Typing tool
|
Complete norovirus genomes
EF202567 | GII.4 Farmington Hills | ||
---|---|---|---|
GII.P4 Farmington Hills |
ORF1: 1..4972 ORF2: 4953..6575 ORF3: 6575..7295LOCUS EF202567 7295 bp RNA linear VRL 23-JUL-2016 DEFINITION Norovirus Hu/GII/Toronto/SK/2002/CAN nonstructural polyprotein gene, partial cds; capsid protein gene, complete cds; and unknown gene. ACCESSION EF202567 VERSION EF202567.1 KEYWORDS . SOURCE Norovirus Hu/GII/Toronto/SK/2002/CAN ORGANISM Norovirus Hu/GII/Toronto/SK/2002/CAN Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7295) AUTHORS Kostela,J., Ayers,M., Nishikawa,J., McIntyre,L., Petric,M. and Tellier,R. TITLE Amplification by long RT-PCR of near full-length norovirus genomes JOURNAL J. Virol. Methods 149 (2), 226-230 (2008) PUBMED 18355931 REFERENCE 2 (bases 1 to 7295) AUTHORS Kostela,J. and Tellier,R. TITLE Direct Submission JOURNAL Submitted (29-DEC-2006) Paediatric Laboratory Medicine, Hospital for Sick Children, 555 University Ave, Toronto, ON M5G 1X8, Canada FEATURES Location/Qualifiers source 1..7295 /organism="Norovirus Hu/GII/Toronto/SK/2002/CAN" /mol_type="genomic RNA" /isolate="SK2002" /isolation_source="stool sample" /db_xref="taxon:440500" /country="Canada: Toronto" /collection_date="2002" /note="genotype: II" CDS <1..4972 /note="ORF 1" /codon_start=2 /product="nonstructural polyprotein" /protein_id="ABQ12780.1" /translation="SKQPPPRETPQRPPRPPTPELVKKIPPPPPNGEDEIVISYSVKD GVSGLPELSTVRQPEEANTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVD RGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDN NCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPTVDDSKLKKVANIFLCA LSSLFTRPIKDIIGKLKPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAM IAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGA YGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYM RTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMI SGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSN PIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSR RIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGK GVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLM DTMRVGRQLKDVRTMPELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTS VQTSNELTGALHHLRCARIRYYVRCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSK PQVENTEEVTNKDGCPKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSD EEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRP TRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWS RIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIR TDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLT GSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLE GGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPS LQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFTQACASLDKT TSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDK IYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERH SRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDF TISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVS TDIKLDPEKLTAKLREYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKL EQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIA ELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 4953..6575 /codon_start=1 /product="capsid protein" /protein_id="ABQ12781.1" /translation="MKMASNDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGML TQTTRGDGSTRGHKATVSTGDVHFTPKLGSIQFNTDTNNDFETGQNTKFTPVGVVQDG NGTHQNEPQQWVLPSYSGRTGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6575..>7295 /note="ORF 3" /codon_start=1 /product="unknown" /protein_id="ABQ12782.1" /translation="MAGAFFAGLASDVLGSGLGSLISAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQGMMEVKRAMLLEGGFSETDASRGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRTNPRATVPARGFSNAPS NTSTATSVYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWIEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTAVSTVPK" ORIGIN 1 gtctaaacag ccccccccga gggaaacacc acaaagaccc ccacgaccac ctactccaga 61 actggtcaaa aagatccctc ctcccccgcc caacggagag gatgaaatag tgatttctta 121 tagtgtcaaa gatggcgttt ccggtttgcc tgagctctcc accgttaggc aaccggaaga 181 agctaatacg gccttcagtg tccccccgct caatcagagg gagaacaggg atgctaagga 241 gccactgact ggaacaattc tggaaatgtg ggatggggaa atctaccatt acggcctgta 301 tgtggaccga ggtcttgtac taggcgtgca caaaccacca gctgccatta gcctcgccaa 361 ggtcgaacta acaccactct ccttgttctg gagacctgtg tatactcctc agtacctcat 421 ctctccagac actctcaaga aattacacgg agaaacgttc ccttacacag cctttgacaa 481 caattgctat gccttttgct gctgggtcct ggacctaaac gactcgtggc tgagtaggag 541 aatgatccag agaacaactg gctttttcag accctaccaa gattggaata ggaaacccct 601 ccccactgtg gatgattcca agttaaagaa ggtagctaat atattcctgt gtgctctgtc 661 ttcgctgttc accaggccca taaaagacat aatagggaag ctaaagcctc ttaacatcct 721 caacatcttg gcctcatgtg attggacttt cgcaggcata gtggagtcct tgatactcct 781 ggcagagctc tttggagttt tctggacacc cccagatgtg tctgcgatga ttgccccctt 841 actcggtgac tacgagttac aaggacccga ggaccttgca gtggagctcg tccctgtagt 901 gatgggggga attggtttgg tgctgggatt caccaaagag aagattggaa aaatgttgtc 961 atctgctgcg tccaccttga gagcttgcaa agatcttggt gcttatgggc tagagatcct 1021 aaagttggtc atgaagtggt tcttcccgaa gaaagaggaa gcaaatgaac tggctatggt 1081 gagatccatc gaggatgcag tgctggacct cgaggcaatt gaaaacaacc atatgaccac 1141 cttgctcaaa gacaaagaca gtctggcaac ctacatgaga acccttgacc ttgaggagga 1201 gaaagccaga aaactctcaa ccaagtctgc ttcacctgac atcgtgggca caatcaatgc 1261 ccttctggcg agaatcgctg ctgcacgttc cctggtgcat cgagcgaagg aggagctttc 1321 cagcagacca agacctgtgg tcttgatgat atcaggtaga ccaggaatag ggaagaccca 1381 ccttgctagg gaagtggcta agagaatcgc agcctccctc acaggagacc agcgtgtagg 1441 cctcatccca cgcaatggcg tcgatcactg ggatgcgtac aagggggaga gggtcgtcct 1501 atgggacgac tatggaatga gcaatcccat ccacgacgcc ctcaggttgc aagaactcgc 1561 tgacacttgc cccctcactc taaactgtga caggattgag aataaaggaa aggtctttga 1621 cagcgatgtc atcattatca ctactaacct ggccaaccca gcaccactgg actatgtcaa 1681 ctttgaagca tgctcgaggc gcatcgattt cctcgtgtat gcagaagccc ctgaagtcga 1741 aaaggcgaag cgtgacttcc caggccaacc tgacatgtgg aagaacgcct ttagttctga 1801 tttttcacac ataaaactag cactggctcc acagggtggc ttcgataaaa acgggaacac 1861 cccgcacggg aagggcgtca tgaagactct caccactggc tcccttattg cccgggcatc 1921 agggctactc catgagaggc tagatgagtt tgaactacag ggcccagctc tcaccacctt 1981 caactttgat cgcaacaaag tgcttgcctt taggcaactt gctgctgaaa acaaatatgg 2041 gttgatggac acaatgagag ttgggaggca gctcaaggat gtcagaacca tgccagagct 2101 taaacaagca ctcaagaata tctcaatcaa gaagtgccag atagtgtaca gtggttgcac 2161 ctacacactt gagtctgacg gcaagggcaa tgtgaaagtt gacagagttc agagcacctc 2221 cgtgcagacc agcaatgagc tgactggcgc cctgcaccac ctaaggtgtg ccagaatcag 2281 gtactatgtc aggtgtgtcc aggaggccct gtattccatc atccagattg ctggggctgc 2341 atttgtcacc acgcgcatcg tcaagcgcat gaacatacaa gacctatggt ccaagccaca 2401 agtggaaaac acagaggagg ttaccaacaa ggacgggtgc ccaaaaccca aagatgatga 2461 ggagttcgtc atttcatccg acgacattaa aactgagggt aagaaaggga agaacaagac 2521 tggtcgcggc aagaagcaca cagccttctc aagcaaaggt ctcagtgatg aagagtatga 2581 tgagtacaag aggattagag aagagaggaa tggcaagtat tccatagaag agtacctcca 2641 ggacagggac aaatactatg aggaggtggc cattgccagg gcgaccgagg aagacttctg 2701 tgaagaggag gaggccaaga tccggcaaag gatctttagg ccaacaagaa aacaacgcaa 2761 ggaggaaaga gcttctctcg gtttagtcac aggttctgaa attaggaaaa gaaacccaga 2821 tgatttcaag cccaagggga agctgtgggc tgacgatgac agaagtgtgg actacaatga 2881 gaaactcagc tttgaggccc caccaagcat ctggtcgagg atagtcaact ttggttcagg 2941 ttggggcttc tgggtctccc ccagtctgtt cataacatca acccatgtca taccccaggg 3001 cgcaaaggag ttctttggag tccccatcaa acaaattcag gtacacaaat caggcgaatt 3061 ctgtcgcttg agattcccaa aaccaatcag gactgatgtg acgggtatga tcttagaaga 3121 aggtgcgccc gaaggcaccg tggtcacact actcataaaa aggtctacag gagaactcat 3181 gcccctagca gctagaatgg ggacccatgc aaccatgaaa attcaagggc gcactgttgg 3241 aggtcagatg ggcatgcttc tgacaggatc taacgccaaa agcatggacc taggcaccac 3301 accaggtgat tgcggctgtc cctacatcta caagagagga aatgactatg tggtcattgg 3361 agtccacacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc aggggagtga 3421 gggggaggct acacttgaag gtggtgacag taaaggaaca tactgtggtg caccaatctt 3481 aggcccaggg agtgccccaa aacttagcac caagaccaaa ttctggagat cgtccacagc 3541 accactccca cctggcacct atgagccagc ttatcttggt ggcaaggacc ccagggtcaa 3601 gggtggccct tcattgcagc aagtcatgag ggatcagttg aaaccattta cagagcccag 3661 gggaaagcca ccaaagccaa gtgtgttaga agctgccaag aaaaccatca tcaatgtcct 3721 tgagcaaaca attgatccac ctgagaaatg gtcattcaca caagcttgcg cgtccctcga 3781 caagaccact tccagtggcc atccgcacca catgcggaaa aacgactgct ggaacgggga 3841 atctttcaca ggcaagctgg cagatcaggc ttccaaggcc aacctgatgt tcgaagaagg 3901 gaagaacatg accccagtct acacaggtgc gcttaaggat gaattggtca aaactgacaa 3961 aatttatggt aagatcaaga agaggcttct ctggggctcg gatttagcga ccatgatccg 4021 atgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg ttacacttcc 4081 tatcagagtt ggtatgaata tgaatgagga tggccccatc atattcgaga ggcattccag 4141 gtacagatat cactatgatg ctgattactc tcggtgggat tcaacacaac agagagctgt 4201 gttggcagca gctctagaaa tcatggttaa attctcctca gaaccacatt tggctcaggt 4261 agtcgcagaa gaccttcttt ctcctagcgt ggtggatgtg ggtgacttca caatatcaat 4321 caacgagggt ctcccctctg gggtaccctg cacctcccaa tggaactcca tcgcccactg 4381 gcttctcact ctctgtgcgc tctctgaagt tacaaatctg tcccctgaca tcatacaggc 4441 taattccctc ttctcctttt atggtgatga tgaaatcgtt agcacggaca taaaattgga 4501 cccagagaag ttgacagcaa agctcaggga atatgggctg aaaccaaccc gccctgacaa 4561 aactgaaggg ccccttgtta tctctgaaga cttaaatggt ctgactttcc tgcggagaac 4621 tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagttcaa tactcaggca 4681 aatgtactgg actaggggcc ccaaccatga agacccatct gaaacaatga ttccacactc 4741 ccaaagaccc atacagttga tgtccttact gggagaggcc gcactccacg gcccagcatt 4801 ctacagcaaa atcagcaagt tagtcattgc agagctaaaa gaaggtggca tggattttta 4861 cgtgcccagg caagagccaa tgttcagatg gatgagattc tcagatctga gcacgtggga 4921 gggcgatcgc aatctggctc ccagctttgt gaatgaagat ggcgtcgaat gacgccaacc 4981 catctgatgg gtccacagcc aacctcgtcc cagaggtcaa caatgaggtt atggctttgg 5041 agcccgttgt tggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc 5101 cctggattag aaataatttt gtacaagccc ctggtggaga gtttacagta tcccctagaa 5161 acgctccagg tgaaatacta tggagcgcgc ccttgggccc cgatctgaat ccctaccttt 5221 ctcatttggc cagaatgtac aatggctatg caggtggctt tgaagtgcag gtaatccttg 5281 cggggaatgc gttcaccgcc gggaaagtca tatttgcagc agtcccacca aatttcccaa 5341 ctgaaggctt gagccccagc caggtcacta tgttccccca tatagtagta gatgttaggc 5401 aactggaacc tgtgttgatc cccttacctg atgttaggaa caatttctat cactacaacc 5461 aatcaaatga ccccaccatt aaattgatag caatgctgta cacaccactt agggctaata 5521 atgctgggga agatgtcttc acagtctctt gtcgagtcct cacgaggcca tcccccgatt 5581 ttgatttcat atttttggtg ccacccacag ttgagtcaag aactaaacca ttcaccgtcc 5641 caattttaac tgttgaggaa atgaccaatt caagattccc cattcctttg gaaaagttgt 5701 tcacgggtcc tagcggtgcc tttgttgttc aaccacaaaa tggcaggtgc acgactgatg 5761 gcgtactctt aggcactacc caactgtctc ctgtcaacat ctgcaccttc agaggggatg 5821 tcacccacat tgcaggtact cataattaca caatgaattt ggcttctcaa aattggaaca 5881 attatgaccc aacagaagaa atcccagccc ctctggggac cccagatttc gtgggaagga 5941 tccaaggcat gctcacccaa actacaaggg gagatggctc tacccgcggc cacaaagcta 6001 cagtgagcac tggggatgtc cacttcactc caaagctggg cagtattcag ttcaacactg 6061 atacaaacaa tgattttgaa actggccaaa acacgaaatt caccccagtc ggtgttgtcc 6121 aggatggtaa tggtacccac caaaatgaac ctcaacaatg ggtgctccca agctactcag 6181 gtagaactgg tcataatgta cacctagccc ccgccgtagc ccccactttt ccgggtgagc 6241 aacttctttt cttcaggtcc actatgcccg gatgcagcgg gtaccctaac atgaatttgg 6301 attgtctact cccccaagaa tgggtgcagc acttctacca agaggcagct ccagcacaat 6361 ctgatgtggc tctgctaaga tttgtgaatc cagacacagg tagggttcta tttgagtgca 6421 agcttcataa atcaggctat gtcacagtgg ctcacactgg ccagcatgat ttggttatcc 6481 cccccaatgg ctactttaga tttgattcct gggtcaacca attctacaca cttgccccca 6541 tgggaaatgg gacggggcgt agacgtgcat tataatggct ggagctttct tcgccgggct 6601 ggcatctgat gtccttggct ctggacttgg ttccctaatc agtgctgggg ctggggccat 6661 caaccaaaaa gttgaatttg aaaataacag aaaattgcaa caagcttcct tccaatttag 6721 tagcaatcta caacaggctt cctttcaaca tgataaagag atgctccaag cacaaattga 6781 ggccactaaa aagttgcaac agggtatgat ggaagttaaa cgggcaatgc tcctagaggg 6841 tggattctct gaaacagatg catctcgtgg ggcaatcaac gcccccatga caaaggcttt 6901 ggactggagc ggaacaaggt actgggctcc tgatgctagg actacaacat acaatgcagg 6961 ccgcttttcc acccctcaac cctcgggggc attgccagga agaaccaatc ccagggctac 7021 tgtccccgct cggggcttct ccaatgcacc ttctaacact tctactgcta cttctgtgta 7081 ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggttctggca ccagtgtctc 7141 gagtctcccg tcaactgcaa gaactaggag ctggattgag gatcaaaaca ggaatttgtc 7201 acctttcatg aggggagctc acaacatatc gtttgtcacc ccaccatcta gtagatcctc 7261 tagccaaggg acagcagtct caaccgtgcc caaaa //