Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| KM198486 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 58..5076
ORF2: 5057..6679
ORF3: 6679..7419
LOCUS KM198486 7419 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/C2H-18/2011/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198486
VERSION KM198486.1
KEYWORDS .
SOURCE Norovirus Hu/GII/C2H-18/2011/VNM
ORGANISM Norovirus Hu/GII/C2H-18/2011/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7419)
AUTHORS Cotten,M., Petrova,V., Phan,M.V., Rabaa,M.A., Watson,S.J.,
Ong,S.H., Kellam,P. and Baker,S.
TITLE Deep sequencing of norovirus genomes defines evolutionary patterns
in an urban tropical setting
JOURNAL J. Virol. 88 (19), 11056-11069 (2014)
PUBMED 25056894
REFERENCE 2 (bases 1 to 7419)
AUTHORS Cotten,M.L., Petrova,V., Phan,M.V.T., Rabaa,M.A., Watson,S.J.,
Kellam,P. and Baker,S.
TITLE Direct Submission
JOURNAL Submitted (13-JUL-2014) Virus Genomics, The Wellcome Trust Sanger
Institute, Hinxton CB10 1SA, United Kingdom
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. 2.4.0
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7419
/organism="Norovirus Hu/GII/C2H-18/2011/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/C2H-18/2011/VNM"
/host="Homo sapiens"
/db_xref="taxon:1527009"
/country="Viet Nam"
/collection_date="30-Aug-2011"
/note="genotype: GII"
CDS 58..5076
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02586.1"
/translation="MFSSMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKVPPP
PPNGEDEVVVSYSAKDGISGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI
LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT
LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT
TDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL
AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM
LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN
HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR
AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA
YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL
ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL
APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK
VLAFRQLAAENKYGLMDTMRVGRQLKDVKTMPELKQALKSISIKKCQIVYSGCTYTLE
SDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV
TTRIIKRVNIQNLWSKPQVENTEEATNKDGCPKPKDDEEFVITSDDIKTEGKKGKNKT
GRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEED
FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV
DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV
HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIKRSTGELMPLAARMGTHATM
KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN
TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE
PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP
PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKSMT
PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR
VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV
VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII
QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF
LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA
LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE
DGVE"
CDS 5057..6679
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02587.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFIVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6679..>7419
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02588.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGSLPGRINPRTPTPARASSSASS
NASTVTSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTKSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTG"
ORIGIN
1 tccgctgccg ctgttgctaa cagcaacaac gacaccgtaa aatcttcaag tgacaaaatg
61 ttttctagca tggctgtcac ttttaaacga gccctcgggg cgcggcctaa acagcctccc
121 ccgagggaaa taccgcaaag acccccacga ccacctactc cagaactggt caaaaaggtc
181 cctcctcccc cgcccaacgg agaggatgaa gtggtggttt cttatagtgc caaagatggc
241 atttctggtc tacctgagct ttccaccgtc agacaaccag aagaaaccaa tacggccttc
301 agtgtccctc cactcaatca gagggagaat agggatgcta aggaaccact gactgggaca
361 attctggaaa tgtgggatgg agaaatctat cattatggcc tgtatgttga acgaggtctt
421 gtgctgggtg tgcacaaacc accagctgcc attagcctcg ccaaggtcga actaacacca
481 ctctccttgt tctggagacc tgtgtacacc ccacagtacc tcatctctcc agacactctc
541 aagaaattac acggagaaac atttccctac acagcctttg acaacaactg ctatgccttt
601 tgttgctggg tcctggatct aaacgactcg tggctgagta ggagaatgat ccagagaaca
661 actggcttct tcagacccta ccaagattgg aataggaaac ccctccctac tacggatgat
721 tccaaattaa agaaggtagc taacatattc ctgtgcaccc tgtcttcgct attcaccagg
781 cccataaaag acataatagg aaagttaagg cctctcaaca tcatcaacat cctagcttca
841 tgtgactgga ctttcgcagg catcgtggaa tccttgatac tcttggcaga gctctttgga
901 gtcttctgga cacccccaga tgtgtctgcg atgattgccc ccttactcgg tgatttcgag
961 ttacaaggac ctgaggacct tgtagtggag ctcgtccctg tggtaatggg gggaattggt
1021 ttggtgctgg gattcaccaa agagaagatt ggaaaaatgt tgtcatctgc tgcgtccacc
1081 ttgagagctt gtaaagatct cggtgcatat gggctagaga tcctaaagct agtcatgaag
1141 tggttctttc cgaagaaaga ggaggcaaat gaactggcta tggtgagatc catcgaggat
1201 gcagtactgg accttgaggc aattgaaaac aaccacatga ccaccttgct caaagataaa
1261 gacagcctgg caacctacat gagaaccctt gacctcgagg aagagaaagc cagaaaactc
1321 tcaaccaagt ctgcttcacc tgacatcgtg ggcacaatca acgcccttct ggcgagaatc
1381 gccgctgcac gctccctggt gcaccgagcg aaggaggagc tttccagcag accaagacct
1441 gtggtcttga tgatatcagg tagaccaggg atagggaaga cccaccttgc tagggaagtg
1501 gctaagagaa tcgcagcctc cctcacagga gaccagcgcg taggcctcat cccacgcaat
1561 ggcgtcgatc actgggatgc gtacaagggg gagagggtcg tcctatggga cgactatgga
1621 atgagcaatc ccatccacga cgccctcagg ctgcaagaac tcgccgacac ttgccccctc
1681 actctaaatt gtgacaggat tgagaataaa ggaaaggtct ttgacagtga tgtcatcatt
1741 atcactacta atctggccaa cccagcacca ctggactatg tcaactttga agcgtgctcg
1801 aggcgcatcg atttcctcgt gtacgcagaa gcccccgagg tcgaaaaggc gaagcgtgac
1861 ttcccgggcc aacctgacat gtggaaaaac gcttttagtt ctgatttctc acacataaaa
1921 ctggcactgg ctccacaagg tggcttcgat aagaacggga acaccccaca tgggaagggc
1981 gtcatgaaga ctctcaccac tggctccctt attgcccggg catcagggct gctccatgag
2041 agattggatg agtttgaact acagggccca gctctcacca ccttcaactt tgaccgcaac
2101 aaagtgcttg ccttcaggca gcttgctgct gaaaacaaat acgggttgat ggacacaatg
2161 agagttggga ggcagctcaa ggatgtcaaa accatgccag aacttaaaca agcactcaag
2221 agcatctcaa tcaagaagtg ccagattgtg tacagtggtt gcacctacac acttgagtct
2281 gatggcaagg gcaatgtgaa ggttgacaga gttcagagca cctccgtgca gaccaacaat
2341 gagctggctg gcgccctgca ccatctgagg tgcgccagaa tcaggtacta tgttaagtgt
2401 gtccaggagg ccctgtattc tatcattcag attgctggag ctgcattcgt caccacgcgc
2461 atcatcaagc gtgtgaacat tcaaaactta tggtccaagc cacaagtgga aaacacagag
2521 gaagccacca acaaggatgg gtgcccaaaa cccaaagatg atgaggagtt cgtcatcaca
2581 tctgacgaca ttaaaactga gggtaagaaa ggaaagaaca agactggccg tggcaagaag
2641 cacacagcct tctcaagtaa aggtctcagt gatgaagagt atgatgagta caagagaatt
2701 agagaggaaa ggaatggcaa gtactccata gaagagtacc ttcaggacag ggacaaatac
2761 tatgaggagg tggccattgc cagggcgacc gaggaagact tctgtgaaga ggaggaggcc
2821 aagatccggc aaaggatctt cagaccaaca aggaaacaac gcaaggaaga aagagcttct
2881 ctcggtttag tcacaggttc tgaaattagg aaaagaaacc cagatgattt caagcccaag
2941 gggaaactat gggctgacga tgacagaagt gtggactaca atgagaaact cagttttgag
3001 gctccgccaa gcatctggtc aaggatagtc aactttggct caggttgggg cttctgggtc
3061 tcccccagcc tgttcataac atcaacccac gtcatacccc agggcgcaaa ggagttcttt
3121 ggagtcccca tcaaacaaat tcaggtgcac aagtcaggcg aattctgtcg cttgaggttc
3181 ccaaaaccaa tcaggactga tgtgactggc atgatcttgg aagaaggcgc gcctgaaggc
3241 accgtggcca cactactcat caaaaggtct actggagaac tcatgcccct agcagccaga
3301 atggggaccc atgcaaccat gaaaattcaa gggcgcactg ttggaggtca gatgggcatg
3361 cttctgacag gatccaacgc caaaagcatg gatctaggca ccacaccagg tgattgcggc
3421 tgtccctaca tctacaagag agggaatgac tatgtggtca ttggagtcca cacggctgcc
3481 gctcgtgggg gaaacactgt tatatgtgcc acccaggggg gtgaggggga agctacactt
3541 gaaggtggtg acagtaaggg aacgtactgc ggtgcgccaa tcctaggccc agggagcgcc
3601 ccaaaactta gtaccaaaac caaattctgg aggtcatcca cagcaccact cccacctggc
3661 acctatgagc cagcctacct tggtggcaag gaccccagag tcaagggtgg cccctcgctg
3721 cagcaagtca tgagagacca gctgaaacca ttcacagagc ccaggggtaa gccaccaaag
3781 ccaagtgtgt tggaagctgc caagaaaacc atcatcaatg ttcttgaaca aacaattgac
3841 ccacctgaga agtggtcgtt cgcacaggct tgcgcgtccc ttgacaagac cacttctagc
3901 ggccatccgc atcacatgcg gaaaaacgac tgctggaacg gggagtcctt cacaggcaag
3961 ctggcagacc aggcttccaa ggccaacctg atgtttgaag aagggaagag catgacccca
4021 gtttacacag gtgcgctcaa ggacgagttg gtcaaaactg ataaaattta tggcaagata
4081 aagaagaggc ttctctgggg ctcggattta gcaaccatga tccggtgtgc tcgagcattc
4141 ggaggcctaa tggatgaact caaagcacac tgtgtcacac ttcctatcag agttggtatg
4201 aatatgaatg aggatggccc catcatcttc gagaagcact ccaggtacag gtaccactat
4261 gatgctgatt actctcgatg ggattcaaca caacagagag ccgtgctggc agctgctcta
4321 gaaattatgg ttaaattctc ctcagaacca catttggctc aggtggtcgc agaagacctt
4381 ctttctccta gcgtggtgga tgtgggtgac ttcacaatat caatcaatga gggtcttccc
4441 tctggggtgc cctgcacttc tcaatggaac tccatcgccc actggcttct cactctatgt
4501 gcactctccg aagttacaaa tttgtcccca gacatcatac aggctaattc tctcttctcc
4561 ttctatggtg atgatgaaat tgttagtaca gacataaaac tagacccaga gaagttgaca
4621 gcaaagctta aggaatatgg gttaaaacca acccgccctg acaaaactga aggacctctt
4681 gttatttctg aagacttaga tggtttgact ttcctgcgga gaactgtgac ccgcgaccca
4741 gctggttggt ttggaaaact ggagcagagc tcaatactca ggcaaatgta ctggactagg
4801 ggccccaacc atgaagatcc atctgaatca atgattccac actctcaaag acccatacaa
4861 ttgatgtccc tgctgggaga ggccgcactc cacggcccaa cattctatag taaaatcagc
4921 aaattagtca ttgcagagct aaaagaaggt ggtatggatt tttacgtgcc caggcaagag
4981 ccaatgttca gatggatgag attctcagat ctgagcacgt gggagggcga tcgcaatctg
5041 gctcccagct ttgtgaatga agatggcgtc gaatgacgcc aacccatctg atgggtccgc
5101 agccaacctc gtcccagagg tcaacaatga ggttatggct ttggagcccg ttgtcggtgc
5161 cgctattgcg gcgcctgtag cgggccaaca aaatgtaatt gacccctgga ttaggaataa
5221 ttttgtacaa gcccctggtg gagaattcac agtatcccct agaaacgctc caggtgaaat
5281 actatggagc gcgcccttag gccctgatct gaatccctac ctatcccatt tggccagaat
5341 gtataatggt tatgcaggtg gctttgaagt gcaggtgatc ctcgcgggga acgcgttcac
5401 cgccggaaaa attatatttg cagcagttcc accaaatttt ccaactgaag gcttgagccc
5461 cagccaggtt actatgttcc cccacataat agtagatgtt aggcaactgg aacctgtgtt
5521 gatcccctta cctgatgtta ggaataactt ctatcattat aatcagtcaa atgattctac
5581 cattaaattg atagcaatgc tgtacacacc acttagggct aataatgctg gggaagatgt
5641 cttcacagtc tcttgtcgag tcctcacgag gccatcccct gattttgatt ttatattttt
5701 ggtgccaccc acagttgagt caagaactaa accatttact gtcccaatct taactgttga
5761 agaaatgacc aattcaagat tccccatccc tttggaaaag ttgttcacgg gccccagcgg
5821 tgcctttatt gttcaaccac aaaatggtag atgcacgacc gatggcgtgc tcttaggcac
5881 cacccaactg tctcctgtca acatctgcac cttcagaggg gatgtcaccc acattgcagg
5941 ttctcgcaat tacacgatga atttggcttc tctaaattgg aataattatg acccaacaga
6001 agaaattcca gccccactgg gaactccaga tttcgtggga aagatccaag gtgtgctcac
6061 tcaaaccaca aagggagatg gctcgacccg tggccataaa gcaacagttt acactgggag
6121 tgcccccttt actccaaagc tgggcagtgt tcaattcagt actgacacag aaaatgattt
6181 tgaagctcac caaaacacaa aattcacccc agtcggtgtc atccaggatg gtggcaccac
6241 ccaccgaaat gaaccccaac aatgggtgct cccaagttat tcaggtagag atgtccacaa
6301 tgtacacctg gcccctgctg tagcccccac ttttccgggt gaacaacttc ttttcttcag
6361 gtccactatg cccggatgca gtgggtatcc caacatggat ttggattgcc tactccctca
6421 ggagtgggtg cagcacttct accaagaggc agctccagca caatctgatg tggctctatt
6481 gagatttgtg aatccagaca cgggtagggt cctgtttgag tgcaaacttc ataaatcagg
6541 ctatgtcaca gtggctcaca ccggccagca tgatttggtc atccccccta atggctattt
6601 taggtttgat tcctgggtta accaattcta cacacttgcc cccatgggaa atggaacggg
6661 gcgtagacgt gctttataat ggctggggct ttctttgctg gattggcatc tgatgtcctt
6721 ggctctggac ttggctccct aatcaatgct ggggctgggg ctatcaacca aaagattgat
6781 tttgaaaata acagaaaatt gcagcaagct tccttccagt ttagcagtaa tctacaacag
6841 gcctcctttc aacatgacaa agagatgctc caagcacaaa ttgaggccac taaaaagttg
6901 caacaggaaa tgatgagagt caaacaggca atgctcttag aaggtgggtt ctctgaaaca
6961 gatgcagctc gtggggcaat caacgccccc atgacaaagg ttttggactg gagtggaaca
7021 aggtactggg cccctgatgc caggactaca acatacaatg caggccgctt ttccaccccc
7081 caaccctcgg ggtcattgcc aggaagaatc aatcccagga ctcctactcc cgctcgggcc
7141 tcctccagtg catcctctaa tgcttctact gttacttcta tatattcaaa tcaaactgtt
7201 tcaacgagac ttggttctac agctggctct ggcaccaatg tctcgagtct cccgtcaact
7261 gcaaggacta agagttgggt tgaggatcaa aacagaaatt tgtcaccttt catgaggggg
7321 gctcacaaca tatcgtttgt caccccacca tctagcagat cctctagcca aggcacagtc
7381 tcaaccgtgc ctaaagaagt tttggactcc tggactggc
//