Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| KM198539 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7414
LOCUS KM198539 7414 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/C2H-36/2011/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198539
VERSION KM198539.1
KEYWORDS .
SOURCE Norovirus Hu/GII/C2H-36/2011/VNM
ORGANISM Norovirus Hu/GII/C2H-36/2011/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7414)
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 7414)
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..7414
/organism="Norovirus Hu/GII/C2H-36/2011/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/C2H-36/2011/VNM"
/host="Homo sapiens"
/db_xref="taxon:1527015"
/country="Viet Nam"
/collection_date="25-Oct-2011"
/note="genotype: GII"
CDS 1..5100
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02745.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKKVPPPPPNGEDEVVVSYSAKDGISGLPELSTVRQPE
ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTTDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVKTM
PELKQALKSISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQNLWSKPQVENTEEATNKDGC
PKPKDDEEFVITSDDIKIEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKSMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5081..6703
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02746.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFIVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6703..>7414
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02747.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGATN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGSLPGRINPRTPTPARASSSTSS
NASTVTSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTKSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGPVSTV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc
61 gcaaaatctt caagtgacaa aatgttttct agcatggctg tcacttttaa acgagccctc
121 ggggcgcggc ctaaacagcc tcccccgagg gaaataccgc aaaggccccc acgaccacct
181 actccagaac tggtcaaaaa ggtccctcct cccccgccca acggagagga tgaagtggtg
241 gtttcttata gtgccaaaga tggcatttct ggtctacctg agctttccac cgtcagacaa
301 ccagaagaaa ccaatacggc cttcagtgtc cctccactca atcagaggga gaatagggat
361 gctaaggaac cactgactgg gacaattctg gaaatgtggg atggagaaat ctatcattat
421 ggcctgtatg ttgaacgagg tcttgtgctg ggtgtgcaca aaccaccagc tgccattagc
481 ctcgccaagg tcgaactaac accactctcc ttgttctgga gacctgtgta caccccacag
541 tacctcatct ctccagacac tctcaagaaa ttacacggag aaacatttcc ctacacagcc
601 tttgacaaca actgctatgc cttttgttgc tgggtcctgg atctaaacga ctcgtggctg
661 agtaggagga tgatccagag aacaactggc ttcttcagac cctaccaaga ttggaatagg
721 aaacccctcc ctactacgga tgattccaaa ttaaagaagg tagctaacat attcctgtgc
781 accctgtctt cgctattcac caggcccata aaagacataa taggaaagtt aaggcctctc
841 aacatcatca acatcctagc ttcatgtgac tggactttcg caggcatcgt ggaatccttg
901 atactcttgg cagagctctt tggagtcttc tggacacccc cagatgtgtc tgcgatgatt
961 gcccccttac tcggtgattt cgagttacaa ggacctgagg accttgtagt ggagctcgtc
1021 cctgtggtaa tggggggaat tggtttggtg ctgggattca ccaaagagaa gattggaaaa
1081 atgttgtcat ctgctgcatc caccctaaga gcttgtaaag atctcggtgc atatgggcta
1141 gagatcctaa agctagtcat gaagtggttc ttcccgaaga aagaggaggc aaatgaactg
1201 gctatggtga gatccatcga ggatgcagta ctggaccttg aggcaattga aaacaaccat
1261 atgaccacct tgctcaaaga taaagacagc ctggcaacct acatgagaac ccttgacctc
1321 gaggaagaga aagccagaaa actctcaacc aagtctgcgt cacctgacat cgtgggcaca
1381 atcaacgccc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag
1441 gagctttcca gcagaccaag acctgtggtc ttgatgatat caggtaggcc agggataggg
1501 aagacccacc ttgctaggga agtggccaag agaatcgcag catccctcac aggagaccag
1561 cgcgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggggagagg
1621 gtcgtcctat gggacgacta tggaatgagc aatcccatcc acgacgccct caggctgcaa
1681 gaactcgccg acacttgccc cctcactcta aattgtgaca gaattgagaa taaaggaaag
1741 gtctttgaca gtgatgtcat cattatcact actaatctgg ccaacccagc accactggac
1801 tatgtcaact ttgaagcgtg ctcgaggcgc atcgatttcc tcgtgtacgc agaagccccc
1861 gaggtcgaaa aggcgaagcg tgacttcccg ggccaacctg acatgtggaa aaacgccttt
1921 agttctgatt tctcacacat aaaactggca ctggctccac aaggtggctt cgataagaac
1981 gggaacaccc cacatgggaa gggcgtcatg aagactctca ccactggctc ccttattgcc
2041 cgggcatcag ggctgctcca tgagagattg gatgagtttg aactacaggg cccagctctc
2101 accaccttca actttgaccg caacaaagtg cttgccttca ggcagcttgc tgctgaaaac
2161 aaatacgggt tgatggacac aatgagagtt gggaggcagc tcaaggatgt caaaaccatg
2221 ccagaactta aacaagcact caagagcatc tcaatcaaga agtgtcagat tgtgtacagt
2281 ggttgcacct acacacttga gtctgatggc aagggcaatg tgaaggttga cagagttcag
2341 agcacctccg tgcagaccaa caatgagctg gctggcgccc tgcaccatct gaggtgcgcc
2401 agaatcaggt actatgttaa gtgtgtccag gaggccctgt attctatcat tcagattgct
2461 ggagctgcgt tcgtcaccac gcgcatcatc aagcgtgtga acattcaaaa cttatggtcc
2521 aagccacaag tggaaaacac agaggaagcc accaacaagg atgggtgccc aaaacccaaa
2581 gatgatgagg agttcgtcat cacatctgac gacattaaaa ttgagggcaa gaaaggaaag
2641 aacaagactg gccgtggtaa gaagcacaca gccttctcaa gtaaaggtct cagtgatgaa
2701 gagtatgatg agtacaagag aattagagag gaaaggaatg gcaagtactc catagaagag
2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa
2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tcttcagacc aacaaggaaa
2881 caacgcaagg aagaaagagc ttctctcggt ttagtcacag gttctgaaat taggaaaaga
2941 aacccagatg atttcaagcc caaggggaaa ctatgggctg acgatgacag aagtgtggac
3001 tacaatgaga aactcagttt tgaggctccg ccaagtatct ggtcaaggat agtcaacttt
3061 ggctcaggtt ggggcttctg ggtctccccc agcctattca taacatcaac ccacgtcata
3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaattcaggt gcacaagtca
3181 ggcgaattct gtcgcttgag gttcccaaaa ccaatcagga ctgatgtaac tggcatgatc
3241 ttggaagaag gcgcgcctga aggcaccgtg gccacactac tcatcaaaag gtctactgga
3301 gaactcatgc ccctagcagc cagaatgggg acccatgcaa ccatgaaaat tcaagggcgc
3361 actgttggag gtcagatggg catgcttctg acaggatcca acgccaaaag catggatcta
3421 ggcaccacac caggtgattg cggctgtccc tacatctaca agagagggaa tgactatgtg
3481 gtcattggag tccacacggc tgccgctcgt gggggaaaca ctgttatatg tgccacccag
3541 gggggtgagg gggaagctac acttgaaggt ggtgacagta agggaacgta ctgcggtgcg
3601 ccaatcctag gcccagggag cgccccaaaa cttagtacca aaaccaaatt ctggagatca
3661 tccacagcac cactcccacc tggcacctat gagccagcct accttggtgg caaggacccc
3721 agagtcaagg gtggcccctc gctgcagcaa gtcatgagag accagctgaa accattcaca
3781 gagcccaggg gtaagccacc aaagccaagt gtgttggaag ctgccaagaa aaccatcatc
3841 aatgttcttg aacaaacaat tgacccacct gagaagtggt cgttcgcaca ggcttgcgcg
3901 tcccttgaca agaccacttc tagcggccat ccgcatcaca tgcggaaaaa cgactgctgg
3961 aacggggagt ccttcacagg caaactggca gaccaggctt ccaaggccaa cctgatgttt
4021 gaagaaggga agagcatgac cccagtttac acaggtgcgc tcaaggacga gttggtcaaa
4081 actgataaaa tttatggcaa gatcaagaag aggcttctct ggggctcgga tttagcaacc
4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc
4201 acacttccta tcagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag
4261 cactccaggt acaggtacca ctatgatgct gattactctc gatgggattc aacacaacag
4321 agagccgtgc tggcagctgc tctagaaatt atggttaaat tctcctcaga accacatttg
4381 gctcaggtgg tcgcagaaga ccttctttct cctagcgtgg tggatgtggg tgacttcaca
4441 atatcaatca atgagggtct tccctctggg gtgccctgca cttctcaatg gaactccatc
4501 gcccactggc ttctcactct atgtgcactc tccgaagtta caaatctgtc cccagacatc
4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacagacata
4621 aaactagacc cagagaagtt gacagcaaag cttaaggaat atgggttaaa accaacccgc
4681 cctgacaaaa ctgaaggacc tcttgttatt tctgaagact tagatggttt gactttcctg
4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata
4801 ctcaggcaaa tgtactggac taggggtccc aaccatgaag atccatctga atcaatgatt
4861 ccacactctc aaagacccat acaattgatg tccctgctgg gagaggccgc actccacggc
4921 ccaacattct atagtaaaat cagcaaatta gtcattgcag agctaaaaga aggtggtatg
4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agctttgtga atgaagatgg cgtcgaatga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
5161 ggctttggag cccgttgtcg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagga ataattttgt acaagcccct ggtggagaat tcacagtatc
5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atctgaaccc
5341 ctacctatcc catttggcca gaatgtataa tggttatgca ggtggctttg aagtgcaggt
5401 gatcctcgcg gggaacgcgt tcaccgccgg gaaaattata tttgcagcag ttccaccaaa
5461 ttttccaact gaaggcttga gccccagcca ggttactatg ttcccccaca taatagtaga
5521 tgttaggcaa ctggaacctg tgttgatccc cttacctgat gttaggaata acttctatca
5581 ttataatcag tcaaatgatt ctaccattaa attgatagca atgctgtaca caccacttag
5641 agctaataat gctggggaag atgtcttcac agtctcttgt cgagtcctca cgaggccatc
5701 ccctgacttt gattttatat ttttggtgcc acccacagtt gagtcaagaa ctaaaccatt
5761 tactgtccca atcttaactg ttgaagaaat gaccaattca agattcccca tccctttgga
5821 aaagttgttc acgggcccca gcggtgcctt tattgttcaa ccacaaaatg gtagatgcac
5881 gactgatggc gtgctcttag gcaccaccca actgtctcct gtcaacatct gcaccttcag
5941 aggggatgtc acccacattg caggttctcg caattacacg atgaatttgg cttctctaaa
6001 ttggaataat tatgacccaa cagaagaaat tccagcccct ctgggaactc cagatttcgt
6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaggga gatggctcga cccgtggcca
6121 taaagcaaca gtttacactg ggagtgcccc ctttactcca aagctgggca gtgttcaatt
6181 cagtactgac acagaaaatg attttgaagc tcaccaaaac acaaaattca ccccagtcgg
6241 tgtcatccag gatggtggca ccacccaccg aaatgaaccc caacaatggg tgctcccaag
6301 ttattcaggt agagatgtcc acaatgtaca cctggcccct gctgtagccc ccacttttcc
6361 gggtgaacaa cttcttttct tcaggtccac tatgcccgga tgcagtgggt atcccaacat
6421 ggatttggat tgcctactcc ctcaggagtg ggtgcagcac ttctaccaag aggcagctcc
6481 agcacaatct gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcctgtt
6541 tgagtgcaaa cttcataaat caggctatgt cacagtggct cacaccggcc agcatgattt
6601 ggtcatcccc cctaatggct attttaggtt tgactcctgg gttaaccaat tctacacact
6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcttta taatggctgg ggctttcttt
6721 gctggattgg catctgatgt ccttggctct ggacttggct ccctaatcaa tgctggggct
6781 ggggctatta accaaaagat tgattttgaa aataacagaa aattgcagca agcttccttc
6841 cagtttagca gtaatctaca acaggcctcc tttcaacatg acaaagagat gctccaagca
6901 caaatcgagg ccactaaaaa gttgcaacag gaaatgatga gagtcaaaca ggcaatgctc
6961 ttagaaggtg ggttctctga aacagatgca gctcgtgggg caaccaacgc ccccatgaca
7021 aaggttttgg actggagtgg aacaaggtac tgggcccctg atgccaggac tacaacatac
7081 aatgcaggcc gcttttccac cccccaaccc tcggggtcat tgccaggaag aatcaatccc
7141 aggactccta ctcccgctcg ggcctcctct agtacatcct ctaatgcttc tactgttact
7201 tctatatatt caaatcaaac tgtttcaacg agacttggtt ctacagctgg ttctggcacc
7261 aatgtctcga gtctcccgtc aactgcaagg actaagagtt gggttgagga tcaaaacaga
7321 aatttgtcac ctttcatgag gggggctcac aacatatcgt ttgtcacccc accatctagc
7381 agatcctcta gccaaggccc agtctcaacc gtgc
//