ID EF043235; SV 1; linear; genomic RNA; STD; VRL; 5665 BP. XX AC EF043235; XX DT 31-OCT-2006 (Rel. 89, Created) DT 31-OCT-2006 (Rel. 89, Last updated, Version 1) XX DE Barley yellow dwarf virus - PAV, complete genome. XX KW . XX OS Barley yellow dwarf virus PAV OC Viruses; Riboviria; Luteoviridae; Luteovirus. XX RN [1] RP 1-5665 RA Beckett R.J., Miller W.A.; RT "BYDV/CYDV Global Sequencing Project"; RL Unpublished. XX RN [2] RP 1-5665 RA Miller W.A.; RT ; RL Submitted (05-OCT-2006) to the INSDC. RL Plant Pathology, Iowa State University, 470 Bessey Hall, Ames, IA 50011, RL USA XX DR MD5; 6442713c9757b693db46e5432ce7ffa4. DR EuropePMC; PMC4422679; 25946037. DR RFAM; RF00434; BTE. DR RFAM; RF01508; BYDV_5_UTR. XX FH Key Location/Qualifiers FH FT source 1..5665 FT /organism="Barley yellow dwarf virus PAV" FT /isolate="003" FT /serotype="PAV" FT /mol_type="genomic RNA" FT /country="USA:Kansas" FT /isolation_source="infected wheat" FT /collected_by="William Bockus" FT /db_xref="taxon:2169986" FT primer_bind 1..19 FT /note="viral specific" FT CDS join(142..1158,1158..2744) FT /codon_start=1 FT /ribosomal_slippage FT /product="RNA-dependent RNA polymerase" FT /note="RdRp; P1-P2 fusion created by -1 ribosomal FT frameshift" FT /db_xref="GOA:A0FLF4" FT /db_xref="InterPro:IPR002166" FT /db_xref="InterPro:IPR007094" FT /db_xref="InterPro:IPR013674" FT /db_xref="UniProtKB/TrEMBL:A0FLF4" FT /protein_id="ABK19883.1" FT /translation="MFFEILIGASAKAVKDFISHCYSRLKSIYYSFKRWLMEISGQFKA FT HDAFVNMCFGHMADIEDFEAELAEEFAEREDEVEEARSLLKLLVAQKSKTGVTEAWTDF FT FTKSRGGVYAPLSCEPTRQELEAKSEKLEKLLEEQHQFEVRAAKKYIKEKGRGFINCWN FT DLRSRLRLVKDVKDEAKDNARAAAKIGAEMFAPVDVQDLYSFTEVKKVETGLMKEVVRE FT KNGEEEKHLEPIMEEVRSIKDTAEARDAASTWITETVKLKNSTLNADELSLATIARYVE FT NVGDKFKLDIASKTYLKQVASMSVPIPTNKDIKLKMVLQSPEARARRERMDVLDSVGFL FT EGLCTASGFESPFSILGLPEIAVTDGARLRKVSSNIRYLSQTHLGLVYKAPNASLHNAL FT VAVERRVFTVGKGDKAIYPPRPEHDIFTDTMDYFQKSIIEEVGYCKTYPAQLLANSYSA FT GKRAMYHKAIASLRTTPYHQKDANVQAFLKKEKHWMTKDIAPRLICPRSKRYNIILGTR FT LKFNEKKIMHAIDSVFGSPTVLSGYDNFKQGRIIAKKWQKFACPVAIGVDASRFDQHVS FT EQALKWEHGIYNGIFGDSELALALEHQITNNIKMFVEDKMLRFKVRGHRMSGDINTSMG FT NKLIMCGMMHAYFKKLGVEAELCNNGDDCVIITDRANEKLFDGMYDHFLQYGFNMVTEK FT PVYELEQLEFCQSKPVSINGKYRMVRRPDSIGKDSTTLLSMLNQSDVKSYMSAVAQCGL FT VLNAGVPILESFYKCLYRSSGYKKVSEEFIKNVISYGTDERLQGRRAYNETPITNHSRM FT SYWESFGVDPKIQQIVERYYDGLTVSAQLQSVKVTTPHLQSILLSIPENHSQNEY" FT CDS 142..1161 FT /codon_start=1 FT /product="P1" FT /note="ORF1" FT /db_xref="GOA:A0FLF5" FT /db_xref="InterPro:IPR013674" FT /db_xref="UniProtKB/TrEMBL:A0FLF5" FT /protein_id="ABK19882.1" FT /translation="MFFEILIGASAKAVKDFISHCYSRLKSIYYSFKRWLMEISGQFKA FT HDAFVNMCFGHMADIEDFEAELAEEFAEREDEVEEARSLLKLLVAQKSKTGVTEAWTDF FT FTKSRGGVYAPLSCEPTRQELEAKSEKLEKLLEEQHQFEVRAAKKYIKEKGRGFINCWN FT DLRSRLRLVKDVKDEAKDNARAAAKIGAEMFAPVDVQDLYSFTEVKKVETGLMKEVVRE FT KNGEEEKHLEPIMEEVRSIKDTAEARDAASTWITETVKLKNSTLNADELSLATIARYVE FT NVGDKFKLDIASKTYLKQVASMSVPIPTNKDIKLKMVLQSPEARARRERMDVLDSVGF" FT CDS 2858..4810 FT /codon_start=1 FT /transl_except=(pos:3458..3460,aa:OTHER) FT /product="aphid transmission protein" FT /note="P3-P5 fusion created by ribosomal read-through of FT the ORF3 stop codon" FT /db_xref="GOA:A0FLF6" FT /db_xref="InterPro:IPR001517" FT /db_xref="InterPro:IPR002929" FT /db_xref="InterPro:IPR029053" FT /db_xref="UniProtKB/TrEMBL:A0FLF6" FT /protein_id="ABK19885.1" FT /translation="MNSVGRRGPRRANQNGTRKRRRRTVRPVVVVQPNRAGPRRRNGRR FT KGRGGANPVFRPTGGTEVFVFSVDNLKANSSGAIKFGPSLSQCPALSDGILKSYHRYKI FT TSIRVEFKSHASATTAGAIFIELDTACKQSALGSYINSFTISRTASKVFRAEAINGKEF FT QESTIDQFWMLYKANGTTTDTAGQFIITMSVSLMTAKXVDSSTPEPKPAPEPTPTPQPT FT PAPQPAPEPTPAPVPKRFFEYIGTPTGTISTRENSDSISVSKLGGQSMQYIENEKCETK FT VIDSFWSTNNNVSAQAAFVYPVPEGSYSVNISCEGFQSVDHIGGNEDGYWIGLIAYSNS FT SGDNWGVGNYKGCSFKNFLATNTWRPGHKDLKLNDCQFTDGQIVERDAVMSFHVEATGT FT DACFYLMAPKTMKTDKYNYVVSYGGYTNKRMEFGTISVTCDESDVEAERITRHAETPIR FT SKHILVSEQYEQPLPTIIDQGLCDVQTPEQEQTLVDEEDKQTVSTEPDIALMEYEAATA FT EIPDAEEDVLPSKEQLSSKPVDTSGNKIPKPKEPEVLGTYQGQNIYPEDVPPIARQKLR FT EAAKAPSTLLYEKTPKKSNNFLTRFVEANRSPTTPAAPTVSTASNMTREQLAEYTRIRK FT SLGLTAAKEYKAQFQ" FT CDS 2858..3460 FT /codon_start=1 FT /product="coat protein" FT /note="ORF3; P3" FT /db_xref="GOA:A0FLF7" FT /db_xref="InterPro:IPR001517" FT /db_xref="InterPro:IPR029053" FT /db_xref="UniProtKB/TrEMBL:A0FLF7" FT /protein_id="ABK19884.1" FT /translation="MNSVGRRGPRRANQNGTRKRRRRTVRPVVVVQPNRAGPRRRNGRR FT KGRGGANPVFRPTGGTEVFVFSVDNLKANSSGAIKFGPSLSQCPALSDGILKSYHRYKI FT TSIRVEFKSHASATTAGAIFIELDTACKQSALGSYINSFTISRTASKVFRAEAINGKEF FT QESTIDQFWMLYKANGTTTDTAGQFIITMSVSLMTAK" FT CDS 2901..3362 FT /codon_start=1 FT /product="movement protein" FT /note="P4; ORF4 product translated via a leaky scanning FT mechanism" FT /db_xref="InterPro:IPR001964" FT /db_xref="UniProtKB/TrEMBL:A0FLF8" FT /protein_id="ABK19886.1" FT /translation="MAQERGAVEQFGQWLWSNPIEQDPDDEMVDAREEEGQILYLDQQA FT GLRYSYSQSTTLKPTLPGQSNSAPVYRNAQRFQTEYLSPTTVTRSQVSVLSLSHTRPQL FT RPALSLLNSTPRANNQPWVATLIPSQSAGPPQRSSEPKRLTGRNSRNQR" FT CDS 4917..5042 FT /codon_start=1 FT /product="P6" FT /note="ORF6; highly variable sequence" FT /db_xref="GOA:A0FLF9" FT /db_xref="InterPro:IPR009426" FT /db_xref="UniProtKB/TrEMBL:A0FLF9" FT /protein_id="ABK19887.1" FT /translation="MDNLHVIAVCIFALTVLTGLGAVIGCCAGCLLPPPSLRSSV" FT primer_bind complement(5650..5665) FT /note="viral specific" XX SQ Sequence 5665 BP; 1672 A; 1377 C; 1386 G; 1230 T; 0 other; agtgaagatt gaccatctca caaaagctgt tacgtgcttg taacacacta cacactcgtt 60 ttgtgttcga gaagtagttg caacaacggt ccccttattg cctgacaagc tgagggccac 120 ccttctatcc ccaccgccat catgttcttc gaaatactta taggagctag cgctaaggcg 180 gtcaaagact tcatcagtca ttgttactct cgtttaaaat ctatatatta ttcttttaaa 240 cgatggctga tggaaatatc tgggcagttt aaggcccatg acgcctttgt caacatgtgc 300 ttcggacaca tggctgacat tgaggacttc gaggcagagc tcgctgagga gtttgccgag 360 agggaggatg aggtggaaga ggcgaggagc ctcttgaaac tgctggtcgc ccaaaaatct 420 aaaactgggg tgaccgaggc ttggaccgac ttctttacga agtcgagagg tggcgtctat 480 gcgccacttt cctgcgagcc taccaggcag gagctagaag ctaagagcga gaagctcgaa 540 aaacttctag aagaacagca ccaattcgag gtgcgagcgg ccaagaaata tatcaaggaa 600 aagggccgcg gcttcatcaa ctgctggaac gacttgcgaa gtcgtctcag gctggtgaag 660 gatgtcaagg acgaggcgaa ggacaacgcc agagctgctg ccaagatcgg agcagaaatg 720 ttcgcccccg ttgacgtgca ggacctctac agttttacag aggtcaagaa ggtggagacc 780 ggcctcatga aggaggtcgt gagagagaaa aacggcgaag aagagaaaca cctcgagccc 840 atcatggaag aggtgagatc tatcaaggat accgccgaag ccagggacgc cgcctccact 900 tggatcacag agacagttaa gctgaaaaac tcaacgctta acgcagatga attatctctg 960 gccaccatcg cccgctacgt tgaaaacgta ggggacaaat tcaaactcga cattgctagc 1020 aagacatatc tcaagcaagt cgcatcgatg tctgtaccaa ttccaactaa caaggacatc 1080 aaattgaaga tggtgctgca gagtcctgaa gcacgtgcca ggcgggaacg catggacgtg 1140 cttgactctg tgggttttta gaggggctct gtaccgcctc tggttttgag agcccattct 1200 ctattctcgg gctgccagag attgcggtca cagacggagc ccggctccgt aaggttagta 1260 gtaatattag ataccttagc caaacccacc taggtcttgt atataaggcg ccaaatgcct 1320 ccctgcacaa tgcgcttgta gcagtggaga gaagagtttt tacagtagga aagggggaca 1380 aagcaatcta ccccccccgc ccagagcatg acattttcac tgatacaatg gattacttcc 1440 aaaaatccat tatagaagag gtgggatact gtaaaacata tccagcgcaa ctcctggcta 1500 acagctatag cgcaggaaag agggccatgt atcacaaagc cattgcatca ctgaggacta 1560 ccccttatca tcagaaggat gccaatgtgc aagctttcct gaagaaggaa aaacattgga 1620 tgaccaagga catcgccccc cgattgattt gcccccgcag caagcggtac aacatcatcc 1680 taggaactcg tttgaaattc aacgagaaga agatcatgca cgctatcgat agcgtgttcg 1740 gatcccccac tgtgctttcc ggctatgaca actttaaaca aggaagaatc atagccaaga 1800 agtggcaaaa gtttgcatgc cccgtcgcca tcggcgtgga tgctagccgc tttgaccaac 1860 acgtgtcaga gcaggcgctt aagtgggaac acgggatata caatgggatc ttcggagata 1920 gcgaactggc tcttgcactt gaacaccaaa tcaccaacaa catcaagatg tttgttgaag 1980 acaagatgct taggttcaag gtgagaggcc acagaatgtc cggtgacatt aataccagca 2040 tgggaaacaa gctcataatg tgcggcatga tgcatgcata tttcaagaag ctgggtgttg 2100 aagctgaact ttgcaacaac ggagacgact gtgtcatcat cactgataga gccaatgaga 2160 agctctttga tggcatgtac gaccatttcc tccagtatgg cttcaacatg gtgaccgaaa 2220 aaccagttta cgaactggag caattggagt tttgccagtc aaaaccggtc tctattaatg 2280 gaaagtatag aatggtcaga aggcccgata gcataggcaa agatagcaca acactactga 2340 gcatgctcaa tcaatccgac gtcaagagct acatgtcggc tgttgctcag tgtggcctgg 2400 tgctcaacgc tggagtaccc atacttgaaa gtttctataa atgcctatat agaagctcgg 2460 ggtacaagaa agtgagtgag gaatttatta aaaacgtcat atcgtatgga acagatgaga 2520 gactacaagg tagacgtgcc tataatgaaa cacctatcac aaaccacagt agaatgtcct 2580 actgggaatc attcggagtt gaccctaaga tacagcaaat cgtcgagagg tactacgacg 2640 gtcttacggt gagtgcccaa ctccagagcg tgaaggtgac gactccacat ctgcaatcaa 2700 tactgctttc cataccggaa aaccactcac aaaacgaata ttaattacca aatcttagct 2760 gggtttggga tagggttcat agttagtatc ccctgtacat tagctctcgc gtactttatt 2820 tacaataaag tttcagacac cactagagag gtggtgaatg aattcagtag gccgtagagg 2880 acctagacgc gcaaatcaaa atggcacaag aaagaggcgc cgtagaacag ttcggccagt 2940 ggttgtggtc caacccaatc gagcaggacc cagacgacga aatggtcgac gcaagggaag 3000 aggaggggca aatcctgtat ttagaccaac aggcgggact gaggtattcg tattctcagt 3060 cgacaacctt aaagccaact cttccggggc aatcaaattc ggccccagtc tatcgcaatg 3120 cccagcgctt tcagacggaa tacttaagtc ctaccaccgt tacaagatca caagtatccg 3180 tgttgagttt aagtcacacg cgtccgcaac tacggccggc gctatcttta ttgaactcga 3240 caccgcgtgc aaacaatcag ccctgggtag ctacattaat tccttcacaa tcagcaggac 3300 cgcctcaaag gtcttcagag ccgaagcgat taacgggaag gaattccagg aatcaacgat 3360 agaccagttt tggatgctct acaaggccaa tggaaccacc actgacacgg caggacaatt 3420 cattatcacg atgagtgtca gtttgatgac ggccaaatag gtagactcct caacaccgga 3480 accgaaacct gcaccagaac ctacaccaac cccacagcca acgccagcac cacagcccgc 3540 acccgaaccg actcccgcac ctgtccccaa aagattcttt gagtatatcg gcactccaac 3600 cggtacaatc tcaacaagag agaactctga cagtatttct gtcagcaagc tcggtgggca 3660 gtcgatgcag tacatagaga atgagaagtg tgaaacaaag gtcattgact ccttctggag 3720 cactaacaac aacgtgtctg cacaggcagc cttcgtttac ccagtgccgg aaggatcata 3780 cagtgtgaac atttcgtgcg aaggctttca atccgttgac cacataggag gcaacgagga 3840 tggttattgg attggtttaa ttgcctactc aaattcgtca ggagacaatt ggggggtagg 3900 caactacaaa gggtgcagtt tcaagaactt cttggcaacc aacacttgga gaccaggcca 3960 taaggatctc aagttgaacg attgccagtt cacagatgga caaatagttg agagggatgc 4020 cgtgatgtct ttccatgtgg aagcaacagg tactgacgcc tgtttctatc tcatggctcc 4080 caaaacaatg aaaactgaca agtacaacta tgttgtctca tatggagggt acacaaacaa 4140 acgaatggaa tttggtacca tatctgtgac atgtgatgaa tccgatgttg aggcagaacg 4200 cataacaagg catgctgaaa cacccatacg ttccaaacac atccttgtgt ccgaacagta 4260 tgagcaacct ttacccacca taatcgatca aggcttgtgt gatgtgcaaa ctcccgagca 4320 agaacaaaca ctggtggatg aagaagacaa acagactgtt tccacagaac ctgatatagc 4380 actcatggag tatgaagctg caacagccga aattccagat gctgaagagg atgttttgcc 4440 ctccaaggaa cagttgtctt ctaaaccggt ggacacgtcc ggcaacaaaa tacctaagcc 4500 caaggaacct gaagtacttg gaacatacca gggacagaat atttaccctg aagacgtgcc 4560 accaattgcg cggcaaaaac tacgtgaagc cgcaaaagca ccctccacac tactctacga 4620 gaaaactccc aagaagagca acaatttctt gactcgtttt gtggaggcga ataggtcccc 4680 tacaactcca gctgccccaa cagtgtcaac tgcatcaaac atgacaaggg aacagcttgc 4740 ggagtacact agaattagga aatcccttgg actcacagca gcgaaggaat acaaggcgca 4800 atttcagtga aggtaacacc actagcacaa atcggatcct gggaaacagg cagaactacg 4860 gttcataagc tcgggtaggc cgtcaaccta ccgccgtatc gtattgtgtt tggccgatgg 4920 acaacctcca cgttatcgcc gtttgtattt ttgctctaac tgtgctgaca gggttaggcg 4980 cggtgatcgg ctgttgtgcc ggttgccttc tccctccccc ctccctccgc tcttctgttt 5040 aagcaaaaat ctctcggtct gtgcgagaga aactcaaaaa tatcggggag cttcggctca 5100 gtgaggggat taacgacccc cagtaaaggc tggtcttggc ggacttgaat aacccgctat 5160 aagacgaagt ggtaaccgcc actgatcaaa tggtgaacat gcttctgtgt cgtacactgc 5220 cccggagcct accgggttaa caaggctatt ccaccagctc gatgagatga gagtggagtg 5280 gacggagtgg gtgacttcgt gatgtacacc cgatcgtcag gattgaagac gttaaaactc 5340 gacgacctag tgcaagtcgt taaactgact agggtggata caccacacct ggcctaactt 5400 gtaggcatac ccacgatacg aaacgtgggt ctcttggagc cactacctgt gatgcaaggt 5460 agggtatgag tcttagcaag ctctgtgcca ggagatggac ataaaccata gcaatcctgc 5520 aagtcatctt ggcgaaccat aggtgaaccg tgccacgggc ctgcctaccg aaaggaaaag 5580 cagtatccaa cacagcaatg tgttgggggt tacacccttc ggggtactct taacgctgac 5640 actcgaaaga gcagttcggc aaccc 5665 //