Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| EF202567 | GII.4 Farmington Hills | |
|
|---|---|---|---|
| GII.P4 Farmington Hills |
ORF1: 1..4972
ORF2: 4953..6575
ORF3: 6575..7295
LOCUS EF202567 7295 bp RNA linear VRL 23-JUL-2016
DEFINITION Norovirus Hu/GII/Toronto/SK/2002/CAN nonstructural polyprotein
gene, partial cds; capsid protein gene, complete cds; and unknown
gene.
ACCESSION EF202567
VERSION EF202567.1
KEYWORDS .
SOURCE Norovirus Hu/GII/Toronto/SK/2002/CAN
ORGANISM Norovirus Hu/GII/Toronto/SK/2002/CAN
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7295)
AUTHORS Kostela,J., Ayers,M., Nishikawa,J., McIntyre,L., Petric,M. and
Tellier,R.
TITLE Amplification by long RT-PCR of near full-length norovirus genomes
JOURNAL J. Virol. Methods 149 (2), 226-230 (2008)
PUBMED 18355931
REFERENCE 2 (bases 1 to 7295)
AUTHORS Kostela,J. and Tellier,R.
TITLE Direct Submission
JOURNAL Submitted (29-DEC-2006) Paediatric Laboratory Medicine, Hospital
for Sick Children, 555 University Ave, Toronto, ON M5G 1X8, Canada
FEATURES Location/Qualifiers
source 1..7295
/organism="Norovirus Hu/GII/Toronto/SK/2002/CAN"
/mol_type="genomic RNA"
/isolate="SK2002"
/isolation_source="stool sample"
/db_xref="taxon:440500"
/geo_loc_name="Canada: Toronto"
/collection_date="2002"
/note="genotype: II"
CDS <1..4972
/note="ORF 1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="ABQ12780.1"
/translation="SKQPPPRETPQRPPRPPTPELVKKIPPPPPNGEDEIVISYSVKD
GVSGLPELSTVRQPEEANTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVD
RGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDN
NCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPTVDDSKLKKVANIFLCA
LSSLFTRPIKDIIGKLKPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAM
IAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGA
YGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYM
RTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMI
SGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSN
PIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSR
RIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGK
GVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLM
DTMRVGRQLKDVRTMPELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTS
VQTSNELTGALHHLRCARIRYYVRCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSK
PQVENTEEVTNKDGCPKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSD
EEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRP
TRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWS
RIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIR
TDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLT
GSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLE
GGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPS
LQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFTQACASLDKT
TSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDK
IYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERH
SRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDF
TISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVS
TDIKLDPEKLTAKLREYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKL
EQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIA
ELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 4953..6575
/codon_start=1
/product="capsid protein"
/protein_id="ABQ12781.1"
/translation="MKMASNDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGML
TQTTRGDGSTRGHKATVSTGDVHFTPKLGSIQFNTDTNNDFETGQNTKFTPVGVVQDG
NGTHQNEPQQWVLPSYSGRTGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6575..>7295
/note="ORF 3"
/codon_start=1
/product="unknown"
/protein_id="ABQ12782.1"
/translation="MAGAFFAGLASDVLGSGLGSLISAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQGMMEVKRAMLLEGGFSETDASRGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRTNPRATVPARGFSNAPS
NTSTATSVYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWIEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTAVSTVPK"
ORIGIN
1 gtctaaacag ccccccccga gggaaacacc acaaagaccc ccacgaccac ctactccaga
61 actggtcaaa aagatccctc ctcccccgcc caacggagag gatgaaatag tgatttctta
121 tagtgtcaaa gatggcgttt ccggtttgcc tgagctctcc accgttaggc aaccggaaga
181 agctaatacg gccttcagtg tccccccgct caatcagagg gagaacaggg atgctaagga
241 gccactgact ggaacaattc tggaaatgtg ggatggggaa atctaccatt acggcctgta
301 tgtggaccga ggtcttgtac taggcgtgca caaaccacca gctgccatta gcctcgccaa
361 ggtcgaacta acaccactct ccttgttctg gagacctgtg tatactcctc agtacctcat
421 ctctccagac actctcaaga aattacacgg agaaacgttc ccttacacag cctttgacaa
481 caattgctat gccttttgct gctgggtcct ggacctaaac gactcgtggc tgagtaggag
541 aatgatccag agaacaactg gctttttcag accctaccaa gattggaata ggaaacccct
601 ccccactgtg gatgattcca agttaaagaa ggtagctaat atattcctgt gtgctctgtc
661 ttcgctgttc accaggccca taaaagacat aatagggaag ctaaagcctc ttaacatcct
721 caacatcttg gcctcatgtg attggacttt cgcaggcata gtggagtcct tgatactcct
781 ggcagagctc tttggagttt tctggacacc cccagatgtg tctgcgatga ttgccccctt
841 actcggtgac tacgagttac aaggacccga ggaccttgca gtggagctcg tccctgtagt
901 gatgggggga attggtttgg tgctgggatt caccaaagag aagattggaa aaatgttgtc
961 atctgctgcg tccaccttga gagcttgcaa agatcttggt gcttatgggc tagagatcct
1021 aaagttggtc atgaagtggt tcttcccgaa gaaagaggaa gcaaatgaac tggctatggt
1081 gagatccatc gaggatgcag tgctggacct cgaggcaatt gaaaacaacc atatgaccac
1141 cttgctcaaa gacaaagaca gtctggcaac ctacatgaga acccttgacc ttgaggagga
1201 gaaagccaga aaactctcaa ccaagtctgc ttcacctgac atcgtgggca caatcaatgc
1261 ccttctggcg agaatcgctg ctgcacgttc cctggtgcat cgagcgaagg aggagctttc
1321 cagcagacca agacctgtgg tcttgatgat atcaggtaga ccaggaatag ggaagaccca
1381 ccttgctagg gaagtggcta agagaatcgc agcctccctc acaggagacc agcgtgtagg
1441 cctcatccca cgcaatggcg tcgatcactg ggatgcgtac aagggggaga gggtcgtcct
1501 atgggacgac tatggaatga gcaatcccat ccacgacgcc ctcaggttgc aagaactcgc
1561 tgacacttgc cccctcactc taaactgtga caggattgag aataaaggaa aggtctttga
1621 cagcgatgtc atcattatca ctactaacct ggccaaccca gcaccactgg actatgtcaa
1681 ctttgaagca tgctcgaggc gcatcgattt cctcgtgtat gcagaagccc ctgaagtcga
1741 aaaggcgaag cgtgacttcc caggccaacc tgacatgtgg aagaacgcct ttagttctga
1801 tttttcacac ataaaactag cactggctcc acagggtggc ttcgataaaa acgggaacac
1861 cccgcacggg aagggcgtca tgaagactct caccactggc tcccttattg cccgggcatc
1921 agggctactc catgagaggc tagatgagtt tgaactacag ggcccagctc tcaccacctt
1981 caactttgat cgcaacaaag tgcttgcctt taggcaactt gctgctgaaa acaaatatgg
2041 gttgatggac acaatgagag ttgggaggca gctcaaggat gtcagaacca tgccagagct
2101 taaacaagca ctcaagaata tctcaatcaa gaagtgccag atagtgtaca gtggttgcac
2161 ctacacactt gagtctgacg gcaagggcaa tgtgaaagtt gacagagttc agagcacctc
2221 cgtgcagacc agcaatgagc tgactggcgc cctgcaccac ctaaggtgtg ccagaatcag
2281 gtactatgtc aggtgtgtcc aggaggccct gtattccatc atccagattg ctggggctgc
2341 atttgtcacc acgcgcatcg tcaagcgcat gaacatacaa gacctatggt ccaagccaca
2401 agtggaaaac acagaggagg ttaccaacaa ggacgggtgc ccaaaaccca aagatgatga
2461 ggagttcgtc atttcatccg acgacattaa aactgagggt aagaaaggga agaacaagac
2521 tggtcgcggc aagaagcaca cagccttctc aagcaaaggt ctcagtgatg aagagtatga
2581 tgagtacaag aggattagag aagagaggaa tggcaagtat tccatagaag agtacctcca
2641 ggacagggac aaatactatg aggaggtggc cattgccagg gcgaccgagg aagacttctg
2701 tgaagaggag gaggccaaga tccggcaaag gatctttagg ccaacaagaa aacaacgcaa
2761 ggaggaaaga gcttctctcg gtttagtcac aggttctgaa attaggaaaa gaaacccaga
2821 tgatttcaag cccaagggga agctgtgggc tgacgatgac agaagtgtgg actacaatga
2881 gaaactcagc tttgaggccc caccaagcat ctggtcgagg atagtcaact ttggttcagg
2941 ttggggcttc tgggtctccc ccagtctgtt cataacatca acccatgtca taccccaggg
3001 cgcaaaggag ttctttggag tccccatcaa acaaattcag gtacacaaat caggcgaatt
3061 ctgtcgcttg agattcccaa aaccaatcag gactgatgtg acgggtatga tcttagaaga
3121 aggtgcgccc gaaggcaccg tggtcacact actcataaaa aggtctacag gagaactcat
3181 gcccctagca gctagaatgg ggacccatgc aaccatgaaa attcaagggc gcactgttgg
3241 aggtcagatg ggcatgcttc tgacaggatc taacgccaaa agcatggacc taggcaccac
3301 accaggtgat tgcggctgtc cctacatcta caagagagga aatgactatg tggtcattgg
3361 agtccacacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc aggggagtga
3421 gggggaggct acacttgaag gtggtgacag taaaggaaca tactgtggtg caccaatctt
3481 aggcccaggg agtgccccaa aacttagcac caagaccaaa ttctggagat cgtccacagc
3541 accactccca cctggcacct atgagccagc ttatcttggt ggcaaggacc ccagggtcaa
3601 gggtggccct tcattgcagc aagtcatgag ggatcagttg aaaccattta cagagcccag
3661 gggaaagcca ccaaagccaa gtgtgttaga agctgccaag aaaaccatca tcaatgtcct
3721 tgagcaaaca attgatccac ctgagaaatg gtcattcaca caagcttgcg cgtccctcga
3781 caagaccact tccagtggcc atccgcacca catgcggaaa aacgactgct ggaacgggga
3841 atctttcaca ggcaagctgg cagatcaggc ttccaaggcc aacctgatgt tcgaagaagg
3901 gaagaacatg accccagtct acacaggtgc gcttaaggat gaattggtca aaactgacaa
3961 aatttatggt aagatcaaga agaggcttct ctggggctcg gatttagcga ccatgatccg
4021 atgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg ttacacttcc
4081 tatcagagtt ggtatgaata tgaatgagga tggccccatc atattcgaga ggcattccag
4141 gtacagatat cactatgatg ctgattactc tcggtgggat tcaacacaac agagagctgt
4201 gttggcagca gctctagaaa tcatggttaa attctcctca gaaccacatt tggctcaggt
4261 agtcgcagaa gaccttcttt ctcctagcgt ggtggatgtg ggtgacttca caatatcaat
4321 caacgagggt ctcccctctg gggtaccctg cacctcccaa tggaactcca tcgcccactg
4381 gcttctcact ctctgtgcgc tctctgaagt tacaaatctg tcccctgaca tcatacaggc
4441 taattccctc ttctcctttt atggtgatga tgaaatcgtt agcacggaca taaaattgga
4501 cccagagaag ttgacagcaa agctcaggga atatgggctg aaaccaaccc gccctgacaa
4561 aactgaaggg ccccttgtta tctctgaaga cttaaatggt ctgactttcc tgcggagaac
4621 tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagttcaa tactcaggca
4681 aatgtactgg actaggggcc ccaaccatga agacccatct gaaacaatga ttccacactc
4741 ccaaagaccc atacagttga tgtccttact gggagaggcc gcactccacg gcccagcatt
4801 ctacagcaaa atcagcaagt tagtcattgc agagctaaaa gaaggtggca tggattttta
4861 cgtgcccagg caagagccaa tgttcagatg gatgagattc tcagatctga gcacgtggga
4921 gggcgatcgc aatctggctc ccagctttgt gaatgaagat ggcgtcgaat gacgccaacc
4981 catctgatgg gtccacagcc aacctcgtcc cagaggtcaa caatgaggtt atggctttgg
5041 agcccgttgt tggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc
5101 cctggattag aaataatttt gtacaagccc ctggtggaga gtttacagta tcccctagaa
5161 acgctccagg tgaaatacta tggagcgcgc ccttgggccc cgatctgaat ccctaccttt
5221 ctcatttggc cagaatgtac aatggctatg caggtggctt tgaagtgcag gtaatccttg
5281 cggggaatgc gttcaccgcc gggaaagtca tatttgcagc agtcccacca aatttcccaa
5341 ctgaaggctt gagccccagc caggtcacta tgttccccca tatagtagta gatgttaggc
5401 aactggaacc tgtgttgatc cccttacctg atgttaggaa caatttctat cactacaacc
5461 aatcaaatga ccccaccatt aaattgatag caatgctgta cacaccactt agggctaata
5521 atgctgggga agatgtcttc acagtctctt gtcgagtcct cacgaggcca tcccccgatt
5581 ttgatttcat atttttggtg ccacccacag ttgagtcaag aactaaacca ttcaccgtcc
5641 caattttaac tgttgaggaa atgaccaatt caagattccc cattcctttg gaaaagttgt
5701 tcacgggtcc tagcggtgcc tttgttgttc aaccacaaaa tggcaggtgc acgactgatg
5761 gcgtactctt aggcactacc caactgtctc ctgtcaacat ctgcaccttc agaggggatg
5821 tcacccacat tgcaggtact cataattaca caatgaattt ggcttctcaa aattggaaca
5881 attatgaccc aacagaagaa atcccagccc ctctggggac cccagatttc gtgggaagga
5941 tccaaggcat gctcacccaa actacaaggg gagatggctc tacccgcggc cacaaagcta
6001 cagtgagcac tggggatgtc cacttcactc caaagctggg cagtattcag ttcaacactg
6061 atacaaacaa tgattttgaa actggccaaa acacgaaatt caccccagtc ggtgttgtcc
6121 aggatggtaa tggtacccac caaaatgaac ctcaacaatg ggtgctccca agctactcag
6181 gtagaactgg tcataatgta cacctagccc ccgccgtagc ccccactttt ccgggtgagc
6241 aacttctttt cttcaggtcc actatgcccg gatgcagcgg gtaccctaac atgaatttgg
6301 attgtctact cccccaagaa tgggtgcagc acttctacca agaggcagct ccagcacaat
6361 ctgatgtggc tctgctaaga tttgtgaatc cagacacagg tagggttcta tttgagtgca
6421 agcttcataa atcaggctat gtcacagtgg ctcacactgg ccagcatgat ttggttatcc
6481 cccccaatgg ctactttaga tttgattcct gggtcaacca attctacaca cttgccccca
6541 tgggaaatgg gacggggcgt agacgtgcat tataatggct ggagctttct tcgccgggct
6601 ggcatctgat gtccttggct ctggacttgg ttccctaatc agtgctgggg ctggggccat
6661 caaccaaaaa gttgaatttg aaaataacag aaaattgcaa caagcttcct tccaatttag
6721 tagcaatcta caacaggctt cctttcaaca tgataaagag atgctccaag cacaaattga
6781 ggccactaaa aagttgcaac agggtatgat ggaagttaaa cgggcaatgc tcctagaggg
6841 tggattctct gaaacagatg catctcgtgg ggcaatcaac gcccccatga caaaggcttt
6901 ggactggagc ggaacaaggt actgggctcc tgatgctagg actacaacat acaatgcagg
6961 ccgcttttcc acccctcaac cctcgggggc attgccagga agaaccaatc ccagggctac
7021 tgtccccgct cggggcttct ccaatgcacc ttctaacact tctactgcta cttctgtgta
7081 ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggttctggca ccagtgtctc
7141 gagtctcccg tcaactgcaa gaactaggag ctggattgag gatcaaaaca ggaatttgtc
7201 acctttcatg aggggagctc acaacatatc gtttgtcacc ccaccatcta gtagatcctc
7261 tagccaaggg acagcagtct caaccgtgcc caaaa
//