Typing tool
|
Complete norovirus genomes
MK641589 | GII.14 | ||
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GII.P7 |
ORF1: 5..5098 ORF2: 5079..6689 ORF3: 6689..7483LOCUS MK641589 7529 bp RNA linear VRL 23-MAR-2019 DEFINITION Norovirus GII isolate CA-RGDS-1023, complete genome. ACCESSION MK641589 VERSION MK641589.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7529) AUTHORS Pan,C.-Y., Huynh,T., Newsum,M., Fitzpatrick,K., Castro,C.J., Ng,T.F., Marine,R.L. and Wadford,D.A. TITLE Norovirus GII.P7-GII.14 genome from a school outbreak, Arizona 2018 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7529) AUTHORS Pan,C.-Y., Huynh,T., Newsum,M., Fitzpatrick,K., Castro,C.J., Ng,T.F., Marine,R.L. and Wadford,D.A. TITLE Direct Submission JOURNAL Submitted (15-MAR-2019) Viral and Rickettsial Disease Laboratory, California Department of Public Health, 850 Marina Bay Parkway, Richmond, CA 94804, USA COMMENT ##Assembly-Data-START## Assembly Method :: Geneious v. R10; SPAdes v. 3.6 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7529 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="CA-RGDS-1023" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA: AZ" /collection_date="Feb-2018" /note="genotype: GII.P7-GII.14" gene 5..5098 /gene="ORF1" CDS 5..5098 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QBM30993.1" /translation="MKMASNDATAALGSQKSVNDSNIATPSNKEEVGTFSNIKVGFKK MLGAVPKGTKAPSSDQHCPTVKIRPKTLTIPPEPPNGEDTVQFDAKSETVIGLPDLTT VQNEHENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSDGKALGVHKPP AAISLATIELTPISLYWRPVYTPNYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLE LNDTWLNRRCISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKD LLGKLKPLNLLHLLASCDWTFAGIVETVILMAELFNVFWTPPDVSNFIASLIGDFELQ GPEDLAVELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMK WFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKAR KLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHM ARHLAKSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGSPVKDALTLQEL ADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESP EIEKVKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSL TARVAGLVHERKDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGAALKS VKTLEDLKVALRDVKFNECEIIYKNSKYRVSSNGKGSVSIDKVEDNASQTVNEVHSAL LRLRQARARYYISCFQDLVYTLIQVAGASFVVSRISRRFCWERWVKPTETQEVNESEK EAAQGRWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKY SIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTRKQRKEERGVLGLVTG SDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNL LITTTHVLPKGIRELFGVEIKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTV CSVLVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCG CPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPG KAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRG RLPRPAILEEAKKTVMNVLEQTIDPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNG ESFTGPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGT MIRCARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDST QQRCILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQ WNSIAHWILTLSAMAEVSGLSPDVIQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREY GLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNH ENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAM FRWMRFSDLSTWEGDRNLAPEGVNEDGVE" mat_peptide 5..1006 /gene="ORF1" /product="p48" mat_peptide 1007..2104 /gene="ORF1" /product="NTPase" mat_peptide 2105..2623 /gene="ORF1" /product="p22" mat_peptide 2624..3022 /gene="ORF1" /product="VPg" mat_peptide 3023..3565 /gene="ORF1" /product="Pro" mat_peptide 3566..5095 /gene="ORF1" /product="RdRp" gene 5079..6689 /gene="ORF2" CDS 5079..6689 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QBM30994.1" /translation="MKMASNDATPSDDGAAGLVPEINNEVMALEPVAGASLAAPVVGQ QNIIDPWIRNNFVQAPAGEFTVSPRNSPGELLLDLELGPELNPYLAHLARMYNGHAGG MEVQIVLAGNAFTAGKILFAAIPPSFPYENLSPAQLTMCPHVIVDVRQLEPVLLPMPD IRNVFYHYNQNNSPKLRLVAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFQFTFLVPP TVESKTKNFTLPVLRVSEMTNSRFPVVLDQMYTSRNENIIVQPQNGRCTTDGELLGTT ILQSVSICNFKGTMQAKLNEEPRYQLQLTNLDGSPIDPTDDMPAPLGTPDFQAMLYGV ASQRSSRDNATRAHDAQVDTAGDTFAPKIGQVRFKSSSNDFDLHDPTKFTPIGVNVDD QHPFRQWSLPNYGGHLALNNHLAPAVTPLFPGEQILFFRSYIPSAGGHTDGAMDCLLP QEWIEHFYQEAAPSQSDIALVRFINPDTGRVLFEAKLHKQGFLTIAASGDHPIVMPTN GYFRFEAWVNPFYTLAPVGTGSGRRRIQ" gene 6689..7483 /gene="ORF3" CDS 6689..7483 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QBM30995.1" /translation="MAGAFLAGLAGDVVASSLGSLVGAGANAINQKVEYDFNRQLQEA SFRHDKDMLKAQVAATAGLQQAMIDIKREALTAGGFSPADAARGAVKAPMTQILDWNG SRYWAPNSMKTTGYSGTFTSQGIRSSPHLSNQTPSAVKPTRPLPSISSSSSVYSSPST APSQSTQSTTLSAGTGSSRPNTVSTKTSTLSRTSDWVRGQNEMLGPFMSGALQTAYVT PPSSKASSQGTVSTVPKAVLDSWTPMFNTHRQPLFAHLRRRGESQI" ORIGIN 1 gtgaatgaag atggcgtcta acgacgctac cgctgccctt ggcagtcaaa aatctgtcaa 61 tgacagtaat atagccaccc cttctaacaa agaagaggtt ggtacattct ccaacattaa 121 agttggattc aagaaaatgc tgggtgccgt acccaaaggt accaaggcac ccagcagtga 181 tcagcattgc cccacagtta agatcaggcc taaaacattg acaatccccc ccgaaccccc 241 aaatggtgaa gacaccgtac aatttgatgc aaagtcagaa actgtaattg ggctaccgga 301 cttgacaacg gtgcaaaacg aacacgaaaa tactccatac actgtccccc cattaagtga 361 gagggagcac agaccggcca ctgaaccact tcctggcaca atattggaga tgtgggatgg 421 tgagttttac cattactccg tgtacgtcag cgatggtaaa gctctagggg tccacaaacc 481 accggcggct ataagtctcg cgacgataga actcaccccc atatcacttt actggagacc 541 cgtctacacc cccaactact tggtctcccc agacacatta aaaggcctcg ctggtgaaaa 601 gttcccctac acggccttca gcaacaactg ttacaacttc tgttgttggg tgcttgagct 661 caacgacacg tggcttaaca gaagatgcat ctccagaact accggcttct ttaaaccata 721 ccagtcttgg aataggaaac ccctcccaac tgttgatgat ggaaagatca aaaaggtggc 781 caacgcgatc ctctgtgcac tcggctcgct gttttcaaaa ccaatcaaag atctattagg 841 taaactcaaa ccattgaatc tactacactt gcttgcgtcc tgtgattgga cgtttgcggg 901 tatagtagag acagtcatct taatggcgga gcttttcaat gtgttctgga ccccgccaga 961 tgtctctaat tttatagcct ccctgatagg tgattttgaa ttgcaaggtc ctgaagactt 1021 ggctgtggag ctcgttcccg tggttatggg tggcataggg atggttctcg gcttcaccgc 1081 tgagaagata ggccgcatgc tgtcgtccgc ggcatcaaca ctacgggcgt gcaaagactt 1141 agggaactat gcccttgaca tactcaaatt ggtcatgaaa tggttcttcc caaagaagga 1201 agagaaagct gagatggaga ccttgagggc gattgaagat gctgtccttg acatggaagc 1261 tatagggaat aaccatctca caacccttct caaggacaaa gacagcctca cggctttcat 1321 gaaaaccctg gatctagaag aggagaaagc aaggaaactg tccactaaat catcttcacc 1381 ggacatagtc ggcaccatta acgccatact agctaggata gctgctgcta gatccctact 1441 acataaggcc aaagaggaaa tgtttagcag aatcagacca gtagttgtca tgatctcagg 1501 cagacctggc attggaaaaa ctcatatggc aagacacttg gctaagagca tcgccaacac 1561 catgagtggc gaccaaaggg tcggactcgt cccacgcaac ggtgtcgatc actgggatgc 1621 ctacagagga gagagagtag tcttgtggga tgactacggc atggggagcc ctgtcaaaga 1681 cgccctgaca ctgcaagaat tggccgacac atgtccagtc actttaaatt gtgataggat 1741 tgagaataag gggaagatgt ttgatagtga tgtcatcata atcacgacca acttagtcaa 1801 ccccgcgccc ctcgactatg tgaacttcga ggcgtgttcc aggagagttg atttcctggt 1861 ttatgcagag tcaccagaaa ttgaaaaggt caagagagat ttccccggcc agcctgacat 1921 gtggaaagac cattttaagc cagacttctc ccacattaag ctgactctag ccccccaggg 1981 tggatttgac aagaatggta acaccccaca tggcaagggc accatgcggt ccctaaccca 2041 ggggtcccta accgcgagag ttgcaggcct tgtccatgaa aggaaggacg agttccagct 2101 ccaaggaaat gaccttcaaa catacaattt tgacaccaac agagtctccg catttagaaa 2161 attggccgca gacaacaagt atgggatcat ggagacgatg agagttggcg cagcgctcaa 2221 gagcgtgaag accttggaag atcttaaagt tgcattgagg gatgtaaaat tcaatgagtg 2281 tgaaataatt tacaagaatt ctaagtaccg agtctcttcc aacggtaaag gctcagtctc 2341 tattgacaaa gttgaagaca atgcttccca gacagtgaac gaggtgcatt cagccctcct 2401 cagactcagg caggcgaggg ccagatacta catcagctgc ttccaagacc tcgtctacac 2461 tctcatacag gttgccgggg catcatttgt tgttagtagg atctccagga ggttctgctg 2521 ggaaaggtgg gtcaaaccga ccgagaccca ggaggtgaat gagtccgaaa aggaagcggc 2581 ccaaggcaga tgggaaattg agcccaagga cacagaacca gaaggcaaga agggtaagaa 2641 caagaaagga aggggcaaga aacacacagc cttctctagc aaaggtctga gtgatgaaga 2701 gtatgatgag ttcaagagga tcagggaaga aagaaatgga aagtactcca ttgaggaata 2761 cctgcaggac cgagaccgct attatgaaga agtagcagtt gctcgagcga cagaggagga 2821 cttctgtgaa gaggaagagg ccaagataag acaaagaatt ttccgcccga caaggaagca 2881 gaggaaggag gaaaggggcg tactcggctt ggtcaccggc tcagacatca ggaagaggag 2941 accagacgat tttcaaccaa aaggcaatct atgggctgat gacaccagaa gtgtggacta 3001 caatgagagg cttgattttg aagcaccccc gagtgtctgg tcaagaatag tcccactagg 3061 cactggttgg gggttttggg tgtcatccaa ccttctgatc acaacaacac acgtcctgcc 3121 taaagggatt agggaacttt ttggagttga aatcaaacaa atccaaattc ataagtctgg 3181 agagttttgc aggtttagat tcccaagacc tatcaggcca gatgtcacag gactcgtgct 3241 ggaggagggc gccccagagg gcactgtctg ttctgtgctc gtgaaaagac ccacaggtga 3301 aatgatcccc cttgcagtga ggatgggcac acacgcatcc atgaaaatac agggtaggac 3361 cgttggtggc cagatgggaa tgctcctcac aggagcaaac gcaaagaaca tggatcttgg 3421 caccggccct ggtgactgcg gttgccccta tatctataag cgtggcaacg acatcgttgt 3481 tgcgggcgtc cacaccgcag cagcccgggg aggcaacact gtgatatgtg ctacccaggg 3541 gcaagatggg gaagcagtcc ttgagggaaa tgaggacctt ggcacctact gtggtgcccc 3601 aattctgggc cctggtaagg cgcctaaact cagcacgaag accaagtttt ggcgctcatc 3661 accagatgcc ctgccacctg gcacatatga acctgcttac ctaggaggca aagaccctag 3721 agtggaaaaa ggtccctccc tgcagcaagt catgagagat cagctgaagc ccttcacaga 3781 acccagaggc agactaccta gacctgcaat tttagaggaa gccaaaaaga cagtaatgaa 3841 tgttctagag caaaccattg accccgccaa gccatggtcc tattcgcagg catgtgcctc 3901 attggacaaa accacttcaa gtggtagccc ccatcacgtt aagaaaaatg accactggaa 3961 tggagagtcc ttcactggtc ctcttgcaga ccaggcttcc aaagccaacc tcatgtatga 4021 gcaggctaaa catgtgcagc ccgtgtatac ggctgcgctg aaagatgagc ttgttaagac 4081 tgacaagatc tacaagaaga taaagaagag gcttctatgg gggtcagacc ttggcacaat 4141 gatcaggtgc gccagggctt ttggcggtct catggacagc atgaaggcaa gttgtatagc 4201 tcttccttgt agggtaggaa tgaacatgaa tgaagatggc cccatcatat ttgacaaaca 4261 ctctaagtac aggtaccact atgatgctga ctattctagg tgggactcaa cccaacaaag 4321 gtgtatcctc tctgccgcta tggaagtgat ggtgcggttt tctgctgagc cagaattggc 4381 acaagtggtt gcagaggacc ttttggcacc tagccagctt gatgttggcg actttgtcat 4441 ctcagtccag gagggcctgc catcaggagt cccatgcaca tcgcaatgga attcaatagc 4501 acactggata ctcactttga gtgcgatggc agaagtgtca ggcctctcac cagatgttat 4561 ccaagctcac tcttgttttt cattttatgg ggatgatgag atcgtcagca ctgacatcaa 4621 ccttgacccc atgaagttaa cacaaaaact tagggagtat ggcctggttc ccacccggcc 4681 tgacaaaact gaaggtcccc tcgtcataac tgaagacctc accggcctga cgttccttcg 4741 taggtcgatt gctcgggacc cagctggctg gtttggaaaa ctagaccaag attcaatcct 4801 caggcaactg tactggacga gggggcctaa ccatgagaac ccgtacgaga gcatggtccc 4861 tcattctcag cgggctacac aactcatggc ccttcttggt gaggcctcac tgcatggtcc 4921 tcagttttac aagaaagtta gcaaaatggt catcaatgaa attaagagtg gtggtctgga 4981 gttttacgtg cccagacaag aggccatgtt cagatggatg aggttctctg acctcagcac 5041 gtgggagggc gatcgcaatc ttgctcccga aggtgtgaat gaagatggcg tcgaatgacg 5101 ctactccatc tgatgatggt gcagccggcc tcgtaccaga gatcaacaat gaggttatgg 5161 ctcttgaacc cgtcgctggg gcctcccttg cagcccctgt agtcggtcaa cagaatataa 5221 ttgatccctg gattagaaac aattttgtac aagcccctgc tggtgaattt acagtttccc 5281 ctagaaactc tcctggagaa ctcctacttg atttggaatt gggtcctgaa cttaacccct 5341 atcttgcaca tttggccagg atgtacaatg ggcacgcagg aggaatggaa gtgcagatag 5401 tactggctgg gaatgcgttc acagctggta agatcctatt tgccgccatc ccacctagct 5461 tcccttatga aaatttgtca cccgcccaat tgactatgtg cccccatgtg atagtggatg 5521 tgaggcaatt ggaaccagtg ctcttgccaa tgccagatat aagaaatgtt ttctatcatt 5581 ataatcagaa caacagtccc aaacttaggc ttgtggctat gctttacact cctctgaggg 5641 ctaataattc aggtgatgat gtgttcacgg tgtcttgtcg cgttctaacg cgaccttctc 5701 cagatttcca gttcactttc ctggtcccac ctacagttga gtctaaaact aagaacttca 5761 cccttcccgt tctcagagtc tcagagatga caaactcaag gttccccgtt gttttggacc 5821 aaatgtacac aagcaggaat gaaaacatca ttgtccaacc ccaaaacggc agatgcacaa 5881 ctgatggtga gctgcttggt accactatct tacaatctgt gtctatttgc aatttcaaag 5941 gaacaatgca ggcgaagctg aatgaagagc cacgatacca attgcaactc accaacttgg 6001 atgggtcacc catagatcca acagatgata tgcctgcccc tcttggcaca ccagacttcc 6061 aggccatgtt atatggcgtt gcaagccaac gctcttccag agacaatgcc accagggcac 6121 atgatgcaca ggttgacact gcgggtgaca cattcgcccc gaagattggc caggttcgat 6181 ttaaatcaag ctccaatgat tttgacctac atgaccctac aaaattcaca cctattggtg 6241 tcaatgtgga tgaccagcac ccttttagac agtggtccct gccaaactac ggtggtcacc 6301 ttgccctgaa caatcattta gccccagctg tgacgccgct cttccctggc gagcaaatct 6361 tgttctttag gtcatacatt ccaagcgccg gaggccatac agacggtgct atggactgtt 6421 tgctgcccca agagtggata gagcacttct accaggaggc ggctccttcc caatctgaca 6481 tcgcactggt aaggttcatc aaccctgaca caggaagagt gctctttgaa gctaaattgc 6541 ataaacaagg tttcctcaca attgcagcat ctggagacca ccctattgtg atgcccacca 6601 atggttactt taggtttgaa gcttgggtta atcctttcta tactctcgcc cccgtgggaa 6661 ctgggtctgg gcgcaggagg attcaataat ggctggagct ttccttgcag gtttggcagg 6721 tgacgttgtg gcttccagct tgggctcact cgtgggtgct ggagccaacg ccatcaatca 6781 gaaagtggag tatgacttca acaggcaact ccaggaggca tcttttagac atgacaagga 6841 tatgctcaaa gcccaggttg cagcaacagc aggccttcaa caggccatga tagacatcaa 6901 gcgggaggca ttgactgcag gcggcttttc ccccgctgat gctgcaagag gtgcagtcaa 6961 agcgcctatg acgcagatcc ttgattggaa tggttctaga tattgggctc ctaactccat 7021 gaagacaact ggctattcag gtacatttac ttctcaaggc attagaagtt cccctcatct 7081 gtctaatcaa accccaagtg ctgttaaacc tactagacct ttaccatcta tatctagttc 7141 ttctagtgtg tatagttctc cctctactgc cccttcacaa tcaacacaat caacaacgct 7201 gtctgcaggg acagggtcct ccagacctaa cactgtgtcc acaaagacct ccacattgtc 7261 gaggacaagt gattgggtca gaggccaaaa tgagatgctt ggcccgttca tgagtggtgc 7321 actccaaact gcttatgtca caccaccatc gagcaaggcc tcatcacaag ggacggtctc 7381 gaccgtaccc aaggctgttt tggactcctg gactcccatg tttaacaccc acaggcagcc 7441 tctcttcgcc cacttgcgta ggcgagggga gtcacagatt tagtgaaaag gatgattagg 7501 gttccttcct tcccccttct tattctttt //