Typing tool

Complete norovirus genomes

JQ911594  GI.3
 GI.P13

Length: 7,696 | 3 CDS

ORF1: 5..5410
ORF2: 5394..7028
ORF3: 7028..7675
LOCUS       JQ911594                7696 bp ss-RNA     linear   VRL 20-SEP-2012
DEFINITION  Norovirus Hu/GI/10360/2010/VNM, complete genome.
ACCESSION   JQ911594
VERSION     JQ911594.1
DBLINK      BioProject: PRJNA70471
KEYWORDS    .
SOURCE      Norovirus Hu/GI/10360/2010/VNM
  ORGANISM  Norovirus Hu/GI/10360/2010/VNM
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7696)
  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., My,P.V.,
            Campbell,J., Farrar,J., Vinh,H., Hoang,N.V., Wentworth,D.E. and
            Baker,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-APR-2012) J. Craig Venter Institute, 9704 Medical
            Center Drive, Rockville, MD 20850, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: clc_ref_assemble_long v. 3.20.50819
            Coverage              :: 2042.16x
            Sequencing Technology :: Illumina; 454
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7696
                     /organism="Norovirus Hu/GI/10360/2010/VNM"
                     /mol_type="genomic RNA"
                     /strain="Hu/GI/10360/2010/VNM"
                     /host="Homo sapiens; sex: F"
                     /db_xref="taxon:1175308"
                     /country="Viet Nam: Ho Chi Minh City"
                     /collection_date="14-Mar-2010"
                     /note="genotype: I"
     gene            5..5410
                     /gene="POL"
     CDS             5..5410
                     /gene="POL"
                     /note="genome polyprotein"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AFI08230.1"
                     /translation="MMMASNDAIAVADVSNNNANTNNENIGSRLMAKIRGRIGPQRGE
                     TTTKIKDANMALDLLRRSQTPSPCRQTNDSAPKAQRDRPPRTASEVKRALGWDAEPEH
                     QESTARAWCDLSKEEKEEIMRNNERLFDAGGVTPSILPSTFERTDSSGATDEQQPVTW
                     SSSGGVDLGINDLTTVRGPFWNMCPLPPLDARNNGPAKEPLIGDMVEFYEGHIFHYAI
                     YIGQGKTIGVHSPQAAFSIPRITIHPLVAWWRVCYVPTNQQRLTYEQLKELENEPWPY
                     ASITNNCYEFCCKVMALDDTWLQRKLVNSGKFNHPTQDWSQDTPDFHQDSKLEMVRDA
                     VLSAINGLVSQPFKNILSKIKPLNVLSLLSNCDWTFMGVVELVVLLAELFDVFWTPPD
                     ISSFIASLLPDFHLQGPEDLAKDLVPLILGGIGLAIGFTRDKITKVMKSAVDGLRSAT
                     QLGQYGLEIFSIIKKYFFGGDQTEKTLRGIEDAVIDMEVLSSTNVTQLVKDKKLAKAY
                     MNVLDSEEEKARKLSVRSADPHIVTSVNNLISRISMARSALAKAQAEMTSRPRPVVIM
                     MCGPPGIGKTKAAEHLAGRLAAEIRPGGKVGLVPRESIDHWDGYHGEDVLLWDDYGMS
                     KITEDCNKLQAIADTAPLSLNCDRIENKGMQFSSDAIIITTNAPGPAPVDFVNLGPVC
                     RRVDFLVYCSAPEIEQTRRAHPGDTNAIKDLFKKDFSHLKMELAPQGGFDSQGNTPFG
                     KGVMKTTTLNRLLIQATALAMERQDEFQLQGTVYNFDEDRVAAFTNLARANGLGLISM
                     ATLGKKLRSVKSMEGLRNALLGYKIGECDIVWNTRVYSVKSDGSNVIIKEKQVPSSPQ
                     HQAISTATLALSRLRAARALAYASCLQSAVLSILQVAGSALVVSRAVKRMFGTRTEQP
                     ILEGKHKEHNCRVHRAEAAGHGPIGHDGIIERYGLCESEQEGEDDHTVELPTADKEGK
                     NKGKTKKGRGRKSNFNAFSRRGLSDEEYEEYKKVREEKGGNYSIQEYLEDRQRYEEEL
                     AEVQAGGDGGIGETEAEIRHRVFYKSKSGMRKQRQEERRQLGLVSGTEIRKRKPIDWT
                     PPKNDWSEDTRTVNYDEHISFEAPPSIWSRVVKFGSGWGFWVSSTVFITTTHVIPPGA
                     KEIFGENLSNIAIHRVGEFTQFRFSKKMRPDLSGMVLEEGCPEGTVCTIMIKRDSGEL
                     LPLAVRMGAVASMKIQGKLMHGQSGMLLTGANAKGMDLGTIPGDCGAPYIHKRGNDWV
                     VCGVHAAATKSGNTVVCAIQGGEGEATLEGGDQNKGHYAGHPILRYGNGPSLSTKTKF
                     WKSNPQPLPPGTYEPAYLGGRDPRVEGGPSLQQVLRDQLKPFAEPRGRLPEAGLLEAA
                     VETVTNAIEQVMDAPVAWSYSDACMSLDKTTSSGYPHHKRKNDDWNGSSFVRELGDQA
                     AHANSMYELGKSMKPVYTAALKDELVKPDKVYNKIKKRLLWGADLGTVIRAARAFGPF
                     CEAIKPHVIKLPIKVGMNAIEDGPLIYAEHSKYKYHFDADYTAWDSTQNREIMMESFN
                     IMCKLTANPSLAAVVAQDLLSPSEMDVGDYVISVKDGLPSGFPCTSQVNSINHWIYTL
                     CALSEVTGLAPDVIQSQSYFSFYGDDEIVSTDIEFDSNRLTQVLKEYGLKPTRPDKTD
                     GPIIVRQQVDGLVFLRRTISKDAIGYQGRLDRNSIERQLWWTRGPNHDDPFETLVPHT
                     QRKVQLISLLGEAALHGEKFYRKIASRVIQEVKEGGLEIYIPGWQAMFRWMRFHDLSL
                     WTGDRDLLPDYVNDDGV"
     mat_peptide     5..1225
                     /gene="POL"
                     /product="protein p37"
     mat_peptide     1226..2314
                     /gene="POL"
                     /product="NTPase"
                     /note="p40"
     mat_peptide     2315..2914
                     /gene="POL"
                     /product="protein p20"
     mat_peptide     2915..3334
                     /gene="POL"
                     /product="viral genome-linked protein"
                     /note="VPg"
     mat_peptide     3335..3877
                     /gene="POL"
                     /product="3C-like protease"
                     /note="3CLpro; calicivirin"
     mat_peptide     3878..5407
                     /gene="POL"
                     /product="RNA-directed RNA polymerase"
     gene            5394..7028
                     /gene="VP1"
     CDS             5394..7028
                     /gene="VP1"
                     /note="p59"
                     /codon_start=1
                     /product="capsid protein VP1"
                     /protein_id="AFI08231.1"
                     /translation="MMMASKDAPTNMDGTSGAGQLVPEANTAEPISMDPVAGAATAVA
                     TAGQINMIDPWIMSNFVQAPQGEFTVSPNNTPGDVLFDLQLGPQLNPFLAHLAQMYNG
                     WVGNMRVKVLLAGNAFTAGKIIISCIPPGFTSQNISIAQMTMFPHVIADVRVLEPIEI
                     PLEDVRNVLFHTNDNRPTMRLVCMLYTPLRANGSSSGTDPFVIAGRVLTCPDSNFSFL
                     FLVPPNVEQKTRPFSVPNIPLNTLSNSRVPSLIKSMTISRDQNQIIQFQNGRVTLDGQ
                     LQGTTPTSVSQLCKIRGTTYHATGGNGINLTELNGEPYHAFESPAPIGFPDLGGCDWH
                     LTATPTQAFNDGAKVVRLSVTQGAAFAPHLGTIHYTTTDTDYNPNTSIICTLDWLSQT
                     AGQSNVDPWQIPTYGSTLTEAAQLAPPIFPPGFGETLVFFLSDFPISNGKNGLSVPCT
                     LPQEFVTHFVNEQAPIRGEAALLHYVDPDTHRNLGEFKLYPEGFMTCVPNTSGGGPQT
                     LPINGVFVFVSWVSRFYQLKPVGTAGAARRLGIRRS"
     gene            7028..7675
                     /gene="VP2"
     CDS             7028..7675
                     /gene="VP2"
                     /note="minor capsid protein; basic protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="AFI08232.1"
                     /translation="MAQAVLGAIAATAAGSAVGAGIQAGTEAALQHQRFQQDLTLQSN
                     TFKHDKEMLAMQVEASTSLLQNSLNTRYNLLTQAGLTSADAARAVAGAPVTRVVDWNG
                     TRIAAPLSTATTLRSGGFMSIPVMYRGAKTEQQKLTGFSNPNYETGSSVSRTSQWVSS
                     QNSMRSSVAPFHPDALRTTWVTPPGSSSTSTVSSASSIPRFFNTERLPLFANNKR"
ORIGIN      
        1 gtgaatgatg atggcgtcta acgacgctat tgccgttgct gatgtcagca ataacaatgc
       61 taacaccaac aatgaaaaca ttgggtctcg cctcatggcg aagatccgtg ggcgtatagg
      121 cccacaacgt ggtgaaacaa ccacaaaaat taaggatgcc aacatggcgc ttgatctttt
      181 acgtcggtca caaacaccat ctccatgtcg gcaaactaat gacagtgccc ccaaagctca
      241 aagggaccgc cccccacgga ccgcttcaga ggtaaaaagg gcactgggat gggatgctga
      301 accagaacat caagaaagca cggctagggc atggtgtgac ctctctaaag aggagaagga
      361 ggagataatg cgtaacaacg agaggctctt tgatgctgga ggtgtcaccc catcaatcct
      421 gcccagcaca tttgagagga ctgactcaag cggtgccact gacgagcaac aaccagtgac
      481 atggtcttct agtggtggag ttgaccttgg catcaatgat ttgaccacag ttcgtggccc
      541 gttttggaac atgtgccccc tcccaccact ggatgcccgt aataatggcc ctgccaagga
      601 accccttata ggggacatgg tcgagttcta tgaaggccac atattccact atgccattta
      661 catcgggcag ggcaaaacca ttggagtcca ctcgccgcag gccgctttct ccatacccag
      721 aataactatc cacccactag tggcctggtg gcgcgtgtgt tatgtcccca ctaatcaaca
      781 acgcctcacc tacgagcaac ttaaggagtt ggaaaatgaa ccatggccct atgcctcaat
      841 caccaacaac tgttatgagt tttgctgtaa agtgatggcg cttgatgata cctggctcca
      901 gaggaaattg gtcaatagtg gaaaatttaa ccaccccaca caggactggt cacaggacac
      961 cccagatttt caccaggatt caaaacttga aatggtaagg gacgctgttc tgtcagccat
     1021 taacggtctt gtgtcacaac ctttcaagaa cattctgtca aaaattaaac cattaaatgt
     1081 gctcagtctt ttatcaaact gtgattggac tttcatgggc gtcgtggagc tggttgtgct
     1141 cctggcagaa ctgtttgatg tgttctggac cccaccggac atttcaagct tcattgcatc
     1201 tctactgcca gactttcatc tacaaggtcc agaagaccta gccaaagact tagtccccct
     1261 tatattaggt ggtataggtc tggcaattgg tttcacaaga gacaaaataa caaaagtgat
     1321 gaagagcgcc gttgatgggc tgcggtcagc aacacagctc ggacaatatg gattggagat
     1381 attctcaatc atcaagaaat acttctttgg aggggatcaa acagaaaaga ccctgcgggg
     1441 tattgaagat gcggtgatag acatggaagt attgtccagt accaatgtga cacaactagt
     1501 caaagataag aagttagcca aagcctacat gaatgtactg gacagtgagg aagaaaaagc
     1561 gaggaagctc tcagtccgta gcgctgaccc acacatagtg acctctgtca acaacttgat
     1621 atcacgcatc tctatggcaa gatcagctct ggctaaagcc caagctgaga tgacgtcccg
     1681 cccacgacca gtggttataa tgatgtgtgg cccccctggt atcggaaaga ctaaggctgc
     1741 cgagcaccta gctggccgac tagctgctga aattagacct ggaggcaaag ttggccttgt
     1801 acctcgggag tccatagatc attgggatgg atatcatggc gaggatgtct tgctctggga
     1861 tgactatggc atgtcaaaga taacagagga ttgtaataaa ttgcaggcta tagccgacac
     1921 tgcaccactg tcgcttaatt gtgacagaat agaaaataaa ggcatgcaat tctcttctga
     1981 tgcaataatt ataaccacca atgctcctgg cccagcccca gtcgactttg tcaacctagg
     2041 ccccgtgtgc aggcgagtgg actttttagt ctactgttct gcacctgaga ttgaacaaac
     2101 gcggagggct catccaggtg acactaatgc catcaaggat ctgtttaaaa aggacttctc
     2161 acacctaaaa atggaattgg ctccacaggg cggctttgat agtcagggca atacaccttt
     2221 tgggaagggt gtcatgaaga ccacaactct caacagactg ctaatacagg ccacagcatt
     2281 agccatggaa cggcaagatg aattccaact ccaggggact gtttataact ttgatgagga
     2341 cagagtggcc gccttcacca atttggctcg cgctaatggc ctagggctta taagcatggc
     2401 aacgttgggt aagaaactaa ggagtgttaa gtccatggaa ggcctgcgta atgcactact
     2461 gggatacaag attggagagt gtgatatagt ttggaacact agggtgtact cagtcaagag
     2521 tgacgggagc aatgtcataa ttaaagaaaa gcaggtaccg tcctcacccc aacatcaagc
     2581 catttccaca gccaccctcg cgctctctag actgcgggct gctagagctc ttgcgtatgc
     2641 ctcctgtctg caaagtgcgg tgctgtcaat actccaggtg gccggctctg ccttagtggt
     2701 gagcagggcc gtaaaacgta tgtttggcac tcgcaccgaa cagcccattc tggagggtaa
     2761 gcataaagaa cataactgca gagtacaccg tgcagaggct gccggccacg gccctattgg
     2821 tcatgatgga atcattgaac gttatggtct gtgtgagagt gagcaagaag gggaagatga
     2881 ccatactgtg gagctgccca ctgctgataa agaaggtaag aacaaaggca aaaccaagaa
     2941 gggccgcggg cggaagtcca atttcaatgc attctctagg cgtggactta gtgatgaaga
     3001 atatgaggag tacaagaaag taagagaaga gaagggtggt aactacagca tacaagagta
     3061 ccttgaggat cgccagcgtt atgaagaaga actcgctgag gtgcaagctg gcggagatgg
     3121 tgggatcggt gaaactgaag cagagatccg ccaccgggtc ttctataaat caaagtctgg
     3181 catgagaaaa caacggcaag aggaacgccg ccagttgggc cttgtgagcg gcactgaaat
     3241 ccgtaagcgt aagcccatag attggacccc ccccaaaaat gattggtcag aggacactag
     3301 aactgttaac tatgatgaac atattagctt tgaagcccct ccttcaattt ggagtagagt
     3361 agtcaaattt ggcagtggct ggggcttctg ggtaagttca acagtgttca tcactacaac
     3421 acatgttata ccacctggtg ctaaggagat ctttggtgag aatcttagta acattgccat
     3481 ccacagggtt ggtgagttca cccaattccg tttctctaag aaaatgaggc ctgatctctc
     3541 tggtatggtc cttgaagagg ggtgccctga aggcacagtg tgcaccataa tgataaaaag
     3601 agactctgga gagctgttgc cgctagccgt tcgtatggga gcagtggcct caatgaagat
     3661 tcaagggaaa ctcatgcacg ggcaatcagg aatgttgctc actggtgcta atgccaaggg
     3721 catggacctt gggaccatac ctggggactg tggagcgcct tacatccata agagagggaa
     3781 tgactgggtg gtttgcggtg tgcatgcagc agccacgaaa tcaggcaaca ccgtggtgtg
     3841 cgccatccag ggtggtgaag gtgaagccac gctagagggt ggcgatcaaa ataagggaca
     3901 ctatgcagga cacccaatat taagatatgg aaatggtcct tcactgtcga ctaaaacaaa
     3961 attctggaaa tcaaaccccc agcctctacc ccctggtaca tatgaaccag cctacctcgg
     4021 tggcagagac cccagagttg aaggcggtcc atctttgcag caggtgttgc gagaccagct
     4081 gaagccattt gctgaacccc gtggcaggtt gcccgaagca ggattgctag aagccgcggt
     4141 tgaaactgtc accaatgcaa ttgagcaggt catggacgca ccagtggcat ggagttacag
     4201 cgacgcctgc atgtccttag ataaaacaac cagttctggc tacccccatc acaaaaggaa
     4261 gaatgatgat tggaatggga gttcatttgt gagagaattg ggagatcaag cagcgcatgc
     4321 taacagcatg tatgagcttg gtaagtctat gaaaccagtg tatacagcag cacttaagga
     4381 tgaactcgtc aaaccagaca aggtgtacaa taaaatcaag aaaagactac tctggggggc
     4441 ggatcttggc actgtcatcc gtgccgctag ggcttttggg ccattttgtg aagcaataaa
     4501 accccatgtg attaagttac ccattaaagt gggtatgaac gccatagagg atggcccctt
     4561 aatttatgca gaacattcca agtataagta tcactttgat gctgactaca cagcatggga
     4621 ttcaacacaa aacagggaga tcatgatgga atcttttaac atcatgtgca aacttactgc
     4681 taacccctcc ctagccgcag tggtggcaca ggacctgctc tccccttctg aaatggacgt
     4741 cggtgattat gtgatcagtg tcaaagatgg tctaccatct ggttttccat gtacctcaca
     4801 agtaaacagc atcaaccatt ggatctacac tttgtgtgcc ctgtcagagg tcactggttt
     4861 agctcctgat gtaatacagt cacaatctta cttttcattt tatggtgatg atgaaatagt
     4921 ttcaacagat attgaatttg actcaaacag actaacacag gtattaaaag agtatggcct
     4981 aaaacccaca agacctgata aaactgacgg cccaatcatt gtaaggcaac aggttgatgg
     5041 cttggttttc ctccggcgca ccatctcgaa ggatgccatc gggtaccagg gtcggcttga
     5101 ccgtaattcc attgaaagac agctctggtg gacccgggga cccaatcacg atgatccatt
     5161 tgaaacctta gtcccacaca cacagaggaa ggtccaactg atatccttgc tgggtgaagc
     5221 tgcactccat ggtgagaaat tctatagaaa gatagctagt agggtgatcc aggaggtcaa
     5281 agaaggagga ttggaaattt acatccctgg ttggcaggcc atgttccgct ggatgcgatt
     5341 ccatgatttg agcttgtgga caggagaccg cgatctcttg cccgattatg taaatgatga
     5401 tggcgtctaa ggacgcccca acaaacatgg atggcaccag tggtgccggt cagctggtac
     5461 cagaggcaaa tacagctgaa cctatatcaa tggacccagt ggctggagcc gcaacagcgg
     5521 ttgcaactgc tggacaaatt aatatgattg acccctggat aatgagtaat tttgtgcaag
     5581 ccccacaagg ggaattcact gtctcaccta ataacacccc tggagatgtt ctgtttgatt
     5641 tacaattggg gcctcaacta aatccattcc tcgcccatct agcccagatg tataatggct
     5701 gggtaggcaa tatgcgtgtg aaggtgctgc ttgctggcaa cgcttttact gcagggaaaa
     5761 taataattag ctgcataccc ccaggtttta cctcccaaaa tatttctatt gcccaaatga
     5821 caatgtttcc tcatgtcatc gctgacgtga gggttctgga acctatagaa ataccccttg
     5881 aggatgtgag gaatgtgctg tttcacacca atgacaaccg cccaacaatg aggcttgtat
     5941 gcatgttgta tacccccttg cgagccaatg gcagttcttc tggcacggac ccttttgtca
     6001 tagctggtcg ggttctcacc tgcccagatt caaatttcag tttcctattt ttagtacccc
     6061 ctaatgtaga acaaaagact agacctttta gtgttcccaa tatacctctg aatacattgt
     6121 caaattcaag ggtaccatca ttgatcaagt ctatgaccat ctctagagat cagaatcaaa
     6181 taattcaatt ccaaaatggc agggtcacat tggatggtca gttacagggc accacaccca
     6241 catcagtgag ccagttgtgt aaaattagag gcactacata ccacgcaact ggaggtaatg
     6301 ggataaattt aacagagttg aatggtgagc cataccatgc ctttgaaagc cccgccccga
     6361 tagggtttcc agaccttggt ggttgcgatt ggcatctcac agcaaccccc acgcaggctt
     6421 tcaatgatgg agcgaaggtc gtgcgcctgt cagtcaccca gggcgcagcc tttgcaccac
     6481 acctgggtac catacattac accactactg atactgatta caaccccaac actagcataa
     6541 tttgcacact agattggctg tcccaaactg ctggtcagag taatgttgac ccttggcaga
     6601 taccaactta tgggtcgact ttaactgaag ccgctcagtt ggcgcctccc atctttcccc
     6661 ctgggtttgg agaaacattg gttttctttc tatcagactt tcctatttcc aatggcaaga
     6721 acggactcag tgtaccgtgc actctcccac aggaatttgt cacccatttt gtgaatgaac
     6781 aggccccaat cagaggagag gccgccctct tacattatgt tgatcctgac actcatcgta
     6841 atcttggaga gtttaaattg tatccagaag gttttatgac ttgtgttcct aatactagtg
     6901 gtggtggtcc ccaaactttg cctatcaatg gagtctttgt ctttgtttct tgggtctctc
     6961 gcttttacca gttgaagcct gtgggaacag ccggtgcggc tcgtaggctt ggaatcagga
     7021 gatcataatg gctcaagctg tcttaggagc aattgcagcc acagccgctg gcagcgcggt
     7081 tggggcaggc attcaggctg gcactgaagc tgcactgcaa catcagcgct ttcaacaaga
     7141 cttgactcta caaagtaaca cattcaaaca tgataaggag atgttggcta tgcaggtgga
     7201 ggcttctact tctttattac agaatagctt gaacactcgc tataacttgt tgacccaggc
     7261 aggtctgact tctgcagatg ccgccagagc agtggcgggg gcccccgtca ctcgtgtggt
     7321 ggactggaat ggcactcgca tcgccgctcc actatcaact gccaccactc tccgctctgg
     7381 aggatttatg tctataccgg tcatgtatag gggtgcaaaa acagaacagc agaaattgac
     7441 aggcttctca aaccccaatt acgagactgg ttcatctgtg tcgcgcacat cgcaatgggt
     7501 ttcctcacaa aactcaatgc ggtctagcgt agcaccattc cacccagatg cacttaggac
     7561 aacttgggtc acaccgcctg gttcgtcttc tacatctact gtttcttcag cttcatctat
     7621 acctagattc tttaatactg aaagattacc cttgttcgca aacaataaga ggtgattttt
     7681 gtaatatgaa aatgtg
//