Dbfetch
ID JQ314460; SV 1; linear; genomic RNA; STD; VRL; 6414 BP. XX AC JQ314460; XX DT 26-APR-2012 (Rel. 112, Created) DT 30-MAY-2012 (Rel. 112, Last updated, Version 2) XX DE Pepino mosaic virus strain US1_EF09_58, complete genome. XX KW . XX OS Pepino mosaic virus OC Viruses; Riboviria; Tymovirales; Alphaflexiviridae; Potexvirus. XX RN [1] RC Publication Status: Online-Only RP 1-6414 RX PUBMED; 22623984. RA Li R., Gao S., Hernandez A.G., Wechter W.P., Fei Z., Ling K.S.; RT "Deep Sequencing of Small RNAs in Tomato for Virus and Viroid RT Identification and Strain Differentiation"; RL PLoS One 7(5):E37127-E37127(2012). XX RN [2] RP 1-6414 RA Li R., Gao S., Hernandez A.G., Wechter W.P., Fei Z., Ling K.-S.; RT ; RL Submitted (22-DEC-2011) to the INSDC. RL Virology Laboratory, USDA-ARS, U.S. Vegetable Laboratory, 2700 Savannah RL Highway, Charleston, SC 29414, USA XX DR MD5; 5f1739b894e30c23f906c5e6df6f9f4c. DR EuropePMC; PMC3356388; 22623984. DR EuropePMC; PMC5485527; 28621718. XX FH Key Location/Qualifiers FH FT source 1..6414 FT /organism="Pepino mosaic virus" FT /host="Solanum lycopersicum (tomato)" FT /strain="US1_EF09_58" FT /mol_type="genomic RNA" FT /country="USA" FT /collection_date="18-Nov-2009" FT /note="genotype: US1" FT /db_xref="taxon:112229" FT 5'UTR 1..84 FT gene 85..4404 FT /gene="rep" FT CDS 85..4404 FT /codon_start=1 FT /gene="rep" FT /product="replicase" FT /note="RNA replication" FT /db_xref="GOA:I1V2B9" 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:I1V2B9" FT /protein_id="AFI25329.1" FT /translation="MSRVRNTLEKIRDPQVQSSICEAAYQHVRPVLKESLINCPYALND FT YEADTLENLGVTINPHAIQTHTHAAAKVVENRMLEIVGHHLPKDEKVTFIFLKRSKLRY FT MRRAAVHKDVFVNHNIEPKDFFRYDEESTSTSFSVNTRIAYISDSLHFMEPADVTHLFD FT RCQNLKTLMATVVLPVEAIHRQTSLFPAIYSINYNEEGFEYIPGSHGGGAYFHKYETLD FT WLKYSRFIGHDPLTGLKYTITIQMVESLGANHLFLFQRGNFETPLYRTFQKNSFVTFPN FT IFHPRHVNATKPMPRSRAIQLYLYVKSVNKVTQRDIFAKVRQLISTAELELYDPDELTH FT VVNYFSYVSQLSSINDYDNMLKSSFFKKLVAPMQHDWRCMIEFFRGKSDFNQLLTALQW FT KDFSYTIKTEELIITTHTAIGQAISGAANTYKERRQLTQLVKQGVISLADFQSEEPKIE FT YTEFERETKPPVDCVTNYNNAVKNLGLSEPVDLPECSYSRNSVPNNEISMAMTDADNFA FT VINEIESLLSEEIAAPTLPALKNKTWASYASDTSSKKNEEIENIIAELEASRKVSNVQQ FT TQHNYHISQCPTSLTADLPWKAWLPLLNAHGFKGDQIQHSPDGQIIQPIQDINNKTPRS FT EYPSSIPADLVSTLRNIKRAVYAIPISHRRASAYSSDVKNNRTGKLLCAQSKEWKESFA FT FKMQHEDIVKSGVVIHGCGGSGKSQALQNFLRTLGDNNDCCTVVVPTVELRNDWVNKLC FT KLPMEHIKTFEKAMIQPGFPVVIFDDYTKLPPGYIEAYLFHHANTELFILTGDSRQSVY FT HESNNEAYIASLDEAVAYYSNYCGFYLNATHRNVRSLANKLGVYSEKEGHLKITFASNA FT LQKCKVPILVPSQMKKNAMQDIGHKAMTYAGCQGLTAPRVQILLDNHTQHCSDRVLYTC FT LSRAVDSIHFINTGPNNSEFWDKLEATPYLKAFIDTYRDEKTEMLNSKPADDSPVEPEA FT PATHFPVSNGNNLEKLASTLPEKFAREIYDKHHGYSNTIQTENPIVQLFQHQQAKDETL FT FWATIEARLSITTPDANLREFTLKKDVGDILFFNYHSAMCLPADPVDFEPRTWEICAAE FT VKNTYLAKPMANLINAASRQSPDFEPNKISLFLKSQWVKKVEKLGAIKSKPGQTIAAFM FT QQTVMLYGTMARYLRKMRQRFQPKHIFINCETTTDDLNNFVLNGWNFNRTAQTNDFTAF FT DQSQDGAMLQFEVMKAKFFNIPADVIEGYINIKLNAKIFLGTLSIMRLSGEGPTFDANT FT ECSIAYTATRYHLSSAVKQVYAGDDMALDGVVMEKPSFKKLQSKLKLTSKTLFPKQVKG FT DYAEFCGWTFTPGGIIKNPLKMHASIMLQEAIGNLHTAARSYAIDMKHSYQMGDKLHEY FT LTPDEAEQHFLAVRKLHKLHQGEAMRLGEKSPPKATH" FT gene 4429..5133 FT /gene="tgbp1" FT CDS 4429..5133 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="AFI25330.1" FT /translation="MERSTLINLLQLHHFEPKLSVEGVIVVHGIAGTGKTTLLRTLFSA FT YPNLVIGSPRPCYLDKANKISQVCLSCFPNTLCDIVDEYHLLESYQEPTLALFGDPCQC FT TFIGRLRIPHYTSFRTHRFGKSTAELLNKLFQLQIVSVKQEDDIVEFFDPFQVDPTENI FT SASEEEVLEFVSDQVVTTSSEELAGLEFTETTFYCTTLAAAVTENPARTFISLTRHTQR FT LTIGELNARIDS" FT gene 5114..5485 FT /gene="tgbp2" FT CDS 5114..5485 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="AFI25331.1" FT /translation="MPGLTPRADLTDTYKIIAIAFLLSACIYFQNSHYQPVAGDNLHRL FT PFGGQYQDGTKKISYFPQQQSYFHSGNKLNVLILIFILTLGIVLTNKFSFSVSRTTHQH FT SCYNTHSAANTTPPLSGHH" FT gene 5337..5585 FT /gene="tgbp3" FT CDS 5337..5585 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="AFI25332.1" FT /translation="MSSYSSSFLHWVSSSPINLVLALAVLLTSILATIHILQPTQHHHC FT QVIIDGAAIVVTNCENTPEVLKAINFAPWNGLSFPSV" FT CDS 5632..6345 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="AFI25333.1" FT /translation="MADNTPVAATSGSPPTAQDAGAKAPADFSNPNTAPSLSDLKKVKY FT VSTVTSVATPTEIEALGKIFTAMGLAANETGPAMWDLARAYADVQSSKSAQLIGATPSN FT PALSRRALAAQFDRINITPRQFCMYFAKVVWNILLDSNIPPANWAKLGYQEDTKFAAFD FT FFDGVTNPASLQPADGLIRQPNEKELAAHSVAKYGALARQKISTGNYITTLGEVTRGHM FT GGANTMYAIDAPPEL" FT 3'UTR 6346..6414 XX SQ Sequence 6414 BP; 2047 A; 1472 C; 1151 G; 1744 T; 0 other; gaaaacaaaa cataaccaaa acaacaaagt cataataaca ctacataacc acgcggaaaa 60 acagctaacg cactttaccg cattatgtct cgtgttagaa atactttgga aaagatcaga 120 gaccctcaag tacagtcaag catatgcgaa gcagcatacc aacatgttcg accagttttg 180 aaggaatctc taatcaattg tccctatgcg ctcaatgatt atgaagccga cacccttgag 240 aatttaggtg tcacaattaa ccctcatgca attcaaaccc atacacacgc agcagctaaa 300 gtggttgaaa acagaatgct agagattgtt ggtcaccatc taccaaaaga tgagaaggtt 360 accttcattt tcctaaaacg tagtaaattg cgttacatga gaagagctgc tgttcataaa 420 gatgtttttg tcaaccataa catagagccc aaagattttt ttaggtatga cgaggagtcc 480 acatcaacaa gcttctccgt gaatactaga atcgcataca tttcagattc cttacatttc 540 atggagccag ctgatgttac acaccttttt gaccgttgcc aaaatcttaa aacattaatg 600 gcaaccgttg tcctacctgt tgaagcaatt catagacaaa catctttatt tcctgcgata 660 tactccatta actacaatga agaaggcttt gagtatatcc ctggttccca tggtggtggt 720 gcatactttc acaagtatga gaccttagac tggcttaaat attccagatt cataggacat 780 gatccattga ctggcctcaa atataccatt acaattcaaa tggttgaaag tctaggcgcc 840 aaccaccttt tccttttcca aagaggaaat tttgaaacgc ccttatatag gacctttcaa 900 aaaaatagtt ttgtgacatt ccctaatata tttcatcccc gacatgttaa tgccacaaaa 960 cctatgccac gctccagggc aatccaattg tacttatatg ttaagtctgt caacaaagtc 1020 acacaaagag acatctttgc aaaagttaga cagcttatat ccacagctga gctggaactg 1080 tatgaccctg atgagcttac tcatgttgtc aattactttt catatgtttc acaattgtca 1140 tctataaatg attatgacaa catgctaaaa tccagtttct tcaagaaatt ggttgcaccc 1200 atgcaacacg actggaggtg catgattgaa ttcttccggg gaaagagtga tttcaatcaa 1260 cttctcaccg ctcttcaatg gaaagatttt tcctatacta tcaaaactga agagctaata 1320 attactacac acactgccat tgggcaagct ataagtggag cagctaatac ttataaggaa 1380 agaaggcaat taacacaact ggtcaagcaa ggagtgattt cactcgctga ttttcaatct 1440 gaagagccca aaatagaata caccgaattc gagcgagaaa caaaaccacc agttgattgt 1500 gtgactaatt acaacaatgc tgttaagaac cttggcctgt ctgaaccagt ggatctgcca 1560 gaatgctcat actctagaaa ctctgttcct aacaatgaga tatctatggc tatgactgat 1620 gctgacaact tcgctgttat aaatgaaatt gaatctctct tgtctgaaga aatcgcagca 1680 ccaacacttc cagcattgaa aaataaaaca tgggctagtt atgcatctga cacttcatca 1740 aagaagaatg aagaaattga aaatataatt gctgagctag aagcttcacg taaggtctcc 1800 aatgtccagc aaacacagca caactaccat atctcacaat gccccacttc cttaactgct 1860 gatcttccat ggaaagcctg gctcccactt ctcaatgccc atggtttcaa aggagatcag 1920 atccaacata gtcccgacgg ccaaataatc caaccaattc aggacatcaa caataaaaca 1980 ccaagatctg aatacccatc tagcatccct gcagatcttg tttcaacctt gcgcaatatt 2040 aaaagagcag tttatgctat tcctatcagc cacagaaggg ccagcgctta tagctcagat 2100 gttaaaaata acagaactgg aaaactgctc tgtgctcaat ccaaagaatg gaaagagagt 2160 tttgctttca aaatgcaaca tgaagacata gtcaaatctg gtgttgtcat acatggttgt 2220 ggcggctccg gaaaatcaca agcattgcaa aacttcctta gaactttggg tgacaataat 2280 gactgctgta cagttgttgt ccccacagta gagctcagga atgactgggt taacaaattg 2340 tgcaagttgc ctatggaaca catcaaaaca tttgaaaaag caatgattca accaggcttt 2400 cctgttgtta tttttgacga ctatactaag ctgccacccg gttacattga agcttatctg 2460 ttccatcacg ccaacactga actcttcatc ctcactggtg actctagaca aagtgtatat 2520 catgagtcca acaacgaagc ttacattgcc tctcttgatg aagctgttgc ctactactcc 2580 aactactgtg gtttctattt gaacgctacg cacagaaatg tacgtagttt agctaacaag 2640 ttgggagtgt acagtgaaaa agaaggacac ctcaaaatta cttttgcatc caatgctcta 2700 caaaaatgca aagtacctat cttggtgccc tctcagatga agaaaaatgc aatgcaagac 2760 attggccata aagcaatgac ttatgcagga tgtcaaggac ttactgctcc aagagttcaa 2820 attttgcttg acaaccacac acagcattgc tcggacagag ttctttacac atgtctttca 2880 cgagctgtgg attctatcca ttttatcaat actggcccca acaattctga attttgggat 2940 aagcttgaag ctacaccata cctcaaagcc tttattgata cataccggga tgaaaagact 3000 gagatgttga attcaaaacc tgcagatgac agccctgtgg aacctgaagc tcctgctact 3060 catttccccg tttctaacgg caacaactta gagaaattag cttccacact acctgaaaag 3120 tttgctcggg agatctatga taagcatcat ggttattcca acaccataca aacagagaac 3180 cccatagtac aacttttcca acatcaacag gcaaaagatg aaactctctt ttgggcaaca 3240 attgaggcaa gactttctat aaccacacca gacgctaacc tcagagaatt tactttgaag 3300 aaagacgttg gagatattct gttctttaac tatcactcag caatgtgtct gccagctgac 3360 cctgtcgact tcgagccaag aacttgggaa atatgtgcag ctgaagtcaa gaatacatac 3420 ctagcaaaac caatggctaa tttgataaat gccgctagtc gacaatctcc tgacttcgag 3480 cctaacaaga tctcactgtt tttaaagtca caatgggtta agaaagtaga gaaattggga 3540 gcaatcaaat ccaagcctgg gcaaacaatt gcggctttta tgcagcaaac cgttatgctg 3600 tacggaacta tggctagata cttaagaaaa atgagacaaa gatttcaacc aaaacacatt 3660 tttatcaact gtgaaactac aaccgacgat ctgaataatt ttgttctcaa tggttggaac 3720 tttaatcgaa ctgctcagac taatgatttc actgcatttg atcaatccca agatggagct 3780 atgttacaat ttgaagtcat gaaagctaaa ttcttcaaca ttcctgcaga cgtgattgaa 3840 gggtatatca acattaagct taacgctaaa attttcctag gcaccctttc aattatgagg 3900 ttatcaggtg aaggtcccac atttgatgca aacactgaat gctctattgc ttacacagca 3960 acaagatacc atctgagttc agcagtgaaa caagtttacg ctggtgatga catggctctt 4020 gacggagtgg tcatggaaaa accctccttt aagaaattac agagcaagct taaattgaca 4080 tcaaaaacat tgtttccaaa acaagttaag ggtgattatg ccgaattttg tgggtggact 4140 tttaccccag gtgggattat taaaaatcct ttgaaaatgc atgcatccat catgttacaa 4200 gaagcaatag gtaacctcca cactgctgct aggtcatatg caatagacat gaagcattca 4260 taccaaatgg gagataaatt gcatgaatac cttactcctg atgaagctga gcaacatttc 4320 ttggctgttc gcaaattgca caaactccac caaggtgaag ccatgagact tggggagaag 4380 agccccccaa aagcaacaca ttgacgggtt aagtttcccc tgttcgaaat ggaaagatcc 4440 actctaataa atttacttca actgcaccac tttgaaccta aactcagcgt tgaaggagtt 4500 attgttgtac acggaatcgc tggaacaggg aaaactaccc tacttagaac tttattttcc 4560 gcttacccga acctagttat aggatcacct aggccttgtt acttagataa agctaataaa 4620 atttcacaag tttgtttatc ttgctttcca aacacccttt gtgatattgt cgatgagtac 4680 catcttctag aaagttacca agaacctact ttggctttgt ttggagaccc ttgtcagtgt 4740 actttcattg gaagacttag aattccacac tacacttcct tcagaacaca tagatttggc 4800 aagtctactg cagagctttt aaacaagttg tttcaacttc aaattgtctc tgtaaaacaa 4860 gaagacgaca tagttgaatt ctttgaccca tttcaagtag acccaactga aaatatttca 4920 gcatctgagg aagaagtttt ggaatttgtc tctgatcaag tagtgacaac cagctctgaa 4980 gaattagcag gattggagtt cactgaaacc actttctact gcactacact agctgcagca 5040 gtcactgaaa atcctgccag aactttcatc tccttaacca gacacactca gagactcacc 5100 attggcgaac taaatgccag gattgactcc tagagctgac ctcactgaca cctacaagat 5160 aattgctatt gcctttttgt tgtcagcttg catttacttc caaaacagcc attaccaacc 5220 tgttgctgga gataatctgc atagattgcc atttggcggc cagtatcaag acggcaccaa 5280 gaagatatca tattttcctc agcaacaatc atactttcac tctggtaaca aattaaatgt 5340 cctcatactc atcttcattc ttacattggg tatcgtcctc accaataaat ttagttttag 5400 cgttagccgt actactcacc agcattcttg ctacaataca cattctgcag ccaacacaac 5460 accaccattg tcaggtcatc attgacggag ctgccatagt tgttactaat tgtgaaaaca 5520 cgcctgaagt tctaaaagca atcaacttcg ccccttggaa cgggttaagt tttcctagtg 5580 tttgaaaatt aactttgagc acttcacaat taagctaaca attcactaat catggctgac 5640 aataccccag ttgctgctac ttctggttcc cctccaactg ctcaagatgc tggtgccaaa 5700 gcccctgctg acttttcaaa tcctaataca gctcctagcc tcagtgattt gaagaaagtc 5760 aagtatgtgt ccacagtcac ttcagtggca acaccaactg aaatagaagc cctcggaaag 5820 atcttcaccg ccatgggact ggctgctaat gaaactggac ccgctatgtg ggatctagcg 5880 cgtgcttatg ctgatgtcca aagttcaaaa tccgcacaac tcataggtgc caccccctca 5940 aatccagcac tctcacgccg cgcacttgct gcccaatttg atcgtattaa catcacaccc 6000 aggcagtttt gcatgtattt tgctaaagtt gtctggaaca ttctgctaga cagcaatatc 6060 ccaccagcaa actgggccaa gcttggttac caagaagaca caaaatttgc tgctttcgac 6120 ttcttcgatg gagtcaccaa tccagcaagt ttgcaaccag ctgacggcct catccggcaa 6180 cccaatgaaa aggagcttgc tgctcactca gttgctaagt atggtgcact agccaggcag 6240 aaaatttcca ctggcaacta cataaccaca cttggagagg tcacacgtgg acacatgggt 6300 ggagctaaca ccatgtacgc aattgatgca cccccagaac tttaaaacac tcgaaactta 6360 atcagagtgg ggttttctat agtttatttt cccaataaat tgcttttgta attt 6414 //