Typing tool
|
Complete norovirus genomes
KC576912 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7509LOCUS KC576912 7509 bp ss-RNA linear VRL 23-OCT-2013 DEFINITION Norovirus Hu/GII.4/NIHIC4.1/2011/USA, complete genome. ACCESSION KC576912 VERSION KC576912.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII.4/NIHIC4.1/2011/USA ORGANISM Norovirus Hu/GII.4/NIHIC4.1/2011/USA Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7509) AUTHORS Madupu,R., Halpin,R.A., Ransier,A., Fedorova,N., Tsitrin,T., McLellan,M., Stockwell,T., Amedeo,P., Appalla,L., Bishop,B., Edworthy,P., Gupta,N., Hoover,J., 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 (01-FEB-2013) 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 :: 228.3x Sequencing Technology :: Sanger; Illumina; 454 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7509 /organism="Norovirus Hu/GII.4/NIHIC4.1/2011/USA" /mol_type="genomic RNA" /strain="Hu/GII.4/NIHIC4.1/2011/USA" /host="Homo sapiens" /db_xref="taxon:1292142" /country="USA: Maryland" /collection_date="31-Jan-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" /PCR_primers="fwd_name: Ampl_7_Forward, fwd_seq: gtgaatgawgatggcgt, rev_name: Ampl_7_Reverse, rev_seq: ccagrctrtctttrtctt" /note="genotype: GII.4" gene 1..5100 /gene="POL" CDS 1..5100 /gene="POL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AGE99602.1" /translation="MKMASNDASAAAVANSNNDTAKSSNDKMFSNMAVTLKRALGARP KQPPPREIPQRPPRPPTPELIKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS HARVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGR LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKIGRQLKDVKTM PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSRGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 1..990 /gene="POL" /product="protein p48" mat_peptide 991..2088 /gene="POL" /product="NTPase" /note="p41" mat_peptide 2089..2625 /gene="POL" /product="protein p22" mat_peptide 2626..3024 /gene="POL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3025..3567 /gene="POL" /product="3C-like protease" /note="3CLpro; calcivirin" mat_peptide 3568..5097 /gene="POL" /product="RNA-directed RNA polymerase" gene 5081..6703 /gene="VP1" CDS 5081..6703 /gene="VP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AGE99603.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRSNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQMILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSADFTPKLGSVQFGTDTDNDFETHQNTRFTPVGVIQDG ATTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPNFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6703..7509 /gene="VP2" CDS 6703..7509 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AGE99604.1" /translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQELMKVKQTILLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRINPRTPIPARGSPSISS NASTATSIHSNQTASTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKDVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caaatgacaa gatgttttct aacatggctg tcactcttaa aagagccctc 121 ggggcgcggc ctaaacagcc ccccccgagg gaaataccac aaagaccccc acgaccacct 181 actccagaac tgatcaaaaa gatccctcct cccccgccca acggagagga tgaagtagtg 241 gtttcttata gtgccaaaga tggcgtttcc ggtttgcctg agctttccac cgtcaggcaa 301 ccggaagaaa ccaatacggc cttcagtgtc cctccactca atcagaggga gaatagggac 361 gctaaggaac cactgactgg aacaattctg gaaatgtggg atggagaaat ctaccattat 421 ggcctgtatg ttgagcgagg tcttgtgctg ggtgtgcaca aaccaccagc tgccattagc 481 cacgccaggg tcgaattaac accactctcc ttgttctgga gacctgtgta cactcctcag 541 tacctcattt ctccagacac tctcaagaag ttacacggag aaacatttcc ctacacagcc 601 tttgacaaca actgctatgc cttttgttgt tgggtcctgg acctaaacga ctcgtggctg 661 agtaggagaa tgatccagag aacaactggc ttcttcagac cctaccaaga ttggaatagg 721 aaacccctcc ccactatgga tgattccaaa ttaaagaagg tagctaacat attcctgtgt 781 gccctgtctt cgctattcac caggcccata aaagacataa taggaaggtt aaggcctctc 841 aacatcatca acatcctggc ctcatgtgat tggactttcg cgggcatagt ggagtccttg 901 atactcttgg cagagctctt tggagttttc tggacacccc cagatgtgtc tgcgatgatt 961 gcccccttac tcggtgattt cgagttacaa ggacctgaag accttgtagt ggagctcgtc 1021 cctgtagtaa tgggggggat tggtctggtg ctaggattca ccaaagagaa gattggaaaa 1081 atgttgtcat ctgctgcatc caccttgaga gcttgtaaag accttggtgc atatgggcta 1141 gaaatcttaa agttagtcat gaagtggttc ttcccgaaga aagaggaagc taatgaactg 1201 gccatggtga gatccatcga ggatgcggta ctggaccttg aggcaattga aaacaaccat 1261 atgaccacct tgctcaaaga caaagatagc ctggcaacct acatgagaac ccttgacctc 1321 gaggaagaga aagccagaaa actctcaacc aagtctgctt cacctgacat cgtgggcaca 1381 atcaacgcgc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag 1441 gagctttcca gcagaccaag acctgtagtc ttgatgatat caggcaggcc aggaataggg 1501 aagacccacc ttgctaggga agtggctaag agaatcgcag cctccctcac aggagaccag 1561 cgtgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggggagagg 1621 gtcgtcctat gggacgacta tggaatgagc aatcccatcc acgacgccct cagactgcaa 1681 gaactcgctg atacttgccc cctcacccta aattgtgaca ggattgagaa taaaggaaag 1741 gtctttgaca gcgatgtcat cattatcact actaatctgg ccaacccagc gccactggac 1801 tatgtcaact ttgaagcatg ctcgaggcgc atcgatttcc tcgtgtacgc agaagccccc 1861 gaggtcgaaa aggcgaagcg cgacttcccg ggccaacctg acatgtggaa aaacgctttt 1921 agttctgatt tctcacacat aaaactggca ctggctccgc aaggtggctt tgataagaac 1981 gggaacaccc cacacgggaa gggcgtcatg aagactctca ccactggctc cctcattgcc 2041 cgggcatcag ggctgctcca cgagagattg gatgagtttg aactacaggg cccagctctc 2101 accaccttca actttgaccg caacaaagtg cttgccttta gacagcttgc tgctgaaaac 2161 aaatatgggt tgatggacac aatgaaaatt gggaggcagc tcaaggatgt caaaaccatg 2221 ccagaactta aacaagcact caagaatatc tcaatcaaga agtgccagat tgtgtacagt 2281 ggttgcacct acacacttga gtctgatggc aaaggcaatg tgaaagttga cagagtccag 2341 agtacctccg ttcagactaa caatgagttg gctggcgccc tgcaccatct aaggtgcgcc 2401 agaatcaggt attatgttaa gtgtgttcag gaggccctgt attctatcat ccagattgct 2461 ggggctgcat ttgtcaccac gcgcatcatc aagcgtgtga acattcaaga cttatggtcc 2521 aagccacaag tggaaaacac agaggaggct accagcaaag acgggtgccc aaaacccaaa 2581 gatgatgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaggggaag 2641 aacaagactg gccgtggtaa aaagcataca gccttctcaa gtaaaggtct cagtgatgaa 2701 gagtatgatg agtacaagag aattagagag gaaagaaatg gcaagtactc catagaagag 2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tcttcagacc aacaaggaaa 2881 caacgcaagg aagaaagggc ttctctcggt ttagtcacag gttctgaaat taggaaaaga 2941 aatccagaag acttcaagcc caaggggaaa ctatgggctg acgatgacag aagtgtggac 3001 tacaatgaaa aactcagttt tgaggcccca ccaagcatct ggtcaaggat agtcaacttt 3061 ggttcaggtt ggggcttctg ggtctccccc agcctgttca taacatcaac ccacgtcata 3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaattcaggt gcacaagtca 3181 ggcgaattct gtcgcttgag gttcccaaaa ccaatcagga ctgatgtgac tggcatgatc 3241 ttggaagaag gtgcgcccga aggcaccgtg gtcacactac tcatcaaaag gcctactgga 3301 gaactcatgc ccctagcagc tagaatggga acccacgcaa ccatgaaaat tcaagggcgc 3361 actgttggag gtcagatggg catgcttctg acagggtcca acgccaaaag catggatcta 3421 ggtaccacac caggtgattg cggctgtccc tacatctaca agagaggaaa cgactatgtg 3481 gtcattggag tccacacggc tgccgctcgt gggggaaaca ctgtcatatg tgccacccag 3541 gggggtgagg gggaagctac acttgaaggt ggtgacagta ggggaacata ctgtggtgca 3601 ccaatcctag gcccagggag tgccccaaaa ctcagcacca aaaccaaatt ctggagatca 3661 tccacagcac cacttccacc tggcacctat gaaccagcct accttggtgg taaagacccc 3721 agagtcaagg gtggcccctc gttgcagcaa gtcatgaggg accagctgaa accatttaca 3781 gagcctaggg gtaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc 3841 aatgtccttg aacagacaat tgacccacct gagaagtggt cgttcgcaca agcttgcgcg 3901 tcccttgata agaccacttc tagcggccat ccgcaccaca tgcggaaaaa cgactgctgg 3961 aacggggagt ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt 4021 gaagaaggga agaacatgac cccagtctac acaggtgcac ttaaggatga attagtcaaa 4081 actgacaaaa tttatggcaa gatcaagaag aggcttctct ggggctcgga tttggcaacc 4141 atgatccggt gtgctcgagc attcggaggt cttatggatg aactcaaagc acactgtgtc 4201 acacttcctg tcagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag 4261 cattccaggt acagatacca ctatgatgct gattactctc ggtgggattc aacacaacag 4321 agagccgtgc tggcagctgc tctagaaatc atggttaaat tctcctcaga accacatttg 4381 gctcaggtag tagcagaaga ccttctttct cctagcgtag tggatgtggg tgacttcaca 4441 atatcaatca acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc 4501 gcccactggc ttctcactct ctgcgcactc tccgaagtca caaatttgtc tccagacatc 4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacagacata 4621 aaattagacc cagagaagtt gacagcaaag cttaaggaat atgggttgaa accaacccgc 4681 cctgacaaaa ctgaagggcc tcttgttatt tctgaagact tagacggttt gacttttctg 4741 cggagaactg tgacccgcga ccctgctggt tggtttggaa aactggagca gagctcaata 4801 ctcaggcaaa tgtactggac taggggcccc aaccatgaag acccatctga atcaatgatc 4861 ccacactctc aaagacccat acaattgatg tccttactgg gagaggccgc actccacggc 4921 ccaacattct acagtaaaat cagcaagtta gtcattgcag agctaaaaga aggtggcatg 4981 gatttttacg tgcccaggca ggagccaatg ttcagatgga tgagattctc ggatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga 5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat 5161 ggctttggag cccgttgtcg gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa gtaactttgt acaagcccct ggtggagagt tcacagtatc 5281 ccctagaaac gctccaggtg aaatactttg gagcgcgccc ttaggccctg atctgaatcc 5341 ctacctatct catttggcca gaatgtataa tggttatgca ggtggttttg aagtgcagat 5401 gatcctcgcg gggaacgcgt tcaccgcggg aaaaattata tttgcagcag tcccaccaaa 5461 ttttccaact gaaggcttga gtcccagcca ggtcactatg ttcccccaca taatagtaga 5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata acttctatca 5581 ctataaccag tcaaatgatc ctaccattaa attgatagca atgctgtata caccactcag 5641 ggccaataat gccggggatg atgtcttcac agtctcttgt cgagtcctca cgaggccatc 5701 ccctgatttt gacttcatat ttctggtgcc acctacagtt gagtcaagaa ctaaaccatt 5761 tactgtccca gtcttgactg ttgaagaaat gaccaattca agattcccca ttcctttgga 5821 gaaattgttc acgggtccca gcagtgcctt tgttgttcaa ccacaaaatg gcagatgcac 5881 aactgatggc gtgctcttag gcaccaccca gctgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacattg cgggttcccg taattacaca atgaatttgg cctctctaaa 6001 ttggaacaat tatgacccaa cagaagagat tccagcccct ctgggaactc cagatttcgt 6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaggga gatggctcga cccggggcca 6121 taaagctaca gtttacactg ggagtgccga cttcactcca aagctgggca gtgttcaatt 6181 tggtactgat acagataatg actttgaaac tcaccaaaac acaagattta ccccagtcgg 6241 tgtcatccag gatggtgcga ccacccaccg aaatgaaccc caacaatggg tgctcccaag 6301 ttattcagga agaaatgtcc ataatgtaca cctagcccct gctgtagccc ccaattttcc 6361 gggcgaacaa cttcttttct tcaggtccac tatgcccgga tgcagcgggt atcccaacat 6421 ggatttggat tgcctactcc cccaggagtg ggtgcaacac ttctaccaag aggcagctcc 6481 agcacaatcc gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcttgtt 6541 tgagtgcaaa ctccataaat caggctatgt cacagtggct cataccggcc aacatgattt 6601 ggtcatcccc cccaatggtt attttaggtt tgattcctgg gttaatcagt tctacacact 6661 tgcccccatg ggaaatggaa cggggcgcag acgtgcttta taatggctgg agctttcttt 6721 gctggattgg catctgatgt ccttagctct ggacttggtt ccctaatcaa tgctggggct 6781 ggggctatca accaaaagat tgattttgaa aataatagaa aattgcagca agcttccttt 6841 cagtttagca gcaatctaca acaagcttcc tttcaacatg ataaagagat gctccaagca 6901 caaattgagg ccactaaaaa gttgcaacag gaactgatga aagtcaaaca gacaatactc 6961 ttagaaggtg gattttctga aacagatgca gcccgtgggg caatcaacgc ccccatgaca 7021 aaggctttgg actggagtgg gacaaggtac tgggcccctg atgctaggac tacaacatac 7081 aatgcaggcc gcttttccac ccctcaacct tcgggggcac tgccaggaag aatcaatccc 7141 aggactccta tccccgcccg gggctccccc agcatatctt ccaatgcttc tactgctact 7201 tctatacatt caaatcaaac tgcttcaacg agacttggtt ctacagctgg ttctggcacc 7261 aatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga 7321 aatttgtcac ctttcatgag gggggctcac aacatatcgt ttgtcacccc accatctagc 7381 agatcctcca gccaaggcac agtctcaacc gtgcctaaag atgttttgga ctcctggact 7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaggcg aggggagtca 7501 cgggtgtaa //