Typing tool
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Typing tool
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Complete norovirus genomes
| KC597139 | GII.17 | |
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| GII.P12 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7441
LOCUS KC597139 7441 bp ss-RNA linear VRL 02-APR-2013
DEFINITION Norovirus Hu/GII.17/C142/1978/GUF, partial genome.
ACCESSION KC597139
VERSION KC597139.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/GII.17/C142/1978/GUF
ORGANISM Norovirus Hu/GII.17/C142/1978/GUF
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7441)
AUTHORS Madupu,R., Halpin,R.A., Ransier,A., Fedorova,N., Tsitrin,T.,
McLellan,M., Stockwell,T., Amedeo,P., Appalla,L., Bishop,B.,
Edworthy,P., Gupta,N., Hoover,J., Katzel,D., Li,K., Schobel,S.,
Shrivastava,S., Thovarai,V., Wang,S., Kim,M., Bok,K.,
Sosnovtsev,S.V., Wentworth,D.E. and Green,K.Y.
TITLE Direct Submission
JOURNAL Submitted (07-FEB-2013) J. Craig Venter Institute, 9704 Medical
Center Drive, Rockville, MD 20850, USA
COMMENT This work was supported by the National Institute of Allergy and
Infectious Diseases (NIAID), Genome Sequencing Centers for
Infectious Diseases (GSCID) program.
The genome sequence was generated using overlapping PCR amplicons
spanning the genome. The amplicons were pooled by sample and then
barcoded and sequenced using Next Generation Sequencing platforms.
The consensus sequences of the internal PCR primer hybridization
sites were manually verified using reads from amplicons that
spanned across the sites.
##Genome-Assembly-Data-START##
Current Finishing Status :: Finished
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Genome Coverage :: 386.3x
Sequencing Technology :: Sanger; Illumina; 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7441
/organism="Norovirus Hu/GII.17/C142/1978/GUF"
/mol_type="genomic RNA"
/strain="Hu/GII.17/C142/1978/GUF"
/host="Homo sapiens"
/db_xref="taxon:1292397"
/country="French Guiana: Cayenne"
/collection_date="11-Jul-1978"
/PCR_primers="fwd_name: Ampl_2_Forward, fwd_seq:
ccgcaaaatcttcaagtg, rev_name: Ampl_1_Reverse, rev_seq:
ttggttgagagyttyctg"
/PCR_primers="fwd_name: Ampl_3_Forward, fwd_seq:
tcaaccaartctgcttcacctg, rev_name: Ampl_2_Reverse, rev_seq:
cwacaggtcttggtctgctrga"
/PCR_primers="fwd_name: Ampl_4_Forward, fwd_seq:
ggcaagaagcacacagcctt, rev_name: Ampl_3_Reverse, rev_seq:
ratcctttgccggatcttgg"
/PCR_primers="fwd_name: Ampl_5_Forward, fwd_seq:
tggyaagatcaagaagaggc, rev_name: Ampl_4_Reverse, rev_seq:
crrctctytgttgtgttgaatccc"
/PCR_primers="fwd_name: Ampl_6_Forward, fwd_seq:
gagrccrtccccygattttg, rev_name: Ampl_5_Reverse, rev_seq:
acaacaaargcacygctrgg"
/PCR_primers="fwd_name: Ampl_7_Forward, fwd_seq:
gtgaatgawgatggcgt, rev_name: Ampl_6_Reverse, rev_seq:
atcaatyttgtcttttcaca"
/PCR_primers="fwd_name: Ampl_8_Forward, fwd_seq:
ygactcgtggctgagyagga, rev_name: Ampl_7_Reverse, rev_seq:
ccagrctrtctttrtctt"
/note="genotype: GII.17"
gene 5..5104
/gene="POL"
CDS 5..5104
/gene="POL"
/note="genome polyprotein"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AGI17591.1"
/translation="MKMASNDASAAAAANSNNDIAKSSSDGVLSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEPVVSYSAKDGVSGLPELSTVRQPD
EINTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
LRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAVVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
AKRDFPGQPDMWKNAFSPDFSHIKLMLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVRTM
PELKQALKNISIKRCQIVYSGCTYTLESDGKGNVKVDRVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEETVNKDGC
PKPKDDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNERLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRENDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWSFTQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFERHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFKISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSETMIPHSQRPVQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNDDGVE"
mat_peptide 5..994
/gene="POL"
/product="protein p48"
mat_peptide 995..2092
/gene="POL"
/product="NTPase"
/note="p41"
mat_peptide 2093..2629
/gene="POL"
/product="protein p22"
mat_peptide 2630..3028
/gene="POL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 3029..3571
/gene="POL"
/product="3C-like protease"
/note="3CLpro; calicivirin"
mat_peptide 3572..5101
/gene="POL"
/product="RNA-directed RNA polymerase"
gene 5085..6707
/gene="VP1"
CDS 5085..6707
/gene="VP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AGI17592.1"
/translation="MMMASNDAAPSNDGATGLVPEINHETLPLEPVAGAAIAAPVTGQ
NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD
VRNTFFHYNNQPANRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP
SVESKTKPFSLPILTISELTNSRFPAPIDSLYTAQNNNLNVQCQNGRCTLDGELQGTT
QLLPSGICAFRGKLTADVHQSHDDRWHMQLTNLNGTPFDPTEDVPAPLGTPDFTGLLF
GVASQRNVVSNPNTTRAHEAVISTTSSQFVPKLGSINFGSTSDDFQLQQPTKFTPVGI
KVESGHDFDQWALPRYSGHLTLNMNLAPPVAPNFPGEQLLFFRSNVPCAGGVSDGVID
CLLPQEWIQYFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRTGYITVAHSGDYPLV
VPSNGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6707..>7441
/gene="VP2"
CDS 6707..>7441
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="putative capsid protein VP2"
/protein_id="AGI17593.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGTNAITQKVDFENNKQLQSA
SFQHDKDMLQAQVAATKQLQADMIAIKQGILTAGGFSPTDAARGAVGAPMTKVLDWSG
TRYWAPNSTRTTGYSGQFTSTPLHTPTKTSQPAPVKRTQPPSSSSGSIYSLPTQSTVL
SKPSFGSSVCSASTQSTKLSSVSSMDRTVNWVNQQRSLSPYMSGALNISHVTPPSSRA
SSSGTVSTVPKEVLDSWTSAFNTHRQP"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaca gcaacaacga
61 catcgcaaaa tcttcgagtg acggagtgct ttctagcatg gctgtcactt ttaagcgagc
121 cctcggggca cggcctaaac agcctccccc gagggaaata ccacagagac ccccaaggcc
181 acctacccca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaacc
241 agtggtttct tatagcgcca aagatggcgt ttccggtttg cctgagcttt ccactgtcag
301 gcagccggat gaaatcaaca cggcgttcag tgttccccct ctcaaccaaa gggagaatag
361 ggatgccaag gaaccactaa ctggaacaat tctggaaatg tgggacgggg agatctacca
421 ttacggcctg tatgtggaac gaggccttgt acttggtgtg cacaaaccac cggctgccat
481 cagcctcgcc aaggttgaac taacaccact ctctctgttc tggagacctg tgtacactcc
541 ccagtatctc atctccccag acactctcag gagactgcac ggagaatcgt tcccctatac
601 agcttttgac aacaattgct atgccttctg ttgttgggtc ttggacctaa acgactcgtg
661 gctgagtagg agaatgatcc agagaacaac tggtttcttt agaccctacc aagactggaa
721 taggaaaccc ctccctacta tggatgactc caaattaaag aaggtagcta acatattcct
781 gtgtgctcta tcttcgctat tcaccaggcc catcaaagac ataataggga agctgagacc
841 tcttaacatc cttaacatct tggcctcatg tgattggact tttgcaggca tagtggaatc
901 cttgatactc ttggcagagc tctttggagt tttctggact cccccagatg tgtctgcgat
961 gattgccccc ttactaggtg attacgagct acaggggcct gaggaccttg cagtggaact
1021 cgttccaata gtgatggggg ggattggttt ggtgctagga tttaccaaag agaagattgg
1081 gaagatgttg tcatctgctg catccacctt aagagcttgt aaagaccttg gtgcatacgg
1141 actggaaatc ttaaaattag tcatgaagtg gttcttccca aagaaagagg aagcaaatga
1201 gctggctgtg gtgagatcca tcgaggatgc ggtgctggac ctcgaggcaa ttgaaaacaa
1261 ccacatgacc accctgctca aagacaaaga cagcctggca acctacatga gaacccttga
1321 ccttgaggag gagaaagcca ggaagctctc aaccaagtct gcttcacctg atatcgtggg
1381 cacaatcaac gctcttctgg cgagaatcgc tgctgcacgt tccctggtgc atcgggcgaa
1441 ggaggagctt tccagcagac caagacctgt tgttgtgatg atatcaggca aaccagggat
1501 agggaagacc caccttgcca gggaattggc caagaggatc gcagcctccc tcacagggga
1561 ccagcgtgtg ggtctcatcc cacgcaatgg cgttgaccat tgggacgcat acaagggaga
1621 aagggtcgtc ctatgggacg actatggtat gagtaatccc atccatgatg ccctcaggtt
1681 gcaagaactc gctgacactt gccccctcac gctaaattgt gacaggattg agaacaaagg
1741 gaaggtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccatt
1801 ggactatgtc aactttgaag catgctcgag gcgcatcgat ttcctcgtgt atgcagatgc
1861 ccctgaggtc gagaaggcga aacgtgattt cccaggccaa cctgacatgt ggaagaatgc
1921 tttcagtcct gacttctcgc acataaaact gatgctggct ccacagggtg gcttcgacaa
1981 gaatggcaac accccacatg ggaaaggcgt catgaagacc ctcaccactg gctccctcat
2041 cgcccgagca tcagggctac tccatgagag gttagatgag tacgagctgc agggcccaac
2101 tctcaccacc ttcaactttg accgcaacaa ggtgcttgct tttagacagc ttgctgctga
2161 aaacaagtac gggttgatgg acacaatgag agttggaaga cagctcaagg atgtcaggac
2221 catgccagaa ctcaaacaag cactcaagaa tatctcaatc aagaggtgcc agatagtgta
2281 tagtggctgc acctacacac ttgagtctga tggcaagggt aatgtgaaag ttgacagagt
2341 tcagagtgcc actgtgcaga ccaataatga actggccggt gccctacacc atctaaggtg
2401 cgccagaatt agatattatg tcaagtgtgt ccaggaggcc ctgtattcca tcatccaaat
2461 tgctggagct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacctctg
2521 gtccaagcca caggtggaag acacagagga gactgtcaac aaggatgggt gcccaaaacc
2581 caaagatgat gaagagttcg tcgtttcatc cgacgacatc aagactgagg gcaagaaggg
2641 gaagaacaag actggccgtg gcaagaagca tacagccttc tcaagcaaag gtctcagtga
2701 tgaagagtac gatgagtaca aaagaatcag agaagaaaga aacggcaagt actccataga
2761 agagtacctt caggacaggg acaagtacta tgaggaggtg gccattgcca gggcgaccga
2821 agaggacttc tgtgaagaag aagaggccaa gattcgacag aggattttca ggccaacaag
2881 gaaacagcgc aaagaggaga gggcctctct cggtttggtc acaggttctg aaatcaggaa
2941 gaggaaccca gatgatttca agcccaaagg aaagctgtgg gctgatgacg acaggagtgt
3001 tgactacaat gagagactca attttgaagc cccaccaagc atctggtcga ggatagtcaa
3061 ctttggttca ggttggggct tttgggtttc ccccagcctg ttcataacat caactcatgt
3121 cataccccag ggcgcacagg agttctttgg agtccccatc aaacaaattc agatacacaa
3181 atcgggcgaa ttctgtcgct tgaggtttcc aaaaccaatt aggactgatg tgacgggcat
3241 gatcttagaa gaaggtgcgc ccgaagggac cgtggtcaca ctactcatca agaggccaac
3301 tggagaactt atgcccttgg cagccagaat gggaacccat gcaaccatga ggattcaagg
3361 gcgcactgtt ggaggtcaaa tgggcatgct tctgacagga tccaacgcca agagtatgga
3421 tctaggcacc acaccaggtg actgtggctg tccctacatt tacaagaggg agaatgacta
3481 cgtggtcatt ggagtccaca cggctgccgc tcgtggagga aatactgtca tatgtgccac
3541 ccaggggagt gagggagaag ccacacttga aggcggtgac aataagggaa cctactgtgg
3601 tgcaccaatc ttaggtccag gaagtgcccc aaaactcagc accaagacta aattttggag
3661 atcatctaca acaccactcc cacctggtac ctatgaacca gcctaccttg gtggcaagga
3721 ccccagagtc aagggtggtc cttcattgca acaagttatg agggaccagc tgaaaccatt
3781 tacagagccc aggggcaaac caccaaaacc aagtgtgtta gaggctgcca agaaaaccat
3841 catcaatgtc cttgaacaaa caattgatcc acctcagaaa tggtcattca cgcaagcttg
3901 cgcgtccctc gacaagacca cctccagtgg ccatccgcac cacatgcgga aaaacgactg
3961 ctggaacggg gaatccttca caggcaaatt ggcagatcag gcttccaagg ccaacctgat
4021 gttcgaagag gggaagaaca tgaccccagt ctacacaggt gcgcttaagg atgagctggt
4081 caaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggtt cggacctggc
4141 gaccatgatc cggtgcgctc gagcatttgg aggcctgatg gatgaactca aggcacattg
4201 tgttacactt cctgtcagag ttggtatgaa catgaatgag gatggtccta tcatctttga
4261 gagacactcc agatacaaat atcattatga tgctgattac tctcggtggg attcaacaca
4321 acaaagggcc gtgttagcag cagccctaga aatcatggtt aaattctccc cagaaccgca
4381 cctggcccag atagttgcgg aagaccttct ctcccccagt gtgatggatg taggtgactt
4441 caaaatatca atcaatgagg gtctcccctc cggggtaccc tgcacctccc aatggaactc
4501 catcgcccac tggctcctca ctctctgtgc actctctgaa gttacaaatc tgtcccctga
4561 catcattcag gctaattccc tcttttcctt ctatggtgat gatgaaattg tgagtacaga
4621 cataaagttg gacccagaga aattgacagc aaaactcaaa gaatacggat tgaaaccaac
4681 tcgccctgac aaaactgagg gaccccttgt tatctctgaa gacctgaatg gtctgacctt
4741 cctgcggaga actgtgaccc gcgacccagc tggctggttt ggaaaattgg aacagagctc
4801 aatacttagg caaatgtact ggactagggg ccccaatcat gaagatccat ccgaaacaat
4861 gataccacac tcccaaagac ccgtacaatt aatgtctttg ctgggcgagg ctgcactcca
4921 cggcccagca ttctacagca aaattagcaa gctagtcatt gcagagctga aggaaggtgg
4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcggattt
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgatg atggcgtcga
5101 atgacgctgc tccatctaat gatggtgcta cgggcctcgt cccagagatc aaccacgaga
5161 cccttcctct ggaaccggtg gcgggtgcag ccattgccgc gcctgtcact ggccaaaata
5221 atataattga tccctggatt agaacaaatt ttgtacaagc acccaatgga gagttcactg
5281 tctcacctag aaactctcct ggagaaattc ttttaaattt ggaattgggt cctgatttaa
5341 acccatattt ggcacactta tctagaatgt acaatgggta tgctggtggc gtggaagttc
5401 aagtcctcct agcagggaac gcgttcactg cagggaaaat tctcttcgct gccgtgccac
5461 caaatttccc agttgaattc ttgagtcctg cacaaatcac catgttgcca cacttaatag
5521 ttgatgttag aacccttgaa cctatcatga taccactccc tgatgttagg aacaccttct
5581 tccattacaa taaccaacct gccaaccgca tgcgactggt agccatgttg tatacccctt
5641 tgagatctaa tggttccggc gatgatgtct tcactgtttc atgtagagtg ctgactaggc
5701 ccaccccaga ttttgagttc acatatttgg tccccccttc agtagagtct aagactaaac
5761 ccttttctct acctatatta accatttctg aattaaccaa ttcaagattt cctgcaccca
5821 tagattcatt gtacacagcc caaaacaaca atctcaatgt ccaatgtcaa aatggtcggt
5881 gcacactgga tggtgaactg cagggaacca ctcagttgct gccttcaggc atatgtgctt
5941 tcaggggcaa attaacagca gatgtacacc aaagccacga tgacagatgg cacatgcagc
6001 tgacaaatct taatgggacc ccctttgatc caacagagga tgtgccagct ccgttaggca
6061 ccccagattt cacaggcctc ctcttcggag tggcgagtca gaggaatgtt gtatccaatc
6121 caaacaccac cagggcacac gaggctgtga tctccacaac cagttcacag tttgtgccaa
6181 aattaggatc aatcaacttt ggtagtacaa gtgatgattt ccagttacaa caacccacca
6241 aatttacacc agttggaatt aaggttgaga gtggacatga ttttgaccaa tgggccctgc
6301 ccagatattc aggtcattta acccttaata tgaatcttgc cccgcctgtt gctccaaatt
6361 tccctggtga acagctgttg ttctttagat caaatgttcc ttgtgctggt ggcgtcagtg
6421 atggtgtcat cgactgtttg ttgcctcagg agtggataca gtacttctac caggagtctg
6481 ctccctccca gtctgatgtg gcccttatca ggtacgtcaa tcctgacacg ggtcgcacac
6541 tcttcgaggc gaaactccac agaacaggct acatcactgt tgctcattca ggtgattatc
6601 cccttgttgt cccctctaat ggatacttca gatttgattc ttgggtgaac cagttttact
6661 cactcgcccc catgggaact ggaaacgggc gcagacgggt gcagtaatgg caggagcttt
6721 tatagcaggt cttgcaggtg acatgctcac caacacagtt ggttcactag tgaatgctgg
6781 aaccaatgcc ataacccaaa aggtggactt tgaaaacaac aaacagctcc agtctgcttc
6841 cttccaacat gacaaagaca tgctccaagc acaagtggct gccaccaagc agttgcaggc
6901 tgacatgatc gccatcaaac aggggatatt gaccgctggc ggcttttccc ccactgatgc
6961 ggcgagagga gcagtgggtg cacccatgac caaggtcctc gattggtccg gtactcgtta
7021 ctgggcgcca aattccacga ggacaactgg ctactcaggg cagttcacat caacgccctt
7081 gcacacaccc acgaaaacaa gtcagcctgc tcctgtcaaa agaacccaac ccccttcttc
7141 ctcttcaggt agtatctata gccttccaac acagagtact gtcttgagta agccttcttt
7201 cggctcttct gtttgttctg cttcaacaca atctacaaaa ttgagttcag tttcttcaat
7261 ggacagaaca gtaaattggg ttaatcagca aagaagcctc agcccctaca tgagtggtgc
7321 tctcaacata tctcatgtaa cacctccatc gagtagggct tcgagttcgg gaacagtctc
7381 aactgtgccc aaagaagttt tggactcctg gacatctgca tttaacacac acagacagcc
7441 g
//