Typing tool
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Typing tool
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Complete norovirus genomes
| MN996299 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5007
ORF2: 4988..6610
ORF3: 6610..7416
LOCUS MN996299 7431 bp RNA linear VRL 15-JUL-2020
DEFINITION Norovirus GII isolate SCD1062_2 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MN996299
VERSION MN996299.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7431)
AUTHORS Zhang,Z., Wang,D., Liu,D., Zhang,Z. and Wu,Q.
TITLE Whole Genome Analysis for Co-Infected Different Genotypes of Human
Norovirus
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7431)
AUTHORS Zhang,Z., Wang,D., Liu,D., Zhang,Z. and Wu,Q.
TITLE Direct Submission
JOURNAL Submitted (28-JAN-2020) School of Agriculture & Biology, Shanghai
Jiao Tong University, 800 Dongchuan Rd. Minhang Dist, Shanghai
200240, China
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC genomics workbench v. 12
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7431
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="SCD1062_2"
/isolation_source="asal swab"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="China: Shanghai"
/collection_date="18-Feb-2018"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5007
/gene="ORF1"
CDS <1..5007
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QHQ73455.1"
/translation="MSSTLKKALGARPKQPTPRDEPQKSPRPPTPELVKRIPPPPPNG
EEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFSVPPLSLRENREAKEPLTGAILE
MWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVELTPLSLYWRVVYTPQYLISPETLR
RLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTTGFFRPYQEWNRKPLPTMD
DSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCDWTFAGIVESLILLAE
LFGVFWTPPDVSAMIAPLLGDYELQGPEDLAIELVPVVMGGIGLVLGFTKEKIGKMLS
SAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIEDAVLDLEAIENNHM
TTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINALLARIAAARSLVHRAK
EELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRVGLIPRNGVDHWDAYK
GERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSEVIIITTNLAN
PAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKDAFKPDFSHIKLQLAP
QGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQGPTITTFNFDRNRIT
AFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKRCRIIYGGSTYDLESD
GKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYVKCVQEAVYSIIQIAGAAFVTT
RIARRMNIQELWSKPQLDQSESEAKEEALKSEDDEFIISSKDIKEEGKKGKNKTGRGK
KHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEE
EEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNE
KLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPAGITEAFGVPIKQIQIHKSG
EFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPLAARMGTHATMKIQG
RMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVIGVHTAAARGGNTVIC
ATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSSNTPLPPGTYEPAYL
GGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTIINVLEQTLDPPQKW
TYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLADQASKANLMFEEGKHMTPVYT
AALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEMKAHCISLPVRVGMN
MNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVRFSAEPQLAQIVAED
LLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTKLSPDIIQANS
MFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLIISEDLNGLTFLRRT
VTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPIQLMALLGEASLHGP
SFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE
"
mat_peptide <1..903
/gene="ORF1"
/product="p48"
mat_peptide 904..2001
/gene="ORF1"
/product="NTPase"
mat_peptide 2002..2532
/gene="ORF1"
/product="p22"
mat_peptide 2533..2931
/gene="ORF1"
/product="VPg"
mat_peptide 2932..3474
/gene="ORF1"
/product="Pro"
mat_peptide 3475..5004
/gene="ORF1"
/product="RdRp"
gene 4988..6610
/gene="ORF2"
CDS 4988..6610
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QHQ73456.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6610..7416
/gene="ORF3"
CDS 6610..7416
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QHQ73457.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSTTTSVNSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 atgtcttcca ccttaaagaa agccctcggg gctaggccca aacagcctac cccgagagac
61 gaaccacaaa agtccccaag accaccaact cccgagttgg tcaagaggat accccctcct
121 ccacctaatg gcgaagaaga agaagaacca gtcattaggt atgaagttaa gagtgggatc
181 tctggcctgc ccgagctcac aacagtcccc caaccggacg tggccaacac agcattcagt
241 gttccaccac tgagcttgag agaaaacagg gaggccaagg aaccgctaac aggggcaata
301 ttagagatgt gggacggaga gatataccac tatggcctgt acgtggagaa aggcttagtg
361 ttgggtgtgc acaaaccacc tgcagccata agcatggcaa gagtggagct gacgccgctg
421 tcattgtact ggcgtgtggt gtacactccc caatacctca tctcccctga aactctcagg
481 aggctcaacg gagaggcgtt cccttacacc gccttcgaca acaactgcta tgccttttgc
541 tgctgggtgc tagacctcaa tgactcatgg cttagcagga ggatggtgca aagaacaacg
601 ggcttcttca gaccttacca agagtggaac agaaaacccc tgcccaccat ggatgattcc
661 aaaataaaga aggtagcaaa tatattccta tgttcattgt ccacattatt caccagaccc
721 ataaaagacc tcataggaaa aattaaacca ttaaacatat tgaacatcct ggcaacgtgt
781 gactggacgt ttgccggaat agtggagtct ctgatattac ttgctgaact cttcggagtt
841 ttctggacac ccccagatgt gtctgctatg atcgctccct tactcgggga ctacgagttg
901 caggggccag aagacctcgc cattgaactc gtacctgtgg taatgggagg gattggtttg
961 gtgttgggat tcaccaaaga gaaaatcggt aaaatgttgt cctcagcagc atcaacactt
1021 agggcttgca aagatcttgg tgcctatggc ttagagatac tcaaattggt catgaagtgg
1081 ttcttcccaa agaaagaaga ggccaatgag ctagccatgg tgagggccat agaggatgcc
1141 gtactagatc ttgaggcaat agaaaataac cacatgacaa ccctgttgaa agacaaagac
1201 agcttagcaa catacatgaa aacactggac atggaggagg agaaagccag aaggttgtcc
1261 acaaaatctg catctcctga catagttggg acaatcaacg ccctgctggc tcgaatagca
1321 gcagccaggt cattagtcca cagggccaag gaagagctat ctagcaggat aagaccagta
1381 gttgttatga tatctggtaa accaggaata ggcaaaactc atctggccag ggaggtggca
1441 agaaaggtag catccactct cacaggagat caaagagtcg gactcatacc aagaaacggt
1501 gtggaccatt gggatgcata caaaggtgag agagtcgtgc tgtgggacga ctatggcatg
1561 agcaacccca ttcatgatgc tcttcgcata caagaattgg ctgatacgtg tccccttacc
1621 ttaaattgtg acagaattga aaacaaggga aaagtttttg atagtgaagt cataataatt
1681 acaacaaacc ttgccaatcc agccccactt gattatgtca actttgaggc ctgttccagg
1741 agaattgatt tcctggtgta cgctgaggcg ccagaagtgg aaaaggcaaa acgggatttt
1801 cctggtcagc cagatatgtg gaaggacgcc ttcaagccgg acttttcaca catcaagcta
1861 caacttgcac ctcaaggcgg ctttgacaag aatggcaaca ccccacatgg gaaaggggtg
1921 atgaagaccc tcactaccgg ttctctgatt gcccgtgcat caggcctatt acatgagagg
1981 atggatgaat ttgaactcca aggtcccaca atcaccacct tcaattttga ccggaacaga
2041 atcacagcat tcagacaatt ggctgcagaa aacaaatatg ggttggtgga taccatgaaa
2101 gttggtaatc aactaaaagg agtgaaaacc atggaagaac tcaaacaagc aatcaggaat
2161 gtgaccatca agaggtgccg gatcatctac ggtggctcca cgtatgacct tgaatctgat
2221 ggcaagggca aagttttggt ggaaaaggtc aagaacacct ctgtgcagac caacaacgag
2281 ttggccgggg ccctgcacca tctcaaacat gcccgaatca ggtactatgt caaatgtgtg
2341 caagaagcag tctattccat catacaaatt gccggcgctg cgtttgtcac cacgcgcatt
2401 gcacgccgca tgaacataca agaactttgg tcgaagccac aattagatca aagtgaatca
2461 gaagctaagg aagaggccct caagtcagaa gatgacgagt tcatcatatc ttctaaggac
2521 atcaaggagg aaggaaagaa gggcaaaaac aaaactggcc gtggcaagaa acacactgca
2581 ttctccagca agggcttgag tgatgaggag tatgacgagt acaagaggat aagagaagag
2641 agaaatggga agtactctat agaggagtat cttcaagaca gagacaggta ctatgaggag
2701 ctcgccattg ccaaggccac ggaagaagac ttctgtgaag aggaggagat caaaatccgc
2761 cagagaattt tccgtcccac caggaaacaa agaaaggaag agagggccac attagggctg
2821 gtaacaggtt cagaaatcag aaaaagaaac cctgatgact tcaaacccaa agggaagctg
2881 tgggccgatg acaacagaag tgttgactac aatgagaaac tggactttga ggccccccca
2941 agcatatggt ctaggattgt gagctttggt tctggctggg gcttctgggt gtcaccaagc
3001 ctgttcataa catcaactca tgtaatcccc gcaggcataa cagaagcatt tggagtcccc
3061 atcaaacaaa ttcagatcca caagtcaggt gaattttgcc gattcagatt cccaaaacca
3121 attagaccag atgtgacagg aatgatcttg gaagaaggtg cgcctgaagg caccgtggca
3181 actgtgctca tcaaacgccc caccggagag cttatgcctc ttgcagccag aatgggaaca
3241 cacgcaacca tgaaaattca aggccgcatg gttggcggac agatgggcat gttgctcact
3301 ggatcaaatg ctaaaggaat ggatttggga acaacccctg gtgactgtgg ctgtccttac
3361 atctataaaa ggggcaatga ctatatagtc attggggtac acactgcagc agcccgtggt
3421 ggaaacaccg tcatctgtgc cacacaggga agtgagggtg aggcaactct tgagggtgga
3481 gatgataaag gaacatactg tggggcaccc attttaggcc ctgggggtgc accaaaattg
3541 agcaccaaaa ccaaattttg gaggtcatcg aacacgcccc ttccaccagg gacatatgag
3601 cctgcctacc tcggtggccg tgatccgcgt gttaagggtg ggccctcctt gcagcaggta
3661 atgagagacc agttaaagcc attcactgaa cccaggggca aacctccaag accaagtgta
3721 ttggaagcag ctaaacaaac cattatcaat gttctcgaac aaaccctgga ccctccacaa
3781 aaatggacat atgcacaggc gtgtgcctca cttgacaaaa ccacctccag cgggcatccc
3841 catcacgttc gaaagaatga attctggaat ggtgagacct tcactggtaa attggcagac
3901 caagcatcaa aagcaaacct aatgtttgag gaagggaaac acatgacacc agtgtataca
3961 gcagcactca aggacgaact agttaagact gagaaaatct atggaaagat caagaagaga
4021 ctgctctggg gctctgactt gtccaccatg atccggtgcg ctaggtcatt tggtgggctc
4081 atggatgaga tgaaggcaca ctgcatatca ctcccagtac gagttggcat gaatatgaat
4141 gaagatggcc caataatatt tgagaaacat tccagatata aataccacta tgatgcagac
4201 tactctcgtt gggattcaac acaacagagg gcagtactag cagcagcctt ggaaatcatg
4261 gtcagattct ctgcagaacc acaattggca cagatagtcg ctgaggatct actggcccct
4321 agtgtagtag atgtgggaga ctttaaaatt acaataaatg aagggctccc atctggtgtg
4381 ccatgcactt ctcaatggaa ctctatcgca cactggctgc taactctctg tgccttgtct
4441 gaagtcacta aactgtcccc tgacattata caagcaaatt ccatgttctc attttacggt
4501 gatgacgaga ttgtcagcac cgacataaaa ttggaccctg aacagttaac cgccaagttg
4561 aaggagtacg gcctgaaacc gacccgccca gacaagaccg agggacccct gatcatcagt
4621 gaagatttga acggactcac tttcctccga aggacggtga ctcgtgaccc agctggctgg
4681 tttggaaaac tggaccaaag ttcaattttg aggcagatgt actggactag aggaccaaat
4741 catgaagacc ccaatgagac aatgataccc cattctcaaa gacccataca gctcatggca
4801 ctgcttggtg aagcctctct tcacggaccc tctttctaca gtagaatcag taaactggtc
4861 ataactgaac tcaaagaagg tgggatggac ttttacgtgc caaggcagga acccatgttc
4921 aggtggatga ggttttctga cttgagcacg tgggagggcg atcgcaatct ggctcccaat
4981 tttgtgaatg aagatggcgt cgagtgacgc caacccatct gatgggtccg cagccaacct
5041 cgtaccagag gtcaacaatg aggttatggc tttggagccc gttgttggtg ccgctattgc
5101 ggcacctgta gcgggccaac aaaatgtaat tgacccctgg attagaaata attttgtaca
5161 agcccctggt ggggaattta cagtgtcccc tagaaacgct ccaggtgaaa tactatggag
5221 cgcgccccta ggccctgacc taaatcccta cctatcccat ttagccagaa tgtacaatgg
5281 ttatgcaggt ggttttgaag tgcaggtaat tctcgcgggg aacgcgttca ctgccgggaa
5341 gattatattt gcagcagtcc caccaaattt tccaactgaa ggcttaagtc ctagccaggt
5401 cactatgttc ccccacataa tagtagatgt tagacagcta gaacccgtgc tgatcccctt
5461 acccgatgtt aggaataatt tctatcatta caatcagtca aatgactcca ctattaagtt
5521 gatagcaatg ttgtatacac cacttagggc taataatgct ggagatgatg ttttcacagt
5581 ttcgtgccga gttcttacga gaccatcccc cgattttgat ttcatatttt tggtgccacc
5641 cacagttgag tcaagaacta aaccattctc tgtcccaatt ttaactgttg aggagatgac
5701 caattcaaga ttccccatcc ctttggaaaa gttgttcaca ggccccagta gtgcctttgt
5761 tgttcaacca caaaacggca ggtgcacaac tgatggcgtg ctcctaggca ccacccaact
5821 ttctcctgtc aacatctgca ccttcagagg ggatgtcacc cacatcacag gtagtcgcaa
5881 ctacacaatg aatttggctt ctcaaaattg gaacaactat gacccaacag aagagatccc
5941 agcccctcta ggaactccag attttgtggg gaagattcaa ggcatgctca cccaaaccac
6001 aaggacagat ggttcaacac gcggccacaa agctacagtt tacactggga gcgccgactt
6061 tgctccaaaa ttgggtagag ttcaatttga aactgacaca gaccatgatt ttgaagctaa
6121 tcaaaacaca aagttcaccc cagtcggtgt catccaagat ggtagcacca cccaccgaaa
6181 cgaaccccaa cagtgggtgc tcccaagtta ctcaggcaga aacactcaca atgtacattt
6241 ggcccccgct gtagccccca cctttccggg tgagcaactt ctcttcttca gatccaccat
6301 gcccggatgc agcgggtacc ccaacatgga tttggactgt ctgctccccc aggaatgggt
6361 gcagtacttc taccaagagg cagccccagc acaatctgat gtggctctgc taagatttgt
6421 gaatccagac acaggtaggg ttttgtttga gtgcaagctc cacaaatcag gctatgttac
6481 agtggctcac actggccaac atgatttggt tatccccccc aacggttact ttaggtttga
6541 ttcctgggtc aaccagttct acacacttgc ccccatggga aatggaacgg ggcgtagacg
6601 tgtagtgtaa tggctggagc tttctttgct ggattggcat ctgatgtcct tggctctgga
6661 cttggttccc ttatcaatgc tggggctggg gccatcaacc aaaaagttga atttgaaaac
6721 aacaggaaat tacaacaagc atccttccaa tttagcagca atctgcaaca ggcttccttt
6781 caacatgata aagagatgct ccaagcacaa attgaggcca ccaaaaagct acaacaggaa
6841 atgatgaaag ttaagcaggc aatgctccta gagggtgggt tctctgagac agatgcagcc
6901 cgcggggcaa ttaacgcccc catgacaaaa gctttggact ggagcgggac aaggtactgg
6961 gctccagatg ctaggattac aacatacaat gcaggccact tttccacccc tcaaccatcg
7021 agggcactgc cagggagagc taatcttagg gatgctgtcc ctgctcgggg accctccaac
7081 aaatcctcta actcttctac taccacctct gtgaactcaa atcaaactat ttcaacgaga
7141 cttggttcta cagctggttc tggaaccagt gtctcgagcc tcccgtcaac tgcaaggact
7201 aggagctggg ttgaggatca aaataggaat ttgtcacctt tcatgagggg ggcccacaac
7261 atatcatttg ttaccccacc atctagcaga tcctctagcc aaggcacagt ctcaaccgtg
7321 cctaaagaga ttttggactc ctggactggc gctttcaaca cgcgcaggca gcctctcttc
7381 gctcacattc gtaagcgagg ggagtcacgg gtgtaatgtg aaaagacaga a
//