Typing tool

Complete norovirus genomes

JX846925  GII.2
 GII.P30

Length: 7,492 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6713
ORF3: 6713..7492
LOCUS       JX846925                7492 bp ss-RNA     linear   VRL 24-OCT-2013
DEFINITION  Norovirus Hu/GII.2/KL109/1978/MYS, complete genome.
ACCESSION   JX846925
VERSION     JX846925.1
DBLINK      BioProject: PRJNA70471
KEYWORDS    .
SOURCE      Norovirus Hu/GII.2/KL109/1978/MYS
  ORGANISM  Norovirus Hu/GII.2/KL109/1978/MYS
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7492)
  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     Genome sequence lacks part of non-coding region.
            
            ##Assembly-Data-START##
            Assembly Method       :: clc_ref_assemble_long v. 3.22.55705
            Coverage              :: 70.9x
            Sequencing Technology :: Sanger; Illumina; 454
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7492
                     /organism="Norovirus Hu/GII.2/KL109/1978/MYS"
                     /mol_type="genomic RNA"
                     /strain="Hu/GII.2/KL109/1978/MYS"
                     /host="Homo sapiens; sex: M"
                     /db_xref="taxon:1260940"
                     /country="Malaysia: Kuala Lumpur"
                     /collection_date="30-May-1978"
                     /note="genotype: GII.2"
     gene            5..5104
                     /gene="POL"
     CDS             5..5104
                     /gene="POL"
                     /note="genome polyprotein"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AFX71658.1"
                     /translation="MKMASNDASAAAAVNSNNDNAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEPVVHYSAKDGITGLPELTTVRQPE
                     EVATAFSVPPLDQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLYWRPVYTPQYLIAPDTLRKLHGELFPYTAFDNNCYAFCCWVLELNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANILLCALSSLFTRPIKDIIGK
                     LRPLNILNILASCDWSFASIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRAIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHLAREL
                     AKKIATTLSGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPVHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDVEK
                     AKRDFPGQPDMWKSAYSPDFSHIKLMLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPNLTTFNFDRNKIQAFRQLAAENKYGLVDTMRVGGQLKSVRTI
                     PELKQALKNILIKRCQIVYGGSTYTLESDGKGSVKVEKVQNTNIQINNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQNLWSRPPVGDAEEVTSQDGC
                     PKPKDDDEFVISSSDITPEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDERVVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGTQEFFGVPIKQIQIHKSGEFCRLRFPKSIRTDVTGMILEEGAPEG
                     TVVSLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGNAPKLSTKTKFWRSSTVPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPKKWSFSQACASLDKTTSSGHPHHIRKNDCW
                     NGESFTGKLADQASKANLMYEEGKNMTPVYTGALKDELVKTDKIYGQIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRFSYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQTVAEDLLAPSVMDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLAPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQIYWTRGP
                     NHEDPSETMIPHSQRPIQLMSLLGEAALHGPTFYTKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     mat_peptide     5..994
                     /gene="POL"
                     /product="protein p48"
     mat_peptide     995..2092
                     /gene="POL"
                     /product="NTPase"
                     /note="p41"
     mat_peptide     2093..2629
                     /gene="POL"
                     /product="protein p22"
     mat_peptide     2630..3028
                     /gene="POL"
                     /product="viral genome-linked protein"
                     /note="VPg"
     mat_peptide     3029..3571
                     /gene="POL"
                     /product="3C-like protease"
                     /note="3CLpro; calicivirin"
     mat_peptide     3572..5101
                     /gene="POL"
                     /product="RNA-directed RNA polymerase"
     gene            5085..6713
                     /gene="VP1"
     CDS             5085..6713
                     /gene="VP1"
                     /codon_start=1
                     /product="capsid protein VP1"
                     /protein_id="AFX71659.1"
                     /translation="MKMASNDAAPSTDGAAGLVPESNSEVMALEPVAGAALAAPVTGQ
                     TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
                     MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
                     VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
                     TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT
                     QLQVSGICAFKGEVTAHLQDNDHLYNITITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
                     VITQRDKQNAAGQSQPANRGHDAVVPTYTAQYTPKLGQVQIGTWQTDDLKVNQPVKFT
                     PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYLPLKGGYGNPA
                     IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
                     VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRIQ"
     gene            6713..7492
                     /gene="VP2"
     CDS             6713..7492
                     /gene="VP2"
                     /note="minor capsid protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="AFX71660.1"
                     /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQRLQQN
                     SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPTDAARGAVNAPMTQALDWNG
                     TRYWAPGSMRTTSYSGRFTSTAPARQADFQHTQNRPSSGSSVSSYTTQSSRPTLTTTT
                     GSSHGTTSSNSTRSTNLSQSTVSRATSRTSEWVRDQNRNLEPYMHGALQTAFVTPPSS
                     RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgtaaaca gcaacaacga
       61 caacgcaaaa tcttcaagtg acggagtact atctagtatg gctgtcactt ttaaacgagc
      121 ccttggggcc cggcctaaac agccgccccc gagggaaata ccacaaaggc ccccaaggcc
      181 acccactcca gaactggtga aaaagatccc acctcccccg cccaacgggg aagatgaacc
      241 ggtcgttcat tatagtgcca aagatggcat aactgggctg cccgaactta caacagtgag
      301 gcagccagaa gaggttgcta cagcattcag cgtcccaccc ctcgaccaga gagagaatag
      361 ggacgctaag gagccattga ccggcaccat cttggagatg tgggatggcg agatctacca
      421 ttatggccta tatgtggagc gagggctggt gcttggcgtg cacaaaccac cagccgccat
      481 cagcctcgct aaagttgagt taacacctct atctttgtat tggagaccag tgtacacccc
      541 ccagtatctc atcgctcctg acaccctcag gaaactgcac ggggagttat ttccatacac
      601 ggcctttgat aacaactgct atgccttctg ctgctgggtg ttggaattaa atgattcttg
      661 gttgagcaga aggatgatac agagaacaac tggctttttc aggccttacc aagattggaa
      721 taggaagccc ctccccacca tggatgactc caagttgaag aaggtggcca acatactttt
      781 gtgtgccttg tcatcactat tcactagacc catcaaggac ataattggga aactcaggcc
      841 tctcaacatc cttaacatcc tggcttcttg tgattggtct ttcgcaagta tagtggaatc
      901 tctaattctc ctggctgaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgccccc ttactgggtg actacgagct gcaaggacct gaagatcttg ctgtggaact
     1021 tgtaccggta gtaatggggg ggataggatt ggtgttgggg ttcaccaagg aaaagattgg
     1081 gaagatgcta tcatctgccg cctccaccct gagggcctgc aaagaccttg gcgcctatgg
     1141 gctggaaatt ctgaaactgg tcatgaaatg gtttttccca aagaaagagg aggcaaacga
     1201 gcttgcgatg gtgagggcta ttgaggacgc agtcctagat ctcgaggcta ttgagaacaa
     1261 ccatatgaca gctctactca aagataaaga tagcctcgcg acatacatga ggactcttga
     1321 tttggaggaa gaaaaggcca gaaagctctc cactaagtcc gcttcacctg atatagtggg
     1381 cacgatcaac gccctactgg ctagaattgc cgctgctcgt tcccttgtac acagggccaa
     1441 ggaagaactg tccagcagac taaggccagt tgtcgtgatg atatctggca aacctggcat
     1501 cgggaagacc catctggcta gagaattggc aaagaagatt gctacaaccc tctcaggaga
     1561 ccagagggta ggcctcatcc cccgcaacgg agtcgaccac tgggatgctt acaagggtga
     1621 gagagtcgtt ctctgggacg actatggaat gagtaaccct gtccacgatg ccctaagact
     1681 ccaagaactt gctgacacct gccccctgac cctaaactgt gacagaattg agaacaaggg
     1741 caaggttttt gacagtgatg ccataatcat cacaaccaac ctggctaacc cagctccact
     1801 tgattatgtc aactttgaag cttgctccag gcgcattgac ttcctcgtgt atgccgatgc
     1861 acctgacgtt gagaaggcga agcgcgactt cccgggacaa cctgacatgt ggaagagcgc
     1921 ttacagtccc gacttctcac acatcaagct aatgctggct ccccagggtg gttttgacaa
     1981 aaatggcaac accccacacg ggaaaggtgt catgaagacc ctcacaacag gctccctcat
     2041 tgcccgtgct tcagggctcc tccatgaaag actggatgaa ttcgaactac aaggacccaa
     2101 cctcacaact ttcaactttg accgtaataa aatacaggct tttaggcagc ttgctgccga
     2161 aaacaaatat ggcctggtag acacaatgag agtgggtgga caactcaaga gtgtcagaac
     2221 tataccagaa ctcaagcagg ccctcaagaa catattaatc aaaaggtgcc agatagtgta
     2281 cggtggcagc acctacacac ttgaatctga tggcaaaggg agtgtgaaag tggaaaaagt
     2341 gcaaaatacc aacatccaaa tcaacaatga gctagctggt gctctacacc acctccgatg
     2401 cgccaggatc aggtattatg ttaaatgtgt tcaggaggct ctttactcca ttatccaaat
     2461 tgctggggcc gcgtttgtaa ccacgcgcat tgtgaagcgc atgaacatac agaacttgtg
     2521 gtcaaggcct ccagtaggag atgcggagga ggtcactagc caggatggtt gcccaaagcc
     2581 caaagatgat gatgagttcg tcatctcgtc tagtgacatc acgcctgaag gcaagaaagg
     2641 aaagaacaag actggccgcg gtaagaaaca cacagccttc tcgagcaagg gtctcagtga
     2701 tgaggagtac gatgagtaca aaagaattag ggaagaaagg aatggtaagt actccataga
     2761 agaatacctt caggacagag acaagtatta tgaggaagtg gccatagcca gggcaactga
     2821 ggaagacttc tgtgaggaag aagaagccaa gatccgacag aggatattta ggccaacgag
     2881 gaagcaacgc aaggaggaga gggcttccct tggccttgtc accggctcag agatcagaaa
     2941 gagaaaccca gacgacttca aacctaaagg aaagctgtgg gctgatgatg aaagggttgt
     3001 tgactataat gagaaactca gtttcgaggc ccccccgagc atctggtcaa ggatagtcaa
     3061 ctttgggtca ggatgggggt tttgggtgtc ccctagcctg ttcattacat caacccatgt
     3121 tataccccaa ggcactcagg aattctttgg tgtacccatc aagcagattc aaattcacaa
     3181 atcaggggag ttctgccgcc tgagattccc taaatcaatc agaactgatg taacaggcat
     3241 gatcctagaa gagggagccc cagaaggaac cgtggtctca ctactcatca agagaccaac
     3301 cggtgagctc atgcccctgg cagccagaat gggcacccat gcgactatga agatccaagg
     3361 tcgcacggtt gggggtcaga tgggcatgtt gctaacaggg tccaatgcta aaagcatgga
     3421 tttgggcacg acgcctggtg actgtggctg cccctacatt tataagagag gcaatgacta
     3481 cgtggtcatc ggcgtgcaca cagccgcggc tcgcggaggt aacactgtca tctgtgcaac
     3541 ccagggtagt gaaggtgagg ccacgctcga aggcggtgat aacaaaggta cctactgtgg
     3601 agctccaata ctaggtcctg gtaacgcacc caaactcagt accaagacta agttctggag
     3661 gtcctccaca gtgccactcc cacccgggac ctatgaacca gcctacttag gtggcaagga
     3721 tcccagggtg aagggtggac cttcactaca acaagtcatg agagaccagc taaaaccatt
     3781 cactgagcct aggggcaaac cacccaagcc aagtgtgctg gaagccgcca agaagaccat
     3841 tatcaatgtg ttggagcaaa caatagatcc ccccaaaaaa tggtcatttt cacaagcatg
     3901 tgcgtcgctt gataaaacca cctccagcgg ccacccccac cacatacgga agaacgattg
     3961 ctggaatgga gagtctttta caggaaaatt ggcagatcaa gcatcaaaag ctaacctaat
     4021 gtatgaggaa ggaaagaaca tgaccccagt ctatacaggg gccctcaagg atgagctggt
     4081 caagactgat aagatttatg ggcagatcaa gaaaaggctt ctttggggct cggacttggc
     4141 aacaatgatc cgttgtgcgc gggcgtttgg agggttgatg gatgagctta aggcccattg
     4201 tgtaacactt cctgtcaggg ttggaatgaa catgaatgag gatggaccca taatctttga
     4261 aaagcactcc aggttctcat accactatga tgcagactac tcacgatggg actcaaccca
     4321 acagagggca gtgctagctg cagccttgga aatcatggta aaattctcac cagaaccaca
     4381 tttggcccaa actgttgcag aggatctcct agcccccagt gtgatggatg taggtgattt
     4441 caaaataaca attaacgagg gtctgccctc gggagtaccc tgcacatcac agtggaattc
     4501 catcgcccac tggctcctca cactctgtgc actatctgaa gtcacaaacc tggctcctga
     4561 catcatacaa gctaactcct tgttctcttt ctatggtgat gatgaaattg tgagcactga
     4621 tataaaatta gacccagaga aactcacagc aaaactcaaa gaatacggac tcaagccaac
     4681 ccgcccggac aaaactgaag gacccctgat catatccgag gacttgaatg gtttgacctt
     4741 tctgcggcgg accgtgaccc gtgatccagc tgggtggttt ggcaagttgg accagagttc
     4801 aattctcagg cagatatact ggactagggg ccccaaccat gaggacccgt ccgaaacaat
     4861 gataccacac tcccaaaggc ctatacagct gatgtctctt ttgggtgaag cagccttgca
     4921 tggtccaacg ttttacacca aaatcagtaa attggtcatc acagagctga aggaaggtgg
     4981 catggatttt tacgtgccca gacaggaacc catgttcagg tggatgaggt tctcggattt
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccgc tccatctact gatggcgcag ccggcctcgt gccagaaagt aatagtgagg
     5161 tcatggctct tgagcctgtg gctggtgctg ccttggcagc cccggttacc ggtcaaacaa
     5221 atattataga cccttggatt agagcaaatt ttgtccaggc ccctaatggt gaattcacag
     5281 tttctccccg caatgcccct ggtgaagtgc tattgaatct agaattgggt ccagaattaa
     5341 atccttatct ggcacatttg gcaagaatgt acaacgggta tgccggtggg atggaggtgc
     5401 aggtcatgct agctgggaac gcgttcacag ctggcaaatt ggtcttcgct gctgtaccac
     5461 ctcattttcc ggttgaaaac cttagcccac agcaaattac catgttcccc catgtgatta
     5521 tagatgttag gactttggaa cctgttttgt tgccactccc cgatgttaga aataatttct
     5581 ttcattataa tcaaaaagat gatcctaaga tgagaattgt ggctatgctt tatactcccc
     5641 tcaggtccaa tggttctggt gatgatgtgt ttacagtctc ttgtagggtg ttgactagac
     5701 cctcccctga ttttgatttt acatacctgg tgccaccaac agtggaatcc aaaacaaaac
     5761 catttactct tccaatcctt acacttgggg agctttccaa ctctagattt ccagtgtcca
     5821 tagatcagat gtacactagc cccaatgaag tcatatctgt gcagtgccag aatggaaggt
     5881 gcacactgga tggggagctc caaggaacaa cacagctcca agttagtggc atttgtgcat
     5941 tcaaaggaga agtgaccgcc cacttgcagg acaatgatca cctatacaac atcaccatca
     6001 caaacttgaa tgggtcccct tttgatccct ctgaggacat ccccgccccc ctgggtgtgc
     6061 ccgactttca gggaagggtc tttggtgtca tcactcaaag agacaaacag aatgccgctg
     6121 gacaaagcca gccggcaaac aggggacacg atgctgtagt tcccacttac acagcccagt
     6181 acaccccaaa attgggtcag gttcaaattg gcacatggca gaccgacgat cttaaagtca
     6241 accaaccagt aaaattcacc ccagtcggtc tcaatgatac agaacatttc aatcagtggg
     6301 tggttcctag gtacgctggt gctttaaatc taaatacaaa tcttgccccc tctgttgctc
     6361 cagtgtttcc aggggagcgt ttgctcttct ttaggtcata cctccccctt aagggtggtt
     6421 atggaaaccc agctattgat tgcctgctac cacaagagtg ggtgcagcat ttttatcagg
     6481 aagcagcccc ctcaatgagt gaggtggccc ttgtcagata catcaatccg gacactggcc
     6541 gggcgctgtt tgaggccaaa ctccacagag ctggtttcat gacagtctcg agtaacacca
     6601 gtgctccggt ggttgtgcct gccaacggat acttcagatt tgactcttgg gtgaaccaat
     6661 tttattctct tgcccccatg ggaactggaa atgggcgtag aaggattcag taatggctgg
     6721 agctttcgta gctggtctcg cgggggatgt gctcagcaat gggctcagtt cactaattaa
     6781 tgcaggtgct aatgcaataa atcagagagc agaatttgat tttaaccaga gattacagca
     6841 aaattctttt aatcatgata aggagatgtt gcaggctcag attcaggcaa ctaagcagct
     6901 gcaggcagac atgatggcta taaagcaggg ggttctgacc gctggcggct tttcccctac
     6961 tgatgcagcc agaggcgctg tgaacgcgcc catgacacag gcgctggatt ggaatggcac
     7021 aaggtattgg gcaccaggct ccatgaggac tacatcctac tctggcaggt tcacatcgac
     7081 cgccccggca aggcaggccg actttcaaca cactcaaaat cggccttcga gtggctcttc
     7141 tgtgtcctct tataccactc aatcttcaag accaactcta accacaacca cagggtcctc
     7201 acacggtaca acctcatcca attcgacccg tagcacaaac ctttcccagt cgacggtctc
     7261 tagggctacc tctaggacta gtgagtgggt tagagatcaa aataggaatt tggaacccta
     7321 catgcatggt gccttacaga cagcctttgt caccccacct tccagcaggg catctgacgg
     7381 gacagtctca accgtcccca aaggtgtttt ggactcctgg acacctgcgt tcaacacccg
     7441 caggcagccg ctttttgcac acctccgtaa gaggggggag tcacgggtgt aa
//