Typing tool
|
Complete norovirus genomes
KJ685409 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 1..5041 ORF2: 5022..6644 ORF3: 6644..7450LOCUS KJ685409 7450 bp ss-RNA linear VRL 28-JAN-2015 DEFINITION Norovirus Hu/GII/BG1C0241-32/2011/BGD, partial genome. ACCESSION KJ685409 VERSION KJ685409.1 DBLINK BioProject: PRJNA242747 KEYWORDS . SOURCE Norovirus Hu/GII/BG1C0241-32/2011/BGD ORGANISM Norovirus Hu/GII/BG1C0241-32/2011/BGD Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7450) 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-Assembly-Data-START## Current Finishing Status :: Finished Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Genome Coverage :: 185.3x Sequencing Technology :: Ion Torrent ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7450 /organism="Norovirus Hu/GII/BG1C0241-32/2011/BGD" /mol_type="genomic RNA" /strain="Hu/GII/BG1C0241-32/2011/BGD" /host="Homo sapiens; sex: F; age: 204D" /db_xref="taxon:1486688" /country="Bangladesh: Dhaka" /collection_date="13-Jul-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..5041 /gene="POL" /locus_tag="DC54_49757gpPOL" CDS <1..5041 /gene="POL" /locus_tag="DC54_49757gpPOL" /note="genome polyprotein" /codon_start=2 /product="nonstructural polyprotein" /protein_id="AHX22034.1" /translation="AKSSSDGVLSSMAVTFKRALGARPKQPPPREKPQRPPRPPTPEL VKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNTAFSVPPLNQRENRDAK EPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELAPLSLYWRPVYTPQ YLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDW NRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNILASCDWTFAGI VESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFT KEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAIVRSIEDAVLD LEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAA ARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRN GVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDV IIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDF SHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTT FNFDRNKVLAFRQLAAENKYGLVDTMRVGKQLKDVRTMPELKQALKNVSIKKCQIVYS GCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQ IAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKDDEEFVISSDDIKTEG KKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAI ARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEIRKRNPDDFKPKGKLW ADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGV PIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAAR MGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHT AAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTKTKFWRSSTAS LPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLEAAKKTIINV LEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMF EEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAH CVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRAVLAAALEIMVKFSP EPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVT NLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTRPDKTEGPLVISE DLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPSETMIPHSQRPIQLM SLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNL APSFVNEDGVE" mat_peptide <1..931 /gene="POL" /locus_tag="DC54_49757gpPOL" /product="putative protein p48" mat_peptide 932..2029 /gene="POL" /locus_tag="DC54_49757gpPOL" /product="NTPase" /note="p41" mat_peptide 2030..2566 /gene="POL" /locus_tag="DC54_49757gpPOL" /product="protein p22" mat_peptide 2567..2965 /gene="POL" /locus_tag="DC54_49757gpPOL" /product="viral genome-linked protein" /note="VPg" mat_peptide 2966..3508 /gene="POL" /locus_tag="DC54_49757gpPOL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3509..5038 /gene="POL" /locus_tag="DC54_49757gpPOL" /product="RNA-directed RNA polymerase" gene 5022..6644 /gene="VP1" /locus_tag="DC54_49757gpVP1" CDS 5022..6644 /gene="VP1" /locus_tag="DC54_49757gpVP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AHX22035.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHISGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFVTNQNTKFTPVGVIQDG STTPRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6644..7450 /gene="VP2" /locus_tag="DC54_49757gpVP2" CDS 6644..7450 /gene="VP2" /locus_tag="DC54_49757gpVP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AHX22036.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRASLRATVPARGSSSMSS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSISSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 cgcaaaatct tcaagtgacg gagtgctttc tagcatggct gtcactttta aacgagccct 61 cggggcgcgg cctaaacagc ctcccccgag ggaaaaacca caaagacccc cacgaccacc 121 tactccagaa ctggttaaaa atattccccc tcccccaccc aacggagagg atgaaatagt 181 ggtttcttat agtgtcaaag atggtgtttc cggcttgcct gacctttcca ccgtcaggca 241 gccggaagaa tccaacacgg ccttcagtgt ccctccactc aatcagaggg agaatagaga 301 tgctaaggag ccactcactg gaacaattct ggaaatgtgg gacggggaaa tctaccatta 361 tggcctgtat gtggagcgag gtcttgtact aggtgtgcac aaaccgccag ctgccatcag 421 cctcgccaag gttgagctag caccactctc cttgtactgg agacctgtgt acactcctca 481 gtacctcatc tctccagaca ctctcaagaa actgtccgga gaaacgttcc cctacacagc 541 ctttgacaac aactgttatg ccttttgttg ctgggtcctg gacctaaatg actcgtggct 601 gagcaggaga atgatccaga gaacaactgg tttcttcagg ccctaccaag actggaatag 661 gaaacccctt cccactatgg atgactccaa aataaagaag gtagctaaca tatttctgtg 721 tgctctgtcc tcgctattca ccagacccat aaaagatata atagggaaga taaggcctct 781 taacatcctc aacatcttag cctcatgtga ttggaccttt gcgggcatag tggagtccct 841 gatactcttg gcagaactct ttggagtttt ctggacaccc ccagatgtgt ctgcgatgat 901 tgccccctta cttggtgact acgagctaca aggacctgag gaccttgcag tggagctcgt 961 ccccgtggtg atggggggaa ttggtttggt gctaggattc accaaagaga agattgggaa 1021 aatgttgtca tctgctgcgt ccactttgag agcttgcaaa gaccttggcg catatgggct 1081 agagatccta aagttagtca tgaagtggtt cttcccgaag aaggaggagg caaatgagct 1141 ggctatagtg aggtccatcg aggatgcagt cctggatctc gaggcaattg aaaacaatca 1201 tatgaccacc ttgcttaaag ataaagacag tctggcaacc tacatgagaa cacttgacct 1261 tgaagaggag aaagccagga aactctcaac caagtctgcc tcacccgaca tcgtgggcac 1321 aatcaacgcc ctcctggcga gaatcgctgc cgcacgttct ctggtgcatc gagcgaagga 1381 ggagctttcc agcagaccaa gacctgtggt gttgatgata tcaggcaggc caggaatagg 1441 gaagacccac ctcgctaggg aagtggctaa gagaatcgca gcctccctta caggagacca 1501 gcgtgtgggc ctcatcccac gcaatggcgt cgaccattgg gatgcgtaca agggggagag 1561 ggtcgtccta tgggacgatt atggaatgag caaccctatt cacgatgccc tcaggctgca 1621 agaactcgct gacacttgcc cccttactct gaactgtgac aggattgaaa ataaaggaaa 1681 ggtctttgac agcgatgtca tcattatcac cactaatctg gccaacccag caccactgga 1741 ctatgtcaac tttgaagcat gctcgaggcg cattgacttc ctcgtgtatg cagaagcccc 1801 tgaagtcgaa aaggcgaagc gtgacttccc aggccagcct gacatgtgga agaacgcttt 1861 cagttctgat ttctcacaca taaaactagc actggcccca cagggtggtt tcgacaagaa 1921 cgggaacacc ccacacggaa agggcgtcat gaagactctc accactggct cccttattgc 1981 ccgggcatca gggctactcc atgagaggtt agatgaattt gaactgcagg gcccagctct 2041 caccaccttc aatttcgatc gcaataaagt gcttgccttt agacagcttg ctgctgaaaa 2101 taaatatgga ttggtggaca caatgagggt tgggaaacag ctcaaggatg tcagaaccat 2161 gccagaactc aaacaagcac tcaagaatgt ctcaatcaag aagtgtcaaa tagtgtatag 2221 tggttgcacc tacatgcttg agtctgatgg caagggcaat gtgaaagttg acagaatcca 2281 aagcgccgcc gtgcagacca acaatgagct ggctggtgcc ttgcaccact tgaggtgcgc 2341 cagaatcaga tactatgtca agtgtgtcca ggaagccctg tattccatca tccaaatcgc 2401 tggggctgca tttgtcacca cgcgcattgc caagcgcatg aacatacaag acctatggtc 2461 caagccacaa gtggaaaaca cagaggagac taccagcaag gacgggtgcc caaaacctaa 2521 ggatgatgag gagtttgtca tttcatccga cgacatcaaa actgagggca agaaagggaa 2581 gaacaagact ggccgtggca agaagcacac agcattttca agtaaaggcc tcagtgatga 2641 agagtacgat gaatacaaga ggattagaga agaaaggaat ggcaagtact ctatagaaga 2701 gtaccttcag gacagggaca aatactatga ggaggtggcc attgccaggg cgactgagga 2761 agacttctgt gaagaggagg aggccaagat ccggcaaagg atctttaggc caacaaggaa 2821 acaacgcaag gaggaaagag tctctctcgg tctggtcaca ggctctgaaa ttaggaaaag 2881 aaacccagat gacttcaaac ccaaggggaa attgtgggct gacgatgaca ggagtgtgga 2941 ctacaatgag aaactcagtt ttgaggcccc accaagcatt tggtcgagaa tagtcaactt 3001 tggttcaggc tggggattct gggtttcccc cagtctgttc ataacatcaa cccatgttat 3061 accccagggc gcaaaggagt tctttggagt ccccatcaaa caaatacagg tacacaagtc 3121 aggcgagttc tgtcgcttga gattccctaa accaatcagg actgatgtga cgggcatgat 3181 cttagaagaa ggcgcacctg agggtaccgt ggtcacacta ctcatcaaaa ggtccactgg 3241 ggaactcatg cccctagcag ctaggatggg gacccatgcg accatgaaga tccaagggcg 3301 cactgttggg ggccagatgg gcatgcttct gacaggatcc aacgccaaga gcatggacct 3361 gggtactaca ccaggtgatt gtggctgccc ctatatctac aagagaggta atgactatgt 3421 ggtcattgga gtccacacgg ctgccgcacg tgggggaaac actgtcatat gtgccaccca 3481 ggggagtgaa ggagaggcta cacttgaggg tggtgacaac aagggaacat actgtggtgc 3541 accaatccta ggcccaggga gtgccccaac acttagcacc aagaccaaat tctggagatc 3601 gtccacagca tcactcccac ctggcaccta tgaaccagcc tatcttggtg gcaaggaccc 3661 tagagtcaag ggtggccctt cactgcagca agtcatgagg gaacagttga agccattcac 3721 agagcccagg ggcaagccac caaaaccaag tgtattagaa gctgccaaga agaccatcat 3781 taatgtcctt gagcaaacaa ttgatccacc tgagaaatgg tcgttcgcac aagcttgcgc 3841 gtcccttgac aagaccactt ccagtggtca tccgcaccac atgcggaaaa acgactgctg 3901 gaacggggag tccttcacag gcaagctggc agaccaggct tccaaggcca acctgatgtt 3961 tgaagaaggg aagaacatga ccccagtcta cacagctgcg ctcaaggatg agttagttaa 4021 aactgacaaa atttatggta agatcaagaa gaggcttctc tggggctcgg acttggcgac 4081 catgatccgg tgtgctcgag cattcggagg cctaatggat gaactcaaag cgcactgtgt 4141 cacacttccc attagagttg gcatgaatat gaatgaggat ggccccatca tcttcgagag 4201 gcattccagg tacacgtacc actatgatgc tgattactct cgatgggatt caacacaaca 4261 gagagccgtg ttggcagcag ctctagaaat catggttaaa ttctccccag aaccacattt 4321 ggctcaggta gtcgcggaag accttctttc tcctagcgtg gtggacgtgg gcgacttcac 4381 aatatcaatc aacgagggtc ttccctctgg ggtgccctgc acctcccaat ggaactccat 4441 cgcccactgg cttctcactc tctgtgcgct ctctgaagtc acaaacctat ctcctgatac 4501 catacaggct aattccctct tctcttttta tggtgatgat gaaattgtta gcacagacat 4561 aaaattggac ccagagaaat tgacagcaaa gctcagagaa tatgggttaa aaccaacccg 4621 ccctgacaaa actgaaggac cccttgtcat ctctgaagac ctgaatggcc taactttcct 4681 gcggagaact gtgacccgcg acccagctgg ttggtttgga aaactggagc agagttcaat 4741 actcaggcaa atgtactgga ctaggggtcc caaccatgga gacccatctg aaacaatgat 4801 tccacactcc caaagaccca tacaattgat gtccctactg ggggaggccg ctctccacgg 4861 cccagcattt tacagcaaaa tcagcaaatt ggtcattgca gagctaaaag aaggtggtat 4921 ggatttttac gtgcccagac aagagccaat gttcagatgg atgagattct cagatctgag 4981 cacgtgggag ggcgatcgca atctggctcc cagttttgtg aatgaagatg gcgtcgagtg 5041 acgccaaccc atctgatggg tccacagcca acctcgtccc agaggtcaac aatgaggtta 5101 tggctttgga gcccgtagtt ggtgctgcta ttgcggcacc tgtagcgggc cagcaaaatg 5161 taattgaccc ctggattaga aacaattttg tacaagcccc tggtggagag tttacagtat 5221 cccctagaaa cgctccaggt gagatactat ggagcgcgcc cttaggccct gatttgaatc 5281 cctacctttc ccatttggcc agaatgtaca atggttatgc aggtggtttt gaagtgcagg 5341 taatcctcgc ggggaatgcg ttcaccgccg ggaaaatcat atttgcagca gtcccaccaa 5401 atttcccaac tgaaggtttg agccccagcc aagtcactat gttcccccac ataatagtag 5461 atgttaggca attggaacct gtgttgatcc ccttacccga tgttaggaat aatttctacc 5521 attataatca gtcaaatgac cccaccatca aattgatagc aatgttgtac acaccactta 5581 gggctaacaa tgccggggac gacgtcttca cagtttcttg tcgagtcctc acgagaccat 5641 cccccgattt tgatttcata tttttggtgc cacccacagt tgaatcaaga actaaaccat 5701 tctctgtccc agttttaact gttgaggaga tgaccaattc aaggttcccc attcctttgg 5761 aaaagttgtt cacgggcccc agtagtgcct ttgttgttca accacaaaac ggcaggtgca 5821 cgactgatgg cgtgctccta ggtactaccc aactgtctcc tgtcaacatc tgcaccttca 5881 gaggggatgt cacccacatt tcaggcagtc gtaactacac aatgaatttg gcctcccaaa 5941 attggaacag ttacgatcca acagaagaaa tcccagcccc cctaggaact ccagatttcg 6001 tggggaagat tcaaggtgtg ctcacccaaa ccacaaggac agatggctcg acccgcggcc 6061 acaaagctac agtgtacact gggagcgccg acttttctcc aaaactgggt agggttcaat 6121 ttgccactga cacagacaat gattttgtaa ctaaccaaaa cacgaagttc accccagtcg 6181 gtgttatcca ggatggtagt actacccccc gaaacgaacc ccaacaatgg gtgctcccaa 6241 gttactcagg cagaaacact cataatgtgc acctggcccc cgctgtagcc cccactttcc 6301 cgggcgagca gctcctcttc ttcagatcta ccatgcccgg atgcagcggg taccccaaca 6361 tggatttgga ctgtctgctc ccccaggaat gggtgcagta tttctaccag gaggcagccc 6421 cagcacaatc tgatgtggcg ctgttaagat ttgtgaatcc agacacaggt agggttttgt 6481 ttgagtgtaa gcttcataaa tcaggctatg ttacagtggc tcacactggc caacatgatc 6541 tagttatccc ccccaatggt tattttagat ttgattcctg ggtcaaccag ttctacacac 6601 ttgcccccat gggaaatggg acggggcgta gacgtgcatt ataatggctg gggccttctt 6661 tgccggattg gcatctgacg tccttggctc tggacttggt tccctaatca atgctggggc 6721 tggggccatc aaccaaaaag ttgaatttga aaacaacaga aaattgcaac aagcctcctt 6781 ccaatttagt agcaatctac aacaggcttc ctttcaacat gacaaagaga tgctccaagc 6841 acaaattgag gccaccaaaa agttgcaaca ggaaatgatg agagttaaac aagcaatgct 6901 cctagagggt ggattctctg agacagatgc agcccgtggg gcaatcaacg cccccatgac 6961 aaaaactttg gactggagcg gaacaaggta ctgggctccc gatgctagga ctacaacata 7021 caatgcaggc cgcttttcca cccctcaacc ctcgggggca ctaccaggaa gagctagtct 7081 tagggctact gtccccgccc ggggttcctc cagcatgtct tctaactctt ctattgctac 7141 ttctgtgtat tcaaatcaaa ccacctcgac gagacttggt tctacagctg gttctggtac 7201 cagtgtctcg agcctcccgt caactgcaag gactaggagc tgggttgagg atcaaaatag 7261 gaatttgtca cctttcatga ggggggccca caacatctcg tttgtcaccc caccatctag 7321 catatcctct agccaaggca cagtctcaac cgtgcccaaa gaagttttgg actcctggac 7381 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgcaagc gaggggagtc 7441 acgggtgtaa //