ID JX866664; SV 1; linear; genomic RNA; STD; VRL; 6413 BP. XX AC JX866664; XX DT 19-APR-2013 (Rel. 116, Created) DT 19-APR-2013 (Rel. 116, Last updated, Version 1) XX DE Pepino mosaic virus isolate BNMX12-1, complete genome. XX KW . XX OS Pepino mosaic virus OC Viruses; Riboviria; Tymovirales; Alphaflexiviridae; Potexvirus. XX RN [1] RC Publication Status: Online-Only RP 1-6413 RX PUBMED; 23587202. RA Ling K.S., Li R., Bledsoe M.; RT "Pepino mosaic virus genotype shift in North America and development of a RT loop-mediated isothermal amplification for rapid genotype identification"; RL Virol J 10(1):117-117(2013). XX RN [2] RP 1-6413 RA Ling K.-S., Li R., Bledsoe M.; RT ; RL Submitted (23-SEP-2012) to the INSDC. RL Virology Laboratory, USDA-ARS, U.S. Vegetable Laboratory, 2700 Savannah RL Highway, Charleston, SC 29414, USA XX DR MD5; 30c31aa2bac390cd4883fb04d0a6a302. DR EuropePMC; PMC3639891; 23587202. XX CC ##Assembly-Data-START## CC Assembly Method :: DNASTAR v. Lasergene 10 CC Sequencing Technology :: Sanger dideoxy sequencing CC ##Assembly-Data-END## XX FH Key Location/Qualifiers FH FT source 1..6413 FT /organism="Pepino mosaic virus" FT /host="Solanum lycopersicum" FT /isolate="BNMX12-1" FT /mol_type="genomic RNA" FT /db_xref="taxon:112229" FT 5'UTR 1..83 FT CDS 84..4403 FT /codon_start=1 FT /gene="rep" FT /product="replicase" FT /function="RNA replication" FT /db_xref="GOA:M9P9D1" FT /db_xref="InterPro:IPR001788" FT /db_xref="InterPro:IPR002588" FT /db_xref="InterPro:IPR007094" FT /db_xref="InterPro:IPR027351" FT /db_xref="InterPro:IPR027417" FT /db_xref="UniProtKB/TrEMBL:M9P9D1" FT /protein_id="AFZ88248.1" FT /translation="MSRVRNTLEKIRDPQVQSSICEAAYQHVRPVLKESLINCPYALND FT YEADTLENLGVTINPHAIQTHTHAAAKVVENRMLEIVGHHLPKDEKVTFIFLKRSKLRY FT MRRAAVHKDVFVNHNIEPKDFFRYDEESTSTSFSVNTKIAYISDSLHFMEPADVTHLFD FT RCQNLKTLMATVVLPVEAIHRQTSLFPAIYSINYNEEGFEYIPGSHGGGAYFHKYETLD FT WLKYSRFIGHDPLTGLKYTITIQMVESLGANHLFLFQRGNFETPLYRTFQKNSFVTFPN FT IFHPRHVNATKPMPRSRAIQLYLYVKSVNKVTQRDIFAKVRQLISTAELELYDPDELTH FT VVNYFSYVSQLSSINDYDNMLKSSFFKKLVAPMQHDWRCMIEFFRGKSDFNQLLTALQW FT KDFSYTIKTEELIITTHTAIGQAISGAANTYKERRQLTQLVKQGVISLADFQSEEPKIE FT YTEFERETKPPVDCVTNYNNAVKNLGLSEPVDLPECSYARKSVPSNEISMAMTDADNFA FT VINEIESLLSEEIAAPTLPALKNKTWASYASDTSSKKNEEIENIIAELEASRKVSNVQQ FT TQHNYHISQCPTSLTADLPWKAWLPLLNAHGFKGDQIQHSPDGQIIQPIQDINNKTPRS FT EYPSSIPADLVSTLRNIKRAVYAIPISHRRASAYSSDVKNNRTGKLLCAQSKEWKESFA FT FKMQHEDIVKSGVVIHGCGGSGKSQALQNFLRTLGDNNDCCTVVVPTVELRNDWVNKLC FT KLPMEHIKTFEKAMIQPGFPVVIFDDYTKLPPGYIEAYLFHHANTELFILTGDSRQSVY FT HESNNEAYIASLDEAVAYYSNYCGFYLNATHRNVRSLANKLGVYSETEGHLKITFASNA FT LQKCKVPILVPSQMKKNAMQDIGHKAMTYAGCQGLTAPRVQILLDNHTQHCSDRVLYTC FT LSRAVDSIHFINTGPNNSEFWDKLEATPYLKAFIDTYRDEKTEMLNSKPADDSPVEPEA FT PATHFPVSNGNNLEKLASTLPEKFAREIYDKHHGYSNTIQTENPIVQLFQHQQAKDETL FT FWATIEARLSITTPEANLREFTLKKDVGDILFFNYHSAMCLPADPVDFEPRTWEICAAE FT VKNTYLAKPMANLINAASRQSPDFEPNKISLFLKSQWVKKVEKLGAIKSKPGQTIAAFM FT QQTVMLYGTMARYLRKMRQRFQPKHIFINCETTTDDLNNFVLNGWNFNRTAQTNDFTAF FT DQSQDGAMLQFEVMKAKFFNIPADVIEGYINIKLNAKIFLGTLSIMRLSGEGPTFDANT FT ECSIAYTATRYHLSSAVKQVYAGDDMALDGVVMEKPSFKKLQSNLKLTSKTLFPKQVKG FT DYAEFCGWTFTPGGIIKNPLKMHASIMLQEAIGNLHTAARSYAIDMKHSYQMGDKLHEY FT LTPDEAEQHFLAVRKLHKLHQGEAMRLGEKSPPKATH" FT gene 84..4303 FT /gene="rep" FT gene 4428..5132 FT /gene="tgbp1" FT CDS 4428..5132 FT /codon_start=1 FT /gene="tgbp1" FT /product="triple gene block protein 1" FT /db_xref="GOA:I1V2C0" FT /db_xref="InterPro:IPR027351" FT /db_xref="InterPro:IPR027417" FT /db_xref="UniProtKB/TrEMBL:I1V2C0" FT /protein_id="AFZ88249.1" FT /translation="MERSTLINLLQLHHFEPKLSVEGVIVVHGIAGTGKTTLLRTLFSA FT YPNLVIGSPRPCYLDKANKISQVCLSCFPNTLCDIVDEYHLLESYQEPTLALFGDPCQC FT TFIGRLRIPHYTSFRTHRFGKSTAELLNKLFQLQIVSVKQEDDIVEFFDPFQVDPTENI FT SASEEEVLEFVSDQVVTTSSEELAGLEFTETTFYCTTLAAAVTENPARTFISLTRHTQR FT LTIGELNARIDS" FT gene 5113..5484 FT /gene="tgbp2" FT CDS 5113..5484 FT /codon_start=1 FT /gene="tgbp2" FT /product="triple gene block protein 2" FT /db_xref="GOA:Q69A02" FT /db_xref="InterPro:IPR001896" FT /db_xref="UniProtKB/TrEMBL:Q69A02" FT /protein_id="AFZ88250.1" FT /translation="MPGLTPRADLTDTYKIIAIAFLLSACIYFQNSHYQPVAGDNLHRL FT PFGGQYQDGTKKISYFPQQQSYFHSGNKLNVLILIFILTLGIVLTNKFSFSVSRTTHQH FT SCYNTHSAANTTPPLSGHH" FT gene 5336..5584 FT /gene="tgbp3" FT CDS 5336..5584 FT /codon_start=1 FT /gene="tgbp3" FT /product="triple gene block protein 3" FT /db_xref="InterPro:IPR003411" FT /db_xref="UniProtKB/TrEMBL:C4PFL5" FT /protein_id="AFZ88251.1" FT /translation="MSSYSSSFLHWVSSSPINLVLALAVLLTSILATIHILQPTQHHHC FT QVIIDGAAIVVTNCENTPEVLKAINFAPWNGLSFPSV" FT CDS 5631..6344 FT /codon_start=1 FT /product="coat protein" FT /db_xref="GOA:Q69A00" FT /db_xref="InterPro:IPR000052" FT /db_xref="UniProtKB/TrEMBL:Q69A00" FT /protein_id="AFZ88252.1" FT /translation="MADNTPVAATSGSPPTAQDAGAKAPADFSNPNTAPSLSDLKKVKY FT VSTVTSVATPTEIEALGKIFTAMGLAANETGPAMWDLARAYADVQSSKSAQLIGATPSN FT PALSRRALAAQFDRINITPRQFCMYFAKVVWNILLDSNIPPANWAKLGYQEDTKFAAFD FT FFDGVTNPASLQPADGLIRQPNEKELAAHSVAKYGALARQKISTGNYITTLGEVTRGHM FT GGANTMYAIDAPPEL" FT 3'UTR 6345..6413 XX SQ Sequence 6413 BP; 2047 A; 1464 C; 1157 G; 1745 T; 0 other; gaaaacaaaa cataaccaaa acaacaaagt cataatacac tacataacca cgcggaaaaa 60 cagctaacgc actttaccgc attatgtctc gtgttagaaa tactttggaa aagatcagag 120 accctcaagt acagtcaagc atatgcgaag cagcatacca acatgttcga ccagttttga 180 aggaatctct aatcaattgt ccctatgcgc tcaatgatta tgaagccgac acccttgaga 240 atttaggtgt cacaattaac cctcatgcaa ttcaaaccca tacacacgca gcagctaaag 300 tggttgaaaa cagaatgcta gagattgttg gtcaccatct accaaaagat gagaaggtta 360 ccttcatttt ccttaaacgt agtaaattgc gttacatgag aagagctgct gtccataaag 420 atgtttttgt caaccataac atagagccca aagatttttt taggtatgac gaggagtcca 480 catcaacaag cttctccgtg aatactaaaa tcgcatacat ttcagattcc ttacatttca 540 tggagccagc tgatgttaca cacctttttg accgttgcca aaatcttaaa acattaatgg 600 caaccgttgt cctacctgtt gaagcaattc atagacaaac atctttattt cctgcgatat 660 actccattaa ctacaatgaa gaaggctttg agtatatccc tggttcccat ggtggtgggg 720 catactttca caagtatgag actttagact ggcttaaata ttccagattc ataggacatg 780 atccattgac tggcctcaaa tataccatta caattcaaat ggttgaaagt ctaggcgcca 840 accacctttt ccttttccaa agaggaaatt ttgaaacgcc cttatatagg acctttcaaa 900 aaaatagttt tgtgacattc cctaatatat ttcatccccg acatgttaat gccacaaaac 960 ctatgccacg ctccagggca atccaattgt acttatatgt taagtctgtc aacaaagtca 1020 cacaaagaga catctttgca aaagttagac agcttatatc cacagctgag ctggaactgt 1080 atgaccctga tgagcttact catgttgtca attacttttc atatgtttca caattgtcat 1140 ctataaatga ttatgacaac atgctaaaat ccagtttctt caagaaattg gttgcaccca 1200 tgcaacacga ctggaggtgc atgattgaat tcttccgggg aaagagtgat ttcaatcaac 1260 ttctcaccgc tcttcaatgg aaagattttt cctatactat caaaactgaa gagctaataa 1320 ttactacaca cactgccatt gggcaagcta taagtggagc agctaatact tataaggaaa 1380 gaaggcaatt aacacaactg gtcaagcaag gagtgatttc gctcgctgat tttcaatctg 1440 aagagcccaa aatagaatac accgaattcg agcgagaaac aaaaccacca gttgactgtg 1500 tgactaatta caacaatgct gttaagaacc ttggcctgtc ggaaccagtg gatctaccag 1560 aatgctcata cgctagaaaa tctgttccta gcaatgagat atctatggct atgactgatg 1620 ctgacaactt cgctgttata aatgaaattg aatctctctt gtctgaagaa atagcagcac 1680 caacacttcc agcattgaaa aataaaacat gggctagtta tgcatctgac acttcatcaa 1740 agaaaaatga agaaattgaa aatataattg ctgagctaga agcttcacgt aaggtctcca 1800 atgtccagca aacacagcat aactaccata tctcacaatg ccccacttcc ttaactgctg 1860 atcttccatg gaaagcctgg ctcccacttc tcaatgccca tggtttcaaa ggagatcaga 1920 tccaacatag tcccgacggc caaataatcc aaccaattca ggacatcaac aataaaacac 1980 caagatctga atacccatct agcatccctg cagatcttgt ttcaaccttg cgcaatatta 2040 aaagagcagt ttatgctatt cctatcagcc acagaagggc cagcgcttat agctcagatg 2100 ttaaaaataa cagaactgga aaactgctct gtgcgcaatc caaagaatgg aaagagagtt 2160 ttgctttcaa aatgcaacat gaagacatag tcaaatctgg tgttgtcata catggttgtg 2220 gcggctccgg aaaatcacaa gcattgcaaa acttccttag aactttgggt gacaataatg 2280 actgctgcac agttgttgtt cccacagtag agctcaggaa tgactgggtt aacaaattgt 2340 gcaagttgcc tatggaacac atcaaaacat ttgaaaaagc aatgattcaa ccaggctttc 2400 ctgttgtcat ttttgacgac tatactaagc tgccacccgg ttacattgaa gcttatctgt 2460 tccaccacgc caacactgaa ctcttcatcc tcactggtga ctctagacaa agtgtgtatc 2520 atgagtctaa caatgaagct tacattgcct ctcttgatga agctgttgcc tactattcca 2580 actactgcgg tttctatttg aacgctacgc acagaaatgt acgtagttta gctaacaagt 2640 tgggagtgta cagtgaaaca gaaggacacc tcaaaattac ttttgcatcc aatgctctac 2700 aaaaatgcaa agtacccatc ttggtgccct ctcagatgaa gaaaaatgca atgcaagaca 2760 ttggccataa agcaatgact tatgcaggat gtcaaggact tactgctcca agagttcaaa 2820 ttttgcttga caaccacaca cagcattgct cggacagagt tctttacaca tgtctttcac 2880 gagctgtgga ttctatccat tttatcaata ctggccccaa caattctgaa ttttgggata 2940 agcttgaagc tacaccatac ctcaaagcct ttattgatac ataccgggat gaaaagactg 3000 agatgttgaa ttcaaaacct gcagatgaca gccctgtgga acctgaagct cctgctactc 3060 atttccccgt ctctaacggc aacaacttag agaaattagc ttcaacacta cctgaaaagt 3120 ttgctcggga gatctatgat aaacatcatg gttattccaa caccatacaa acagagaacc 3180 ccatagtaca acttttccaa catcaacagg caaaagatga aactctcttt tgggcaacaa 3240 ttgaggcaag actttctata accacaccag aagctaacct cagagaattt actttgaaga 3300 aagacgttgg agatattctg ttctttaact atcactcagc aatgtgtctg ccagctgacc 3360 ctgtcgactt cgagccaaga acttgggaaa tatgtgcagc tgaagtcaag aatacatacc 3420 tagcaaaacc aatggctaat ttgataaatg ccgctagtcg acaatctcct gacttcgagc 3480 ctaacaagat ctcactgttt ttgaagtcac aatgggttaa gaaagtagag aaattgggag 3540 caatcaaatc aaagcctggg cagacaattg cggcttttat gcagcaaacc gttatgctgt 3600 acggaactat ggctaggtac ttaagaaaaa tgagacaaag atttcaacca aaacacattt 3660 tcatcaattg tgaaactaca actgatgatc tgaataattt tgttctcaat ggttggaact 3720 ttaatcgaac tgctcagact aatgatttca ctgcatttga tcaatcccaa gatggagcta 3780 tgttacaatt tgaagtcatg aaggctaaat tcttcaacat tcctgcagac gtgattgaag 3840 ggtatatcaa cattaagctt aacgctaaaa ttttcctagg taccctttca attatgaggt 3900 tatcaggtga aggtcccaca tttgatgcaa acactgaatg ctctattgct tacacagcaa 3960 caagatacca tctgagttca gcagtgaaac aagtttacgc tggtgatgac atggctcttg 4020 acggagtggt catggaaaaa ccctccttta agaaattaca gagcaatctt aaattgacat 4080 caaaaacatt gtttccaaaa caagttaagg gtgattatgc tgaattttgc gggtggactt 4140 ttaccccagg tgggattatc aaaaatcctt tgaaaatgca tgcatccatc atgttacaag 4200 aagcaatagg taacctccac actgctgcta ggtcatatgc aatagacatg aagcattcat 4260 accaaatggg agataaattg catgaatacc ttactcctga tgaagctgag caacatttct 4320 tggctgttcg caaattgcac aaactccacc aaggtgaagc catgagactt ggggagaaga 4380 gccccccaaa agcaacacat tgacgggtta agtttcccct gttcgaaatg gaaagatcca 4440 ctctaataaa tttacttcaa ctgcaccact ttgaacctaa actcagcgtt gaaggagtca 4500 ttgttgtaca cggaattgct ggaacaggga aaaccaccct acttagaact ttattttccg 4560 cttacccgaa cctagttata ggatcaccta ggccttgtta cttagataaa gctaataaaa 4620 tttcacaagt ttgtttatct tgctttccaa acaccctttg tgatattgtc gatgagtacc 4680 atcttctaga aagttaccaa gaacctactt tggctttgtt tggagaccct tgtcagtgta 4740 ctttcattgg aagacttaga attccacact acacttcctt cagaacacat agatttggca 4800 agtctactgc agagctttta aacaagttgt ttcaacttca aattgtctct gtaaaacaag 4860 aagacgacat agttgaattc tttgacccat ttcaagtaga cccaactgaa aatatttcag 4920 catctgagga agaagttttg gaatttgtct ctgatcaagt agtgacaacc agctctgaag 4980 aattagcagg attggagttc actgaaacca ctttctactg cactacacta gctgcagcag 5040 tcactgaaaa tcctgccaga actttcatct ccttaaccag acacactcag agactcacca 5100 ttggcgaact aaatgccagg attgactcct agagctgacc tcactgacac ctacaagata 5160 attgctattg cctttttgtt gtcagcttgc atttacttcc aaaatagcca ttaccaacct 5220 gttgctggag ataatctgca tagattgcca tttggtggcc agtatcaaga cggcaccaag 5280 aagatatcat attttcctca gcaacaatca tactttcact ctggtaacaa attaaatgtc 5340 ctcatactca tcttcattct tacattgggt atcgtcctca ccaataaatt tagttttagc 5400 gttagccgta ctactcacca gcattcttgc tacaatacac attctgcagc caacacaaca 5460 ccaccattgt caggtcatca ttgacggagc tgccatagtt gttactaatt gtgaaaacac 5520 gcctgaagtt ctaaaagcaa tcaacttcgc cccttggaac gggttaagtt ttcctagtgt 5580 ttgaaaatta actttgagca tttcacaatt aagctaacaa ttcactaatc atggctgaca 5640 ataccccagt tgctgctact tctggttccc ctccaactgc tcaagatgct ggtgccaaag 5700 cccctgctga cttttcaaat cctaatacag ctcctagcct cagtgatttg aagaaagtca 5760 agtatgtgtc cacagtcact tcagtggcaa caccaactga aatagaagcc ctaggaaaga 5820 tcttcaccgc catgggactg gctgctaatg aaactggacc cgctatgtgg gatctagcgc 5880 gtgcttatgc tgatgtccaa agttcaaaat ccgcacaact cataggtgcc accccctcaa 5940 atccagcact ctcacgccgc gcacttgctg cccaatttga tcgtattaac atcacaccca 6000 ggcagttttg catgtatttt gctaaagttg tctggaacat tctgctagac agcaatatcc 6060 caccagcaaa ctgggccaag cttggttacc aagaagacac aaaatttgct gctttcgatt 6120 tcttcgatgg agtcaccaat ccagcaagtt tgcaaccagc tgacggcctc atccggcaac 6180 ccaatgaaaa ggagcttgct gctcactcag ttgctaagta tggcgcacta gccaggcaga 6240 aaatttccac tggcaactac ataaccacac ttggagaggt cacacgtgga cacatgggtg 6300 gagctaacac catgtacgca attgatgcac ccccagaact ttaaaacact cgaaacttaa 6360 ttagagtggg gttttctata gtttattttc ccaataaatt gcttttgtaa ttt 6413 //