ID AY488137; SV 2; linear; genomic RNA; STD; VRL; 8066 BP. XX AC AY488137; XX DT 01-JUN-2004 (Rel. 80, Created) DT 24-SEP-2009 (Rel. 102, Last updated, Version 6) XX DE Strawberry pallidosis-associated virus segment RNA 1, complete sequence. XX KW . XX OS Strawberry pallidosis-associated virus OC Viruses; Riboviria; Closteroviridae; Crinivirus. XX RN [1] RP 1-8066 RX DOI; 10.1007/s00705-004-0410-z. RX PUBMED; 15503221. RA Tzanetakis I.E., Reed J., Martin R.R.; RT "Nucleotide sequence, genome organization and phylogenetic analysis of RT Strawberry pallidosis associated virus, a new member of the genus RT Crinivirus"; RL Arch. Virol. 150(2):273-286(2005). XX RN [2] RP 1-8066 RA Tzanetakis I.E., Martin R.R.; RT ; RL Submitted (26-NOV-2003) to the INSDC. RL Molecular & Cellular Biology Program, Dept. of Botany and Plant Pathology, RL Oregon State University and USDA-ARS, 3420 Orchard Ave, Corvallis, OR RL 97330, USA XX RN [3] RC Sequence update by submitter RP 1-8066 RA Tzanetakis I.E.; RT ; RL Submitted (23-SEP-2009) to the INSDC. RL Dept. of Botany and Plant Pathology, Oregon State University and USDA-ARS, RL 3420 Orchard Ave, Corvallis, OR 97330, USA XX DR MD5; 69e560ddaa16eddafc8b40edc6e2e0fc. DR EuropePMC; PMC2786829; 19793810. XX CC On Sep 23, 2009 this sequence version replaced gi:45935310. XX FH Key Location/Qualifiers FH FT source 1..8066 FT /organism="Strawberry pallidosis-associated virus" FT /segment="RNA 1" FT /isolate="M1" FT /mol_type="genomic RNA" FT /country="USA:Maryland" FT /isolation_source="strawberry; Fragaria x ananassa" FT /db_xref="taxon:227507" FT CDS join(265..6101,6103..7621) FT /codon_start=1 FT /ribosomal_slippage FT /product="ORF 1a/1b fusion polyprotein" FT /note="contains ORF 1a motifs and viral polymerase" FT /db_xref="GOA:Q6JGW4" 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:Q6JGW4" FT /inference="non-experimental evidence, no additional FT details recorded" FT /protein_id="AAS79673.2" FT /translation="MSVRSKLVSPYTPSADIEFSSFLNRVIDYPIKSIDLNRLDFLRQY FT FNIPLCRFNKLPKPIVYMFGRDFQAISNFIDQKMSLKTGNSPNPGNEVVETIEGKTAFG FT DGYFVRVWEKPLVIDVFVSLGRYHSPDYDYKYRLNFRRHPNNKRIYTSVMCNICKADKV FT SKAFCENYNLFSVLNPTQFMTQCLLLSVMEKIQEFKTLVNYHVNSSFRQPLKSYQEKLA FT KYNEEYRKTKEGDTLIGVKSNVKGTETKKSLIPQPFLLKKRRAPFASVRHHVDVRGREY FT FTICYTDGSVKYVPNHRNVIVNMFNLTLGGGTYVIHEMCLTPDGSRYGMHKNGYCWLEA FT FCMANRFIPRHTVPFPELKYGYLLSCGLRDIMKGRIEDYGNGLGHFSRELTSSKREVYL FT TTHIGIKTDGEGDISLKNADVFFDDLFSGIVNNTNVKSENDVMSNIVRRVSNKLNETFN FT RKKELNISVCLSSNEKKELCEVFPEICMEFSDSSFSSHALFTAIRECENYSLSKRNNFC FT DFIDAGGNVVKYIRENVKDIHICAPVVDIKDSHRMMTRSNILDKTAGLSETITMCDKMC FT QVCDVQKQNIVAVEVYDMTLSDMAKSILSHKAKRFDFSVIIPPEVYEENCDVSMFGGGL FT RVKGNNLTCSYYYGKSGECYTHDINNLRDILKIQIFSVDGVIFKKTLESSRRGLHFFSI FT VPCLGMKNDTYTLKTYYPKTESDKVLMLVPVKNKFGIVENVRVKTDRSIVYHLLEYVMN FT TAQRIDEKSYEYLMSQFRARKSINIKGGKVIQEPFDLPLDLYPGYLGVILGEGLRLREK FT TLQMAKLSYFKHYLPTILRIMIHFMYRTLAKTRQAMYHGAIHCMKWIMSEEFIEEVING FT DRRIFDIQETYEFSQVVTITGEEYNNYAINESFNVFVRESEKNLRAIDSELLPFDDSFE FT TTELDRFKDLLTGGGGGFSCFSKTAYKIYERIFRLFSWTTLTPKKVHDLTGVLTNLIFY FT MLRCGSYTFETMKKYCKMVFNSITGIGCGLSVSIKTFLKDVVSLMRRKIVERNDKLYDE FT FMDNFKSDDELELSSMDSQTTLDANICSEEEVSSESDEVEVLCHDSQLSTLSFRRPIRC FT FISWRSLKSYLDSIFRYPYELIENIRFAIKSYAYKIYRLYLNSIEVAEIIKETFNELKD FT AFFGWLTSEGGLEFIIDGVSLSIVNTIFYGLMGRFSLMSNLAVLLVYSSLKLSGIGKKY FT LGHESIVVQLADFLNVGCFLNVQHPFGFLIMPVRHLAMKCISNKLKKKAATKESLKTSA FT TSLIAKDFVSLKFYDKFSYKALRQAICILLIFIVIFPKLVLVSILSLLLIGEHKKYLNS FT TVLQANLQLSFASVFKKTSKSNRMIVFKKLIAEKFSRKKTLEEDEEIQQSLDIAGKIRD FT GDCVDDDIEVDFDYDGSYVERKGKMTEGLLARIPEVSKKDIPWGDRSEHSMNSAEYENL FT NFSSLTPTTDRHYIKCEVNLKLSNAILLYPNSGNCVPTVTGNMEVDAISEFYYLESRRM FT NIELGKLDNAIRVFASKYHTVKKFQDIVWDMRNNLDDSTLYMSNNGNSWYRLKQSDGKS FT MTLEGACKMTVDSDLVSFTKNVSGYQFTSDELLGMFTNNRCMGLESFKDDKGDFHVNRI FT MNDVVIHNKPPGAGKTTTIVKNILDDLKNRETCLAFTCTSAGKKEIVDKLKKFNVPNAY FT QYVTTYDSYLMKNKKNKIQKVYCDEVFMVHAGEWIACMNLIENDYVRCYGDKNQIPFIN FT RVPNTTCHLSFDLYLKFQMIHDNVSYRCPVDVCYLLSNLTDPIGNKLYPNGVYPAGDNS FT KILRSVDVVGINCAEDLKPDEKKKYITFTQYEKEEVSKITGKKMKVSGTANTVNEVQGG FT TFPKVELIRLKQFDNPIYTNMNQFIVSISRHTEKLDYKVVSSKLNDFVGEKISALNTIA FT DYVIKEHNFKQCVDVYEMVVEDLCLPATFSRPPSSHHRSINEFMCFINPGLSAYNYIHR FT TLIFEYEQYELPVVGEVDLVLSRSKPYNPGLYVIPDLLGKGERSRPDTWRQVLLSLSHR FT NFSAPRVNENCDTLASAEILAQSLMKAFDFLKLSENFDTVLPDIWSITKWIEDREPNKV FT RKLKRSFGHDLMNSQFSRMKLMIKGEMKPKMDMSSYGTYGPSSNIIYYEQIVNMFYSPM FT FLRIFDRIGYCLNSKVVLYSGMNLETLGKLIRSKLDFPIQEYRTTEIDFSKFDKSQGVI FT FKLYEEIIYKFFKFDSKTYEAIKFSEYFCRAKSSCGISVELGAQRRTGSPNTWLSNTLV FT TLAMILTHYDLDDIDLLLVSGDDSLIFSRKDLGNKANEINRDFGMEAKFIMNSVPYFCS FT KFIIEDRGEIKVVPDPVRFFEKLSVPISLQDFQVGDLLRERFVSFKDLMIGYDSDAVII FT LVDNLISIRYDIPRMTSYAALCYIHCLTSNVLAYTKLFIEGFTVAI" FT mat_peptide join(265..6101,6103) FT /product="ORF 1a" FT /note="methyltransferase, helicase and polymerase" FT misc_feature 3847..3915 FT /note="transmembrane region" FT misc_feature 4195..4263 FT /note="transmembrane region" FT mat_peptide 6104..7618 FT /product="ORF 1b" FT /note="RdRp" FT CDS 7630..7869 FT /codon_start=1 FT /product="ORF 2 precursor" FT /note="p9; contains two transmembrane domain-helices" FT /db_xref="GOA:Q6JGW3" FT /db_xref="UniProtKB/TrEMBL:Q6JGW3" FT /protein_id="AAS79674.1" FT /translation="MLSTLLSIIFSILYISCVVHLELCFTKYLIYRSHNPCSELQCINM FT FYIIGKTNSILMLLDFTFIIISNLLASIYSKINP" FT sig_peptide 7630..7692 XX SQ Sequence 8066 BP; 2442 A; 1419 C; 1706 G; 2499 T; 0 other; gtaaaagtac acaagtttac cgttgactaa ttagcatttt gctatttagt ttatttgttt 60 gcttgctgcg cggcctcggc tgatcagtac tttttgtgcg acacttcggt gtatcacata 120 atatatatat cacgtttata tatattttct tcctttccat tctgcctcgt gcaacacaac 180 aaatcaaatc accctcgcca gttccctaaa ctgaaattaa tccagggtac ttggaatcag 240 acttggctta tctgattcta cataatgtct gtaagaagta agttggtttc cccttatacc 300 ccatctgccg atattgaatt ttcatctttc cttaataggg tgattgatta ccctattaag 360 agtattgatt taaatcggct tgatttcctc aggcagtatt ttaatattcc cttgtgccgt 420 tttaataaac ttcccaaacc aatcgtgtat atgtttggta gggactttca ggctatctcc 480 aactttatcg atcagaaaat gtccctaaag accggtaatt ccccgaatcc tggtaatgaa 540 gtcgtcgaga ccattgaggg aaagaccgct tttggagatg gatactttgt tagggtctgg 600 gagaagcccc ttgttattga tgtttttgta tctctcggtc gttatcatag tccagactat 660 gattataaat atcgactcaa cttcagaagg caccccaata acaagaggat atacacaagt 720 gttatgtgta atatatgtaa agctgataag gtttctaaag ccttttgtga gaattacaat 780 cttttctcag tcctgaatcc cactcaattc atgactcagt gtctcctcct atctgttatg 840 gagaagatac aagaatttaa aactttggtg aattatcatg tcaattcctc cttccgtcaa 900 ccactcaaga gctatcaaga gaaattagct aaatacaatg aagagtatag gaagacgaag 960 gagggtgaca cgctcattgg cgtgaaaagc aacgtgaagg gtactgagac caaaaagagt 1020 ttgattcccc aacccttcct gctcaagaag aggagagctc ccttcgcgtc agttcgtcat 1080 catgtagacg tccgagggcg cgaatatttc accatctgct acaccgatgg ttccgttaaa 1140 tacgttccaa atcataggaa tgttattgtg aatatgttca acctcacgtt aggtggcgga 1200 acttatgtta ttcatgagat gtgtctcact ccagatggtt cccgctatgg aatgcataag 1260 aatggatatt gctggttgga agccttttgc atggctaata ggtttattcc ccgtcacacc 1320 gttccctttc cagagttgaa atatggatat ttgctctcat gtggcttgag agacataatg 1380 aaggggagaa ttgaggacta tgggaacggt ttgggccact tttcgaggga gttgacttca 1440 tctaagcgtg aagtctatct caccacccat ataggcataa agactgacgg tgaaggtgac 1500 ataagcctta agaacgctga tgtgttcttt gatgatttgt tttctggcat tgttaataat 1560 actaacgtta aatcggaaaa cgacgtcatg tctaacatcg ttaggagggt gtccaacaag 1620 ttgaatgaga ctttcaatcg taagaaagag ctcaatatct ccgtatgtct ctctagtaac 1680 gagaagaagg agttgtgcga agtttttcct gagatatgca tggagttctc agactcatcc 1740 ttctcctctc atgcgctttt cactgccata agagaatgcg aaaattattc gttgtccaag 1800 aggaataatt tttgtgactt tattgacgct ggaggaaatg tagtgaaata catcagggag 1860 aatgtcaagg acattcacat ttgcgcacca gtagttgata tcaaagactc tcacaggatg 1920 atgacaagga gtaacatcct tgacaaaacc gcgggtcttt cagagacgat aacgatgtgc 1980 gacaaaatgt gccaagtttg cgatgtccaa aagcagaata tagtcgccgt ggaagtttac 2040 gatatgactc tttcagacat ggcgaagtct attctttctc ataaggcgaa acgtttcgat 2100 ttttccgtca taatacctcc agaagtttat gaagagaatt gtgatgtgtc aatgtttggc 2160 ggaggactgc gcgttaaggg caacaattta acatgctctt attattatgg caagagtggt 2220 gaatgttaca ctcatgacat caacaatctt cgtgacattt tgaagatcca aatcttttca 2280 gttgatggag tgatttttaa aaagactctc gaatcatcca ggaggggtct tcactttttc 2340 tctatcgttc cttgcttggg tatgaagaat gacacctata ctcttaagac gtactatccg 2400 aagactgaat ctgataaagt cttgatgttg gtgcctgtca agaataaatt tggtatcgtc 2460 gagaacgtcc gagtgaaaac ggataggtcc atcgtctacc atcttttgga atatgtgatg 2520 aacacagcgc agaggattga tgagaagtct tatgaatatc ttatgtctca attcagggcc 2580 cgaaagagca taaatattaa gggaggtaag gtaattcaag aaccctttga ccttccttta 2640 gatttatacc cgggttattt gggagtgatt ttgggagagg gtttgagatt gagagaaaag 2700 acattgcaga tggcaaagtt aagttatttc aaacattatc tccccacaat tttgagaata 2760 atgatacatt tcatgtacag aactctcgcc aagaccagac aggccatgta tcacggagcg 2820 atacattgca tgaagtggat tatgtctgag gagtttattg aggaagtcat aaatggcgac 2880 aggagaattt ttgacataca agagacctac gagttctctc aagttgtcac aattacgggt 2940 gaagaataca acaactatgc catcaatgaa tctttcaacg tctttgtgag agaatcagag 3000 aagaatctaa gagcgataga ttctgagttg ttgccgtttg atgattcttt tgagaccacg 3060 gagttggaca gattcaaaga tctactcaca ggaggtggcg ggggtttctc atgtttctca 3120 aaaacggcat ataaaattta tgagcgaatc ttccgtttgt tttcatggac aactctcaca 3180 ccaaagaagg tccatgattt aacaggagtg ttgaccaatc tgatcttcta catgttgcgt 3240 tgcggtagtt atacctttga gactatgaag aagtattgta agatggtctt caactctatc 3300 actggcattg gatgtggtct ctccgtcagt attaagacct tccttaaaga tgtggtatcc 3360 ttaatgagaa ggaagatcgt tgagaggaat gacaagttgt atgatgaatt catggacaat 3420 tttaaaagtg atgatgagct tgaattgtcg tctatggatt cccaaactac tctggacgcc 3480 aatatttgtt cagaagagga agtatcttcc gagtctgacg aagtcgaggt tttgtgtcac 3540 gactctcaac tgtcgacctt atctttcaga aggcccatca ggtgttttat aagctggaga 3600 agtctgaaaa gttacttgga ttctattttt aggtatcctt atgaattaat tgagaatatc 3660 agatttgcca tcaaaagtta tgcatacaag atatacagat tgtatcttaa ttctattgaa 3720 gttgccgaga taatcaaaga aactttcaat gaattaaaag atgctttctt tggatggttg 3780 acatcagaag gaggtcttga atttatcata gacggcgttt cgttgtcaat tgtcaatacg 3840 atcttctatg gtcttatggg tagatttagc cttatgagca atttggcggt tcttctcgta 3900 tactctagtt tgaaattgtc tggtataggg aagaaatatt tgggtcatga atccattgtt 3960 gtccaattgg ctgacttcct gaacgttggc tgcttcctga acgtacaaca tcctttcggc 4020 tttcttataa tgccagttag acatttggct atgaagtgta tttcaaacaa gttgaaaaag 4080 aaagccgcca ccaaggaatc gctgaaaact tcagctacca gcttaattgc taaggatttt 4140 gttagcttaa aattctatga caagttttca tataaggctt tgagacaagc aatctgtatt 4200 ttgctgatat tcattgtcat atttccaaaa ttggttcttg tctcaatttt atctttgctg 4260 cttattggtg aacacaaaaa gtatttgaat tccaccgttt tgcaagccaa cttgcagctg 4320 agttttgctt cagtctttaa gaaaacttcg aagagcaaca gaatgatcgt tttcaagaaa 4380 ttgatcgctg aaaagttttc acggaagaag actttagaag aagatgagga aatccaacag 4440 agtctggaca ttgccggaaa aattagggac ggagactgcg tggatgatga cattgaggtg 4500 gattttgact atgatggatc atacgtggag aggaagggta aaatgacaga ggggttgctt 4560 gctagaattc ccgaagttag caagaaagac attccttggg gagacaggag tgaacattct 4620 atgaactctg cggagtatga gaacttaaac ttctcaagcc tcaccccaac cacagatcgg 4680 cattacatca aatgtgaagt aaacctgaaa ttgagcaatg ccattttgct ttatcccaat 4740 tcaggcaact gcgttccaac tgtgactggg aatatggaag tcgatgccat ttccgagttt 4800 tattatttag agagcagaag aatgaatatt gaactgggaa agctggataa tgccatcagg 4860 gtcttcgcgt ccaaatacca cacagtgaag aaattccagg atatcgtttg ggatatgagg 4920 aacaaccttg atgactcaac attgtacatg tccaacaacg gtaattcttg gtaccgattg 4980 aaacaatctg atgggaaatc catgacgctt gaaggcgctt gtaaaatgac agttgattcg 5040 gatttggtca gctttaccaa gaatgtttcc ggttatcaat tcactagtga tgagcttttg 5100 ggtatgttta ccaataaccg gtgcatgggt cttgaaagtt ttaaggatga taaaggagac 5160 ttccatgtta acagaataat gaatgatgtt gtcattcata acaagccacc cggtgctgga 5220 aaaacaacaa caattgtgaa gaacatcctg gatgatttaa agaaccggga aacgtgcctc 5280 gcttttacct gcacctctgc cggaaagaag gagatagtgg ataagctgaa aaaatttaac 5340 gttcctaatg cgtatcagta tgtcaccact tatgactcat acctgatgaa gaataagaag 5400 aataagattc agaaggtata ctgtgatgag gtgttcatgg tacacgctgg agagtggata 5460 gcttgcatga atctgattga gaatgattat gtgaggtgtt acggtgacaa gaatcaaatt 5520 ccttttataa atcgagtacc aaacaccacc tgtcatttat cgtttgacct ttacttgaag 5580 tttcaaatga tccatgacaa tgtatcatac aggtgtcccg tggatgtatg ctatttacta 5640 tctaatctca cggaccctat tggtaacaag ttatatccca atggtgttta tcccgctgga 5700 gacaattcga aaatcttgag aagcgttgat gttgtgggta tcaactgcgc ggaagatttg 5760 aaaccagatg agaagaagaa gtacataacc tttacccagt atgaaaagga agaggtgtca 5820 aaaataactg gcaagaaaat gaaggtatct ggtaccgcca acactgtcaa tgaagtccaa 5880 ggaggtactt tcccaaaggt agagttaatc agattgaaac aatttgataa tccaatttac 5940 actaacatga atcaattcat cgttagcata tccagacaca ctgaaaaatt ggattacaag 6000 gttgtttcaa gcaaattgaa tgactttgtg ggtgagaaga tatcagcatt gaacacaatt 6060 gctgattacg ttattaagga acacaacttc aagcagtgcg tttgacgtat atgaaatggt 6120 ggtcgaagat ctttgtctac ctgcgacctt tagtagacca ccatcctccc atcatagatc 6180 cataaatgag tttatgtgtt tcatcaatcc aggattgagt gcttacaact atattcacag 6240 gaccctcatc tttgagtatg agcagtatga actcccagtt gttggtgaag ttgatttagt 6300 gttgagtcga tctaagccct acaatccagg attatacgtt atcccagatt tattgggaaa 6360 aggggaaagg tcacgacccg acacatggag acaagtgctt ttgtcgttgt ctcatagaaa 6420 cttttcggct ccgagggtga atgagaattg cgatacatta gcctccgccg aaattcttgc 6480 ccaaagtctc atgaaagctt ttgactttct aaagttatcg gagaattttg atactgttct 6540 tcccgatatt tggagtatta ccaagtggat tgaagacagg gaacccaata aggtgaggaa 6600 gttgaagaga agtttcgggc atgacttgat gaattctcaa ttctctcgta tgaaacttat 6660 gatcaaaggg gagatgaaac cgaaaatgga catgtcaagt tatgggacat atggaccatc 6720 ctcaaacatc atttattacg aacagattgt aaatatgttt tattcgccca tgtttttgag 6780 aatttttgat cgaattggtt attgcttgaa ttcaaaggta gttttgtatt ctggtatgaa 6840 tttggaaact ctaggcaaat tgataagatc taaattggac tttccaattc aagagtacag 6900 gactaccgaa attgatttta gcaaatttga taaatctcaa ggtgtcatat ttaaactcta 6960 tgaagaaatt atttataaat tcttcaaatt tgattcaaaa acctatgagg cgataaaatt 7020 ttctgaatat ttttgtcgag cgaagagcag ttgtgggatt tctgtggagc tgggagctca 7080 gagaagaact ggatctccaa acacgtggtt atcaaacact ctcgtcacct tggccatgat 7140 acttacacac tatgatctag atgatataga tctattactc gtaagtggag atgacagtct 7200 cattttctca aggaaagatc tcgggaacaa agcaaatgaa attaacagag actttgggat 7260 ggaggccaag tttataatga attctgttcc ctacttttgt tccaaattca tcattgaaga 7320 tagaggggaa attaaggtag tccctgaccc ggtcagattt tttgaaaaat tgtctgtacc 7380 gatttctttg caagacttcc aagtcgggga tttacttaga gagcgattcg tatcctttaa 7440 agatcttatg ataggttatg atagcgacgc tgtgatcata ttggttgata atttgatatc 7500 gattcgctat gacataccta gaatgacgtc ttatgccgca ctgtgttata ttcattgttt 7560 gacttcaaac gtgttagcgt acacgaaact ttttattgaa ggtttcacag ttgcaattta 7620 ggttcagaaa tgttgtcaac attactttct attatttttt ctatcttgta catatcttgc 7680 gttgtacatc tagaactttg cttcactaaa tatttaattt atagatcaca taacccttgc 7740 tcagagttac agtgcattaa tatgttttat attataggaa aaaccaattc aattttaatg 7800 ttgctagatt ttacttttat aataataagt aatttgcttg catctattta tagtaaaata 7860 aatccataaa atattattaa gcccttttct gtattatgtt tttgggctta gagtcatata 7920 cgtgcttttc agtgtagtgt gtattataaa atctcgaaaa atacaaaaaa ttttattgtt 7980 aattatgtaa ttacaatatt atcggcgctc aaaagagaag gttgtacctt ccgccatgag 8040 cgtctagtat ttaataaaat aaggcg 8066 //