Typing tool
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Typing tool
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Complete norovirus genomes
| KF712492 | GII.4 Yerseke | |
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| GII.P4 Hunter |
ORF1: 1..4872
ORF2: 4853..6472
ORF3: 6472..7278
LOCUS KF712492 7278 bp ss-RNA linear VRL 26-OCT-2013
DEFINITION Norovirus Hu/GII.4/NIHIC1.8/2012/USA, partial genome.
ACCESSION KF712492
VERSION KF712492.1
DBLINK BioProject: PRJNA70471
KEYWORDS STANDARD_DRAFT.
SOURCE Norovirus Hu/GII.4/NIHIC1.8/2012/USA
ORGANISM Norovirus Hu/GII.4/NIHIC1.8/2012/USA
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7278)
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 (29-SEP-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 :: Standard Draft
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Genome Coverage :: 139.1x
Sequencing Technology :: Sanger; Illumina
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7278
/organism="Norovirus Hu/GII.4/NIHIC1.8/2012/USA"
/mol_type="genomic RNA"
/strain="Hu/GII.4/NIHIC1.8/2012/USA"
/host="Homo sapiens"
/db_xref="taxon:1406811"
/country="USA: Maryland"
/collection_date="31-Jul-2012"
/PCR_primers="fwd_name: 1_Forward, fwd_seq:
gtgaatgawgatggcgt, rev_name: 1_Reverse, rev_seq:
ccagrctrtctttrtctt"
/PCR_primers="fwd_name: 2_Forward, fwd_seq:
ygactcgtggctgagyagga, rev_name: 2_Reverse, rev_seq:
gytgggccctgyagttcawa"
/PCR_primers="fwd_name: 3_Forward, fwd_seq:
tcaaccaartctgcttcacctg, rev_name: 3_Reverse, rev_seq:
aagtcytcctcrgtcgccct"
/PCR_primers="fwd_name: 4_Forward, fwd_seq:
gggaaraacaagrctggycg, rev_name: 4_Reverse, rev_seq:
crrctctytgttgtgttgaatccc"
/PCR_primers="fwd_name: 5_Forward, fwd_seq:
tggyaagatcaagaagaggc, rev_name: 5_Reverse, rev_seq:
atcagtcgtgcayctgccrt"
/PCR_primers="fwd_name: 6_Forward, fwd_seq:
cagtytcttgtcgrgtyctca, rev_name: 6_Reverse, rev_seq:
atcaatyttgtcttttcaca"
/note="genotype: GII.4"
gene <1..4872
/gene="POL"
/locus_tag="H649_46727gpPOL"
CDS <1..4872
/gene="POL"
/locus_tag="H649_46727gpPOL"
/note="genome polyprotein"
/codon_start=1
/product="putative nonstructural polyprotein"
/protein_id="AGX85888.1"
/translation="DEVVVSYSAKDGVSGLPELSTVRQPEEANTAFSVPPLNQRENRD
AKEPLTGTILEMWDGEIYHYGLYVERGFVLGVHKPPAAISLAKVELTPLSLYWRPVYT
PQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQ
DWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNILNILASCDWSFA
GIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLG
FTKEKIGKMLSSAASTLRACKDLGAYGLEILKLAVKWFFPKKEEANELAIVRSIEDAV
LDLEAIENNHMTTLLKDKSSLAAYMKTLDLEEEKARKLSTKSASPDIVGTVNALLARI
AAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTYLAREVAKRIAASLTGDQRVGLVP
RNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELADTCPLTLNCDRIENKGKVFDS
DVIIITTNLANPAPLDYVNFEACSRRIDFLAYAEAPEVEKAKRDFPGQPDMWKNAFSP
DFTHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPTL
TTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTMPELKQALKNISIKKCQIV
YSGSTYTLESDGKGNVKVDRVQSASVQTNNELAGALHHLRTARMRYYVRCVQEALYSI
IQIAGAAFVTTRIVKRMNIQSLWSKPQVENTEETTSRDGCPKPKDDEEFVISSDDIKT
EGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEV
AIARAIEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGK
LWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFF
GVPIKQIQVHKSGEFCRLRFPKPIRADVTGMILEEGAPEGTVVTLLIKRSTGELMPLA
ARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGV
HTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPKLSTKTKFWRSST
APLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTII
NVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANL
MFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELK
AHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRAVLAAALEIMVKF
SPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSE
VTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTRPDKTEGPLAI
SEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGSNHEDPSETMIPHSQRPIQ
LMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDR
NLAPSFVNEDGVE"
mat_peptide <1..762
/gene="POL"
/locus_tag="H649_46727gpPOL"
/product="putative protein p48"
mat_peptide 763..1860
/gene="POL"
/locus_tag="H649_46727gpPOL"
/product="NTPase"
/note="p41"
mat_peptide 1861..2397
/gene="POL"
/locus_tag="H649_46727gpPOL"
/product="protein p22"
mat_peptide 2398..2796
/gene="POL"
/locus_tag="H649_46727gpPOL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 2797..3339
/gene="POL"
/locus_tag="H649_46727gpPOL"
/product="3C-like protease"
/note="3CLpro; calicivirin"
mat_peptide 3340..4869
/gene="POL"
/locus_tag="H649_46727gpPOL"
/product="RNA-directed RNA polymerase"
gene 4853..6472
/gene="VP1"
/locus_tag="H649_46727gpVP1"
CDS 4853..6472
/gene="VP1"
/locus_tag="H649_46727gpVP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AGX85889.1"
/translation="MKMASSDANPSDGSTANLVPEANNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLSRMYNGYAGG
FEVQVILAGNAFAAGKIIFAAVPPNFPTEGLSPSQVTMFPHLIVDVRQLEPVMIPLPD
IRNNFYHYNQSNDPTIKLIAMLYTPLRANNVGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESKTNPFSVPILTIEEMTNSRFPIPLEKLFTGPSSALVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHTTKTHTYQMNLAAQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGNGSTRAHKATVYTGSAEFTPKLGRIQLFTDTDNDLEANQNTKFTPVGVIQDG
DTHQNEPQQWVLPSYSGRNNHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDC
LLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGHHDLFI
PPNGYFRFDSWVSPFYTLAPMGNGTGRRRAL"
gene 6472..7278
/gene="VP2"
/locus_tag="H649_46727gpVP2"
CDS 6472..7278
/gene="VP2"
/locus_tag="H649_46727gpVP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AGX85890.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQD
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPGARTTTYNAGYFSTPQHSGALPGRANLRAAVPARGSSRVSS
NSSTATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLNSQTGVFNTRRQPLFAHIRRRGESRA"
ORIGIN
1 gatgaagtag tggtttctta tagtgccaaa gatggcgttt ccggtttgcc tgagctttcc
61 accgtcaggc aaccggaaga agccaatacg gccttcagtg tccccccact caatcagagg
121 gagaataggg atgctaagga accactaact gggacaattc tggaaatgtg ggatggagaa
181 atctatcatt acggcctgta tgttgagcga ggttttgtgc tgggcgtaca caagccacca
241 gctgccatta gcctcgccaa ggtcgaatta acaccactct ccttgtactg gagacctgtg
301 tacactcctc agtacctcat ttctccagac actctcaaga aattacacgg agaaacattt
361 ccctacacag cctttgacaa caattgctat gccttttgtt gctgggtcct ggatttaaac
421 gactcgtggc tgagtaggag aatgatccag agaacaactg gcttcttcag accctaccaa
481 gattggaata ggaaacccct ccccactatg gatgactcca aattaaagaa ggtggctaac
541 atattcctgt gtgcattgtc ttcgctattc accaggccta taaaagatat aatagggaag
601 ctaaggcctc ttaacatcct taacatcttg gcttcatgtg attggtcttt tgcaggcata
661 gtggagtcct tgatactctt ggcagaactc tttggagttt tctggacacc cccagatgtg
721 tctgcgatga ttgccccctt actcggtgac tacgaactgc agggacctga ggaccttgca
781 gtggagctcg tccctgtagt gatgggggga attggtttgg tgctaggatt caccaaagag
841 aagattggaa aaatgttgtc atctgctgca tccaccctga gagcttgtaa agatcttggt
901 gcatatgggc tagagatcct aaagttggct gtgaagtggt tcttcccgaa gaaagaggaa
961 gcaaatgaac tggctatagt gagatccatc gaggatgcag tcctggatct cgaagcaatt
1021 gaaaacaacc atatgaccac cttgctcaaa gacaaaagca gtctggcagc ctacatgaaa
1081 acccttgacc ttgaggagga gaaagccagg aaactctcaa ccaagtctgc ttcacctgac
1141 attgtgggca cagtcaacgc ccttctggcg agaatcgctg ctgcacgttc tctggtgcat
1201 cgagcgaagg aggaactttc tagcagacca agacctgtag tgttgatgat atcaggcaga
1261 ccaggaatag ggaagaccta ccttgccaga gaagtggcta agagaatcgc agcctccctt
1321 acaggagacc agcgtgtagg cctcgtccca cgcaatggcg tcgaccactg ggatgcgtac
1381 aagggggaga gggtcgttct atgggacgac tatggaatga gcaatcccat ccaagatgcc
1441 ctcagattgc aagaactcgc tgacacttgt cccctcaccc tgaactgtga caggattgag
1501 aacaaaggaa aggtctttga cagcgatgtc atcattatca ccactaacct ggctaaccca
1561 gcaccactgg actatgtcaa cttcgaagca tgctcgaggc gcatcgactt cctcgcgtat
1621 gcagaagccc ctgaggtcga aaaggcgaag cgtgacttcc caggccaacc cgatatgtgg
1681 aagaacgcct tcagtcctga tttcacacac ataaaactaa cattggctcc acagggtggt
1741 ttcgacaaga acgggaacac cccacacggg aagggcgtca tgaagactct caccaccggc
1801 tccctcattg cccgggcatc agggctactc catgagaggc tagatgaatt tgaactacag
1861 ggcccaactc tcaccacttt caactttgat cgcaataaag tgcttgcctt tagacaactt
1921 gctgctgaaa acaaatatgg gttgatggac acaatgaaag ttgggaggca gctcaaggat
1981 gtcagaacaa tgccagagct caagcaagca ctcaagaata tttcaatcaa gaagtgccag
2041 atagtgtaca gtggtagcac ctacacactt gagtctgatg gcaagggtaa tgtgaaggtt
2101 gacagagtcc aaagcgcctc cgtgcagacc aacaatgagc tggctggcgc cctacaccat
2161 ctaaggacag ccagaatgag atactatgtc aggtgtgtcc aggaggccct gtattccatc
2221 atccagattg ctggggctgc atttgtcacc acgcgcatcg tcaagcgcat gaacatacaa
2281 agcctatggt ctaaaccaca agtggaaaac acagaggaga ctaccagcag ggacgggtgt
2341 ccaaaaccca aagatgatga ggagttcgtc atttcatccg acgacatcaa gactgaaggc
2401 aagaaaggga aaaacaagac tggccgcggt aagaagcaca cagccttctc aagcaaaggt
2461 ctcagtgatg aagagtacga tgagtacaag aggattagag aagaaaggaa tggtaagtac
2521 tccatagaag agtaccttca agacagggac aaatactatg aggaggtggc cattgccagg
2581 gcgatcgagg aagacttctg tgaagaggag gaggccaaga tccggcaaag gatcttcagg
2641 ccaacaagga aacaacgcaa ggaggaaaga gcttctctcg gtttagtcac aggttctgaa
2701 attaggaaaa gaaatccaga tgatttcaaa cccaagggga aattgtgggc tgacgatgac
2761 agaagtgtgg actacaatga gaaactcagt tttgaagccc caccaagcat ctggtcgagg
2821 atagtcaact ttggttcagg ttggggattc tgggtttccc ccagtttgtt cataacatca
2881 acccatgtca taccccaggg agcaaaggag ttctttggag tccccatcaa acaaattcag
2941 gtacataagt caggcgaatt ctgtcgcttg agattcccaa aaccaatcag ggctgatgtg
3001 acgggcatga tcttagaaga aggtgcaccc gagggcaccg tggttacact actcatcaaa
3061 aggtccactg gggaactcat gcccctagca gctaggatgg ggacccatgc aaccatgaaa
3121 atccaaggac gcactgttgg aggtcaaatg ggcatgcttc tgacaggatc caacgccaaa
3181 agcatggacc tgggtaccac accaggtgat tgtggctgtc cctacatcta caagagagga
3241 aatgactatg tagtcattgg agtccacacg gctgccgctc gtgggggcaa cactgtcatc
3301 tgtgccaccc aggggagtga gggagaggct acacttgaag gtggtgacaa caaagggaca
3361 tactgtggtg caccaatcct aggcccaggg agtgccccaa aacttagcac caagaccaaa
3421 ttctggagat cgtccacagc accactccca cctggcacct atgaaccagc ctatcttggt
3481 ggtaaggatc ccagagttaa gggtgggcct tcactacagc aggtcatgag ggatcagctg
3541 aagccattca cagagcccag gggcaagcca ccaaagccaa gtgtgttgga agctgctaag
3601 aaaaccatca tcaatgtcct tgagcaaaca attgatccac ctgagaaatg gtcgttcgca
3661 caagcttgcg cgtcacttga taagaccacc tccagtggtc acccgcacca catgcggaaa
3721 aacgactgct ggaacgggga gtccttcaca ggcaagctgg cagaccaggc ttccaaggcc
3781 aacctgatgt ttgaagaggg gaagaacatg acgccagtct atacagctgc gcttaaggat
3841 gaattagtta aaactgacaa gatttatggt aagatcaaga aaaggcttct ctggggctcg
3901 gatttggcga ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa
3961 gcgcactgtg tcacacttcc catcagagtt ggtatgaata tgaatgagga tggccccatc
4021 atcttcgaga ggcactccag gtacacgtac cactatgatg ctgattactc tcgatgggat
4081 tcaacacaac agagagccgt gttggcagca gctctagaaa ttatggttaa gttctcccca
4141 gaaccacatt tggcccaggt agtcgcagaa gaccttcttt cccctagcgt ggtggacgtg
4201 ggtgacttta caatatcaat taacgagggt cttccctctg gagtgccctg cacctcccaa
4261 tggaactcca tagcccactg gcttctcacc ctctgtgcgc tctctgaagt tacaaacttg
4321 tctcctgaca ccatacaagc taattccctc ttctcttttt atggtgatga tgaaattgtt
4381 agcacagaca taaaattgga cccagaaaag ttgacagcaa agctcaggga atatgggtta
4441 aaaccaaccc gccccgacaa aactgaagga ccccttgcca tctctgaaga cttggatggc
4501 ctgactttct tgcgaagaac tgtgacccgc gacccagctg gttggtttgg aaaactggag
4561 cagagctcaa tactcaggca aatgtactgg actaggggtt ccaaccatga agacccatct
4621 gaaacaatga ttccacactc ccaaaggccc atacaactga tgtccctact gggggaggcc
4681 gcactccacg gcccaacatt ctacagcaaa atcagcaagt tagtcattgc agagctaaaa
4741 gaaggtggca tggattttta cgtgcccaga caagagccaa tgttcagatg gatgagattc
4801 tcagatctga gcacgtggga gggcgatcgc aatctggctc ccagttttgt gaatgaagat
4861 ggcgtcgagt gacgccaacc catctgatgg gtccacagcc aacctcgtcc cagaggccaa
4921 caatgaggtt atggctttgg agcccgttgt tggtgccgct attgcggcac ctgtagcggg
4981 ccaacaaaat gtaattgacc cctggattag aaataatttt gtacaagccc ctggtggaga
5041 gttcacagta tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccttaggccc
5101 tgatctaaac ccctatctat ctcatttgtc cagaatgtat aatggttatg caggtggttt
5161 tgaagtgcag gtaatcctcg cggggaacgc gttcgccgcc ggaaaaatca tattcgcagc
5221 agtcccacca aatttcccaa ctgaaggctt gagccccagc caggtcacta tgttccccca
5281 cttaatagta gatgttaggc aactggaacc tgtgatgatc cccttacccg atattaggaa
5341 taatttctat cattacaatc aatcaaatga tcccaccatc aaattgatag caatgttgta
5401 tacacctctt agggctaata atgttggtga cgatgtcttc acagtttctt gtcgggtact
5461 cacgagacca tcccccgatt ttgatttcat atttctagtg ccacccacag ttgaatcaaa
5521 aaccaaccca ttctctgttc caattctaac tattgaggag atgaccaatt caagattccc
5581 cattcctttg gaaaagctgt tcacgggccc cagcagtgcc cttgttgttc aaccacaaaa
5641 cggcaggtgc acgactgatg gcgtgctcct gggtaccacc caactgtctc ctgtcaacat
5701 ctgcaccttc agaggggatg tcacccatac tacaaaaact catacctacc aaatgaattt
5761 ggctgctcaa aattggaaca gttatgaccc aacagaagaa atcccagccc ccctaggaac
5821 tccagatttc gtgggaaaga tccaaggtgt gctcacccaa accacgaagg gaaatggctc
5881 aacccgtgcc cacaaagcta cagtgtacac tgggagcgcc gagttcactc caaaactggg
5941 tagaatccaa cttttcactg acacagacaa cgatcttgaa gctaaccaaa acacaaagtt
6001 caccccagtc ggtgtcatcc aggatggtga tacccaccaa aatgaacccc aacaatgggt
6061 actcccaagt tactcaggta gaaataatca caatgtgcac ctggcccccg ctgtagcccc
6121 cacttttccg ggcgagcaac ttctcttctt cagatccact atgcccggat gcagcgggta
6181 ccccaacatg aatttggact gtctgcttcc ccaggaatgg gtgcaatatt tctatcaaga
6241 ggcagcccca gcacaatctg atgtggcttt gctaagattt gtgaatccag atacaggtag
6301 ggttttgttt gagtgcaagc ttcataaatc aggttatgtc acagtggctc acaccggcca
6361 ccatgatttg tttatccccc ctaatggtta tttcagattt gattcctggg tcagcccctt
6421 ctacacactt gcccccatgg gaaatggaac ggggcgtaga cgtgcattat aatggctgga
6481 gctttctttg ctggattggc atctgacgtc cttggatccg gacttggttc tctgatcaat
6541 gccggggctg gggccatcaa ccaaaaagtt gaatttgaaa acaacagaaa attgcaacaa
6601 gattccttcc aatttagtag caatctgcaa caggcttcct ttcaacatga taaagagatg
6661 ctccaagcac aaattgaggc caccaaaaag ttgcaacagg aaatgatgag agttaaacag
6721 gcaatgctcc tagagggtgg gttctctgag acagatgcag cccgtggggc aatcaacgcc
6781 cccatgacaa aggttttgga ctggagtggg acaaggtact gggctcccgg tgctaggact
6841 acaacataca atgcaggcta cttttccact ccccaacact cgggggcact gccaggaaga
6901 gctaatctta gggctgctgt ccccgctcgg ggctcctcta gagtatcttc taattcttct
6961 actgctacct ctgtgtattc aaatcaaact gcttcaacga gacttggttc tacagctggt
7021 tctggtacca gtgtctcgag cctcccgtca actgcaagga ctaggagttg ggttgaggat
7081 caaaatagga atttgtcacc tttcatgagg ggggcccaca acatatcgtt tgtcacccca
7141 ccatctagca gatcctctag tcaaggcaca gtctcaaccg tgcccaaaga agttttgaac
7201 tcccagactg gcgttttcaa tacgcgcagg cagcctctct ttgctcacat tcgtaggcga
7261 ggggagtcac gggcgtaa
//