LOCUS JX289822 5642 bp RNA linear VRL 15-NOV-2012
DEFINITION Norovirus Hu/GII.1/7EK/Hawaii/1971/USA, partial genome.
ACCESSION JX289822
VERSION JX289822.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/GII.1/7EK/Hawaii/1971/USA
ORGANISM Norovirus Hu/GII.1/7EK/Hawaii/1971/USA
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 5642)
AUTHORS Madupu,R., Halpin,R., 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 (06-JUL-2012) J. Craig Venter Institute, 9704 Medical
Center Drive, Rockville, MD 20850, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: clc_ref_assemble_long v. 3.20.50819
Coverage :: 5.2x
Sequencing Technology :: Sanger; Illumina; 454
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..5642
/organism="Norovirus Hu/GII.1/7EK/Hawaii/1971/USA"
/mol_type="genomic RNA"
/strain="Hu/GII.1/7EK/Hawaii/1971/USA"
/isolate="7EK"
/host="Homo sapiens"
/db_xref="taxon:1208060"
/country="USA: Hawaii"
/collection_date="1971"
/note="genotype: GII.1"
gene <1..3815
/gene="POL"
CDS <1..>1555
/gene="POL"
/note="genome polyprotein; coding region disrupted by
sequencing gap"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="AFS33554.1"
/translation="SLAAYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARS
LVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELAKKIAATLTGDQRVGLIPRNGVD
HWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSDAIII
TTNLANPAPLDYVNFEACSRRIDFLVYADAPDVEKAKRDFPGQPDMWKNAFSPDFSHI
KLMLAPQGGFDKNGNTPHGKGVMKTLTVGSLIARASGLLHERLDEYELQGPALTTYNF
DRNKVLAFRQLAAENKYGLMDTMRVGGQLKGVRTMSELKQALKNISVKRCQIVYSGCT
YTLESDGKGSVRVDRVQNTTVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAG
AAFVTTRIAKRMNIQDLWSKPQLDDTGEAVSKEGCPKPKDDEEFVVSSDDIKVEGKKG
KNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARA
TEEDFCEEEE"
mat_peptide <1..802
/gene="POL"
/product="NTPase"
/note="p41"
mat_peptide 803..1339
/gene="POL"
/product="protein p22"
mat_peptide 1340..>1555
/gene="POL"
/product="viral genome-linked protein"
/note="VPg"
gap 1556..2085
/estimated_length=530
CDS <2086..3815
/gene="POL"
/note="genome polyprotein; coding region disrupted by
sequencing gap"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="AFS33557.1"
/translation="QMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAA
ARGGNTVICATQGNEGEAILEGGDDKGTYCGAPILGPGSAPKLSTKTKFWRSSTTPLP
PGTYEPAYLGGKDPRVKSGPSLQQVMRDQLKPFTEPRGKQPKPSVLEAAKKTIINVLE
QTIDPPQKWSFAQACASLDKTTSSGHPHHIRKNDCWNGDSFTGKLADQASKANLMFEE
GKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCV
TLPVRVGMNMNEDGPIIFEKHSRYKYHYEANYARGDSTQQRAVLAAALEIMVKFSPEP
HLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQWNSITHWLLTLCALSEVTDL
SPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLIISEDL
DGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSL
LGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAP
SFVNEDGVE"
mat_peptide <2086..2282
/gene="POL"
/product="3C-like protease"
/note="3CLpro; calicivirin"
mat_peptide 2283..3812
/gene="POL"
/product="RNA-directed RNA polymerase"
gene 3796..5403
/gene="VP1"
CDS 3796..5403
/gene="VP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AFS33555.1"
/translation="MKMASNDAAPSNDGAAGLVPEVNNETMALEPVAGASIAAPLTGQ
NNVIDPWIRMNFVQAPNGEFTVSPRNSPGEILLNLELGPELNPFLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKLVFAAIPPHFPLENLSPGQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQQPEPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFNYLVPP
TVESKTKPFTLPILTIGELSNSRFPVPIDELYTSPNEGVIVQPQNGRSTLDGELLGTT
QLVPSNICALRGRINAQVPDDHHQWNLQVTNTNGTPFDPTEDVPAPLGTPDFLANIYG
VTSQRNPNNTCRAHDGVLATWSPKFTPKLGSVILGTWEESDLDLNQPTRFTPVGLFNT
DHFDQWALPSYSGRLTLNMNLAPSVSPLFPGEQLLFFRSHIPLKGGTSDGAIDCLLPQ
EWIQHFYQESAPSPTDVALIRYTNPDTGRVLFEAKLHRQGFITVANSGSRPIVVPPNG
YFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 5403..>5642
/gene="VP2"
CDS 5403..>5642
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AFS33556.1"
/translation="MAGAFIAGLAGDIVTNSVGSLVNAGANAINQKVDFENNKQLQQA
SFNHDKEMLQAQIQATKQLQADMIALRQGVLTAGGF"
BASE COUNT 1418 a 1285 c 1242 g 1167 t
ORIGIN
1 cagcctggcg gcttacatga gaactctcga ccttgaggaa gagaaagcca gaaagctctc
61 aaccaaatct gcttcacccg acatcgtggg cacaatcaac gctctcttgg cgaggatcgc
121 agccgctcgc tccctcgtgc atcgggcaaa ggaagagctc tccagtaggc cgagacccgt
181 tgttgtgatg atatcgggaa aaccagggat agggaagacc catcttgcca gagaactggc
241 caaaaagatc gcagctactc tcacagggga tcagagagtg ggtctcattc cacgcaatgg
301 cgttgaccac tgggacgcat acaaggggga gagggtcgtc ctttgggatg actacgggat
361 gagcaacccc atccatgatg ctctcagaat acaggagctt gctgacactt gccccctaac
421 attaaactgt gatagaattg aaaacaaagg gaaagttttt gacagtgatg ccataatcat
481 caccaccaac ttggccaacc ctgcaccact agactatgtc aattttgagg catgctcgag
541 gcgcattgat ttcctcgtgt atgccgacgc ccctgatgtc gaaaaggcga agcgcgactt
601 cccaggccaa cctgacatgt ggaaaaatgc ttttagtcct gacttctcac acataaaatt
661 gatgctagcc ccacagggtg gttttgataa gaacggcaac accccacatg ggaagggcgt
721 catgaaaacc ctcaccgttg gttccctcat cgcccgtgca tcaggactcc tccatgagag
781 actggatgag tacgaactac agggcccagc tctcacaacc tacaactttg accgaaacaa
841 agtgcttgct ttcaggcagc ttgctgctga aaacaagtac ggtttaatgg acacaatgag
901 agtcggaggg cagctcaagg gtgtcagaac catgtcagag ctcaaacaag cactcaaaaa
961 catctcagtt aaaaggtgcc agatagtgta cagtggttgc acttacacac ttgaatctga
1021 tggtaagggc agtgtgaggg ttgacagagt tcagaacacc actgtgcaga ccaacaacga
1081 gttagccggc gccctgcacc atctcaggtg cgccaggatt aggtactatg tcaagtgtgt
1141 tcaagaggcc ctgtattcca tcatccaaat tgcaggggct gcgtttgtca ccacgcgcat
1201 tgccaaacgc atgaacatac aggacctttg gtccaagcca cagctggacg acacaggaga
1261 agctgtcagc aaagaagggt gcccaaaacc caaggatgat gaggagttcg ttgtttcatc
1321 tgacgacatc aaggtcgagg gcaagaaagg gaaaaacaag actggtcgcg gcaagaaaca
1381 cacagccttc tcgagtaaag gtctcagtga tgaggagtac gacgagtaca aaagaatcag
1441 ggaggaaaga aacggcaagt actctataga agagtatctc caggacagag acaagtatta
1501 cgaggaggtt gccattgcta gggcgactga ggaggacttc tgtgaagaag aagaannnnn
1561 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
1621 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
1681 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
1741 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
1801 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
1861 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
1921 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
1981 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
2041 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnngccaa atgggtatgc
2101 tcctaacagg atccaatgct aaaagtatgg acctgggcac tacacccggt gactgtggtt
2161 gtccctacat ctataagaga gggaatgact atgtggtcat cggggttcac acagctgctg
2221 cccgtggggg gaacactgtc atatgtgcca cccagggtaa tgaaggtgag gccatacttg
2281 agggcggaga tgacaaaggc acctactgtg gtgccccaat cctgggtcca ggaagtgccc
2341 caaagctcag caccaagacc aaattttgga ggtcatccac aacgccactc ccgcctggca
2401 cctacgaacc agcctacctc ggtggcaagg accccagagt caagagtggc ccctcattac
2461 aacaagtcat gagagaccag ttgaaaccat tcacagaacc aagaggtaaa caaccaaaac
2521 caagtgtgtt ggaggctgcc aagaaaacca tcatcaatgt tcttgaacaa acaatagacc
2581 cgcctcaaaa atggtcattt gcgcaagctt gtgcgtctct tgacaagacc acctccagtg
2641 gccacccaca ccacatacgg aagaatgact gctggaatgg ggactctttc acaggcaagt
2701 tggcagatca ggcctcgaag gccaacttga tgtttgagga ggggaagaac atgaccccag
2761 tctacacagg tgccctcaag gatgagttag tcaaaactga caagatatat ggtaagatca
2821 agaagaggtt actctggggc tcggacctgg caaccatgat ccggtgtgca cgagcgttcg
2881 gaggtctgat ggacgaactt aaagcccact gtgtcacact ccctgtcaga gttggtatga
2941 acatgaatga ggatggcccc attatctttg agaaacactc caggtataaa tatcattatg
3001 aggcaaatta tgctcgaggg gactcaacac agcagagagc cgtactagct gcagccctag
3061 agatcatggt caaattctcc ccagagccac acttggccca ggtagttgca gaagaccttc
3121 tttcccccag tgtgatggat gtgggtgact tcaagatatc aatcaacgag ggtcttccct
3181 ctggggtgcc ctgcacctcg caatggaact ccatcaccca ctggctcctc actctttgtg
3241 cactctctga agtcacggac ctgtcccctg acatcattca agccaattcc ttattctctt
3301 tctatggtga tgatgaaatt gtgagtacag acataaaatt ggacccagaa aaactgacag
3361 caaaactgaa agagtatggg ctgaagccaa cccgccctga caagactgag ggacctctga
3421 tcatttctga ggatctggat ggtttaacct ttctgcggag aactgtaacc cgtgatccag
3481 ctggttggtt tggtaaatta gaacagagct caatacttag gcagatgtac tggactaggg
3541 gccccaacca tgaggatcca tctgaaacaa tgataccaca ttcccaaagg cccatacagt
3601 tgatgtctct gctaggtgaa gctgcattgc acggtccagc attctacagc aaaatcagta
3661 aactagtcat tgcagagttg aaggaaggtg gcatggactt ttacgtgccc aggcaagagc
3721 cgatgttcag atggatgaga ttctcagacc tgagcacgtg ggagggcgat cgcaatctgg
3781 ctcccagttt tgtgaatgaa gatggcgtcg aatgacgccg ccccatctaa tgatggtgca
3841 gccggtctcg taccagaggt caacaacgag acgatggccc tcgaaccggt ggctggggct
3901 tctatagccg cccctctaac cggtcaaaat aatgtgatag acccctggat tagaatgaac
3961 tttgtccaag ccccaaatgg agaattcaca gtgtctcccc gcaattctcc tggtgaaatc
4021 ttgctaaatt tggaattagg ccctgaatta aatccattct tagcacacct ttcaagaatg
4081 tataatggtt atgccggcgg ggttgaagtg caggtactac tcgctgggaa cgcgttcaca
4141 gcgggaaaac tggtgtttgc agcaatcccc ccgcacttcc ctcttgagaa tctgagtcct
4201 ggacaaatta caatgttccc tcatgtgatt attgatgtta gaacattaga acctgtgctt
4261 ttgccccttc cagatgttag aaataatttc tttcattaca atcagcagcc cgagccccgt
4321 atgagacttg tagctatgtt gtatactcct cttagatcta atggttctgg tgatgatgtg
4381 ttcacagttt cttgcagggt tctcacccgc ccttctccag attttgattt taattatttg
4441 gttcccccaa ctgtggagtc taaaactaaa ccattcaccc tgccaatcct aactattgga
4501 gaattgtcaa attctagatt cccagttcca atagatgaat tgtacaccag ccccaatgaa
4561 ggagtgatcg tgcagcccca aaatggcaga tcaacacttg atggtgaatt gttgggcacc
4621 acgcaactcg tgccctcaaa catctgtgcg ctacgagggc gcattaacgc ccaggtgcca
4681 gatgatcacc atcaatggaa cctacaggta acaaacacaa atgggactcc tttcgacccc
4741 accgaagacg tccctgcacc actgggcaca ccggatttcc tggcgaatat ctatggagtc
4801 accagccaga gaaaccccaa caacacttgc cgtgcccatg atggggtttt ggcaacttgg
4861 agccccaaat ttacacccaa gttaggatct gtgattttgg gcacttggga agaaagtgat
4921 cttgatctca atcagcccac aaggttcaca cctgttggtc tgtttaacac tgaccacttt
4981 gatcagtggg ccttgcctag ttattctgga agattaaccc taaacatgaa tttggcaccc
5041 tctgtttccc ccctctttcc aggtgaacag ctacttttct tcaggtccca tataccactc
5101 aaaggaggta cctctgatgg tgccattgat tgtctactcc cccaggaatg gattcagcat
5161 ttttatcagg agtcagcccc atcgcccacg gacgtggctc taattagata caccaatcct
5221 gacacaggcc gcgttttgtt tgaagctaaa ctgcacaggc aaggattcat cacagtggca
5281 aactctggtt ctaggcctat tgttgtccct ccgaatggct attttaggtt tgattcttgg
5341 gttaatcaat tctattctct cgcccccatg ggaactggga acgggcgcag aagagtgcag
5401 taatggctgg agcttttata gcagggcttg ctggtgacat agtcaccaat agtgttggct
5461 cacttgtgaa cgctggagct aatgcaataa accaaaaagt ggactttgaa aacaacaagc
5521 aactacagca ggcttctttc aatcatgaca aagagatgct gcaagctcaa atccaagcca
5581 ccaaacagct acaggctgac atgattgctc tcagacaagg ggtgttgacc gcaggcggct
5641 tc
//