Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| KU311162 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 1..5093
ORF2: 5074..6693
ORF3: 6693..7499
LOCUS KU311162 7524 bp RNA linear VRL 01-JAN-2016
DEFINITION Norovirus Hu/GII.4/AlbertaSP1/2012/CA isolate SP1 non-structural
polyprotein gene, partial cds; and major capsid protein and minor
capsid protein genes, complete cds.
ACCESSION KU311162
VERSION KU311162.1
KEYWORDS .
SOURCE Norovirus Hu/GII.4/AlbertaSP1/2012/CA
ORGANISM Norovirus Hu/GII.4/AlbertaSP1/2012/CA
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7524)
AUTHORS Hasing,M.E., Hazes,B., Lee,B.E., Preiksaitis,J.K. and Pang,X.L.
TITLE Analysis of the intra-host genetic diversity of norovirus in
patients with acute and chronic infection using next generation
sequencing
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7524)
AUTHORS Hasing,M.E., Hazes,B., Lee,B.E., Preiksaitis,J.K. and Pang,X.L.
TITLE Direct Submission
JOURNAL Submitted (15-DEC-2015) Provincial Laboratory for Public Health,
8440-112 Street, Edmonton, Alberta T6G 2J2, Canada
COMMENT ##Assembly-Data-START##
Assembly Method :: Bowtie v. 2-2.2.5
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7524
/organism="Norovirus Hu/GII.4/AlbertaSP1/2012/CA"
/mol_type="genomic RNA"
/isolate="SP1"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:1772262"
/country="Canada"
/collection_date="Dec-2012"
CDS <1..5093
/codon_start=3
/product="non-structural polyprotein"
/protein_id="ALT54490.1"
/translation="ASNDASAAAVANSNNDTAKSSNDKMFSNMAVTLKRALGARPKQP
PPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETN
TAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISFAK
VELTPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLS
RRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGRLRP
LNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVV
ELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKE
EANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSA
SPDIVGTINALLARIAAARSLVHRAKEELSSRLRPVVLMISGKPGIGKTYFAREVAKR
IAASLTGDQRIGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIYDALRLQELADTCPLT
LNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKR
DFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTSSLIARASGL
LHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKIGRQLKDVKTMPEL
KQALKNISIKKCQIVYNGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLRCAR
IRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEAASKDGCPKP
KDDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYS
IEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGS
EIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLF
ITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVV
TLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGC
PYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILGPGS
APKLSTKTKYWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGK
PPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGE
SFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATM
IRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQ
QRVVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQW
NSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYG
LKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHE
DPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMF
RWMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5074..6693
/note="VP1"
/codon_start=1
/product="major capsid protein"
/protein_id="ALT54491.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRSNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSKDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSNAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTQIASTQTYTMNLASLNWNNYDPTEEIPAPLGAPDFMGKIQGVL
TQTTRQGGSTRGHKATVSTGSVHFTPKLGSVRFDTDTNNDLQPHQSTRFTPVGVIQDG
DTHQNEPQQWALPCYSGRDVNNVHLAPAVAPSFPGEQLLFFRSTMPGCSGYPNMDLDC
LLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHNLVI
PPNGYFRFDSWVNQFYTLAPMGNGTGRRRVL"
CDS 6693..7499
/note="VP2"
/codon_start=1
/product="minor capsid protein"
/protein_id="ALT54492.1"
/translation="MAGALFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRELQQA
SFQFSSNLQQASFQHDKEMLHAQIEATKKLQQELMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRINPRTPIPARGSPSISS
NVSSATSIHSNQTASTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKDVLDSWTGAFNTRRQPLFAHIRRRGESRV"
3'UTR 7500..>7524
ORIGIN
1 tggcgtctaa cgacgcttcc gctgccgctg ttgctaacag caacaacgac accgcaaaat
61 cttcaaatga caaaatgttt tctaacatgg ctgtcactct taaacgagcc ctcggggcgc
121 ggcctaaaca gccccccccg agggaaatac cacaaagacc cccacgacca cctactccag
181 aactggtcaa aaagatccct ccccccccgc ccaacggaga ggatgaagta gtggtttctt
241 atagtgccaa agatggcgtt tccggtttgc ctgagctttc caccgtcagg caaccggaag
301 aaaccaatac ggccttcagc gtccctccac tcaaccagag ggagaatagg gatgctaagg
361 aaccactgac tggaacgatt ctggaaatgt gggatggaga aatctaccat tatggcctgt
421 atgttgagcg aggtctcgtg ctgggcgtac acaaaccacc agctgccatt agcttcgcca
481 aggtcgaatt aacaccactc tccttgtact ggagacctgt gtacactcct cagtacctca
541 tttctccaga cactctcaag aagttacacg gagaaacatt tccctacaca gcctttgaca
601 acaactgcta cgccttttgt tgttgggtct tggatctaaa cgactcgtgg ctgagcagga
661 gaatgatcca gagaacaact ggcttcttca gaccctacca agattggaat aggaaacccc
721 tccccactat ggatgattcc aaactaaaga aggtagctaa catattcctg tgcaccctgt
781 cttcgctatt caccaggccc ataaaagaca taataggaag gttaaggcct ctcaacatca
841 tcaacatcct ggcttcatgt gattggactt tcgcaggcat agtggagtcc ttgatactct
901 tggcagagct ctttggagtt ttctggacac ccccagatgt gtctgcgatg atcgccccct
961 tactcggtga ttttgagtta caagggcctg aagaccttgt agtggaactc gtccctgtag
1021 taatgggggg gattggtctg gtgctaggat tcaccaaaga gaagattgga aaaatgttgt
1081 catctgctgc atccactctg agagcttgta aagaccttgg tgcatatggg ctagaaatcc
1141 tgaagttagt catgaagtgg ttcttcccga agaaagagga agctaatgaa ctggctatgg
1201 tgagatccat cgaggatgcg gtactggacc ttgaggcaat tgaaaacaac catatgacca
1261 ccttgctcaa agacaaagat agcctggcaa cctacatgag aacccttgac ctcgaggaag
1321 agaaagccag aaaactctca accaaatctg cttcacctga catcgtgggc acaatcaacg
1381 cacttctggc gagaatcgcc gctgcacgct ccctggtgca ccgagcgaag gaggagcttt
1441 ccagcagact aagacctgta gtcttgatga tatcaggcaa gccaggaata gggaagacct
1501 actttgctag ggaagtggct aagagaatcg cagcctccct cacaggagac cagcgtatag
1561 gcctcatccc acgcaatggc gtcgatcact gggatgcgta caagggggag agggtcgtcc
1621 tatgggacga ctatggaatg agcaatccca tctacgacgc cctcaggctg caagaactcg
1681 ctgacacttg ccccctcacc ctaaattgtg acaggattga gaataaagga aaggtctttg
1741 acagcgatgt catcatcatc accactaatc tggccaaccc agcaccactg gactatgtca
1801 actttgaagc atgctcgagg cgcatcgact tcctcgtgta cgcagaagcc cccgaggtcg
1861 aaaaggcgaa acgcgacttc ccgggccaac ctgacatgtg gaaaaacgca tttagttctg
1921 acttctcaca cataaaactg gcactggccc cacaaggtgg ctttgataag aacgggaaca
1981 ccccacacgg gaagggcgtc atgaagactc tcaccactag ctctctcatt gcccgggcat
2041 cagggctgct ccacgagaga ttggatgagt ttgaactaca gggcccagct ctcaccacct
2101 tcaactttga ccgcaacaaa gtgcttgcct tcaggcagct tgctgctgaa aacaaatatg
2161 gattgatgga cacaatgaaa attgggaggc agctcaagga tgtcaaaacc atgccagaac
2221 ttaaacaagc actcaagaat atctcaatca agaagtgcca gattgtgtac aatggttgca
2281 cctacacact tgagtctgat ggcaaaggca atgtgaaagt tgacagagtc cagagcactt
2341 ccgttcagac taacaatgag ttggctggcg ccctgcacca tctaaggtgc gctagaatca
2401 ggtattatgt taagtgtgtt caggaggccc tgtattctat catccagatt gccggggccg
2461 catttgtcac cacgcgcatc atcaagcgtg tgaacattca agacttatgg tccaagccac
2521 aagtggaaaa cacagaggag gctgccagca aagacgggtg cccaaaaccc aaagatgatg
2581 aggagttcgt cgtttcatct gacgacatta aaactgaggg taagaaaggg aagaacaaga
2641 ctggccgtgg taaaaagcat acagccttct caagtaaagg tctcagtgat gaagagtatg
2701 atgagtacaa gagaattaga gaggaaagaa acggcaagta ctccatagaa gagtaccttc
2761 aggacaggga caaatactat gaggaggtgg ccattgccag ggcgaccgag gaagacttct
2821 gtgaagagga ggaggccaag atccggcaaa ggatcttcag accaacaagg aaacaacgca
2881 aggaagaaag ggcttctctc ggtttagtca caggttctga aattaggaag agaaatccag
2941 aagacttcaa gcccaaggga aaactatggg ctgacgatga caggagtgtg gactacaatg
3001 aaaaactcag ttttgaggcc ccaccaagca tctggtcaag gatagtcaac tttggttcag
3061 gttggggctt ctgggtctcc cccagcctgt tcataacatc aacccacgtc ataccccagg
3121 gcgcgaagga gttctttggg gtccccatca aacaaattca ggtgcacaag tcaggcgaat
3181 tctgtcgctt gaggttccca aaaccaatca ggactgatgt gactggcatg atcttggaag
3241 agggtgcgcc tgaaggcacc gtggtcacac tactcatcaa aaggtctact ggagaactca
3301 tgcccctagc agctagaatg ggaacccacg caaccatgaa gattcaaggg cgcactgttg
3361 gaggtcagat gggcatgctt ctgacagggt ccaacgccaa aagcatggat ttaggtacca
3421 caccaggtga ttgcggctgt ccctacatct acaagagagg aaacgactat gtggtcattg
3481 gagtccacac ggctgccgct cgtgggggaa acactgtcat atgtgccacc caggggggtg
3541 agggggaagc tacacttgaa ggtggtgaca gtaagggaac atactgtggt gcaccaatct
3601 taggcccagg gagtgcccca aaactcagca ccaaaaccaa atactggaga tcatccacag
3661 caccacttcc acctggcacc tacgaaccag cctaccttgg tggtaaagac cccagagtca
3721 agggtggccc ctcgttgcag caagtcatga gagaccagct gaaaccattt acagagccta
3781 ggggtaagcc accaaagcca agtgtgttag aagctgccaa gaaaaccatc atcaatgtcc
3841 ttgaacagac aatcgaccca cctgagaagt ggtcgttcgc acaagcttgc gcgtcccttg
3901 ataagaccac ttctagcggc catccgcatc acatgcggaa aaacgactgc tggaacgggg
3961 agtcctttac aggcaagctg gcagatcagg cttccaaggc taacctgatg tttgaagaag
4021 ggaagaacat gaccccagtc tacacaggtg cacttaagga tgaattagtc aaaactgata
4081 aaatttatgg caagatcaag aagaggcttc tctggggctc ggatttggcg accatgatcc
4141 ggtgtgctcg agcattcgga ggccttatgg atgaactcaa agcacactgt gtcacactcc
4201 ctgtcagagt tggtatgaac atgaatgagg atggtcccat catcttcgag aaacattcca
4261 ggtatagata ccactatgat gctgattact ctcggtggga ttcaacacaa cagagagtcg
4321 tgctggcagc tgctctagaa atcatggtta aattctcctc agaaccacat ttggctcagg
4381 tggtagcaga ggaccttctt tctcctagcg tagtggatgt gggtgacttc acaatatcga
4441 tcaacgaggg ccttccctct ggggtgccct gcacctccca atggaactct atcgcccact
4501 ggcttctcac tctctgcgca ctctccgaag tcacaaattt gtctccagac atcatacagg
4561 ccaattctct cttctccttc tatggtgatg atgaaattgt tagcacagac ataaaattag
4621 acccagagaa gttgacagca aagcttaagg aatatgggtt gaaaccaacc cgccctgata
4681 aaactgaagg acctcttgtt atttctgaag acttagatgg tttgactttc ctgcggagaa
4741 ctgtgacccg cgaccctgct ggttggtttg gaaaactgga gcagagctca atacttaggc
4801 aaatgtactg gactaggggc cccaaccatg aagacccatc tgaatcaatg atcccacact
4861 ctcaaagacc catacaattg atgtccttgc tgggagaggc cgcactccac ggcccaacat
4921 tctacagtaa aatcagcaaa ttagtcattg cagagcttaa agaaggtggc atggattttt
4981 acgtgcccag gcaggagcca atgttcagat ggatgagatt ctcggatctg agcacgtggg
5041 agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgaa tgacgccaac
5101 ccatctgatg ggtccgcagc caacctcgtc ccagaggtca acaatgaggt tatggctttg
5161 gagcccgttg tcggtgccgc tattgcggcg cctgtagcgg gccaacaaaa tgtaattgac
5221 ccctggatta gaagtaactt tgtacaagcc cctggtggag agttcacagt atcccctaga
5281 aacgctccag gtgaaatact atggagcgcg cccttaggcc ctgatctgaa tccctaccta
5341 tctcatttgg ccagaatgta taatggttat gcaggtggtt ttgaagtgca ggtgatcctc
5401 gcggggaacg cgttcaccgc gggaaaaatt atatttgctg cagtcccacc aaattttcca
5461 actgaaggct tgagtcccag ccaggtcact atgttccccc acataatagt agatgttagg
5521 caattggaac ctgtgttgat ccccttacct gatgttagga ataacttcta tcactataac
5581 cagtcaaaag attctaccat taaattgata gcaatgctgt acacaccact cagggccaat
5641 aatgccgggg atgacgtctt cacagtctct tgtcgagtcc tcacgaggcc atcccctgat
5701 tttgacttca tatttctggt gccacctaca gttgagtcaa gaactaagcc atttactgtc
5761 ccaatcttaa ctgttgaaga aatgaccaat tcaagattcc ccattccttt ggagaaattg
5821 ttcacgggtc ccagcaatgc ctttgttgtt caaccacaaa atggcagatg cacaactgat
5881 ggcgtactct taggcaccac ccaactgtct cctgtcaaca tctgcacctt cagaggggat
5941 gtcacccaaa ttgcgagtac ccaaacttac acaatgaatt tggcctctct aaattggaac
6001 aattatgacc caacagaaga gattccagcc cctctgggag ctccagactt catgggaaag
6061 atccaaggtg tgctcactca aaccacaagg caaggtggct cgacccgggg ccataaagct
6121 acagtttcca ctgggagtgt ccacttcact ccaaagctgg gcagtgttcg atttgacact
6181 gatacaaaca atgaccttca acctcatcaa agcacaagat ttaccccagt cggcgtcatc
6241 caggatggtg acacccacca aaatgaaccc caacaatggg cgctcccatg ttattcaggt
6301 agagatgtca acaatgtaca cctagcccct gctgtagccc ccagttttcc gggtgaacaa
6361 cttctcttct tcaggtccac tatgcccgga tgcagcgggt atcccaacat ggatttggat
6421 tgcctactcc cccaggagtg ggtgcaacac ttctaccaag aggcagctcc agcacaatct
6481 gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcttgtt tgagtgcaaa
6541 ctccataaat caggctatgt cacagtggct cataccggcc aacataattt ggtcatcccc
6601 cccaatggtt attttaggtt tgattcctgg gttaatcagt tctacacact tgcccccatg
6661 ggaaatggaa cggggcgtag acgtgtttta taatggctgg agctctcttt gctggattgg
6721 cttctgatgt ccttagctct ggacttggtt ccctaatcaa tgctggggct ggggctatca
6781 accaaaagat tgattttgaa aataatagag aattgcagca agcttccttt cagtttagta
6841 gcaatctaca acaagcttcc tttcaacatg ataaagagat gctccatgca caaattgagg
6901 ccactaaaaa gttgcaacag gaattgatga aggtcaaaca ggcaatgctc ttagaaggtg
6961 gattttctga aacagatgca gcccgtgggg caatcaacgc ccccatgact aaggctttgg
7021 actggagtgg aacaaggtac tgggcccctg atgctaggac tacaacatac aatgcaggcc
7081 gcttttccac ccctcaacct tcgggggcac taccaggaag aatcaatccc aggactccta
7141 tccccgcccg gggctcccca agtatatctt ccaatgtttc ttctgctact tctatacatt
7201 caaatcaaac tgcttcaacg agacttggtt ctacagctgg ttctggcacc aatgtctcga
7261 gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga aatttgtcac
7321 ctttcatgag gggggcgcac aacatatcgt ttgtcacccc accatctagc agatcctcca
7381 gccaaggcac agtctcaacc gtgcctaaag atgttttgga ctcctggact ggcgctttca
7441 acacgcgcag gcagcctctc ttcgctcaca ttcgtaggcg aggggagtca cgggtgtaat
7501 gtgaaaagac aaaactgatt atct
//