Typing tool

Complete norovirus genomes

JX846924  GII.3
 GII.P41

Length: 7,527 | 3 CDS

ORF1: 5..5110
ORF2: 5091..6737
ORF3: 6737..7501
LOCUS       JX846924                7527 bp ss-RNA     linear   VRL 24-OCT-2013
DEFINITION  Norovirus Hu/GII.3/HK71/1978/CHN, complete genome.
ACCESSION   JX846924
VERSION     JX846924.1
DBLINK      BioProject: PRJNA70471
KEYWORDS    .
SOURCE      Norovirus Hu/GII.3/HK71/1978/CHN
  ORGANISM  Norovirus Hu/GII.3/HK71/1978/CHN
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7527)
  AUTHORS   Madupu,R., Halpin,R., Ransier,A., Fedorova,N., Stockwell,T.,
            Amedeo,P., Bishop,B., Edworthy,P., Gupta,N., 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 (31-JUL-2012) J. Craig Venter Institute, 9704 Medical
            Center Drive, Rockville, MD 20850, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: clc_ref_assemble_long v. 3.22.55705
            Coverage              :: 65.0x
            Sequencing Technology :: Sanger; Illumina; 454
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7527
                     /organism="Norovirus Hu/GII.3/HK71/1978/CHN"
                     /mol_type="genomic RNA"
                     /strain="Hu/GII.3/HK71/1978/CHN"
                     /host="Homo sapiens"
                     /db_xref="taxon:1260941"
                     /country="China: Hong Kong"
                     /collection_date="05-Jan-1978"
                     /note="genotype: GII.3"
     gene            5..5110
                     /gene="POL"
     CDS             5..5110
                     /gene="POL"
                     /note="genome polyprotein"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AFX71655.1"
                     /translation="MKMASNDASAAAAAASNNDNAKSSSDGVLNSMAVTFKRALGARP
                     KQPPPRETTQKQKPPRPPTPELVKKIPPPPPNGEDELVVSYSIKDGVSGLPELSTVSQ
                     PDEANTAFSVPPLNQRENRDAKEPLPGTILEMWDGEIYHYGLYVERGLVLGVHKPPAA
                     ISLAKVELTPLSLYWRPVYTPQYLMSPDTLRKLHGELFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKMANIILCALSSLFTRPIKDII
                     GKLRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKDEANELAMVRSIEDAVLDLEAIENNHMTSLLKDKDSLATYMRTLDLEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAR
                     ELAKKIAATLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELAD
                     TCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLMLAPQGGFDKNGNTPHGKGVMKTLTSGSLIA
                     RASGLLHERLDEYELQGPTPTTFNFDQNKVFAFRQLAAENKYGLMDTMRVGSQLKGVK
                     TVSELKQALKNIAIKRCQIVYSGSTYSLESDGKGNVKVEKVQSTTVQTNNELSGALHH
                     LRCARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDAEETINKD
                     GCPKPKDDEEFVISSEDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREER
                     NGKYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLG
                     LVTGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWV
                     SPSLFITSTHVIPQGSQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAP
                     EGTVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTP
                     GDCGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAMLEGGDNKGTYCGAPI
                     LGPGNAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRIKGGPSLQQVMRDQLKPFT
                     EPRGKPPNPSVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNE
                     CWNGESFTGKLADQASKANLMYEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGS
                     DLATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYNYHYDADYSR
                     WDSTQQRAVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFKISITEGLPSGVP
                     CTSQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAK
                     LKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTR
                     GPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVIAELKEGGMDFYVPR
                     QEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     mat_peptide     5..1000
                     /gene="POL"
                     /product="protein p48"
     mat_peptide     1001..2098
                     /gene="POL"
                     /product="NTPase"
                     /note="p41"
     mat_peptide     2099..2635
                     /gene="POL"
                     /product="protein p22"
     mat_peptide     2636..3034
                     /gene="POL"
                     /product="viral genome-linked protein"
                     /note="VPg"
     mat_peptide     3035..3577
                     /gene="POL"
                     /product="3C-like protease"
                     /note="3CLpro; calicivirin"
     mat_peptide     3578..5107
                     /gene="POL"
                     /product="RNA-directed RNA polymerase"
     gene            5091..6737
                     /gene="VP1"
     CDS             5091..6737
                     /gene="VP1"
                     /codon_start=1
                     /product="capsid protein VP1"
                     /protein_id="AFX71656.1"
                     /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
                     QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
                     FEVQVVLAGNAFTAGKVIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPINLPMPD
                     VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
                     TVESKTKPFTLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
                     QLLPSQICAFRGTLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPAP
                     LGTPDFRGKVFGVASQRNPDSTTRAHEAKVDTTSGRFTPKLGSLEISTESDDFDPNQP
                     TRFTPVGIGVDNEADFQQWSLPDYSGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
                     GRSNGILDCLVPQEWVQHFYQESAPAQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
                     KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
     gene            6737..7501
                     /gene="VP2"
     CDS             6737..7501
                     /gene="VP2"
                     /note="minor capsid protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="AFX71657.1"
                     /translation="MAGAFIAGLAGDMLTSTVGSLVNAGASAINQKVDFENNKYLQNA
                     SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPITRVLDWSG
                     TRYWAPNATSTTSMSGGFTSQTVHRTTPNFKTNQAPKSTPSSGSSVRSNSTQLTSLSS
                     HSSGSSRSSGSTVVSSLPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASNSD
                     TVSTVPKSVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgctgcca gcaacaacga
       61 caacgcaaaa tcttcaagtg acggagtact aaatagtatg gctgtcactt ttaaacgagc
      121 cctcggggcc cggcccaaac agccgccccc gagggaaaca acacaaaaac aaaaaccccc
      181 acgaccgccc actccggagt tggtcaaaaa gatcccgcct cccccgccca acggggagga
      241 cgagttagtg gtctcctata gtattaaaga tggcgtctcc ggtttgcctg agctctccac
      301 cgtcagtcaa ccagacgagg ccaacacagc atttagtgtc cccccattaa accaaaggga
      361 gaacagagat gctaaggaac cactgcccgg caccatcctg gagatgtggg acggagagat
      421 ctaccattat ggcctgtacg tggaacgggg tctggtgctt ggggtacaca aaccaccagc
      481 ggctattagt cttgccaagg ttgagttgac accattgtct ctatattgga gaccagtgta
      541 caccccccag taccttatgt ccccggacac tctcagaaag ctacatggag aactattccc
      601 ttatacggcc tttgataata actgttatgc cttctgttgt tgggttttag atctaaacga
      661 ctcttggctt agcaggagaa tgatacagag aacaactggc tttttccggc cctaccagga
      721 ctggaacaga aagccccttc ccaccatgga tgattccaaa ttgaaaaaga tggccaatat
      781 aatactgtgt gctttgtcat cgctgtttac caggcccatt aaggacataa ttggaaagtt
      841 gagaccccta aacatcctca atatattggc ttcctgcgat tggacttttg caggtatagt
      901 agaatcccta atcctcttgg cagagctctt tggagttttc tggacgcccc cagatgtgtc
      961 tgcgatgatc gcccccttac taggtgacta cgagctacag ggacctgaag accttgctgt
     1021 ggagctcgta ccagtagtaa tgggggggat aggtttggtt ctaggtttca ccaaagaaaa
     1081 gattggaaaa atgctatcat ctgctgcatc cactcttagg gcttgtaaag accttggagc
     1141 atacgggttg gaaatcttaa aattggtcat gaagtggttc ttcccgaaga aagatgaggc
     1201 aaacgagctc gcaatggtga gatccatcga ggacgcagta ttggatctcg aagcaattga
     1261 aaacaaccac atgacctctt tgctcaaaga caaggacagt ttggcaacct acatgagaac
     1321 tctagatctt gaagaggaga aggctagaag actctccacc aagtctgcct ctcctgacat
     1381 cgtgggcaca atcaatgccc tattggcgcg gatcgcagcc gcccgctccc tggtgcatcg
     1441 ggcaaaagaa gagctctcta gcaggccaag gcccgttgtt gtgatgatat caggcaaacc
     1501 aggaatagga aagactcacc tcgctagaga gttagcaaag aaaattgcag ccaccctcac
     1561 aggagatcag agggtgggcc ttgtcccacg gaacggtgtt gaccactggg acgcatacaa
     1621 aggtgagaga gtcgtccttt gggatgacta tgggatgagc aaccccattc acgacgccct
     1681 cagactgcaa gaacttgctg acacgtgccc cctaacacta aattgtgata ggattgagaa
     1741 caagggaaaa gtctttgaca gtgacgctat aatcattaca actaatctgg ccaacccagc
     1801 accactggac tatgtcaact ttgaagcatg ctcaaggcgc attgacttcc tcgtgtatgc
     1861 tgacgcccct gatgttgaaa aggcgaagcg cgactttcca ggacaacctg atatgtggaa
     1921 ggacgctttc aaacccgact tctcacacat aaaactaatg ctggcccctc aaggtgggtt
     1981 tgataagaac ggcaacaccc cacacggaaa gggcgtcatg aaaaccctca catctggttc
     2041 tctcattgca cgtgcatcag ggctcctcca tgaaagattg gacgaatacg agttgcaagg
     2101 cccaacgccc acaaccttca atttcgacca gaacaaggtc tttgctttca ggcaactcgc
     2161 tgctgaaaac aaatacgggt tgatggacac tatgagagtg ggaagccagc tcaagggagt
     2221 caaaactgtg tcagagctta agcaggcgct caagaacatc gcaattaaaa ggtgccagat
     2281 agtctacagt ggttccacat actcacttga atctgatggc aaaggtaatg tgaaagttga
     2341 gaaggtacag agtacaactg tgcaaacaaa caatgagcta tctggtgcgc tacaccacct
     2401 cagatgcgcc aggatcagat attatgttaa gtgtgtccag gaggcccttt attccatcat
     2461 ccaaattgct ggggccgcgt ttgtcaccac gcgcattgca aaacgcatga acatacaaaa
     2521 tctctggtct aagccacagg tggaggatgc agaagaaacc atcaataaag atgggtgccc
     2581 aaagccaaaa gatgatgagg aatttgtcat ctcgtctgaa gacatcaaag tcgagggcaa
     2641 gaagggaaag aacaagtctg gccgtggcaa gaaacacaca gccttttcaa gcaagggtct
     2701 cagtgatgag gagtacgatg aatacaaaag aattagagaa gaaagaaatg gtaagtactc
     2761 catagaagaa taccttcagg acagggacaa atactatgaa gaggtggcca tagccagggc
     2821 tactgaagag gacttctgtg aggaagagga agccaaaatc cgacagagga ttttcagacc
     2881 aacgaggaaa caacgtaaag aggagagggc ttctcttggc ctggtcacag gctcagaaat
     2941 caggaagagg aacccagacg acttcaaacc caagggaaag ttgtgggctg atgacgacag
     3001 gagtgtcgat tacaatgaga aactcagctt tgaagctccc ccaagcatct ggtcaagaat
     3061 agtcaacttt ggttcaggtt ggggtttctg ggtttcacca agtttgttta taacatccac
     3121 ccatgttata cctcagggat cacaggagtt cttcggggtt tccattaaac agatccaaat
     3181 ccacaaatcg ggtgagttct gccgactaag atttccaaaa ccaatcagaa ctgatgtgac
     3241 aggcatgatc ctggaggaag gggcccctga aggaacagtg gccacactac tcataaagag
     3301 accaactggg gagctcatgc cactggcagc taggatgggc acccacgcaa ctatgaagat
     3361 ccagggtcgc actgttgggg gccaaatggg aatgctcttg acaggatcca acgccaagag
     3421 catggacctg ggtactacac caggtgattg tgggtgccca tatatctaca aaagaggaaa
     3481 tgactacgtg gtcattggag tccacactgc cgccgctcgc ggggggaaca ccgtcatctg
     3541 tgcaacccag ggaagcgagg gtgaggccat gcttgaaggt ggtgacaaca aaggcaccta
     3601 ttgcggtgcc ccaatcctag gtccaggaaa tgcccccaag ctcagtacta agaccaaatt
     3661 ttggaggtcc tcaacagctc cactcccacc tggcacatac gaaccagcct acctcggagg
     3721 taaggacccc aggatcaaag gtggcccctc attacaacaa gtcatgagag atcaattaaa
     3781 gccattcacg gaacccaggg gcaaaccacc aaacccaagt gtgctagaag ctgccaaaaa
     3841 gaccatcatt aatgttcttg aacaaacaat agacccacca caaaaatggt catttgcaca
     3901 agcatgcgca tcgcttgaca aaaccacctc cagtggccac ccgcaccaca tgcggaagaa
     3961 tgaatgttgg aatggagagt ccttcacagg aaaattggca gaccaagctt caaaagctaa
     4021 cctaatgtat gaggaaggta aaaacatgac cccggtctac acaggtgccc tcaaggatga
     4081 gctagtcaaa actgacaaaa tatatggcaa gattaagaag aggctcctct gggggtcaga
     4141 cctggcaacc atgatccggt gcgctcgagc attcggaggg ctaatggatg aactcaaggc
     4201 ccactgcgtc acactcccta ttagggttgg gatgaacatg aatgaggatg gccccatcat
     4261 ctttgagaag cactccaggt acaactacca ttatgatgca gattactctc ggtgggattc
     4321 aacacaacag agggctgtgt tagctgcagc tctagaaatc atggtaaaat tttccccaga
     4381 accacaccta gcccagatag tcgcagaaga ccttttgtcc cccagtgtga tggacgtggg
     4441 cgatttcaaa atatcaatca ctgaagggct cccctctggg gtgccttgca cctcacaatg
     4501 gaactccatc gcccattggc tcctcacact ctgtgcactc tctgaggtaa caaatttgtc
     4561 ccctgacacc atccaagcaa attctctttt ctctttctat ggtgatgatg aaattgtgag
     4621 cacagatatt aaattggatc cagaaaagct gacagctaaa ttgaaagagt atgggctaaa
     4681 accaactcgc cctgacaaga ctgaaggacc tctggtcatc tctgaggact tgaatggtct
     4741 gaccttcctg cggagaactg taacccgcga cccagctggt tggtttggaa aattggaaca
     4801 gagttcaata cttagacaaa tgtattggac caggggcccc aatcatgagg acccctccga
     4861 aacaatgata ccacattccc aaagacccat acagctaatg tccctactag gtgaagctgc
     4921 actgcatggc ccatcattct acagcaagat cagtaagcta gttattgcag agttgaagga
     4981 aggtggcatg gatttttacg tgcccagaca agaaccaatg tttcgatgga tgaggttctc
     5041 agacttgagc acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg
     5101 cgtcgaatga cgctgctcca tctaacgatg gtgccgccgg cctcgtccca gagatcaaca
     5161 atgaggcaat ggcgctagag ccagtggcgg gtgcagcgat agcagcaccc ctcactggcc
     5221 agcaaaacat aattgatccc tggattatga ataattttgt gcaagcacct ggtggtgagt
     5281 ttacagtgtc acctaggaat tcccctggtg aagtgcttct taatttagaa ttaggtccag
     5341 aaataaaccc ctatttggct caccttgcta ggatgtacaa tggttatgca ggtgggtttg
     5401 aagtgcaggt agtcctggct ggaaacgcgt ttacagcagg aaaggtgatc tttgcagcta
     5461 taccccccaa ttttccaatt gataatctga gcgcagcaca aattacaatg tgcccgcatg
     5521 tgattgtgga tgtcaggcag ctggaaccaa ttaatcttcc gatgcctgat gtccgcaaca
     5581 atttctttca ttataatcaa gggtctgatt cgaggttacg cttaattgca atgctgtata
     5641 cacctcttag ggcaaacaat tccggagatg atgtttttac tgtgtcctgt agagtattaa
     5701 ctaggcctag ccctgatttc tcattcaatt ttcttgtccc acccactgtg gaatcaaaga
     5761 caaaaccctt caccctcccc attctgacta tctctgaaat gtctaattcc aggtttccag
     5821 tgccaattga ctctctacac accagcccga ctgagaacat tgttgtccag tgccaaaatg
     5881 ggcgcgtcac tcttgacggt gagttaatgg gtaccaccca actcttgccg agtcagatat
     5941 gtgctttcag gggcacgctc accagatcaa caagcagggc cagtgatcaa gccgacacag
     6001 caacccctag gttattcaat tattattggc acatacaatt ggacaatcta aatggaaccc
     6061 cctacgaccc tgcagaggac ataccagccc ctctgggaac accagacttc cggggcaagg
     6121 tctttggcgt agccagccag agaaaccctg acagcacaac aagagcacat gaagcaaaag
     6181 tggacacaac atctggtcgc ttcaccccga aattgggttc cctagaaata tccactgaat
     6241 ccgatgactt tgacccaaac caaccaacaa gattcacccc agttggcatt ggggttgaca
     6301 atgaggcaga ttttcagcaa tggtccttac ctgactattc cggtcagttc actcacaaca
     6361 tgaacttagc cccagctgtc gcccccaatt tccctggtga gcagcttctt ttcttccgct
     6421 cacagttgcc atcttctggt gggcggtcta acgggattct agactgcctg gtcccccagg
     6481 aatgggttca acacttctac caggaatcag cccctgccca aacacaggtg gccctggtta
     6541 ggtatgtcaa ccctgacact ggtagagtgc tatttgaggc caagctacat aaattaggtt
     6601 tcatgactat agctaagaat ggtgactctc caataaccgt ccctccaaat gggtacttta
     6661 ggtttgaatc ttgggtgaac cccttttata cacttgcccc catgggaact ggaaatgggc
     6721 gcagaaggat tcaataatgg ctggagcctt tatagcagga ttggctggtg acatgctcac
     6781 aagtactgtg ggatctttag ttaatgcagg ggctagtgct atcaatcaaa aagttgattt
     6841 tgaaaataat aaatatttac aaaatgcatc ttttaatcat gataaggaga tgttaaatgc
     6901 acaaattgag gcaacaaaga ggctacaggc tgacatgatt gctatcaaac aaggggtctt
     6961 gaccgctggc ggcttttccc ccactgatgc agcccgtggg gcaattaatg cccccataac
     7021 aagagttttg gactggagtg gaacgaggta ctgggcacca aacgccacct ccacaacctc
     7081 aatgtcaggt ggcttcacaa gccaaactgt acacagaacc acaccaaatt ttaaaacgaa
     7141 ccaggccccc aagtccacac ccagcagtgg gtcttcagtg agatcaaact caacccaact
     7201 cactagcttg agctcacact catccgggtc gtctcgatcc agcgggtcta cggttgttag
     7261 ctcattgcca tcttccaaca ggactaggga ttgggtcaat caacagaatt tcaatttgga
     7321 accacacatg cctggatctc tcaggacagc ttttgtcact ccaccatcta gtacagcctc
     7381 taattcagac acggtctcaa ccgtgcccaa aagtgttttg gactcctgga catctgcgtt
     7441 taatacgcgc agacagccgc tattcgcaca ccttcgcaga aggggggagt caaatgttta
     7501 gtgaaaagat tatcttaaat ttagttt
//