Typing tool
|
Complete norovirus genomes
MN996299 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5007 ORF2: 4988..6610 ORF3: 6610..7416LOCUS MN996299 7431 bp RNA linear VRL 15-JUL-2020 DEFINITION Norovirus GII isolate SCD1062_2 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MN996299 VERSION MN996299.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7431) AUTHORS Zhang,Z., Wang,D., Liu,D., Zhang,Z. and Wu,Q. TITLE Whole Genome Analysis for Co-Infected Different Genotypes of Human Norovirus JOURNAL Unpublished REFERENCE 2 (bases 1 to 7431) AUTHORS Zhang,Z., Wang,D., Liu,D., Zhang,Z. and Wu,Q. TITLE Direct Submission JOURNAL Submitted (28-JAN-2020) School of Agriculture & Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd. Minhang Dist, Shanghai 200240, China COMMENT ##Assembly-Data-START## Assembly Method :: CLC genomics workbench v. 12 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7431 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="SCD1062_2" /isolation_source="asal swab" /host="Homo sapiens" /db_xref="taxon:122929" /country="China: Shanghai" /collection_date="18-Feb-2018" /note="genotype: GII.4 Sydney[P16]" gene <1..5007 /gene="ORF1" CDS <1..5007 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QHQ73455.1" /translation="MSSTLKKALGARPKQPTPRDEPQKSPRPPTPELVKRIPPPPPNG EEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFSVPPLSLRENREAKEPLTGAILE MWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVELTPLSLYWRVVYTPQYLISPETLR RLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTTGFFRPYQEWNRKPLPTMD DSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCDWTFAGIVESLILLAE LFGVFWTPPDVSAMIAPLLGDYELQGPEDLAIELVPVVMGGIGLVLGFTKEKIGKMLS SAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIEDAVLDLEAIENNHM TTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINALLARIAAARSLVHRAK EELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRVGLIPRNGVDHWDAYK GERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSEVIIITTNLAN PAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKDAFKPDFSHIKLQLAP QGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQGPTITTFNFDRNRIT AFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKRCRIIYGGSTYDLESD GKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYVKCVQEAVYSIIQIAGAAFVTT RIARRMNIQELWSKPQLDQSESEAKEEALKSEDDEFIISSKDIKEEGKKGKNKTGRGK KHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEE EEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNE KLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPAGITEAFGVPIKQIQIHKSG EFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPLAARMGTHATMKIQG RMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVIGVHTAAARGGNTVIC ATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSSNTPLPPGTYEPAYL GGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTIINVLEQTLDPPQKW TYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLADQASKANLMFEEGKHMTPVYT AALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEMKAHCISLPVRVGMN MNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVRFSAEPQLAQIVAED LLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTKLSPDIIQANS MFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLIISEDLNGLTFLRRT VTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPIQLMALLGEASLHGP SFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE " mat_peptide <1..903 /gene="ORF1" /product="p48" mat_peptide 904..2001 /gene="ORF1" /product="NTPase" mat_peptide 2002..2532 /gene="ORF1" /product="p22" mat_peptide 2533..2931 /gene="ORF1" /product="VPg" mat_peptide 2932..3474 /gene="ORF1" /product="Pro" mat_peptide 3475..5004 /gene="ORF1" /product="RdRp" gene 4988..6610 /gene="ORF2" CDS 4988..6610 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QHQ73456.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6610..7416 /gene="ORF3" CDS 6610..7416 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QHQ73457.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS NSSTTTSVNSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 atgtcttcca ccttaaagaa agccctcggg gctaggccca aacagcctac cccgagagac 61 gaaccacaaa agtccccaag accaccaact cccgagttgg tcaagaggat accccctcct 121 ccacctaatg gcgaagaaga agaagaacca gtcattaggt atgaagttaa gagtgggatc 181 tctggcctgc ccgagctcac aacagtcccc caaccggacg tggccaacac agcattcagt 241 gttccaccac tgagcttgag agaaaacagg gaggccaagg aaccgctaac aggggcaata 301 ttagagatgt gggacggaga gatataccac tatggcctgt acgtggagaa aggcttagtg 361 ttgggtgtgc acaaaccacc tgcagccata agcatggcaa gagtggagct gacgccgctg 421 tcattgtact ggcgtgtggt gtacactccc caatacctca tctcccctga aactctcagg 481 aggctcaacg gagaggcgtt cccttacacc gccttcgaca acaactgcta tgccttttgc 541 tgctgggtgc tagacctcaa tgactcatgg cttagcagga ggatggtgca aagaacaacg 601 ggcttcttca gaccttacca agagtggaac agaaaacccc tgcccaccat ggatgattcc 661 aaaataaaga aggtagcaaa tatattccta tgttcattgt ccacattatt caccagaccc 721 ataaaagacc tcataggaaa aattaaacca ttaaacatat tgaacatcct ggcaacgtgt 781 gactggacgt ttgccggaat agtggagtct ctgatattac ttgctgaact cttcggagtt 841 ttctggacac ccccagatgt gtctgctatg atcgctccct tactcgggga ctacgagttg 901 caggggccag aagacctcgc cattgaactc gtacctgtgg taatgggagg gattggtttg 961 gtgttgggat tcaccaaaga gaaaatcggt aaaatgttgt cctcagcagc atcaacactt 1021 agggcttgca aagatcttgg tgcctatggc ttagagatac tcaaattggt catgaagtgg 1081 ttcttcccaa agaaagaaga ggccaatgag ctagccatgg tgagggccat agaggatgcc 1141 gtactagatc ttgaggcaat agaaaataac cacatgacaa ccctgttgaa agacaaagac 1201 agcttagcaa catacatgaa aacactggac atggaggagg agaaagccag aaggttgtcc 1261 acaaaatctg catctcctga catagttggg acaatcaacg ccctgctggc tcgaatagca 1321 gcagccaggt cattagtcca cagggccaag gaagagctat ctagcaggat aagaccagta 1381 gttgttatga tatctggtaa accaggaata ggcaaaactc atctggccag ggaggtggca 1441 agaaaggtag catccactct cacaggagat caaagagtcg gactcatacc aagaaacggt 1501 gtggaccatt gggatgcata caaaggtgag agagtcgtgc tgtgggacga ctatggcatg 1561 agcaacccca ttcatgatgc tcttcgcata caagaattgg ctgatacgtg tccccttacc 1621 ttaaattgtg acagaattga aaacaaggga aaagtttttg atagtgaagt cataataatt 1681 acaacaaacc ttgccaatcc agccccactt gattatgtca actttgaggc ctgttccagg 1741 agaattgatt tcctggtgta cgctgaggcg ccagaagtgg aaaaggcaaa acgggatttt 1801 cctggtcagc cagatatgtg gaaggacgcc ttcaagccgg acttttcaca catcaagcta 1861 caacttgcac ctcaaggcgg ctttgacaag aatggcaaca ccccacatgg gaaaggggtg 1921 atgaagaccc tcactaccgg ttctctgatt gcccgtgcat caggcctatt acatgagagg 1981 atggatgaat ttgaactcca aggtcccaca atcaccacct tcaattttga ccggaacaga 2041 atcacagcat tcagacaatt ggctgcagaa aacaaatatg ggttggtgga taccatgaaa 2101 gttggtaatc aactaaaagg agtgaaaacc atggaagaac tcaaacaagc aatcaggaat 2161 gtgaccatca agaggtgccg gatcatctac ggtggctcca cgtatgacct tgaatctgat 2221 ggcaagggca aagttttggt ggaaaaggtc aagaacacct ctgtgcagac caacaacgag 2281 ttggccgggg ccctgcacca tctcaaacat gcccgaatca ggtactatgt caaatgtgtg 2341 caagaagcag tctattccat catacaaatt gccggcgctg cgtttgtcac cacgcgcatt 2401 gcacgccgca tgaacataca agaactttgg tcgaagccac aattagatca aagtgaatca 2461 gaagctaagg aagaggccct caagtcagaa gatgacgagt tcatcatatc ttctaaggac 2521 atcaaggagg aaggaaagaa gggcaaaaac aaaactggcc gtggcaagaa acacactgca 2581 ttctccagca agggcttgag tgatgaggag tatgacgagt acaagaggat aagagaagag 2641 agaaatggga agtactctat agaggagtat cttcaagaca gagacaggta ctatgaggag 2701 ctcgccattg ccaaggccac ggaagaagac ttctgtgaag aggaggagat caaaatccgc 2761 cagagaattt tccgtcccac caggaaacaa agaaaggaag agagggccac attagggctg 2821 gtaacaggtt cagaaatcag aaaaagaaac cctgatgact tcaaacccaa agggaagctg 2881 tgggccgatg acaacagaag tgttgactac aatgagaaac tggactttga ggccccccca 2941 agcatatggt ctaggattgt gagctttggt tctggctggg gcttctgggt gtcaccaagc 3001 ctgttcataa catcaactca tgtaatcccc gcaggcataa cagaagcatt tggagtcccc 3061 atcaaacaaa ttcagatcca caagtcaggt gaattttgcc gattcagatt cccaaaacca 3121 attagaccag atgtgacagg aatgatcttg gaagaaggtg cgcctgaagg caccgtggca 3181 actgtgctca tcaaacgccc caccggagag cttatgcctc ttgcagccag aatgggaaca 3241 cacgcaacca tgaaaattca aggccgcatg gttggcggac agatgggcat gttgctcact 3301 ggatcaaatg ctaaaggaat ggatttggga acaacccctg gtgactgtgg ctgtccttac 3361 atctataaaa ggggcaatga ctatatagtc attggggtac acactgcagc agcccgtggt 3421 ggaaacaccg tcatctgtgc cacacaggga agtgagggtg aggcaactct tgagggtgga 3481 gatgataaag gaacatactg tggggcaccc attttaggcc ctgggggtgc accaaaattg 3541 agcaccaaaa ccaaattttg gaggtcatcg aacacgcccc ttccaccagg gacatatgag 3601 cctgcctacc tcggtggccg tgatccgcgt gttaagggtg ggccctcctt gcagcaggta 3661 atgagagacc agttaaagcc attcactgaa cccaggggca aacctccaag accaagtgta 3721 ttggaagcag ctaaacaaac cattatcaat gttctcgaac aaaccctgga ccctccacaa 3781 aaatggacat atgcacaggc gtgtgcctca cttgacaaaa ccacctccag cgggcatccc 3841 catcacgttc gaaagaatga attctggaat ggtgagacct tcactggtaa attggcagac 3901 caagcatcaa aagcaaacct aatgtttgag gaagggaaac acatgacacc agtgtataca 3961 gcagcactca aggacgaact agttaagact gagaaaatct atggaaagat caagaagaga 4021 ctgctctggg gctctgactt gtccaccatg atccggtgcg ctaggtcatt tggtgggctc 4081 atggatgaga tgaaggcaca ctgcatatca ctcccagtac gagttggcat gaatatgaat 4141 gaagatggcc caataatatt tgagaaacat tccagatata aataccacta tgatgcagac 4201 tactctcgtt gggattcaac acaacagagg gcagtactag cagcagcctt ggaaatcatg 4261 gtcagattct ctgcagaacc acaattggca cagatagtcg ctgaggatct actggcccct 4321 agtgtagtag atgtgggaga ctttaaaatt acaataaatg aagggctccc atctggtgtg 4381 ccatgcactt ctcaatggaa ctctatcgca cactggctgc taactctctg tgccttgtct 4441 gaagtcacta aactgtcccc tgacattata caagcaaatt ccatgttctc attttacggt 4501 gatgacgaga ttgtcagcac cgacataaaa ttggaccctg aacagttaac cgccaagttg 4561 aaggagtacg gcctgaaacc gacccgccca gacaagaccg agggacccct gatcatcagt 4621 gaagatttga acggactcac tttcctccga aggacggtga ctcgtgaccc agctggctgg 4681 tttggaaaac tggaccaaag ttcaattttg aggcagatgt actggactag aggaccaaat 4741 catgaagacc ccaatgagac aatgataccc cattctcaaa gacccataca gctcatggca 4801 ctgcttggtg aagcctctct tcacggaccc tctttctaca gtagaatcag taaactggtc 4861 ataactgaac tcaaagaagg tgggatggac ttttacgtgc caaggcagga acccatgttc 4921 aggtggatga ggttttctga cttgagcacg tgggagggcg atcgcaatct ggctcccaat 4981 tttgtgaatg aagatggcgt cgagtgacgc caacccatct gatgggtccg cagccaacct 5041 cgtaccagag gtcaacaatg aggttatggc tttggagccc gttgttggtg ccgctattgc 5101 ggcacctgta gcgggccaac aaaatgtaat tgacccctgg attagaaata attttgtaca 5161 agcccctggt ggggaattta cagtgtcccc tagaaacgct ccaggtgaaa tactatggag 5221 cgcgccccta ggccctgacc taaatcccta cctatcccat ttagccagaa tgtacaatgg 5281 ttatgcaggt ggttttgaag tgcaggtaat tctcgcgggg aacgcgttca ctgccgggaa 5341 gattatattt gcagcagtcc caccaaattt tccaactgaa ggcttaagtc ctagccaggt 5401 cactatgttc ccccacataa tagtagatgt tagacagcta gaacccgtgc tgatcccctt 5461 acccgatgtt aggaataatt tctatcatta caatcagtca aatgactcca ctattaagtt 5521 gatagcaatg ttgtatacac cacttagggc taataatgct ggagatgatg ttttcacagt 5581 ttcgtgccga gttcttacga gaccatcccc cgattttgat ttcatatttt tggtgccacc 5641 cacagttgag tcaagaacta aaccattctc tgtcccaatt ttaactgttg aggagatgac 5701 caattcaaga ttccccatcc ctttggaaaa gttgttcaca ggccccagta gtgcctttgt 5761 tgttcaacca caaaacggca ggtgcacaac tgatggcgtg ctcctaggca ccacccaact 5821 ttctcctgtc aacatctgca ccttcagagg ggatgtcacc cacatcacag gtagtcgcaa 5881 ctacacaatg aatttggctt ctcaaaattg gaacaactat gacccaacag aagagatccc 5941 agcccctcta ggaactccag attttgtggg gaagattcaa ggcatgctca cccaaaccac 6001 aaggacagat ggttcaacac gcggccacaa agctacagtt tacactggga gcgccgactt 6061 tgctccaaaa ttgggtagag ttcaatttga aactgacaca gaccatgatt ttgaagctaa 6121 tcaaaacaca aagttcaccc cagtcggtgt catccaagat ggtagcacca cccaccgaaa 6181 cgaaccccaa cagtgggtgc tcccaagtta ctcaggcaga aacactcaca atgtacattt 6241 ggcccccgct gtagccccca cctttccggg tgagcaactt ctcttcttca gatccaccat 6301 gcccggatgc agcgggtacc ccaacatgga tttggactgt ctgctccccc aggaatgggt 6361 gcagtacttc taccaagagg cagccccagc acaatctgat gtggctctgc taagatttgt 6421 gaatccagac acaggtaggg ttttgtttga gtgcaagctc cacaaatcag gctatgttac 6481 agtggctcac actggccaac atgatttggt tatccccccc aacggttact ttaggtttga 6541 ttcctgggtc aaccagttct acacacttgc ccccatggga aatggaacgg ggcgtagacg 6601 tgtagtgtaa tggctggagc tttctttgct ggattggcat ctgatgtcct tggctctgga 6661 cttggttccc ttatcaatgc tggggctggg gccatcaacc aaaaagttga atttgaaaac 6721 aacaggaaat tacaacaagc atccttccaa tttagcagca atctgcaaca ggcttccttt 6781 caacatgata aagagatgct ccaagcacaa attgaggcca ccaaaaagct acaacaggaa 6841 atgatgaaag ttaagcaggc aatgctccta gagggtgggt tctctgagac agatgcagcc 6901 cgcggggcaa ttaacgcccc catgacaaaa gctttggact ggagcgggac aaggtactgg 6961 gctccagatg ctaggattac aacatacaat gcaggccact tttccacccc tcaaccatcg 7021 agggcactgc cagggagagc taatcttagg gatgctgtcc ctgctcgggg accctccaac 7081 aaatcctcta actcttctac taccacctct gtgaactcaa atcaaactat ttcaacgaga 7141 cttggttcta cagctggttc tggaaccagt gtctcgagcc tcccgtcaac tgcaaggact 7201 aggagctggg ttgaggatca aaataggaat ttgtcacctt tcatgagggg ggcccacaac 7261 atatcatttg ttaccccacc atctagcaga tcctctagcc aaggcacagt ctcaaccgtg 7321 cctaaagaga ttttggactc ctggactggc gctttcaaca cgcgcaggca gcctctcttc 7381 gctcacattc gtaagcgagg ggagtcacgg gtgtaatgtg aaaagacaga a //