Typing tool

Complete norovirus genomes

JQ911597  GII.4 Den Haag
 GII.P4 Den Haag

Length: 7,510 | 3 CDS

ORF1: 2..5101
ORF2: 5082..6704
ORF3: 6704..7510
LOCUS       JQ911597                7510 bp ss-RNA     linear   VRL 13-MAR-2013
DEFINITION  Norovirus Hu/GII/10012/2009/VNM, complete genome.
ACCESSION   JQ911597
VERSION     JQ911597.1
DBLINK      BioProject: PRJNA70471
KEYWORDS    .
SOURCE      Norovirus Hu/GII/10012/2009/VNM
  ORGANISM  Norovirus Hu/GII/10012/2009/VNM
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7510)
  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     Genome sequence lacks part of non-coding region.
            
            ##Assembly-Data-START##
            Assembly Method       :: clc_ref_assemble_long v. 3.20.50819
            Coverage              :: 296.20x
            Sequencing Technology :: Illumina; 454; Sanger
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7510
                     /organism="Norovirus Hu/GII/10012/2009/VNM"
                     /mol_type="genomic RNA"
                     /strain="Hu/GII/10012/2009/VNM"
                     /host="Homo sapiens; sex: F"
                     /db_xref="taxon:1175311"
                     /country="Viet Nam: Ho Chi Minh City"
                     /collection_date="05-Jul-2009"
                     /note="genotype: II"
     gene            2..5101
                     /gene="POL"
     CDS             2..5101
                     /gene="POL"
                     /note="genome polyprotein"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AFI08239.1"
                     /translation="MKMASNDASAAAVANGNNDTVKSSSDKMFSNMAVTFKRALGARP
                     KQPPPGEIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE
                     ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
                     LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
                     LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVKTM
                     PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRVVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTSLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     mat_peptide     2..991
                     /gene="POL"
                     /product="protein p48"
     mat_peptide     992..2089
                     /gene="POL"
                     /product="NTPase"
                     /note="p41"
     mat_peptide     2090..2626
                     /gene="POL"
                     /product="protein p22"
     mat_peptide     2627..3025
                     /gene="POL"
                     /product="viral genome-linked protein"
                     /note="VPg"
     mat_peptide     3026..3568
                     /gene="POL"
                     /product="3C-like protease"
                     /note="3CLpro; calicivirin"
     mat_peptide     3569..5098
                     /gene="POL"
                     /product="RNA-directed RNA polymerase"
     gene            5082..6704
                     /gene="VP1"
     CDS             5082..6704
                     /gene="VP1"
                     /codon_start=1
                     /product="capsid protein VP1"
                     /protein_id="AFI08240.1"
                     /translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
                     GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6704..7510
                     /gene="VP2"
     CDS             6704..7510
                     /gene="VP2"
                     /note="minor capsid protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="AFI08241.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRTNPRTPTPARGSSSASS
                     NASTATSILSNQTASTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN      
        1 aatgaagatg gcgtctaacg acgcttccgc tgccgctgtt gctaacggca acaacgacac
       61 cgtaaaatct tcaagtgaca aaatgttttc taacatggct gtcactttta aacgagccct
      121 cggggcgcgg cctaaacagc cccccccggg ggaaatacca caaagacccc cacgaccacc
      181 tactccagaa ctggtcaaaa agatccctcc tcccccgccc aacggagagg atgaagtagt
      241 ggtttcttat agtgccaaag atggcgtttc cggtttacct gagctttcca ccgtcaggca
      301 accggaagaa accaatacgg ccttcagtgt ccctccactc aaccagaggg agaatagaga
      361 tgctaaggaa ccactgactg gaacaattct ggaaatgtgg gatggagaaa tctaccatta
      421 tggcctgtat gttgagcgag gtcttgtgct gggtgtgcac aaaccaccag ctgccataag
      481 cctcgccaag gtcgaactaa caccactctc cttgttctgg agacctgtgt acactcccca
      541 gtacctcatc tctccagaca ctctcaagaa attacacgga gaaacgtttc cctacacagc
      601 ctttgacaac aattgctatg ccttttgttg ttgggtcctg gatctaaatg actcgtggct
      661 gagtaggaga atgatccaga gaacaactgg cttcttcaga ccctaccaag actggaatag
      721 gaaacccctc cccactatgg atgattccaa attaaagaag gtagctaaca tattcctgtg
      781 cgccctgtct tcgctattca ccaggcccat aaaagacata ataggaaagc taagacctct
      841 caacatcatc aacatcctgg cttcatgtga ttggactttc gcaggcatag tggagtcctt
      901 gatactcttg gcagagctct ttggagtctt ctggacaccc ccagatgtgt ctgcgatgat
      961 tgccccctta ctcggtgatt tcgagttaca aggacctgag gaccttgtag tggagctcgt
     1021 ccctgtagta atggggggaa ttggtttggt gctgggattc accaaagaga agattgggaa
     1081 aatgttgtca tctgctgcat ccaccttgag agcttgtaaa gatcttggtg catatgggct
     1141 agagatccta aagttagtca tgaagtggtt cttcccgaag aaagaggagg caaatgaact
     1201 ggctatggtg agatccatcg aggatgcagt actggacctt gaggcaattg aaaacaacca
     1261 tatgaccacc ttgctcaaag acaaagacag cctggcaacc tacatgagaa cccttgacct
     1321 cgaggaagag aaagccagaa aactctcaac caagtctgct tcacctgaca tcgtgggcac
     1381 aatcaacgcc cttttggcga gaatcgccgc tgcgcgctcc ctggtgcacc gagcgaagga
     1441 ggagctttcc agcagaccaa gacctgtagt cttgatgata tcaggcagac cagggatagg
     1501 aaaaacccac cttgctaggg aagtggctaa gagaatcgca gcctccctca caggagacca
     1561 gcgtgtaggc ctcatcccac gcaatggcgt cgatcactgg gatgcgtaca agggggagag
     1621 ggtcgtccta tgggacgact atggaatgag caaccccatt cacgacgccc ttaggctgca
     1681 agaactcgcc gacacttgcc cccttactct aaattgtgac aggattgaga ataaaggaaa
     1741 ggtctttgac agcgatgtca tcattatcac cactaatctg gccaacccag caccactgga
     1801 ctatgtcaac tttgaagcgt gctcgaggcg catcgatttc ctcgtgtatg cagaagcccc
     1861 cgaggtcgaa aaggcgaagc gtgacttccc gggccaacct gacatgtgga aaaacgcttt
     1921 tagttctgat ttctcacaca taaaattggc actggctcca caaggtggct ttgataagaa
     1981 cgggaacacc ccacacggga agggcgtcat gaagactctc accactggct ccctcattgc
     2041 ccgggcatca gggctgctcc atgagagatt ggatgagttt gaactacagg gcccagctct
     2101 taccaccttc aactttgacc gcaacaaagt gcttgccttc agacagcttg ctgctgaaaa
     2161 caaatatggg ttgatagaca caatgaaagt tgggaggcag ctcaaggatg tcaaaaccat
     2221 gccagaactt aaacaagcac tcaagaacat ctcaatcaag aagtgccaga ttgtgtatag
     2281 tggttgcacc tacacacttg aatctgatgg caagggcaat gtgaaagttg acagaatcca
     2341 gagcacctcc gtacagacca acaatgagct ggctggcgcc ctgcatcatc tgaggtgcgc
     2401 cagaatcagg tactatgtca agtgtgtcca ggaggccctg tattctatca tccagattgc
     2461 tggggctgca tttgtcacca cgcgcatcat caagcgtgtg aacattcaag acttatggtc
     2521 caagccacaa gtggaaaaca cagaggaggc taccaacaag gacgggtgcc caaaacccaa
     2581 agatgatgag gagttcgtca tttcatctga cgacattaaa actgagggta agaaagggaa
     2641 gaacaagact ggccgtggca agaagcatac agccttctca agtaaaggtc tcagtgatga
     2701 agagtatgat gagtacaaga gaattagaga ggaaaggaat ggcaagtatt ccatagaaga
     2761 gtaccttcag gacagggaca aatactatga ggaggtggcc attgccaggg cgaccgagga
     2821 agacttctgt gaagaggagg aggccaagat ccggcaaagg atcttcagac caacaaggaa
     2881 acaacgcaag gaagaaagag cttctctcgg tttagtcaca ggttctgaga ttaggaaaag
     2941 aaacccagaa gatttcaagc ctaagggaaa actatgggct gacgatgaca gaagtgtgga
     3001 ctacaatgag aaactcagtt ttgaggcccc accaagcatc tggtcaagga tagtcaactt
     3061 tggttcaggt tggggcttct gggtctcccc tagcctgttc ataacatcaa cccacgtcat
     3121 accccagggc gcaaaggagt tctttggagt ccccatcaaa caaattcagg tacacaagtc
     3181 aggcgaattc tgtcgcttga ggttcccaaa accaatcagg actgacgtga ctggcatgat
     3241 cttggaagaa ggtgcgcccg aaggcaccgt ggtcacacta ctcatcaaaa ggtctactgg
     3301 agaactcatg cccctagcag ctagaatggg gacccatgca accatgaaaa ttcaagggcg
     3361 caccgttgga ggtcagatgg gcatgcttct gacaggatcc aacgccaaaa gcatggatct
     3421 aggcaccaca ccaggtgatt gcggctgtcc ctacatctac aagagaggaa atgactatgt
     3481 ggtcattgga gtccacacgg ctgccgctcg tgggggaaac actgtcatat gtgccaccca
     3541 ggggggcgag ggggaagcta cacttgaagg tggtgacagt aagggaacat actgtggtgc
     3601 accaatccta ggcccaggga gtgccccaaa acttagcacc aaaaccaaat tctggagatc
     3661 atccacagca ccactcccac ctggcaccta tgaaccagcc taccttggtg gcaaggaccc
     3721 cagagtcaag ggtggccctt cgttgcagca agtcatgagg gaccagctga aaccatttac
     3781 agagcccagg ggtaagccac caaagccaag tgtgttagaa gctgccaaga aaaccatcat
     3841 caatgtcctt gaacaaacaa ttgacccacc tgagaagtgg tcgttcgcgc aagcttgcgc
     3901 ctcccttgac aagaccactt ctagcggcca tccgcaccat atgcggaaaa acgactgctg
     3961 gaatggggag tccttcacag gcaagctggc agaccaggct tccaaggcta acctgatgtt
     4021 tgaagaaggg aagaacatga ccccagtcta cacaggtgca cttaaggatg aattagtcaa
     4081 aactgacaaa atttatggta agatcaagaa gaggcttctc tggggctcgg atttagcaac
     4141 catgatccgg tgtgctcgag cattcggagg cctaatggat gaactcaaag cacactgtgt
     4201 cacacttcct attagagttg gtatgaatat gaatgaggat ggccccatca tcttcgagaa
     4261 gcattccagg tacagatacc actacgatgc tgattactct cggtgggatt caacacaaca
     4321 gagagtcgtg ctggcagctg ctctagaaat catggttaaa ttctcctcag aaccacattt
     4381 ggctcaggta gtcgcagaag atcttctttc ccctagcgtg gtggatgtgg gtgacttcac
     4441 aatatcaatc aacgagggcc ttccctctgg ggtgccctgc acctcccaat ggaactccat
     4501 cgcccactgg cttctcactc tttgtgcact ctccgaagtc acaagtttgt ctccagatat
     4561 catacaggct aattctctct tctccttcta tggtgatgat gaaattgtta gtacagacat
     4621 aaaattggac ccagagaagt tgacagcaaa gctcaaggaa tatgggttga aaccaacccg
     4681 ccccgacaaa actgaaggac ctctcgttat ctctgaagac ttagatggtt tgactttcct
     4741 gcggagaact gtgacccgcg acccagctgg ttggtttgga aaactggagc agagctcaat
     4801 actcaggcaa atgtactgga ctaggggccc caaccatgaa gatccatctg aatcaatgat
     4861 tccacactct caaagaccca tacaattgat gtccttactg ggagaggccg cactccacgg
     4921 cccaacattc tacagtaaaa tcagcaaact agtcattgca gagctaaaag aaggtggtat
     4981 ggatttttac gtgcccaggc aagagccaat gttcagatgg atgagattct cagatctgag
     5041 cacgtgggag ggcgatcgca atctggctcc cagttttgtg aatgaagatg gcgtcgaatg
     5101 acgccaaccc atctgatggg tccgcagcca acctcgtccc agaggtcagc aatgaggtta
     5161 tggctttgga gcccgttgtc ggtgccgcta ttgcggcgcc tgtagcgggc caacaaaatg
     5221 taattgaccc ctggattaga aacaattttg tacaagcccc tggtggagag ttcacagtat
     5281 cccctagaaa cgctccaggt gagatactat ggagcgcgcc cttaggccct gatctgaatc
     5341 cctacctatc tcacttggcc agaatgtata atggttatgc aggtggtttt gaagtgcagg
     5401 tgatcctcgc ggggaacgcg ttcaccgccg gaaaaattat atttgcagca gtcccaccaa
     5461 attttccaac tgaaggcctg agtcccagcc aggtcactat gttcccccac ataatagtag
     5521 atgttaggca attggaacct gtgttgatcc ccttacctga tgttaggaat aatttctatc
     5581 attataatca gacaaatgat tctaccatta aattgatagc aatgctgtat acaccactta
     5641 gggccaataa tgctggggaa gacgtcttca cagtctcttg tcgagtcctc actaggccgt
     5701 cccctgattt tgattttata tttttggtgc cacccacagt tgagtcaaga actaaaccat
     5761 ttactgtccc aatcttaacc gttgaagaaa tgaccaattc aagattcccc attcctttgg
     5821 aaaagttgtt cacgggtccc agcggtgcct ttgttgtcca accacaaaat ggcaggtgca
     5881 cgactgatgg cgtgctctta ggcaccaccc aactgtctcc tgtcaacatc tgtaccttca
     5941 gaggggatgt cacccacatt gcaggttctc gtaattacac aatgaatttg gcatctctaa
     6001 attggaacaa ttatgaccca acagaagaaa ttccagcccc tctaggaact ccagatttcg
     6061 tgggaaagat ccaaggtgtg ctcactcaaa ccacaaaagg agatggctcg acccgtggcc
     6121 ataaagctac agtttacact gggagtgccc cctttactcc aaagctgggc agtgttcaat
     6181 tcagtactga cacagaaaat gattttgaaa ctcaccaaaa cacaaaattc accccagtcg
     6241 gtgtcatcca ggatggtggc accacccacc gaaatgaacc ccaacaatgg gtgctcccaa
     6301 gttattcagg tagagatgtt cataatgtac acctagcccc tgctgtagcc cccacttttc
     6361 cgggtgaaca acttcttttc ttcaggtcca ctatgcccgg atgcagcggg tatcccaaca
     6421 tggatttgga ttgcctactc ccccaggagt gggtgcagca cttctaccaa gaggcagctc
     6481 cagcacaatc tgatgtggct ctattgagat ttgtgaatcc agacacgggt agggtcctgt
     6541 ttgagtgcaa acttcataaa tcaggctatg tcacagtggc tcacaccggt cagcatgatt
     6601 tggtcatccc ccccaatggc tattttaggt ttgattcctg ggttaatcag ttttacacac
     6661 ttgcccccat gggaaacgga acggggcgta ggcgcgcttt ataatggctg gagctttctt
     6721 tgctggattg gcatctgatg tccttggctc tggacttggt tccctaatca atgctggggc
     6781 tggggctatc aaccaaaaga ttgattttga aaataataga aaattgcagc aagcttcctt
     6841 ccagtttagc agtaatctac aacaggcttc ctttcaacac gataaagaga tgctccaagc
     6901 acaaattgag gccactaaaa agttgcaaca ggaaatgatg aaagtcaaac aggcaatgct
     6961 cctagaaggt ggattctctg aaacagatgc agcccgtggg gcaatcaacg cccccatgac
     7021 aaaggttttg gactggagcg gaacaaggta ctgggcccct gatgctagga ctacaacata
     7081 caatgcgggc cgcttttcca cccctcaacc ttcggggacg ctgccaggaa gaaccaatcc
     7141 caggactcct acccccgctc ggggctcctc tagcgcatct tctaatgctt ctactgctac
     7201 ttctatactt tcaaatcaaa ctgcttcaac gagacttggt tctacagctg gttctggtac
     7261 caatgtctcg agtctcccgt caactgcaag gactaggagt tgggttgagg atcaaaacag
     7321 aaatttgtca cctttcatga ggggggctca caacatatcg tttgtcaccc caccatctag
     7381 cagatcctct agccaaggca cagtctcaac cgtgcctaaa gaagttttgg actcctggac
     7441 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaggc gaggggagtc
     7501 acgggtgtaa
//