LOCUS EF521833 5647 bp RNA linear VRL 24-APR-2007 DEFINITION Barley yellow dwarf virus - PAV isolate 015, complete genome. ACCESSION EF521833 VERSION EF521833.1 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 REFERENCE 1 (bases 1 to 5647) AUTHORS Beckett,R.J. and Miller,W.A. TITLE BYDV/CYDV Global Sequencing Project JOURNAL Unpublished REFERENCE 2 (bases 1 to 5647) AUTHORS Beckett,R.J. and Miller,W.A. TITLE Direct Submission JOURNAL Submitted (27-MAR-2007) Plant Pathology, Iowa State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..5647 /mol_type="genomic RNA" /country="USA: Iowa" /collected_by="W.A. Miller" /host="oat IA04116" /db_xref="taxon:12040" /isolate="015" /serotype="PAV" /organism="Barley yellow dwarf virus-PAV" primer_bind 1..19 /note="derived from viral specific primer used for RT-PCR" CDS join(142..1158,1158..2744) /ribosomal_slippage /codon_start=1 /protein_id="ABP68707.1" /translation="MFFEILIGASAKAVKDFISHCYSRLKSIYYSFKRWLMEISGQFK AHDAFVNMCFGHMADIEDFEAELAEEFAEREDEVEEARSLLKLLVAQKSKTGVTEAWT DFFTKSRGGVYAPLSCEPTRQELEVKSEKLEKLLEEQHQFEVRAAKKYIREKGRGFIN CWNDLRSRLRLVKDVKDEAKDNARAAAKIGAEMFAPVDVQDLYSFTEVKKVETGLMKE VVKERNGEEEKHLEPIMEEVRSIKDTAEARDAASTWITETVKLKNSTLNADELSLATI ARYVENVGDKFKLDIASKTYLKQVASMSVPIPTNKDIKLKMVLQSPEARARRERMDVL DSVGFLEGLCTASGFESPFPILGLPEIAVTDGARLRKVSSNIRYLSQTHLGLVYKAPN ASLHNALVAVERRVFTVGKGDKAIYPPRPEHDIFTDTMDYFQKSIIEEVGYCRTYPAQ LLANSYSAGKRAMYHKAIASLRTVPYHQKDANVQAFLKKEKHWMTKDIAPRLICPRSK RYNIILGTRLKFNEKKIMHAIDSVFGSPTVLSGYDNFKQGRIIAKKWQKFAYPVAIGV DASRFDQHVSEQALKWEHGIYNGIFGDSELALALEHQITNNIKMFVEDKMLRFKVRGH RMSGDINTSMGNKLIMCGMMHAYFKKLGVEAELCNNGDDCVIITDRANEKLFDGMYDH FLQYGFNMVTEKPVYELEQLEFCQSKPVSINGKYRMVRRPDSIGKDSTTLLSMLNQSD VKSYMSAVAQCGLVLNAGVPILESFYKCLYRSSGYKKVSEEFIKNVISYGTDERLQGR RTYNETPITNHSRMSYWESFGVDPKIQQIVERYYDGLTVSAQLQSVKVTTPHLQSILL SIPENHSQNEY" /product="RNA-dependent RNA polymerase" /note="RdRp; P1-P2 fusion created by -1 ribosomal frameshift" CDS 142..1161 /codon_start=1 /protein_id="ABP68708.1" /translation="MFFEILIGASAKAVKDFISHCYSRLKSIYYSFKRWLMEISGQFK AHDAFVNMCFGHMADIEDFEAELAEEFAEREDEVEEARSLLKLLVAQKSKTGVTEAWT DFFTKSRGGVYAPLSCEPTRQELEVKSEKLEKLLEEQHQFEVRAAKKYIREKGRGFIN CWNDLRSRLRLVKDVKDEAKDNARAAAKIGAEMFAPVDVQDLYSFTEVKKVETGLMKE VVKERNGEEEKHLEPIMEEVRSIKDTAEARDAASTWITETVKLKNSTLNADELSLATI ARYVENVGDKFKLDIASKTYLKQVASMSVPIPTNKDIKLKMVLQSPEARARRERMDVL DSVGF" /product="P1" /note="ORF1" CDS 2858..4792 /codon_start=1 /protein_id="ABP68709.1" /translation="MNSVGRRGPRRANQNGTRRRRRRTVRPVVVVQPNRAGPRRRNGR RKGRGGANPVFRPTGGTEVFVFSVDNLKANSSGAIKFGPSLSQCPALSDGILKSYHRY KITSIRVEFKSHASATTAGAIFIELDTACKQSALGSYINSFTISRTASKVFRAEAING KEFQESTIDQFWMLYKANGTTTDTAGQFIITMSVSLMTAKXVDSSTPEPKPAPEPTPA PQPAPEPTPAPVPKRFFEYIGTPTGTISTRENSDSISVSKLGGQSMQYIENEKCETKV IDSFWSTNNNVSAQAAFVYPVPEGSYSVNISCEGFQSVDHIGGNEDGYWIGLIAYSNS SGDNWGVGNYKGCSFKNFLATNTWRPGHKDLKLNDCQFTDGQIVERDAVMSFHVEATG TDACFYLMAPKTMKTDKYNYVVSYGGYTNKRMEFGTISVTCDESDVEAERITRHAETP IRSKHILVSEQYERPLPTIINQGLCDVQTPEQEQTLVDEEDKQTVSTEPDIALMEYEA ATAEIPDAEEDVLPSKEQLSSKPVDTSGNKIPKPKEPEVLGTYQGQNIYPEDVPPIAR QKLREAANAPSTLLYEKTPKKSNNFLTRFVEANRSPTTPAAPTVSTVSNMTREQLAEY TRIRKSLGLTAAKEYRAQFQ" /product="aphid transmission protein" /transl_except=(pos:3458..3460,aa:OTHER) /note="P3-P5 fusion created by ribosomal read-through of the ORF3 stop codon" CDS 2858..3460 /codon_start=1 /protein_id="ABP68710.1" /translation="MNSVGRRGPRRANQNGTRRRRRRTVRPVVVVQPNRAGPRRRNGR RKGRGGANPVFRPTGGTEVFVFSVDNLKANSSGAIKFGPSLSQCPALSDGILKSYHRY KITSIRVEFKSHASATTAGAIFIELDTACKQSALGSYINSFTISRTASKVFRAEAING KEFQESTIDQFWMLYKANGTTTDTAGQFIITMSVSLMTAK" /product="coat protein" /note="ORF3; P3" CDS 2901..3362 /codon_start=1 /protein_id="ABP68711.1" /translation="MAQEGGAVEQFGQWLWSNPIEQDPEDEMVDAREEEGQILYLDQQ AGLRYSYSQSTTLKPTLPGQSNSAPVYRNAQRFQTEYLSPTTVTRSQVSVLSLSHTRP QLRPALSLLNSTPRANNQPWVATLIPSQSAGPPQRSSEPKRLTGRNSRNQR" /product="movement protein" /note="P4; ORF4 translated via a leaky scanning mechanism" CDS 4899..5024 /codon_start=1 /protein_id="ABP68712.1" /translation="MDDLHVIAVCIFALTVLTGLGAVIGCCAGCLHPPLSLRPSV" /product="P6" /note="ORF6; highly variable sequence" primer_bind complement(5632..5647) /note="derived from viral specific primer used for RT-PCR" ORIGIN 1 agtgaagatt gaccatctca caaaagctgt tacgtgcttg taacacacta cacactcgtt 61 ttgttttcga gaagtagttg caacaacggt ccccttattg cctgacaagc tgagggccac 121 ccttctatcc ccaccgccat catgttcttc gaaatactta taggagctag cgctaaggcg 181 gtcaaagact tcatcagtca ttgttactct cgtttgaaat ctatatatta ttcgttcaaa 241 cgatggctga tggagatatc tgggcagttt aaggcccatg acgcctttgt caacatgtgc 301 ttcgggcaca tggctgacat tgaggacttc gaggcagagc tcgctgagga gtttgccgag 361 agggaggatg aggtggaaga ggcaaggagc ctcttgaaac tgctggtcgc ccaaaaatct 421 aaaactgggg tgaccgaggc ttggaccgac ttcttcacga agtcgagagg tggcgtctat 481 gcgccgcttt cctgcgagcc taccaggcag gagctagaag ttaagagcga gaagctcgaa 541 aaacttctag aagaacagca ccaattcgag gtgcgagcgg ccaagaaata cattagggaa 601 aaaggccgcg gcttcatcaa ctgctggaac gacttgcgaa gtcgtctcag gctggtgaag 661 gacgtcaagg acgaggcgaa ggacaacgcc agagctgctg ccaagatcgg agcagaaatg 721 ttcgcccctg ttgacgtgca agacctctac agtttcacag aggtcaagaa ggtggagacc 781 ggcctcatga aggaggtcgt gaaagagaga aacggcgaag aagagaaaca cctcgagccc 841 atcatggaag aggtgagatc tatcaaggac accgccgaag ccagggatgc cgcctccact 901 tggataacag agacagttaa gctgaagaac tctacgctta acgccgatga attgtctctg 961 gccaccatcg cccgctacgt tgaaaacgta ggggacaaat tcaaactcga cattgctagc 1021 aagacatatc taaagcaagt cgcatcgatg tctgtaccaa ttccaactaa caaggacatc 1081 aaattaaaga tggtgctgca gagtcctgaa gcacgtgcca ggcgggaacg catggacgtg 1141 cttgactctg tgggttttta gaggggctct gtaccgcctc tggttttgag agcccattcc 1201 ccattctcgg gctgccagag attgcggtca cagacggagc ccggctccgt aaggttagta 1261 gtaatattag ataccttagc caaacccacc taggtcttgt atataaggca ccaaatgcct 1321 ccctgcacaa tgcgcttgta gcagtggaga gaagagtttt tacagtagga aagggggaca 1381 aagcaatcta ccccccccgc ccagagcatg acattttcac tgatacgatg gattacttcc 1441 aaaaatccat tatagaagag gtgggatact gtagaacata tccagcgcaa ctcctggcta 1501 acagctatag cgcaggaaag agggccatgt atcacaaagc cattgcatct ttgaggactg 1561 tcccttatca tcagaaggat gctaatgtgc aagctttcct gaagaaggag aaacattgga 1621 tgaccaagga cattgccccc cgattgattt gcccccgcag caagcggtac aacatcatcc 1681 taggaactcg tttgaaattc aacgagaaga agatcatgca cgctatcgat agtgtgtttg 1741 gatcccccac tgtgctttct ggctacgaca actttaaaca aggaagaatc atagccaaga 1801 agtggcaaaa gtttgcatac cccgtcgcca tcggcgtgga tgctagccgc tttgaccaac 1861 acgtgtcaga gcaggcgctt aagtgggaac acgggatata caatgggatc ttcggagaca 1921 gtgaactggc tcttgcactt gaacaccaaa tcaccaacaa cattaagatg tttgttgaag 1981 ataaaatgct taggttcaag gtaagaggcc acagaatgtc cggtgacatt aataccagca 2041 tgggaaataa gctcataatg tgcggcatga tgcatgcata tttcaagaag ctgggtgttg 2101 aagctgaact ttgtaacaac ggagacgact gtgtcatcat cactgataga gccaatgaga 2161 agctctttga tggcatgtac gaccatttcc tccagtatgg cttcaacatg gtgaccgaaa 2221 aaccagttta cgaactggag caattggagt tttgccagtc aaaaccggtc tctattaatg 2281 gaaagtatag aatggtcaga aggcccgata gcataggcaa agatagcaca acactactga 2341 gcatgctcaa tcaatccgac gtcaagagct acatgtcggc tgttgctcag tgtggcctgg 2401 tgctcaacgc tggagtaccc atacttgaaa gtttctataa atgcctatat agaagctcgg 2461 ggtacaagaa agtgagtgag gaatttatca aaaacgtcat atcgtatgga acagatgaga 2521 gactacaagg tagacgtacc tataatgaaa cacctatcac aaaccacagt agaatgtcct 2581 actgggaatc attcggagtt gaccctaaga tacagcaaat cgtcgagagg tactacgacg 2641 gtcttacggt aagtgcccaa ctccagagcg tgaaggtgac gactccacat ctgcaatcaa 2701 tactactttc cataccggaa aaccactcac aaaacgaata ttaattacca gatcttagct 2761 gggtttggga tagggttcat agttagtata ccctgtacat tagctctcgc gtactttatt 2821 tacaataaag tttcagacac cactagagag gtggtgaatg aattcagtag gccgtagagg 2881 acctagacgc gcaaatcaaa atggcacaag aaggaggcgc cgtagaacag ttcggccagt 2941 ggttgtggtc caacccaatc gagcaggacc cagaagacga aatggtcgac gcaagggaag 3001 aggaggggca aatcctgtat ttagaccaac aggcgggact gaggtattcg tattctcagt 3061 cgacaacctt aaagccaact cttccggggc aatcaaattc ggccccagtc tatcgcaatg 3121 cccagcgctt tcagacggaa tacttaagtc ctaccaccgt tacaagatca caagtatccg 3181 tgttgagttt aagtcacacg cgtccgcaac tacggccggc gctatcttta ttgaactcga 3241 caccgcgtgc aaacaatcag ccctgggtag ctacattaat tccttcacaa tcagcaggac 3301 cgcctcaaag gtcttcagag ccgaagcgat taacgggaag gaattccagg aatcaacgat 3361 agaccagttt tggatgctct acaaggccaa tggaaccacc actgacacgg caggacaatt 3421 cattatcacg atgagtgtca gtttgatgac ggccaaatag gtagactcct caacaccgga 3481 accgaaacct gcaccagaac ctacgccggc tccacagccc gcacccgaac cgactcctgc 3541 acctgtcccc aaaagattct ttgagtatat cggcactcca accggtacaa tctcaacaag 3601 agagaactct gacagtattt ctgtcagcaa gctcggcgga cagtcaatgc agtatataga 3661 gaatgagaag tgtgaaacaa aggtcattga ctccttctgg agcactaaca acaacgtgtc 3721 tgcacaggca gccttcgttt acccagtgcc agaaggatca tacagtgtga acatttcgtg 3781 cgaaggcttt caatccgttg accacatagg gggcaacgag gatggttatt ggattggttt 3841 aattgcctac tccaattcgt caggagacaa ttggggggtg ggcaactaca aagggtgcag 3901 tttcaagaac ttcttggcaa ccaatacttg gagaccaggc cataaggatc tcaagttgaa 3961 cgattgccag ttcacagatg gacaaatagt tgagagggat gccgtgatgt ctttccatgt 4021 ggaagcaaca ggtactgacg cctgtttcta tctcatggcc cccaaaacaa tgaaaactga 4081 caaatacaac tatgttgtct catatggggg gtacacaaac aaacggatgg aatttggtac 4141 catatctgtg acatgtgatg aatccgatgt tgaggcagaa cgcataacaa ggcacgctga 4201 aacacccata cgttccaaac acattcttgt gtctgaacag tatgagcgac ctttacccac 4261 cataatcaat caaggcttgt gtgatgtgca aactcccgag caagaacaaa cactggtgga 4321 tgaagaagac aaacagactg tttccacaga acctgatata gcactcatgg aatatgaagc 4381 tgcaacagct gaaattccgg atgctgaaga ggatgttttg ccctccaagg aacagctgtc 4441 ttctaaaccg gtggacacgt ccggcaacaa aatacctaag cccaaggaac ctgaagtact 4501 tggaacatac cagggacaga atatttaccc tgaagacgtg ccaccaatcg cgcggcaaaa 4561 gctacgcgaa gccgcaaatg caccctccac attactttac gagaaaactc ccaagaagag 4621 caacaatttc ttaactcgtt ttgtggaggc gaataggtcc cctacaactc cagctgcccc 4681 aacagtgtca actgtatcaa acatgacaag ggaacagctt gcggagtata ctagaattag 4741 gaaatccctt ggactcacag cagcgaagga atacagggcg caatttcagt gaaggtaaca 4801 ccactagcac aaatcggatc ctgggaaaca ggcagaacta cggttcataa gctcgggtag 4861 gccgtcaacc taccgccgta tcgtattgtg tttggccgat ggatgacctc cacgttatcg 4921 ccgtttgtat ttttgctcta actgtgctga cagggttagg cgcggtgatc ggctgttgtg 4981 ccggttgcct ccaccccccc ctttccctcc gcccttctgt ttaagcaaaa atctctcggt 5041 ctgtgcgaga gaaactcaaa aatatcgggg agctccggct cagtgagggg attaacgacc 5101 cccagtagag gctggtcttg gcggacttga ataacccgct ataggacgaa gtggtaaccg 5161 ccactgatca aatggtgaac atgcttctgt gttgtacact gccccggagc ccaccgggtt 5221 aacaaggcta ttccaccagc tcaatgaaat gagagtggag tggacggagt gggtgacttc 5281 gtgatgtaca cccgatcgtc aggattgaag acgttaaaac tcgacgacct agtgcaagtc 5341 gttaaactga ctagggtgga tacaccacac ccggcctaac ttgtaggcat acccacgata 5401 cgaaacgtgg gtctcttgga gccactacct gtgatgcaag gtagggtatg agtcttagca 5461 agctctgtgc caggagatgg acataaacca tagcaatcct gcaagtcatc atggcgaacc 5521 ataggtgaac cgtgccacgg gcctgtctac cgaaaggaaa agcagtatcc aacacagcaa 5581 tgtgttgggg gttacaccct tcggggtact cttaacgctg acactcgaaa gagcagttcg 5641 gcaaccc //