Sequence of DPV Strawberry pallidosis-associated virus
Strawberry pallidosis-associated virus segment RNA 1, complete sequence.
ACC No: AY488137
Dated: 2009-09-24 | Length: 8066 | CRC: -803209220
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; ssRNA positive-strand viruses, no DNA stage; Closteroviridae;
OC 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 EMBL/GenBank/DDBJ databases.
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 EMBL/GenBank/DDBJ databases.
RL Dept. of Botany and Plant Pathology, Oregon State University and USDA-ARS,
RL 3420 Orchard Ave, Corvallis, OR 97330, USA
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:IPR007094"
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="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;
ay488137 Length: 8066 24-SEP-2009 Type: N Check: 3331 ..
1 gtaaaagtac acaagtttac cgttgactaa ttagcatttt gctatttagt
51 ttatttgttt gcttgctgcg cggcctcggc tgatcagtac tttttgtgcg
101 acacttcggt gtatcacata atatatatat cacgtttata tatattttct
151 tcctttccat tctgcctcgt gcaacacaac aaatcaaatc accctcgcca
201 gttccctaaa ctgaaattaa tccagggtac ttggaatcag acttggctta
251 tctgattcta cataatgtct gtaagaagta agttggtttc cccttatacc
301 ccatctgccg atattgaatt ttcatctttc cttaataggg tgattgatta
351 ccctattaag agtattgatt taaatcggct tgatttcctc aggcagtatt
401 ttaatattcc cttgtgccgt tttaataaac ttcccaaacc aatcgtgtat
451 atgtttggta gggactttca ggctatctcc aactttatcg atcagaaaat
501 gtccctaaag accggtaatt ccccgaatcc tggtaatgaa gtcgtcgaga
551 ccattgaggg aaagaccgct tttggagatg gatactttgt tagggtctgg
601 gagaagcccc ttgttattga tgtttttgta tctctcggtc gttatcatag
651 tccagactat gattataaat atcgactcaa cttcagaagg caccccaata
701 acaagaggat atacacaagt gttatgtgta atatatgtaa agctgataag
751 gtttctaaag ccttttgtga gaattacaat cttttctcag tcctgaatcc
801 cactcaattc atgactcagt gtctcctcct atctgttatg gagaagatac
851 aagaatttaa aactttggtg aattatcatg tcaattcctc cttccgtcaa
901 ccactcaaga gctatcaaga gaaattagct aaatacaatg aagagtatag
951 gaagacgaag gagggtgaca cgctcattgg cgtgaaaagc aacgtgaagg
1001 gtactgagac caaaaagagt ttgattcccc aacccttcct gctcaagaag
1051 aggagagctc ccttcgcgtc agttcgtcat catgtagacg tccgagggcg
1101 cgaatatttc accatctgct acaccgatgg ttccgttaaa tacgttccaa
1151 atcataggaa tgttattgtg aatatgttca acctcacgtt aggtggcgga
1201 acttatgtta ttcatgagat gtgtctcact ccagatggtt cccgctatgg
1251 aatgcataag aatggatatt gctggttgga agccttttgc atggctaata
1301 ggtttattcc ccgtcacacc gttccctttc cagagttgaa atatggatat
1351 ttgctctcat gtggcttgag agacataatg aaggggagaa ttgaggacta
1401 tgggaacggt ttgggccact tttcgaggga gttgacttca tctaagcgtg
1451 aagtctatct caccacccat ataggcataa agactgacgg tgaaggtgac
1501 ataagcctta agaacgctga tgtgttcttt gatgatttgt tttctggcat
1551 tgttaataat actaacgtta aatcggaaaa cgacgtcatg tctaacatcg
1601 ttaggagggt gtccaacaag ttgaatgaga ctttcaatcg taagaaagag
1651 ctcaatatct ccgtatgtct ctctagtaac gagaagaagg agttgtgcga
1701 agtttttcct gagatatgca tggagttctc agactcatcc ttctcctctc
1751 atgcgctttt cactgccata agagaatgcg aaaattattc gttgtccaag
1801 aggaataatt tttgtgactt tattgacgct ggaggaaatg tagtgaaata
1851 catcagggag aatgtcaagg acattcacat ttgcgcacca gtagttgata
1901 tcaaagactc tcacaggatg atgacaagga gtaacatcct tgacaaaacc
1951 gcgggtcttt cagagacgat aacgatgtgc gacaaaatgt gccaagtttg
2001 cgatgtccaa aagcagaata tagtcgccgt ggaagtttac gatatgactc
2051 tttcagacat ggcgaagtct attctttctc ataaggcgaa acgtttcgat
2101 ttttccgtca taatacctcc agaagtttat gaagagaatt gtgatgtgtc
2151 aatgtttggc ggaggactgc gcgttaaggg caacaattta acatgctctt
2201 attattatgg caagagtggt gaatgttaca ctcatgacat caacaatctt
2251 cgtgacattt tgaagatcca aatcttttca gttgatggag tgatttttaa
2301 aaagactctc gaatcatcca ggaggggtct tcactttttc tctatcgttc
2351 cttgcttggg tatgaagaat gacacctata ctcttaagac gtactatccg
2401 aagactgaat ctgataaagt cttgatgttg gtgcctgtca agaataaatt
2451 tggtatcgtc gagaacgtcc gagtgaaaac ggataggtcc atcgtctacc
2501 atcttttgga atatgtgatg aacacagcgc agaggattga tgagaagtct
2551 tatgaatatc ttatgtctca attcagggcc cgaaagagca taaatattaa
2601 gggaggtaag gtaattcaag aaccctttga ccttccttta gatttatacc
2651 cgggttattt gggagtgatt ttgggagagg gtttgagatt gagagaaaag
2701 acattgcaga tggcaaagtt aagttatttc aaacattatc tccccacaat
2751 tttgagaata atgatacatt tcatgtacag aactctcgcc aagaccagac
2801 aggccatgta tcacggagcg atacattgca tgaagtggat tatgtctgag
2851 gagtttattg aggaagtcat aaatggcgac aggagaattt ttgacataca
2901 agagacctac gagttctctc aagttgtcac aattacgggt gaagaataca
2951 acaactatgc catcaatgaa tctttcaacg tctttgtgag agaatcagag
3001 aagaatctaa gagcgataga ttctgagttg ttgccgtttg atgattcttt
3051 tgagaccacg gagttggaca gattcaaaga tctactcaca ggaggtggcg
3101 ggggtttctc atgtttctca aaaacggcat ataaaattta tgagcgaatc
3151 ttccgtttgt tttcatggac aactctcaca ccaaagaagg tccatgattt
3201 aacaggagtg ttgaccaatc tgatcttcta catgttgcgt tgcggtagtt
3251 atacctttga gactatgaag aagtattgta agatggtctt caactctatc
3301 actggcattg gatgtggtct ctccgtcagt attaagacct tccttaaaga
3351 tgtggtatcc ttaatgagaa ggaagatcgt tgagaggaat gacaagttgt
3401 atgatgaatt catggacaat tttaaaagtg atgatgagct tgaattgtcg
3451 tctatggatt cccaaactac tctggacgcc aatatttgtt cagaagagga
3501 agtatcttcc gagtctgacg aagtcgaggt tttgtgtcac gactctcaac
3551 tgtcgacctt atctttcaga aggcccatca ggtgttttat aagctggaga
3601 agtctgaaaa gttacttgga ttctattttt aggtatcctt atgaattaat
3651 tgagaatatc agatttgcca tcaaaagtta tgcatacaag atatacagat
3701 tgtatcttaa ttctattgaa gttgccgaga taatcaaaga aactttcaat
3751 gaattaaaag atgctttctt tggatggttg acatcagaag gaggtcttga
3801 atttatcata gacggcgttt cgttgtcaat tgtcaatacg atcttctatg
3851 gtcttatggg tagatttagc cttatgagca atttggcggt tcttctcgta
3901 tactctagtt tgaaattgtc tggtataggg aagaaatatt tgggtcatga
3951 atccattgtt gtccaattgg ctgacttcct gaacgttggc tgcttcctga
4001 acgtacaaca tcctttcggc tttcttataa tgccagttag acatttggct
4051 atgaagtgta tttcaaacaa gttgaaaaag aaagccgcca ccaaggaatc
4101 gctgaaaact tcagctacca gcttaattgc taaggatttt gttagcttaa
4151 aattctatga caagttttca tataaggctt tgagacaagc aatctgtatt
4201 ttgctgatat tcattgtcat atttccaaaa ttggttcttg tctcaatttt
4251 atctttgctg cttattggtg aacacaaaaa gtatttgaat tccaccgttt
4301 tgcaagccaa cttgcagctg agttttgctt cagtctttaa gaaaacttcg
4351 aagagcaaca gaatgatcgt tttcaagaaa ttgatcgctg aaaagttttc
4401 acggaagaag actttagaag aagatgagga aatccaacag agtctggaca
4451 ttgccggaaa aattagggac ggagactgcg tggatgatga cattgaggtg
4501 gattttgact atgatggatc atacgtggag aggaagggta aaatgacaga
4551 ggggttgctt gctagaattc ccgaagttag caagaaagac attccttggg
4601 gagacaggag tgaacattct atgaactctg cggagtatga gaacttaaac
4651 ttctcaagcc tcaccccaac cacagatcgg cattacatca aatgtgaagt
4701 aaacctgaaa ttgagcaatg ccattttgct ttatcccaat tcaggcaact
4751 gcgttccaac tgtgactggg aatatggaag tcgatgccat ttccgagttt
4801 tattatttag agagcagaag aatgaatatt gaactgggaa agctggataa
4851 tgccatcagg gtcttcgcgt ccaaatacca cacagtgaag aaattccagg
4901 atatcgtttg ggatatgagg aacaaccttg atgactcaac attgtacatg
4951 tccaacaacg gtaattcttg gtaccgattg aaacaatctg atgggaaatc
5001 catgacgctt gaaggcgctt gtaaaatgac agttgattcg gatttggtca
5051 gctttaccaa gaatgtttcc ggttatcaat tcactagtga tgagcttttg
5101 ggtatgttta ccaataaccg gtgcatgggt cttgaaagtt ttaaggatga
5151 taaaggagac ttccatgtta acagaataat gaatgatgtt gtcattcata
5201 acaagccacc cggtgctgga aaaacaacaa caattgtgaa gaacatcctg
5251 gatgatttaa agaaccggga aacgtgcctc gcttttacct gcacctctgc
5301 cggaaagaag gagatagtgg ataagctgaa aaaatttaac gttcctaatg
5351 cgtatcagta tgtcaccact tatgactcat acctgatgaa gaataagaag
5401 aataagattc agaaggtata ctgtgatgag gtgttcatgg tacacgctgg
5451 agagtggata gcttgcatga atctgattga gaatgattat gtgaggtgtt
5501 acggtgacaa gaatcaaatt ccttttataa atcgagtacc aaacaccacc
5551 tgtcatttat cgtttgacct ttacttgaag tttcaaatga tccatgacaa
5601 tgtatcatac aggtgtcccg tggatgtatg ctatttacta tctaatctca
5651 cggaccctat tggtaacaag ttatatccca atggtgttta tcccgctgga
5701 gacaattcga aaatcttgag aagcgttgat gttgtgggta tcaactgcgc
5751 ggaagatttg aaaccagatg agaagaagaa gtacataacc tttacccagt
5801 atgaaaagga agaggtgtca aaaataactg gcaagaaaat gaaggtatct
5851 ggtaccgcca acactgtcaa tgaagtccaa ggaggtactt tcccaaaggt
5901 agagttaatc agattgaaac aatttgataa tccaatttac actaacatga
5951 atcaattcat cgttagcata tccagacaca ctgaaaaatt ggattacaag
6001 gttgtttcaa gcaaattgaa tgactttgtg ggtgagaaga tatcagcatt
6051 gaacacaatt gctgattacg ttattaagga acacaacttc aagcagtgcg
6101 tttgacgtat atgaaatggt ggtcgaagat ctttgtctac ctgcgacctt
6151 tagtagacca ccatcctccc atcatagatc cataaatgag tttatgtgtt
6201 tcatcaatcc aggattgagt gcttacaact atattcacag gaccctcatc
6251 tttgagtatg agcagtatga actcccagtt gttggtgaag ttgatttagt
6301 gttgagtcga tctaagccct acaatccagg attatacgtt atcccagatt
6351 tattgggaaa aggggaaagg tcacgacccg acacatggag acaagtgctt
6401 ttgtcgttgt ctcatagaaa cttttcggct ccgagggtga atgagaattg
6451 cgatacatta gcctccgccg aaattcttgc ccaaagtctc atgaaagctt
6501 ttgactttct aaagttatcg gagaattttg atactgttct tcccgatatt
6551 tggagtatta ccaagtggat tgaagacagg gaacccaata aggtgaggaa
6601 gttgaagaga agtttcgggc atgacttgat gaattctcaa ttctctcgta
6651 tgaaacttat gatcaaaggg gagatgaaac cgaaaatgga catgtcaagt
6701 tatgggacat atggaccatc ctcaaacatc atttattacg aacagattgt
6751 aaatatgttt tattcgccca tgtttttgag aatttttgat cgaattggtt
6801 attgcttgaa ttcaaaggta gttttgtatt ctggtatgaa tttggaaact
6851 ctaggcaaat tgataagatc taaattggac tttccaattc aagagtacag
6901 gactaccgaa attgatttta gcaaatttga taaatctcaa ggtgtcatat
6951 ttaaactcta tgaagaaatt atttataaat tcttcaaatt tgattcaaaa
7001 acctatgagg cgataaaatt ttctgaatat ttttgtcgag cgaagagcag
7051 ttgtgggatt tctgtggagc tgggagctca gagaagaact ggatctccaa
7101 acacgtggtt atcaaacact ctcgtcacct tggccatgat acttacacac
7151 tatgatctag atgatataga tctattactc gtaagtggag atgacagtct
7201 cattttctca aggaaagatc tcgggaacaa agcaaatgaa attaacagag
7251 actttgggat ggaggccaag tttataatga attctgttcc ctacttttgt
7301 tccaaattca tcattgaaga tagaggggaa attaaggtag tccctgaccc
7351 ggtcagattt tttgaaaaat tgtctgtacc gatttctttg caagacttcc
7401 aagtcgggga tttacttaga gagcgattcg tatcctttaa agatcttatg
7451 ataggttatg atagcgacgc tgtgatcata ttggttgata atttgatatc
7501 gattcgctat gacataccta gaatgacgtc ttatgccgca ctgtgttata
7551 ttcattgttt gacttcaaac gtgttagcgt acacgaaact ttttattgaa
7601 ggtttcacag ttgcaattta ggttcagaaa tgttgtcaac attactttct
7651 attatttttt ctatcttgta catatcttgc gttgtacatc tagaactttg
7701 cttcactaaa tatttaattt atagatcaca taacccttgc tcagagttac
7751 agtgcattaa tatgttttat attataggaa aaaccaattc aattttaatg
7801 ttgctagatt ttacttttat aataataagt aatttgcttg catctattta
7851 tagtaaaata aatccataaa atattattaa gcccttttct gtattatgtt
7901 tttgggctta gagtcatata cgtgcttttc agtgtagtgt gtattataaa
7951 atctcgaaaa atacaaaaaa ttttattgtt aattatgtaa ttacaatatt
8001 atcggcgctc aaaagagaag gttgtacctt ccgccatgag cgtctagtat
8051 ttaataaaat aaggcg