LOCUS EF521828 5679 bp RNA linear VRL 24-APR-2007 DEFINITION Barley yellow dwarf virus - PAV isolate 0109, complete genome. ACCESSION EF521828 VERSION EF521828.1 KEYWORDS . SOURCE Barley yellow dwarf virus-PAV ORGANISM Barley yellow dwarf virus-PAV Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Luteoviridae; Luteovirus. REFERENCE 1 (bases 1 to 5679) AUTHORS Beckett,R.J. and Miller,W.A. TITLE BYDV/CYDV Global Sequencing Project JOURNAL Unpublished REFERENCE 2 (bases 1 to 5679) AUTHORS Beckett,R.J. and Miller,W.A. TITLE Direct Submission JOURNAL Submitted (27-MAR-2007) Plant Pathology, Iowa State University, 470 Bessey Hall, Ames, IA 50011, USA FEATURES Location/Qualifiers source 1..5679 /mol_type="genomic RNA" /country="USA: Iowa" /collected_by="W.A. Miller" /host="barley" /db_xref="taxon:12040" /isolate="0109" /serotype="PAV" /organism="Barley yellow dwarf virus-PAV" primer_bind 1..30 /note="derived from viral specific primer used for RT-PCR" CDS join(143..1162,1162..2748) /ribosomal_slippage /codon_start=1 /protein_id="ABP68677.1" /translation="MLLFELLIGASVKAVKDFISHCYSRLKSIYYAFKRWLLEISGQF KAHDAFVNMCFGHIADIEDFEAELAEEFAVKEEEIEEARSLMRLLTAQRAKSGVAEAW TDFFVKSRGGVYAPLSCEPSKAELEVKADKLERLLEDMHKFEVQAAKKYIKEKGRGFI NCWNDLRSRLKLVKEVRDEAKDNIKAASKIGVEFSAPTNIQDLYTFTKVEKVETGLIK EVTKMVQGEETKHMEPITEDMRSIKDTAEDREAASKWITEVVKLKNSTLSADELSMAT IARYVENIGEKYKLDIASKTYLKQCAMMSVPIPTQKDIKMKMVIQSPAARAARERVAV LDSQGFLEGLCASSGFESPFSLLGLPEIKVTDGARLRKISSNIRYLTQTHLGLVYKAP NASLHNALVAVERRVFTVGKGDKAIYPPHPEHDIFTETMDYFAESVIDKVGHCKTYTP QQLALSYSAGKRAQYFKAVESLKKEPYQMKDSNVQAFLKKEKHWMTKAIAPRLICPRS KRYNIILGTRLKFNEKKIMHAIDSVFGSPTVLSGYDSFTQGEIIAEKWQKFASPVAIG VDASRFDQHVSEQALKWEHGIYNGIFGDIELATALEHQLVNNIKMFVEDKMLTFKVRG HRMSGDINTSMGNKLIMCGMMHAYFKMLGVEAELCNNGDDCVIITERANEKLFDGMYD HFLKYGFNMVTEAPVYELGELEFCQSKPVRIDGKYRMVRRPDCIGKDSCTLLSMLNEA DVKSYMSAVAQCGLVLNAGVPILESFYRCLYRSSGYKKVSEEYIKNVISYGTDERLQG RRTFKETPITNDNRMSYWESFGVDPKIQQLVERYFDGLTVSAQLQRVKVTSPHLQSIL LSIPENNSQNEY" /product="RNA-dependent RNA polymerase" /note="RdRp; P1-P2 fusion created by -1 ribosomal frameshift" CDS 143..1165 /codon_start=1 /protein_id="ABP68678.1" /translation="MLLFELLIGASVKAVKDFISHCYSRLKSIYYAFKRWLLEISGQF KAHDAFVNMCFGHIADIEDFEAELAEEFAVKEEEIEEARSLMRLLTAQRAKSGVAEAW TDFFVKSRGGVYAPLSCEPSKAELEVKADKLERLLEDMHKFEVQAAKKYIKEKGRGFI NCWNDLRSRLKLVKEVRDEAKDNIKAASKIGVEFSAPTNIQDLYTFTKVEKVETGLIK EVTKMVQGEETKHMEPITEDMRSIKDTAEDREAASKWITEVVKLKNSTLSADELSMAT IARYVENIGEKYKLDIASKTYLKQCAMMSVPIPTQKDIKMKMVIQSPAARAARERVAV LDSQGF" /product="P1" /note="ORF1" CDS 2862..4820 /codon_start=1 /protein_id="ABP68679.1" /translation="MNSVGRRGPRRANQNGPRRRRRRAIRPVVVVQPNRAGPRRRNGR RAGRRGPDSIPGSAGRTEVFIFSVDNLKANSSGTIKFGPSLSQCPALSDGILKSYHRY KITSIRVEFKSHASATTSGAIFVELDTACKQSALGSYINSFTISKTASKSFRAEAING KDFQESTIDQFWLLYKANGTTTDTAGQFIIRINVSMLTPKXVDSSTPEPKPAPEPEPT PTPGPTPAPQPTPEPTPAPAPKRFFEYVGTPTGTISTRENSDSISVSKLGGQSMQYIE NEKCETKVIDSFWSTNNNVSAQAAFVYPVPEGSYSVNISCEGFQSVDHIGGNEDGYWI GLIAYSNSSGDNWGVGNYRGCSFKNFLATNTWRPGHKDLKLNDCQFTDGQIVERDAVM SFHVEATGNDACFYLMAPKTMKTDKYNYVVSYGGYTNKRMEFGTISVTCDESDVEAKR ITRHAETPIRYKHILVSERYEEPLPTITDQGLCDVKTPEQEQTLVDEEDRQTVSTEPD IALQEYEAATAEIPDAEEDVLPSKEQLSSKPLDTSGNIIPKSKEPEVLGTYQGQNIYP EDVPPLARQRLREAAKAPSTLLYERTSKKSNNFLTRFMEANRSPTTPAAPTVSTTSNM TREQLAEYTRIRKSLGLTAAKEYKAQFQ" /product="aphid transmission protein" /transl_except=(pos:3462..3464,aa:OTHER) /note="P3-P5 fusion created by ribosomal read-through of the ORF3 stop codon" CDS 2862..3464 /codon_start=1 /protein_id="ABP68680.1" /translation="MNSVGRRGPRRANQNGPRRRRRRAIRPVVVVQPNRAGPRRRNGR RAGRRGPDSIPGSAGRTEVFIFSVDNLKANSSGTIKFGPSLSQCPALSDGILKSYHRY KITSIRVEFKSHASATTSGAIFVELDTACKQSALGSYINSFTISKTASKSFRAEAING KDFQESTIDQFWLLYKANGTTTDTAGQFIIRINVSMLTPK" /product="coat protein" /note="ORF3; P3" CDS 2905..3366 /codon_start=1 /protein_id="ABP68681.1" /translation="MAQEGGAVEQFGQWLWSNPIEQDPDDEMVDAQEEEGQILYLDQQ AGLRYSYSQSTTLKPTLPGQSNSAPVYRNAQRFQTEYLSPTTVTRSQVSVLSLSHTRP PLRRALSLLNSTPRASNQPWVATLIPSPSAKLPPNPSEPRRLMGRTSKNQR" /product="movement protein" /note="P4; ORF4 translated via a leaky scanning mechanism" CDS 4927..5052 /codon_start=1 /protein_id="ABP68682.1" /translation="MDDLHVIAVCIFALTVLTGLGAVIGCCAGCLLPPPSFRSSV" /product="P6" /note="ORF6; highly variable sequence" primer_bind complement(5653..5679) /note="derived from viral specific primer used for RT-PCR" ORIGIN 1 agtgaaggtt gaccacctac acaaaaagac tttgtgcttg aagtctacag ctcacctgtt 61 ttgtattcag gacgttgtct gcaacaacgg tcaacagtac gcccgacacc gtactgccac 121 ctccctatcc ccccccgcca acatgcttct ttttgaactt ttgatcggag ctagcgtcaa 181 agctgttaag gacttcatca gccactgcta ttcacgactt aaaagcatat attatgcttt 241 caaaagatgg ctgttggaaa tatccgggca atttaaggcc catgacgctt ttgtcaacat 301 gtgctttggg cacatcgctg acatcgaaga cttcgaggct gaactcgctg aagagttcgc 361 cgtgaaggag gaagagatcg aggaggcaag aagcctcatg cgactgctca ccgcccaacg 421 agccaaatct ggggtggcgg aggcttggac cgacttcttc gtgaagtcga gaggcggggt 481 ttatgccccg ctttcctgcg agccttccaa agcagagctt gaggtcaaag ccgacaagct 541 cgaaagacta cttgaggaca tgcacaaatt cgaagtgcaa gcggcaaaaa aatatataaa 601 agaaaaaggc cgcgggttca tcaactgctg gaacgatctc cgttccagac tcaagttagt 661 caaggaggta agagacgagg ccaaagacaa catcaaggcc gcctccaaaa tcggcgtgga 721 attctccgca cccaccaaca tccaggacct atacaccttc acaaaggttg aaaaggtcga 781 gactggcctc ataaaggagg tcacaaagat ggtgcaaggg gaggaaacca agcacatgga 841 gcctatcact gaggatatgc gctccattaa ggacacggcg gaagaccgag aggccgcctc 901 caagtggata acggaggtgg ttaaattgaa aaattcaacc ctgtctgccg acgaactgtc 961 catggccacc atcgcccggt atgtggaaaa tatcggagaa aaatacaaac tcgacattgc 1021 ttccaaaaca tatcttaagc aatgtgcaat gatgtctgtt ccaattccca ctcaaaaaga 1081 catcaaaatg aagatggtga tccagagccc tgcggcacga gctgcgcgtg agcgcgtagc 1141 tgtgcttgat tcccagggtt tttagagggg ctctgtgcct cctccggttt tgaaagtccc 1201 ttttctctat taggactgcc ggagattaag gtcacagacg gagcccgttt acgtaagatt 1261 agtagtaata ttaggtacct aactcaaacc cacctcggct tggtttacaa agccccaaac 1321 gcctccctgc acaatgcctt ggttgcagtg gagagaagag tgtttacagt tggtaagggg 1381 gacaaagcta tctacccccc ccacccagag catgatattt tcactgagac tatggactac 1441 ttcgccgagt ccgtaattga caaggtggga cactgtaaga cttacactcc acagcagcta 1501 gctcttagct atagcgcagg gaaaagagcc caatacttca aagccgtcga gtcacttaag 1561 aaagaacctt accaaatgaa ggactcgaat gttcaggcat tcctcaagaa ggagaagcat 1621 tggatgacca aagccatcgc ccctcgcctg atctgccccc gctccaagcg gtataatatc 1681 atccttggaa ctcgcttgaa attcaacgag aagaagatca tgcacgctat cgatagtgtg 1741 tttggatccc ccactgtgct ttccggctat gatagcttca ctcagggtga aattatagcc 1801 gaaaagtggc aaaagtttgc atcacccgtc gccatcggtg ttgatgctag ccgctttgac 1861 cagcatgtgt cagagcaggc gcttaagtgg gaacacggga tatacaatgg catatttggc 1921 gacattgaat tggccaccgc tctcgaacat cagcttgtaa ataacatcaa aatgttcgtt 1981 gaggataaaa tgcttacatt taaggtgaga ggccatagga tgtccgggga cataaacacc 2041 agcatgggaa acaaactcat aatgtgcggc atgatgcatg catactttaa aatgctgggt 2101 gttgaagctg agttgtgcaa caacggagac gactgtgtca tcatcactga gagagccaat 2161 gagaagctct ttgatggcat gtacgaccat ttcttgaaat acggcttcaa catggtgacg 2221 gaagccccag tttatgaact cggggaactc gaattttgtc aatcaaaacc cgtcagaata 2281 gatggtaagt acagaatggt aaggagacca gactgtattg gaaaagatag ctgcacactt 2341 ttgagcatgt tgaatgaggc tgacgtcaag agttacatgt cagctgtggc tcagtgtgga 2401 ctcgttttga atgcgggtgt gcccattttg gaaagcttct accgctgcct gtacagaagc 2461 tctgggtaca agaaagtgag tgaggaatac atcaaaaacg tcatatcata tggaacagat 2521 gaacgccttc aaggtagacg taccttcaag gagacaccta tcacaaacga caatcgaatg 2581 tcgtactggg aatcattcgg agttgaccct aagatacaac aactcgtcga gcggtacttc 2641 gacggtctta cggtaagtgc ccaactccag agagtgaagg tgacatctcc acatctgcaa 2701 tcaatcctcc tctccattcc ggagaacaac tcgcaaaacg aatattaatt accaaatctt 2761 agccgggttt gggatagggt ttatagtaag tattccctgt acattagctc tcacgtactt 2821 tatttacaat aaagtttcag acaccactag agaggtggtg aatgaattca gtaggccgta 2881 gaggacctag acgagcaaat caaaatggcc caagaaggcg gcgccgtaga gcaattcggc 2941 cagtggttgt ggtccaaccc aatcgagcag gacccagacg acgaaatggt cgacgcgcag 3001 gaagaagagg gccagattct atacctggat cagcaggcag gactgaggta ttcatattct 3061 cagtcgacaa ccttaaagcc aactcttccg ggacaatcaa attcggcccc agtctatcgc 3121 aatgcccagc gctttcagac ggaatactta agtcctacca ccgttacaag atcacaagta 3181 tccgtgttga gtttaagtca cacgcgtccg ccactacgtc gggcgctatc tttgttgaac 3241 tcgacaccgc gtgcaagcaa tcagccctgg gtagctacat taattccttc accatcagca 3301 aaactgcctc caaatccttc agagccgagg cgattaatgg gaaggacttc caagaatcaa 3361 cgatagacca gttctggcta ctatacaagg caaatgggac aactactgac actgctggac 3421 aatttataat aaggataaat gtcagtatgc tgactcccaa ataggtagac tcctcaacac 3481 cggaaccgaa accagcacca gaaccagaac caactccaac accagggccc acaccagcgc 3541 cgcagcctac acctgagccc actcctgcac cagcccccaa gagattcttt gagtatgtcg 3601 gaactccaac cggcacaatc tcaactagag agaattctga cagcatctct gtcagcaaac 3661 ttggtgggca gtcgatgcag tacatagaga atgagaaatg tgagacaaaa gtcattgact 3721 ctttctggag cactaacaac aacgtatctg cccaggcagc attcgtttat ccagtgccag 3781 aaggttcata cagcgtcaac atttcgtgtg aaggctttca atccgttgac cacatcggtg 3841 gtaacgagga tgggtactgg attggtctta tagcctactc caattcatca ggcgacaatt 3901 ggggagtagg taattataga gggtgcagtt tcaaaaactt cttggcaacc aatacttgga 3961 gacctggcca caaagatctc aagttgaacg attgccagtt cacagatgga cagatagttg 4021 aaagggacgc cgtgatgtct tttcacgtag aagcaacagg caatgatgcc tgtttctatc 4081 tcatggctcc caaaacaatg aaaactgaca aatacaacta tgttgtctca tatggagggt 4141 acacaaacaa acgaatggaa tttggtacca tatctgtgac atgcgatgaa tccgatgttg 4201 aggcaaaacg cataacaagg cacgctgaaa ctcccatccg ctacaagcac atccttgtgt 4261 ccgagcggta tgaggagcca ttgcccacca taaccgatca aggcttgtgt gatgtgaaaa 4321 ctcccgagca agaacaaaca ttggtggatg aagaagacag acaaactgtt tccactgaac 4381 ctgatatagc actccaggaa tacgaagctg ccacagctga aattcctgat gctgaagagg 4441 atgttttgcc ctccaaggaa cagctgtcct ctaagccatt ggacacgtct ggcaatataa 4501 tacccaaatc caaggaacct gaagtacttg gaacatacca gggccagaac atttaccctg 4561 aagacgtgcc accgctagcg cggcagagat tgcgcgaagc cgcgaaagca ccctccacgt 4621 tgctatatga gcgaacgtcg aagaagagca acaacttctt gactcgtttt atggaggcga 4681 ataggtcccc taccactccc gctgccccaa cagtgtcaac tacatcaaac atgacaaggg 4741 aacagcttgc ggagtacact agaattagga aatcccttgg actcacagca gctaaggaat 4801 acaaggcgca atttcagtga aggtaccacc actagcacaa atcggatcct ggtaaacagg 4861 cagaactacg gttcataagc tcgggtaggc cgtcaaccta ccgccgtatc gtattgtgtt 4921 tggccgatgg atgacctcca tgttatcgcc gtttgtattt ttgctctaac tgtgttgaca 4981 gggttaggcg cggtgatcgg ctgttgcgcc ggttgccttc tcccccctcc ctccttccgc 5041 tcttctgttt aagcaaaaat ctctcggtct gtgcgagaga aactcaaaaa tatcggggag 5101 cttcggctca gtgaggggat taacgacccc cagcaatggc tggtcttggc ggacatgaat 5161 aacccgctat gagacgaagt ggtaaccgcc actgatcaaa aggtaaacat gcttctgtgt 5221 tgtacactgc cccggggcct accgggtcaa caaggctatc ccaccaactc aatgaaatga 5281 gagtggagtg ggcggagtgg gtgacttcgt gatgtacacc cgatcgtcag gattgaagac 5341 gttaaaactc gacgacctag tgcaagtcgt taaactgact cgggtggata caccacaccc 5401 gaccaggcat gcaggcatac ccacgatacg aaacgtgggt ttcttggagc cactacctgt 5461 gatgcaaggt agggtatgag tcttagcaag ctctgtgcca ggaaatggac ataaaccata 5521 gcaatcctgc acatgtttgt cactggtgaa tcataggtga acgtgccact ggcctgttgc 5581 aagcaatcta gctctgcttg caacagtatc ccttagaagc aattctttgg ggggactgga 5641 ttctgactgc cggcactcga aagagaagcc cggcatccc //