Typing tool
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Typing tool
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Complete norovirus genomes
| JQ911597 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
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; Norovirus norwalkense.
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"
/geo_loc_name="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
//