age: 295D" /db_xref="taxon:1486685" /country="Bangladesh: Dhaka" /collection_date="15-Mar-2011" /PCR_primers="fwd_name: Ampl_1_Forward, fwd_seq: gtgaatgawgatggcgt, rev_name: Ampl_1_Reverse, rev_seq: ttggttgagagyttyctg" /PCR_primers="fwd_name: Ampl_2_Forward, fwd_seq: ccgcaaaatcttcaagtg, rev_name: Ampl_2_Reverse, rev_seq: cwacaggtcttggtctgctrga" /PCR_primers="fwd_name: Ampl_3_Forward, fwd_seq: tcaaccaartctgcttcacctg, rev_name: Ampl_3_Reverse, rev_seq: ratcctttgccggatcttgg" /PCR_primers="fwd_name: Ampl_4_Forward, fwd_seq: ggcaagaagcacacagcctt, rev_name: Ampl_4_Reverse, rev_seq: crrctctytgttgtgttgaatccc" /PCR_primers="fwd_name: Ampl_5_Forward, fwd_seq: tggyaagatcaagaagaggc, rev_name: Ampl_5_Reverse, rev_seq: acaacaaargcacygctrgg" /PCR_primers="fwd_name: Ampl_6_Forward, fwd_seq: gagrccrtccccygattttg, rev_name: Ampl_6_Reverse, rev_seq: atcaatyttgtcttttcaca" /note="genotype: GII" gene 1..5100 /gene="POL" /locus_tag="DC54_49735gpPOL" CDS 1..5100 /gene="POL" /locus_tag="DC54_49735gpPOL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AHX22031.1" /translation="MKMASIDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPSPREKPQRPPRPPTPELVKNMPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGNIKKRLLWGSDL ATMIRCARAFGGLMDEFKAHCVTLPIRVGMNMNEDGPIIFEKHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 1..990 /gene="POL" /locus_tag="DC54_49735gpPOL" /product="protein p48" mat_peptide 991..2088 /gene="POL" /locus_tag="DC54_49735gpPOL" /product="NTPase" /note="p41" mat_peptide 2089..2625 /gene="POL" /locus_tag="DC54_49735gpPOL" /product="protein p22" mat_peptide 2626..3024 /gene="POL" /locus_tag="DC54_49735gpPOL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3025..3567 /gene="POL" /locus_tag="DC54_49735gpPOL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3568..5097 /gene="POL" /locus_tag="DC54_49735gpPOL" /product="RNA-directed RNA polymerase" gene 5081..6703 /gene="VP1" /locus_tag="DC54_49735gpVP1" CDS 5081..6703 /gene="VP1" /locus_tag="DC54_49735gpVP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AHX22032.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQTILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHISGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG GTTHQNEPQQWVLPSYSGRDTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6703..7509 /gene="VP2" /locus_tag="DC54_49735gpVP2" CDS 6703..7509 /gene="VP2" /locus_tag="DC54_49735gpVP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AHX22033.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQVMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALSGRANLRATAPARGSSSTSS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSPPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 atgaagatgg cgtctatcga cgcttccgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caagtgacgg agtgctttct agcatggctg tcacttttaa acgagccctc 121 ggggcgcggc ctaaacagcc ttccccgagg gaaaaaccac aaagaccccc acgaccacct 181 actccagaac tggttaaaaa tatgccccct cccccaccca acggagagga tgaaatagtg 241 gtctcttata gtgtcaaaga tggtgtttcc ggcttgcctg acctttccac cgtcaggcaa 301 ccggaagaat ctaacacggc ctttagtgtc cctccactca atcagaggga gaatagagat 361 gctaaggagc cacttactgg aacaatcctg gaaatgtggg atggggaaat ctaccattat 421 ggcctgtatg tggagcgagg tcttgtacta ggtgtgcaca aaccaccagc tgccatcagc 481 ctcgctaagg ttgaactagc accactctcc ttgtactgga ggcctgtgta cacccctcag 541 tacctcatct ctccagacac tctcaagaaa ttatccggag aaacgttccc ctacacagcc 601 tttgacaaca actgttatgc cttttgttgc tgggtcctgg atctaaatga ctcgtggctg 661 agcaggagaa tgatccagag aacaactggt ttcttcaggc cctaccaaga ctggaatagg 721 aaacccctcc ccactatgga tgactccaaa ataaagaagg tggctaacat attcctgtgt 781 gccctgtcct cgctgttcac cagacccata aaagatataa tagggaagat aaggcctctt 841 aacatcctca acatcttagc ctcatgtgat tggacttttg caggcatagt ggagtccctg 901 atactcttgg cagaactctt cggagttttc tggacacccc cagatgtgtc tgcgatgatt 961 gcccccttgc ttggtgacta cgagctacaa ggacctgagg accttgcagt ggagctcgtc 1021 cccgtggtga tggggggaat tggtttggtg ctaggattca ccaaagagaa gattggaaaa 1081 atgttgtcat ctgctgcgtc caccttgaga gcctgtaaag accttggtgc atatgggcta 1141 gagatcctaa agttggtcat gaagtggttc ttcccgaaga aggaggaggc aaatgagctg 1201 gctatagtga ggtctatcga ggatgcagtc ctggatctcg aggcaattga aaacaaccat 1261 atgaccacct tgctcaaaga caaagacagt ctggcaacct atatgagaac acttgacctt 1321 gaggaggaga aagccaggaa actctcaacc aagtctgcct cacccgacat cgtgggcaca 1381 atcaacgccc tcctggcgag aatcgctgcc gcacgttctc tggtgcatcg agcgaaggag 1441 gagctttcca gcagaccaag acctgtggtg ttgatgatat caggcaggcc aggaataggg 1501 aagacccacc tcgctaggga agtggctaag agaatcgcag cctcccttac aggagaccag 1561 cgtgtgggcc tcatcccacg caatggcgtc gaccattggg atgcgtacaa gggggagagg 1621 gtcgtcctat gggacgatta tggaatgagc aaccctattc acgatgccct caggcttcaa 1681 gaactcgctg acacttgccc cctcactcta aactgtgaca ggattgaaaa taaaggaaag 1741 gtctttgaca gcgatgtcat cattatcacc actaatctgg ccaacccagc accactggac 1801 tatgtcaact ttgaagcatg ctcgaggcgc atcgacttcc tcgtgtatgc agaagcccct 1861 gaagtcgaaa aggcaaagcg tgacttccca ggccagcctg acatgtggaa gaacgctttc 1921 agttctgatt tctcacacat aaaactagca ctggccccac agggtggctt cgacaagaac 1981 gggaacaccc cacacggaaa gggcgtcatg aagactctca ccactggctc ccttattgcc 2041 cgggcatcag ggctactcca tgagaggtta gatgaatttg aactacaggg cccagctctc 2101 accaccttca atttcgatcg caataaagta cttgccttta ggcagcttgc tgctgaaaat 2161 aaatatggat tgatggacac aatgagagtt gggaaacagc ttaaggatgt cagaaccatg 2221 ccagaactca aacaagcact caagaatgtc tcaatcaaga agtgccaaat agtgtacagt 2281 ggctgcacct acatacttga gtctgatggc aagggcaatg tgaaagttga cagaatccaa 2341 agcgccgccg tgcagaccaa caatgagctg gctggtgccc tgcaccattt gaggtgcgcc 2401 agaatcagat actatgtcaa gtgtgtccag gaggccctgt attccatcat tcaaattgct 2461 ggggctgcat ttgtcaccac gcgcattgcc aagcgcatga acatacaaga cctatggtcc 2521 aagccacaag tggagaacac agaggagact accagcaagg acgggtgccc aaaacctaag 2581 gatgatgagg agtttgtcat ttcatccgac gacatcaaaa ctgagggtaa gaaagggaag 2641 aacaaaactg gccgcggcaa gaagcacaca gcattttcaa gcaaaggcct cagtgatgaa 2701 gagtacgacg agtacaagag gattagagaa gaaaggaatg gcaagtactc catagaagag 2761 taccttcagg acagggacaa atactatgag gaggtggcca tcgccagggc gactgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tctttaggcc aacaaggaaa 2881 caacgcaagg aggaaagggc ctctctcggt ctggtcacag gctctgaaat taggaaaaga 2941 aacccagacg acttcaaacc caaggggaaa ttgtgggctg acgatgacag gagcgtggac 3001 tacaacgaga aactcagttt tgaggcccca ccaagcatct ggtcgagaat agtcaacttt 3061 ggttcaggct ggggattctg ggtctccccc agtctgttca taacatcaac ccatgtcata 3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaatacaggt gcacaagtca 3181 ggcgagttct gtcgcttgag attcccaaaa ccaatcagga ctgatgtgac gggcatgatc 3241 ttagaagagg gcgcacctga gggcaccgta gtcacactac tcatcaaaag gtccaccggg 3301 gaactcatgc ccctagcagc taggatgggg acccatgcga ccatgaagat ccaagggcgc 3361 actgttggag gccagatggg catgcttctg acaggatcca acgccaagag catggacctg 3421 ggtactacac caggtgattg tggctgcccc tatatctaca agagaggtaa tgattatgtg 3481 gtcattggag tccacacggc tgccgcacgt ggggggaaca ctgtcatatg tgccacccag 3541 gggagtgaag gagaggctac acttgaaggt ggtgacaaca aggggacata ctgtggtgca 3601 ccaatcctag gcccagggag tgccccaaca cttagcacca agaccaaatt ctggagatcg 3661 tccacagcac cactcccacc tggcacctat gaaccagctt atcttggtgg caaggaccct 3721 agagtcaagg gtggcccttc tctgcagcaa gtcatgaggg aacagttgaa gccattcaca 3781 gagcccaggg gcaagccacc aaaaccaagt gtattagaag ctgccaagaa gaccatcatc 3841 aatgtccttg agcaaacaat tgatccacct gagaaatggt cgttcgcaca agcttgcgcg 3901 tcccttgaca aaaccacttc cagtggtcat ccgcaccaca tgcggaaaaa cgactgctgg 3961 aacggggagt ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt 4021 gaagaaggga agaacatgac cccagtctac acagctgcgc tcaaggatga gttagttaaa 4081 actgataaaa tttatggtaa tatcaagaag aggctcctct ggggctcgga cctggcgacc 4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aattcaaagc acactgtgtc 4201 acacttccca ttagagttgg catgaatatg aatgaggatg gccccatcat cttcgagaag 4261 cattccaggt acacatatca ctatgatgct gattactctc gatgggattc aacacaacag 4321 agagccgtgt tggcagcagc tctagaaatc atggtcaagt tctccccaga accacatttg 4381 gctcaagtag tcgcggaaga ccttctttct cctagcgtgg tggacgtggg cgacttcaca 4441 atatcaatca acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc 4501 gcccactggc ttctcactct ctgtgcgctc tctgaagtca caaacctgtc ccctgatacc 4561 atacaggcta actccctctt ctctttttat ggtgatgatg aaattgttag cacagacata 4621 aaattggacc cagagaaatt gacagcaaag ctcagagaat atgggttaaa accaacccgc 4681 cctgacaaaa ccgaaggacc ccttgtcatc tctgaagacc tgaatggcct aactttcctg 4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagttcaata 4801 ctcaggcaaa tgtactggac tagaggtccc aaccatggag acccatctga aacaatgatt 4861 ccacactccc aaagacccat acaattgatg tccctactag gggaggccgc tctccacggc 4921 ccagcatttt acagcaaaat cagcaaattg gtcattgcag agctaaaaga aggtggcatg 4981 gatttttacg tgcccagaca ggagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga 5101 cgccaaccca tctgatgggt ccacagccaa cctcgtccca gaggtcaaca atgaggttat 5161 ggctttggag cccgtggttg gtgccgcaat tgcggcacct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagagt ttacagtatc 5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atttgaaccc 5341 ctacctttcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcagac 5401 aatcctcgcg gggaacgcgt tcaccgccgg gaaaatcata tttgcagcag tcccaccaaa 5461 tttcccaact gaaggtttga gccccagcca ggttactatg ttcccccaca taatagtaga 5521 tgttaggcaa ttggaacctg tgttgattcc cttacccgat gttagaaata atttctacca 5581 ttacaatcaa acaaatgacc ccaccatcaa attgatagca atgttgtaca caccacttag 5641 ggccaataat gccggggacg atgtcttcac agtttcttgt cgagttctca caagaccatc 5701 ccccgatttt gatttcatat ttttggtgcc acccacagtt gaatcaagaa ctaaaccatt 5761 ctctgtcccg gttttaactg ttgaggagat gaccaattca aggttcccca ttcctttgga 5821 gaaattattc acgggcccca gtagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac 5881 gactgatggc gtgctcctag gtactaccca actgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacattt caggcagtcg taactacaca atgaatttgg cctcccaaaa 6001 ttggaacagt tacgatccaa cagaagaaat cccagcccct ctaggaactc cagatttcgt 6061 ggggaagatt caaggtgtgc tcacccaaac cacaaggaca gatggctcga cccgcggcca 6121 caaagctaca gtgtacactg ggagcgccga cttttctcca aaactgggca gagttcaatt 6181 tgccactgat acagacaatg attttgaaac taaccaaaat acaaagttca ccccagtcgg 6241 tgttatccag gatggtggta ccacccacca aaatgaaccc caacaatggg tactcccaag 6301 ttactcaggc agagacactc acaatgtgca cctggccccc gctgtagctc ccactttccc 6361 gggcgagcag ctcctcttct tcagatctac tatgcccgga tgcagcgggt accccaacat 6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtat ttttaccagg aggcagcccc 6481 agcacaatct gatgtggctc tgttaagatt tgtgaatcca gatacaggta gggtcttgtt 6541 tgagtgtaaa cttcataaat caggctatgt tacagtggct cacactggcc aacatgattt 6601 ggttatcccc cccaatggtt attttagatt tgactcctgg gtcaaccagt tctacacact 6661 tgcccccatg ggaaatggga cggggcgtag acgtgcacta taatggctgg agctttcttt 6721 gctggattgg catctgacgt ccttggctct ggacttggtt ccctaatcaa tgctggggct 6781 ggggccatca accaaaaagt tgaatttgaa aacaacagaa aactgcaaca agcttccttc 6841 caatttagca gcaatctaca acaggcttcc tttcaacatg acaaagagat gcttcaagca 6901 caaattgagg ccaccaaaaa gttgcaacag gaaatgatga gagttaaaca agtaatgctc 6961 ctagagggtg gattctctga gacagatgca gcccgtgggg caatcaacgc ccccatgaca 7021 aaagctttgg actggagcgg gacaaggtac tgggctcccg atgctaggac tacaacatat 7081 aatgcaggcc gcttttccac ccctcaaccc tcgggggcac tatcaggaag agctaatctt 7141 agggctactg cccccgcccg gggttcctcc agtacgtctt ctaactcttc tattgctact 7201 tctgtgtatt caaatcaaac cacctcaacg agacttggtt ctacagctgg ttctggtacc 7261 agtgtctcga gccccccgtc aactgcaagg actaggagct gggttgagga tcaaaacagg 7321 aatttatcac ctttcatgag gggggcccac aacatctcat ttgtcacccc accatctagc 7381 agatcctcta gccaaggcac agtctcaacc gtgcccaaag aagttttgga ctcctggact 7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcata ttcgcaagcg aggggagtca 7501 cgggtgtaa //