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reference.gb
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LOCUS NC_009942 11029 bp RNA linear VRL 24-AUG-2016
DEFINITION West Nile virus lineage 1, complete genome.
ACCESSION NC_009942
VERSION NC_009942.1
DBLINK BioProject: PRJNA30293
KEYWORDS RefSeq.
SOURCE West Nile virus (WNV)
ORGANISM West Nile virus
Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
stage; Flaviviridae; Flavivirus; Japanese encephalitis virus group.
REFERENCE 1 (sites)
AUTHORS Faggioni,G., Pomponi,A., De Santis,R., Masuelli,L.,
Ciammaruconi,A., Monaco,F., Di Gennaro,A., Marzocchella,L.,
Sambri,V., Lelli,R., Rezza,G., Bei,R. and Lista,F.
TITLE West Nile alternative open reading frame (N-NS4B/WARF4) is produced
in infected West Nile Virus (WNV) cells and induces humoral
response in WNV infected individuals
JOURNAL Virol. J. 9, 283 (2012)
PUBMED 23173701
REMARK Publication Status: Online-Only
REFERENCE 2 (bases 1 to 11029)
AUTHORS Borisevich,V., Seregin,A., Nistler,R., Mutabazi,D. and
Yamshchikov,V.
TITLE Biological properties of chimeric West Nile viruses
JOURNAL Virology 349 (2), 371-381 (2006)
PUBMED 16545851
REFERENCE 3 (bases 1 to 11029)
CONSRTM NCBI Genome Project
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2007) National Center for Biotechnology
Information, NIH, Bethesda, MD 20894, USA
REFERENCE 4 (bases 1 to 11029)
AUTHORS Borisevich,V., Seregin,A. and Yamshchikov,V.
TITLE Direct Submission
JOURNAL Submitted (19-SEP-2005) Molecular Biosciences, University of
Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, USA
COMMENT VALIDATED REFSEQ: This record has undergone validation or
preliminary review. The reference sequence was derived from
DQ211652.
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..11029
/organism="West Nile virus"
/mol_type="genomic RNA"
/strain="NY99"
/isolate="385-99"
/db_xref="taxon:11082"
/country="USA"
/note="lineage 1; Vero cell passage 2 after isolation"
CDS 97..465
/gene="capsid"
CDS 466..966
/gene="prM"
CDS 967..2469
/gene="env"
CDS 2470..3525
/gene="NS1"
CDS 3526..4218
/gene="NS2A"
CDS 4219..4611
/gene="NS2B"
CDS 4612..6468
/gene="NS3"
CDS 6469..6846
/gene="NS4A"
CDS 6847..6915
/gene="2K"
CDS 6916..7680
/gene="NS4B"
CDS 7681..10395
/gene="NS5"
ORIGIN
1 agtagttcgc ctgtgtgagc tgacaaactt agtagtgttt gtgaggatta acaacaatta
61 acacagtgcg agctgtttct tagcacgaag atctcgatgt ctaagaaacc aggagggccc
121 ggcaagagcc gggctgtcaa tatgctaaaa cgcggaatgc cccgcgtgtt gtccttgatt
181 ggactgaaga gggctatgtt gagcctgatc gacggcaagg ggccaatacg atttgtgttg
241 gctctcttgg cgttcttcag gttcacagca attgctccga cccgagcagt gctggatcga
301 tggagaggtg tgaacaaaca aacagcgatg aaacaccttc tgagttttaa gaaggaacta
361 gggaccttga ccagtgctat caatcggcgg agctcaaaac aaaagaaaag aggaggaaag
421 accggaattg cagtcatgat tggcctgatc gccagcgtag gagcagttac cctctctaac
481 ttccaaggga aggtgatgat gacggtaaat gctactgacg tcacagatgt catcacgatt
541 ccaacagctg ctggaaagaa cctatgcatt gtcagagcaa tggatgtggg atacatgtgc
601 gatgatacta tcacttatga atgcccagta ctgtcggctg gtaatgatcc agaagacatc
661 gactgttggt gcacaaagtc agcagtctac gtcaggtatg gaagatgcac caagacacgc
721 cactcaagac gcagtcggag gtcactgaca gtgcagacac acggagaaag cactctagcg
781 aacaagaagg gggcttggat ggacagcacc aaggccacaa ggtatttggt aaaaacagaa
841 tcatggatct tgaggaaccc tggatatgcc ctggtggcag ccgtcattgg ttggatgctt
901 gggagcaaca ccatgcagag agttgtgttt gtcgtgctat tgcttttggt ggccccagct
961 tacagcttca actgccttgg aatgagcaac agagacttct tggaaggagt gtctggagca
1021 acatgggtgg atttggttct cgaaggcgac agctgcgtga ctatcatgtc taaggacaag
1081 cctaccatcg atgtgaagat gatgaatatg gaggcggcca acctggcaga ggtccgcagt
1141 tattgctatt tggctaccgt cagcgatctc tccaccaaag ctgcgtgccc gaccatggga
1201 gaagctcaca atgacaaacg tgctgaccca gcttttgtgt gcagacaagg agtggtggac
1261 aggggctggg gcaacggctg cggactattt ggcaaaggaa gcattgacac atgcgccaaa
1321 tttgcctgct ctaccaaggc aataggaaga accatcttga aagagaatat caagtacgaa
1381 gtggccattt ttgtccatgg accaactact gtggagtcgc acggaaacta ctccacacag
1441 gttggagcca ctcaggcagg gagactcagc atcactcctg cggcgccttc atacacacta
1501 aagcttggag aatatggaga ggtgacagtg gactgtgaac cacggtcagg gattgacacc
1561 aatgcatact acgtgatgac tgttggaaca aagacgttct tggtccatcg tgagtggttc
1621 atggacctca acctcccttg gagcagtgct ggaagtactg tgtggaggaa cagagagacg
1681 ttaatggagt ttgaggaacc acacgccacg aagcagtctg tgatagcatt gggctcacaa
1741 gagggagctc tgcatcaagc tttggctgga gccattcctg tggaattttc aagcaacact
1801 gtcaagttga cgtcgggtca tttgaagtgt agagtgaaga tggaaaaatt gcagttgaag
1861 ggaacaacct atggcgtctg ttcaaaggct ttcaagtttc ttgggactcc cgcagacaca
1921 ggtcacggca ctgtggtgtt ggaattgcag tacactggca cggatggacc ttgcaaagtt
1981 cctatctcgt cagtggcttc attgaacgac ctaacgccag tgggcagatt ggtcactgtc
2041 aacccttttg tttcagtggc cacggccaac gctaaggtcc tgattgaatt ggaaccaccc
2101 tttggagact catacatagt ggtgggcaga ggagaacaac agatcaatca ccattggcac
2161 aagtctggaa gcagcattgg caaagccttt acaaccaccc tcaaaggagc gcagagacta
2221 gccgctctag gagacacagc ttgggacttt ggatcagttg gaggggtgtt cacctcagtt
2281 gggaaggctg tccatcaagt gttcggagga gcattccgct cactgttcgg aggcatgtcc
2341 tggataacgc aaggattgct gggggctctc ctgttgtgga tgggcatcaa tgctcgtgat
2401 aggtccatag ctctcacgtt tctcgcagtt ggaggagttc tgctcttcct ctccgtgaac
2461 gtgcacgctg acactgggtg tgccatagac atcagccggc aagagctgag atgtggaagt
2521 ggagtgttca tacacaatga tgtggaggct tggatggacc ggtacaagta ttaccctgaa
2581 acgccacaag gcctagccaa gatcattcag aaagctcata aggaaggagt gtgcggtcta
2641 cgatcagttt ccagactgga gcatcaaatg tgggaagcag tgaaggacga gctgaacact
2701 cttttgaagg agaatggtgt ggaccttagt gtcgtggttg agaaacagga gggaatgtac
2761 aagtcagcac ctaaacgcct caccgccacc acggaaaaat tggaaattgg ctggaaggcc
2821 tggggaaaga gtattttatt tgcaccagaa ctcgccaaca acacctttgt ggttgatggt
2881 ccggagacca aggaatgtcc gactcagaat cgcgcttgga atagcttaga agtggaggat
2941 tttggatttg gtctcaccag cactcggatg ttcctgaagg tcagagagag caacacaact
3001 gaatgtgact cgaagatcat tggaacggct gtcaagaaca acttggcgat ccacagtgac
3061 ctgtcctatt ggattgaaag caggctcaat gatacgtgga agcttgaaag ggcagttctg
3121 ggtgaagtca aatcatgtac gtggcctgag acgcatacct tgtggggcga tggaatcctt
3181 gagagtgact tgataatacc agtcacactg gcgggaccac gaagcaatca caatcggaga
3241 cctgggtaca agacacaaaa ccagggccca tgggacgaag gccgggtaga gattgacttc
3301 gattactgcc caggaactac ggtcaccctg agtgagagct gcggacaccg tggacctgcc
3361 actcgcacca ccacagagag cggaaagttg ataacagatt ggtgctgcag gagctgcacc
3421 ttaccaccac tgcgctacca aactgacagc ggctgttggt atggtatgga gatcagacca
3481 cagagacatg atgaaaagac cctcgtgcag tcacaagtga atgcttataa tgctgatatg
3541 attgaccctt ttcagttggg ccttctggtc gtgttcttgg ccacccagga ggtccttcgc
3601 aagaggtgga cagccaagat cagcatgcca gctatactga ttgctctgct agtcctggtg
3661 tttgggggca ttacttacac tgatgtgtta cgctatgtca tcttggtggg ggcagctttc
3721 gcagaatcta attcgggagg agacgtggta cacttggcgc tcatggcgac cttcaagata
3781 caaccagtgt ttatggtggc atcgtttctc aaagcgagat ggaccaacca ggagaacatt
3841 ttgttgatgt tggcggctgt tttctttcaa atggcttatc acgatgcccg ccaaattctg
3901 ctctgggaga tccctgatgt gttgaattca ctggcggtag cttggatgat actgagagcc
3961 ataacattca caacgacatc aaacgtggtt gttccgctgc tagccctgct aacacccggg
4021 ctgagatgct tgaatctgga tgtgtacagg atactgctgt tgatggtcgg aataggcagc
4081 ttgatcaggg agaagaggag tgcagccgca aaaaagaaag gagcaagtct gctatgcttg
4141 gctctagcct caacaggact tttcaacccc atgatccttg ctgctggact gattgcatgt
4201 gatcccaacc gtaaacgcgg atggcccgca actgaagtga tgacagctgt cggcctaatg
4261 tttgccatcg tcggagggct ggcagagctt gacattgact ccatggccat tccaatgact
4321 atcgcggggc tcatgtttgc tgctttcgtg atttctggga aatcaacaga tatgtggatt
4381 gagagaacgg cggacatttc ctgggaaagt gatgcagaaa ttacaggctc gagcgaaaga
4441 gttgatgtgc ggcttgatga tgatggaaac ttccagctca tgaatgatcc aggagcacct
4501 tggaagatat ggatgctcag aatggtctgt ctcgcgatta gtgcgtacac cccctgggca
4561 atcttgccct cagtagttgg attttggata actctccaat acacaaagag aggaggcgtg
4621 ttgtgggaca ctccctcacc aaaggagtac aaaaaggggg acacgaccac cggcgtctac
4681 aggatcatga ctcgtgggct gctcggcagt tatcaagcag gagcgggcgt gatggttgaa
4741 ggtgttttcc acaccctttg gcatacaaca aaaggagccg ctttgatgag cggagagggc
4801 cgcctggacc catactgggg cagtgtcaag gaggatcgac tttgttacgg aggaccctgg
4861 aaattgcagc acaagtggaa cgggcaggat gaggtgcaga tgattgtggt ggaacctggc
4921 aagaacgtta agaacgtcca gacgaaacca ggggtgttca aaacacctga aggagaaatc
4981 ggggccgtga ctttggactt ccccactgga acatcaggct caccaatagt ggacaaaaac
5041 ggtgatgtga ttgggcttta tggcaatgga gtcataatgc ccaacggctc atacataagc
5101 gcgatagtgc agggtgaaag gatggatgag ccaatcccag ccggattcga acctgagatg
5161 ctgaggaaaa aacagatcac tgtactggat ctccatcccg gcgccggtaa aacaaggagg
5221 attctgccac agatcatcaa agaggccata aacagaagac tgagaacagc cgtgctagcg
5281 ccaaccaggg ttgtggctgc tgagatggct gaagcactga gaggactgcc catccggtac
5341 cagacatccg cagtgcccag agaacataat ggaaatgaga ttgttgatgt catgtgtcat
5401 gctaccctca cccacaggct gatgtctcct cacagggtgc cgaactacaa cctgttcgtg
5461 atggatgagg ctcatttcac cgacccagct agcattgcag caagaggtta catttccaca
5521 aaggtcgagc taggggaggc ggcggcaata ttcatgacag ccaccccacc aggcacttca
5581 gatccattcc cagagtccaa ttcaccaatt tccgacttac agactgagat cccggatcga
5641 gcttggaact ctggatacga atggatcaca gaatacaccg ggaagacggt ttggtttgtg
5701 cctagtgtca agatggggaa tgagattgcc ctttgcctac aacgtgctgg aaagaaagta
5761 gtccaattga acagaaagtc gtacgagacg gagtacccaa aatgtaagaa cgatgattgg
5821 gactttgtta tcacaacaga catatctgaa atgggggcta acttcaaggc gagcagggtg
5881 attgacagcc ggaagagtgt gaaaccaacc atcataacag aaggagaagg gagagtgatc
5941 ctgggagaac catctgcagt gacagcagct agtgccgccc agagacgtgg acgtatcggt
6001 agaaatccgt cgcaagttgg tgatgagtac tgttatgggg ggcacacgaa tgaagacgac
6061 tcgaacttcg cccattggac tgaggcacga atcatgctgg acaacatcaa catgccaaac
6121 ggactgatcg ctcaattcta ccaaccagag cgtgagaagg tatataccat ggatggggaa
6181 taccggctca gaggagaaga gagaaaaaac tttctggaac tgttgaggac tgcagatctg
6241 ccagtttggc tggcttacaa ggttgcagcg gctggagtgt cataccacga ccggaggtgg
6301 tgctttgatg gtcctaggac aaacacaatt ttagaagaca acaacgaagt ggaagtcatc
6361 acgaagcttg gtgaaaggaa gattctgagg ccgcgctgga ttgatgccag ggtgtactcg
6421 gatcaccagg cactaaaggc gttcaaggac ttcgcctcgg gaaaacgttc tcagataggg
6481 ctcattgagg ttctgggaaa gatgcctgag cacttcatgg ggaagacatg ggaagcactt
6541 gacaccatgt acgttgtggc cactgcagag aaaggaggaa gagctcacag aatggccctg
6601 gaggaactgc cagatgctct tcagacaatt gccttgattg ccttattgag tgtgatgacc
6661 atgggagtat tcttcctcct catgcagcgg aagggcattg gaaagatagg tttgggaggc
6721 gctgtcttgg gagtcgcgac ctttttctgt tggatggctg aagttccagg aacgaagatc
6781 gccggaatgt tgctgctctc ccttctcttg atgattgtgc taattcctga gccagagaag
6841 caacgttcgc agacagacaa ccagctagcc gtgttcctga tttgtgtcat gacccttgtg
6901 agcgcagtgg cagccaacga gatgggttgg ctagataaga ccaagagtga cataagcagt
6961 ttgtttgggc aaagaattga ggtcaaggag aatttcagca tgggagagtt tcttctggac
7021 ttgaggccgg caacagcctg gtcactgtac gctgtgacaa cagcggtcct cactccactg
7081 ctaaagcatt tgatcacgtc agattacatc aacacctcat tgacctcaat aaacgttcag
7141 gcaagtgcac tattcacact cgcgcgaggc ttccccttcg tcgatgttgg agtgtcggct
7201 ctcctgctag cagccggatg ctggggacaa gtcaccctca ccgttacggt aacagcggca
7261 acactccttt tttgccacta tgcctacatg gttcccggtt ggcaagctga ggcaatgcgc
7321 tcagcccagc ggcggacagc ggccggaatc atgaagaacg ctgtagtgga tggcatcgtg
7381 gccacggacg tcccagaatt agagcgcacc acacccatca tgcagaagaa agttggacag
7441 atcatgctga tcttggtgtc tctagctgca gtagtagtga acccgtctgt gaagacagta
7501 cgagaagccg gaattttgat cacggccgca gcggtgacgc tttgggagaa tggagcaagc
7561 tctgtttgga acgcaacaac tgccatcgga ctctgccaca tcatgcgtgg gggttggttg
7621 tcatgtctat ccataacatg gacactcata aagaacatgg aaaaaccagg actaaaaaga
7681 ggtggggcaa aaggacgcac cttgggagag gtttggaaag aaagactcaa ccagatgaca
7741 aaagaagagt tcactaggta ccgcaaagag gccatcatcg aagtcgatcg ctcagcggca
7801 aaacacgcca ggaaagaagg caatgtcact ggagggcatc cagtctctag gggcacagca
7861 aaactgagat ggctggtcga acggaggttt ctcgaaccgg tcggaaaagt gattgacctt
7921 ggatgtggaa gaggcggttg gtgttactat atggcaaccc aaaaaagagt ccaagaagtc
7981 agagggtaca caaagggcgg tcccggacat gaagagcccc aactagtgca aagttatgga
8041 tggaacattg tcaccatgaa gagtggagtg gatgtgttct acagaccttc tgagtgttgt
8101 gacaccctcc tttgtgacat cggagagtcc tcgtcaagtg ctgaggttga agagcatagg
8161 acgattcggg tccttgaaat ggttgaggac tggctgcacc gagggccaag ggaattttgc
8221 gtgaaggtgc tctgtcccta catgccgaaa gtcatagaga agatggagct gctccaacgc
8281 cggtatgggg ggggactggt cagaaaccca ctctcacgga attccacgca cgagatgtat
8341 tgggtgagtc gagcttcagg caatgtggta cattcagtga atatgaccag ccaggtgctc
8401 ctaggaagaa tggaaaaaag gacctggaag ggaccccaat acgaggaaga tgtaaacttg
8461 ggaagtggaa ccagggcggt gggaaaaccc ctgctcaact cagacaccag taaaatcaag
8521 aacaggattg aacgactcag gcgtgagtac agttcgacgt ggcaccacga tgagaaccac
8581 ccatatagaa cctggaacta tcacggcagt tatgatgtga agcccacagg ctccgccagt
8641 tcgctggtca atggagtggt caggctcctc tcaaaaccat gggacaccat cacgaatgtt
8701 accaccatgg ccatgactga cactactccc ttcgggcagc agcgagtgtt caaagagaag
8761 gtggacacga aagctcctga accgccagaa ggagtgaagt acgtgctcaa cgagaccacc
8821 aactggttgt gggcgttttt ggccagagaa aaacgtccca gaatgtgctc tcgagaggaa
8881 ttcataagaa aggtcaacag caatgcagct ttgggtgcca tgtttgaaga gcagaatcaa
8941 tggaggagcg ccagagaagc agttgaagat ccaaaatttt gggagatggt ggatgaggag
9001 cgcgaggcac atctgcgggg ggaatgtcac acttgcattt acaacatgat gggaaagaga
9061 gagaaaaaac ccggagagtt cggaaaggcc aagggaagca gagccatttg gttcatgtgg
9121 ctcggagctc gctttctgga gttcgaggct ctgggttttc tcaatgaaga ccactggctt
9181 ggaagaaaga actcaggagg aggtgtcgag ggcttgggcc tccaaaaact gggttacatc
9241 ctgcgtgaag ttggcacccg gcctgggggc aagatctatg ctgatgacac agctggctgg
9301 gacacccgca tcacgagagc tgacttggaa aatgaagcta aggtgcttga gctgcttgat
9361 ggggaacatc ggcgtcttgc cagggccatc attgagctca cctatcgtca caaagttgtg
9421 aaagtgatgc gcccggctgc tgatggaaga accgtcatgg atgttatctc cagagaagat
9481 cagaggggga gtggacaagt tgtcacctac gccctaaaca ctttcaccaa cctggccgtc
9541 cagctggtga ggatgatgga aggggaagga gtgattggcc cagatgatgt ggagaaactc
9601 acaaaaggga aaggacccaa agtcaggacc tggctgtttg agaatgggga agaaagactc
9661 agccgcatgg ctgtcagtgg agatgactgt gtggtaaagc ccctggacga tcgctttgcc
9721 acctcgctcc acttcctcaa tgctatgtca aaggttcgca aagacatcca agagtggaaa
9781 ccgtcaactg gatggtatga ttggcagcag gttccatttt gctcaaacca tttcactgaa
9841 ttgatcatga aagatggaag aacactggtg gttccatgcc gaggacagga tgaattggta
9901 ggcagagctc gcatatctcc aggggccgga tggaacgtcc gcgacactgc ttgtctggct
9961 aagtcttatg cccagatgtg gctgcttctg tacttccaca gaagagacct gcggctcatg
10021 gccaacgcca tttgctccgc tgtccctgtg aattgggtcc ctaccggaag aaccacgtgg
10081 tccatccatg caggaggaga gtggatgaca acagaggaca tgttggaggt ctggaaccgt
10141 gtttggatag aggagaatga atggatggaa gacaaaaccc cagtggagaa atggagtgac
10201 gtcccatatt caggaaaacg agaggacatc tggtgtggca gcctgattgg cacaagagcc
10261 cgagccacgt gggcagaaaa catccaggtg gctatcaacc aagtcagagc aatcatcgga
10321 gatgagaagt atgtggacta catgagttca ctaaagagat atgaagacac aactttggtt
10381 gaggacacag tactgtagat atttaatcaa ttgtaaatag acaatataag tatgcataaa
10441 agtgtagttt tatagtagta tttagtggtg ttagtgtaaa tagttaagaa aattttgagg
10501 agaaagtcag gccgggaagt tcccgccacc ggaagttgag tagacggtgc tgcctgcgac
10561 tcaaccccag gaggactggg tgaacaaagc cgcgaagtga tccatgtaag ccctcagaac
10621 cgtctcggaa ggaggacccc acatgttgta acttcaaagc ccaatgtcag accacgctac
10681 ggcgtgctac tctgcggaga gtgcagtctg cgatagtgcc ccaggaggac tgggttaaca
10741 aaggcaaacc aacgccccac gcggccctag ccccggtaat ggtgttaacc agggcgaaag
10801 gactagaggt tagaggagac cccgcggttt aaagtgcacg gcccagcctg gctgaagctg
10861 taggtcaggg gaaggactag aggttagtgg agaccccgtg ccacaaaaca ccacaacaaa
10921 acagcatatt gacacctggg atagactagg agatcttctg ctctgcacaa ccagccacac
10981 ggcacagtgc gccgacaatg gtggctggtg gtgcgagaac acaggatct
//