LOCUS NC_002160 5695 bp ss-RNA linear VRL 13-JAN-2004 DEFINITION Barley yellow dwarf virus-PAS, complete genome. ACCESSION NC_002160 VERSION NC_002160.2 GI:30090015 KEYWORDS . SOURCE Barley yellow dwarf virus-PAS ORGANISM Barley yellow dwarf virus-PAS Viruses; ssRNA positive-strand viruses, no DNA stage; Luteoviridae; Luteovirus. REFERENCE 1 (bases 1 to 5695) AUTHORS Beckett,R.J. and Miller,W.A. TITLE Sequences of novel luteovirus and polerovirus isolates JOURNAL Unpublished REFERENCE 2 (bases 1 to 5695) AUTHORS Beckett,R.J. and Miller,W.A. TITLE Direct Submission JOURNAL Submitted (23-DEC-1999) Plant Pathology, Iowa State University, 474 Bessey Hall, Ames, IA 50011, USA COMMENT VALIDATED REFSEQ: This record has undergone preliminary review of the sequence, but has not yet been subject to final review. The reference sequence was derived from AF218798. On Apr 24, 2003 this sequence version replaced gi:9634102. FEATURES Location/Qualifiers source 1..5695 /organism="Barley yellow dwarf virus-PAS" /virion /mol_type="genomic RNA" /serotype="PAV-129" /db_xref="taxon:228581" gene 139..2744 /locus_tag="BYDVgp1" /db_xref="GeneID:1489887" CDS join(139..1155,1155..2744) /locus_tag="BYDVgp1" /note="low-abundance product derived from -1 ribosomal frameshift" /codon_start=1 /product="RNA-dependent RNA polymerase P1-P2 fusion protein" /protein_id="NP_037635.1" /db_xref="GI:9634108" /db_xref="GeneID:1489887" /translation="MLLFELLIGASVKAVKDFISHCYSRLKSIYYAFKRWLMEISGQF KAHDAFVNMCFGHIADIEDFEAELAEEFALKEDEIEEARSLMRLLTAQKAKTGVVEAW TDFFVKSRGGVYAPLSCEPSKAELEAKADKLERLLEDMHKFEVQAAKKYIKEKGRGFI NCWNDLRSRLKLVKEVNEEAKDNIKAASKIGVEFSAPTNIQDLYAFTKVEKVETGLMK EVTKMVHGEETKHMEPITEDMRSIKDTAEDREAASKWITEVVKLKNSTLSADELSLAT IARYVENIGEKYKLDIASKTYLKQCAMMSVPIPTQKDIKMKMVIQSPAARAARERVAV LDSQGFLEGLCAASGFESPFSLLRLPEIKVTDGARLRKVSSNIRYLTQTHLGLVYKAP NASLHNALVAVERRVFTVGKGDKAIYPPHPEHDIFTETMDYFAESIIDKVGYCKTYPA QQLALSYSAGKRSQYFKAIESLKKEPYQQKDSNVQAFLKKEKHWMTKAIAPRLICPRS KRYNIILGTRLKFNEKKIMHAIDSVFRSPTVLSGYDNFTQGRIIASKWQKFASPVAIG VDASRFDQHVSEQALKWEHGIYNGIFGDTELATALEHQLVNNIKMFVEDKMLSFQVRG HRMSGDINTSMGNKLIMCGMMHAYFKMLGVEAELCNNGDDCVIITERANEKLFDGMYD HFLKYGFNMVTEAPVYELGELEFCQSKPVRIDGKYRMVRRPDCIGKDSCTLLSMLNEA DVKSYMSAVAQCGLVLNAGVPILESFYRCLYRSSGYKKVSEEYIKNVISYGTDERLQG RRTFKETPITSDNRMSYWESFGVDPKIQQLVERYFDDLTVSAQLQSVKVTSPHLQSIL LSIPENNSQNEY" gene 139..1161 /locus_tag="BYDVgp2" /db_xref="GeneID:1489884" CDS 139..1161 /locus_tag="BYDVgp2" /note="ORF1" /codon_start=1 /product="RNA-dependent RNA polymerase P1" /protein_id="NP_037636.1" /db_xref="GI:9634103" /db_xref="GeneID:1489884" /translation="MLLFELLIGASVKAVKDFISHCYSRLKSIYYAFKRWLMEISGQF KAHDAFVNMCFGHIADIEDFEAELAEEFALKEDEIEEARSLMRLLTAQKAKTGVVEAW TDFFVKSRGGVYAPLSCEPSKAELEAKADKLERLLEDMHKFEVQAAKKYIKEKGRGFI NCWNDLRSRLKLVKEVNEEAKDNIKAASKIGVEFSAPTNIQDLYAFTKVEKVETGLMK EVTKMVHGEETKHMEPITEDMRSIKDTAEDREAASKWITEVVKLKNSTLSADELSLAT IARYVENIGEKYKLDIASKTYLKQCAMMSVPIPTQKDIKMKMVIQSPAARAARERVAV LDSQGF" gene 2858..4810 /locus_tag="BYDVgp3" /db_xref="GeneID:1489885" CDS 2858..4810 /locus_tag="BYDVgp3" /note="translated from subgenomic RNA1 as a fusion protein via read-through of the coat protein (P3) stop codon; may play a role in systemic movement" /codon_start=1 /transl_except=(pos:3458..3460,aa:OTHER) /product="aphid transmission protein P5" /protein_id="NP_037637.1" /db_xref="GI:9634106" /db_xref="GeneID:1489885" /translation="MNSVGRRGPRRANQNGPRRRSRRTIRPVVVVQPNRAGPRRRNGR RSGRRGPNSIPGSTGRTEVFIFSVDNLKANSSGTIKFGPSLSQCPALSDGILKSYHRY KITSIRVKFQSHASAATSGAIFVELDTACKQSALGSYINSFTISKTASKSFRAEAING KEFQESTIDQFWLLYKANGTTTDTAGQFIITINVSMLTPKXVDSSTPEPKPAPEPTPA PQPTPTPQPTPEPTPAPVPKRFFEYVGTPTGVISTRENSDSISVSKLGGQSMQYIENE KCESKVIDSFWSTNNNVSAQAAFVFPVPEGSYSVNISCEGFQSVDHIGGNEDGYWIGL IAYSNSSGDNWGIGNYKGCSFKNFLATNTWRPGHKDLKLNDCQFTDGQIVERDGVISF HVDATGTDACFYLAAPKTMKTDKYNYVVSYGGYTNKRMEFGTISVTFDESDVEAERIA RHSETPARHNHILLSESYEEPLPTIIDQGLCDVKTPEQEIVKVDEEDRQTVSTEPDIA LQEYEAATAEIPDAEEDVLPSKEQLSVKPVDSSGTPLPKSKEPEVLGTYQGMNIYPED VPPVARQKLREAAKAPSTMLYDKAPKGSKSILSRFVEGNRSKATPAAPTVSTTSNMTR EQLREYTRIRNSLGVTAAKEYKAQFQ" gene 2858..3460 /locus_tag="BYDVgp4" /db_xref="GeneID:1489888" CDS 2858..3460 /locus_tag="BYDVgp4" /note="ORF3; translated from subgenomic RNA1; occasional read-through of stop codon produces P3-P5 fusion protein" /codon_start=1 /product="coat protein P3" /protein_id="NP_037638.1" /db_xref="GI:9634104" /db_xref="GeneID:1489888" /translation="MNSVGRRGPRRANQNGPRRRSRRTIRPVVVVQPNRAGPRRRNGR RSGRRGPNSIPGSTGRTEVFIFSVDNLKANSSGTIKFGPSLSQCPALSDGILKSYHRY KITSIRVKFQSHASAATSGAIFVELDTACKQSALGSYINSFTISKTASKSFRAEAING KEFQESTIDQFWLLYKANGTTTDTAGQFIITINVSMLTPK" gene 2901..3362 /locus_tag="BYDVgp5" /db_xref="GeneID:1489889" CDS 2901..3362 /locus_tag="BYDVgp5" /note="ORF4; translated via leaky scanning on subgenomic RNA1" /codon_start=1 /product="movement protein P4" /protein_id="NP_037639.1" /db_xref="GI:9634105" /db_xref="GeneID:1489889" /translation="MAQEGGAVEQFGQWLWSNPIEQDPDDEMVDAQEEEGQILYLDQQ AGLRYSYSQSTTLKPTLPGQSNSAPVYRNAQRFQTEYLSPTTVTRSQVSVLSFSHTRP PLRRALSLLNSTPRASNQPWVATLIPSPSAKLPPSPSEPRRLMGRNSKNQR" gene 4940..5059 /locus_tag="BYDVgp6" /db_xref="GeneID:1489886" CDS 4940..5059 /locus_tag="BYDVgp6" /note="ORF6; highly variable sequence among BYDV isolates" /codon_start=1 /product="P6 protein" /protein_id="NP_037640.1" /db_xref="GI:9634107" /db_xref="GeneID:1489886" /translation="MDDLHVIAVCMLAMTTFTAVGVVLGCCIGCIEALCGSKR" ORIGIN 1 tgaaggttga ccacctacac aaaaagactt tgtgcttgaa gtctacaacc cacctgtttt 61 gtattcagga agttgtctgc aacaacggtc aacagtacgt ctgacaccgt actgccccct 121 cccccccccc ccgccaacat gcttcttttt gaacttttga tcggcgctag cgtcaaagct 181 gtaaaagact tcatcagcca ctgctactcc agactaaaaa gcatatatta tgctttcaaa 241 agatggttga tggagatctc tgggcaattt aaggcccacg acgcttttgt caacatgtgc 301 ttcgggcaca ttgctgacat cgaagacttc gaggcggaac tcgctgaaga gttcgccttg 361 aaggaggatg aaatcgagga ggcgagaagc ctcatgcgtc tgctcaccgc ccaaaaagca 421 aaaactgggg tggtggaggc ttggaccgac ttctttgtga agtcgagagg cggggtttat 481 gccccgcttt cctgcgagcc ttccaaagca gagcttgagg ccaaagccga caagctcgaa 541 agactacttg aggacatgca caaatttgag gtgcaagcgg caaaaaaata cataaaagaa 601 aagggccgcg ggttcatcaa ctgctggaac gaccttcgtt ccagactcaa gttagtcaag 661 gaggtaaatg aagaggccaa agacaacatc aaggccgcct ccaagatcgg cgtggaattc 721 tccgcaccca ccaacatcca ggacctctac gccttcacca aggttgaaaa ggtcgagact 781 ggcctcatga aggaggtcac caaaatggtg cacggagaag aaaccaagca catggagccg 841 ataactgaag acatgcgctc catcaaggac accgcggaag accgagaggc cgcctccaag 901 tggataacgg aggtggttaa attgaaaaat tcaaccctgt ctgccgacga gctgtccctg 961 gccaccatcg cccgatatgt ggaaaacatc ggggaaaaat acaagctcga cattgcctcc 1021 aaaacatatc tcaagcaatg cgcaatgatg tctgttccaa ttcctactca aaaagacatc 1081 aaaatgaaga tggtgatcca gagccctgca gcacgagctg cgcgtgagcg cgtagctgtg 1141 cttgattctc agggttttta gaggggctct gtgccgcctc cggttttgaa agtccctttt 1201 ctctattaag actgccggag attaaggtca cagacggagc ccgtttacgt aaggttagta 1261 gtaatattag gtacctaacc caaacccacc tcggcttggt atacaaagcc ccaaatgcct 1321 ccctgcacaa tgccttggtt gcagtggaga gaagagtgtt tacagtagga aagggggaca 1381 aagctatata ccccccccac ccggaacatg acattttcac tgagactatg gactacttcg 1441 cagagtccat aattgacaag gtgggatact gtaaaacata ccctgcacag caattagctc 1501 ttagttatag tgcagggaag cggtcacaat acttcaaagc catagagtct ctcaagaagg 1561 aaccttatca acaaaaggac tctaatgtgc aggcattcct caagaaggag aagcattgga 1621 tgaccaaagc catcgccccg cgcctaatct gcccccgctc taagcggtac aatatcatcc 1681 ttggaactcg tttaaaattc aacgagaaga agatcatgca tgctatcgat agtgtgttta 1741 gatcccccac tgtgctttct ggctatgaca acttcactca aggaagaatc atagccagca 1801 agtggcaaaa gtttgcatca cccgttgcta tcggtgttga tgctagccgc ttcgaccaac 1861 acgtgtctga gcaggcgctt aagtgggaac acgggatata caatggcata tttggcgaca 1921 ctgaattggc cactgctctc gaacatcaac ttgtaaataa tatcaaaatg ttcgttgagg 1981 acaagatgct ttcatttcaa gtgagaggcc acagaatgtc cggggatata aacaccagca 2041 tgggaaacaa actgataatg tgtggcatga tgcacgcata ctttaaaatg ctgggtgttg 2101 aagctgaact gtgcaacaat ggggacgact gtgtcatcat cactgagaga gccaatgaga 2161 agctctttga tggcatgtac gaccacttcc taaagtacgg cttcaacatg gtgacggaag 2221 ccccagttta cgaactcggg gagcttgaat tttgtcaatc aaaacccgtc agaatagatg 2281 gcaaatacag gatggtgagg agaccagact gtattgggaa agatagctgc acacttctga 2341 gcatgttgaa tgaagctgac gtcaagagtt atatgtcagc tgtggctcag tgtgggctcg 2401 ttctgaacgc gggtgtaccc attctggaaa gcttctaccg ctgtttgtac agaagctctg 2461 ggtacaagaa agtaagtgag gaatacatca aaaacgtcat atcatatgga acagatgaac 2521 gccttcaagg tagacgtacc ttcaaggaga cacctatcac aagcgacaat cgaatgtcgt 2581 actgggaatc attcggagtt gaccctaaga tacaacaact cgtcgagcgg tacttcgacg 2641 atcttacggt aagtgcccaa ctccaaagtg tgaaggtgac atctccacat ctgcaatcaa 2701 tcctcctctc cattccggag aacaactcgc aaaacgaata ttaattacca aatcttagcc 2761 gggtttggga tagggtttat agtaagtatt ccctgtacat tagctctcac gtactttatt 2821 tacaataaag tttcagacac cactagagag gtggtgaatg aattcagtag gccgtagagg 2881 acctagacga gcaaatcaaa atggcccaag aaggcggagc cgtagaacaa ttcggccagt 2941 ggttgtggtc caacccaatc gagcaggacc cagacgacga aatggtcgac gctcaggaag 3001 aagagggcca aattctatac ctggatcaac aggcaggact gaggtattca tattctcagt 3061 cgacaacctt aaagccaact cttccgggac aatcaaattc ggccccagtt tatcgcaatg 3121 cccagcgctt tcagacggaa tacttaagtc ctaccaccgt tacaagatca caagtatccg 3181 tgttaagttt cagtcacacg cgtccgccgc tacgtcgggc gctatctttg ttgaactcga 3241 caccgcgtgc aagcaatcag ccttgggtag ctacattaat tccttcacca tcagcaaaac 3301 tgcctccaag tccttcagag ccgaggcgat taatgggaag gaattccaag aatcaacgat 3361 agaccaattc tggctactct acaaggcaaa tgggaccact actgacaccg ctggacagtt 3421 catcataacg ataaacgtca gtatgttaac tcccaaatag gtagactcct caacaccgga 3481 accgaaacca gcaccagagc caacaccagc cccacaaccc actccaaccc cacagcccac 3541 accagaacca actcctgcac ctgtccccaa gagattcttt gaatacgtcg gaactccaac 3601 cggcgtgatt tcaacgcgag aaaactctga cagtatttct gtcagcaagc ttggtggaca 3661 atccatgcag tacatcgaga atgagaaatg tgaatcaaag gttattgatt ccttctggag 3721 caccaacaac aacgtttctg cccaggcagc attcgttttt ccagtgccag aagggtcata 3781 cagtgttaac atttcgtgtg aaggctttca atccgttgac cacatcggtg gtaacgagga 3841 tggctactgg attgggctca tcgcttactc caattcatca ggagacaact ggggaatcgg 3901 taattacaaa gggtgcagtt tcaaaaattt cttggcaaca aacacttgga gacctggcca 3961 caaagatctc aagttgaatg actgccagtt cacagatgga caaatagttg aaagggatgg 4021 cgtgatatct tttcatgtag atgcaacagg tactgacgcc tgtttctacc ttgcagcccc 4081 caagacaatg aaaactgaca aatacaacta tgttgtttcc tatggagggt acacgaacaa 4141 acggatggag ttcggtacca tatctgtgac atttgatgaa tccgatgttg aggcagaacg 4201 cattgccagg cattcagaga ccccggctcg tcacaaccat atactcctat ctgagagtta 4261 cgaagagcca ttacccacca taatcgacca aggcttgtgt gatgtgaaaa ctcccgagca 4321 agaaattgtg aaggtggatg aagaggacag acagactgtt tccactgaac ctgatatagc 4381 attgcaggaa tatgaagctg ccacagctga aatacctgat gctgaagagg acgttttgcc 4441 ctccaaggaa caactgtctg tcaaacccgt ggactcatcc ggaacaccac ttccaaaatc 4501 taaggaacct gaagtacttg gaacgtatca gggtatgaat atatacccag aggatgtgcc 4561 accggtggct cgtcaaaagc tgcgcgaggc agcaaaagcc ccttccacca tgctttacga 4621 caaggccccc aaggggagca aatcaattct gtcgcgattt gtggaaggca ataggtccaa 4681 ggcaacccct gctgctccta cagtgtcaac tacttccaat atgacaagag agcagttgcg 4741 agagtacact cgtattagaa atagtttagg tgttaccgca gcaaaagagt acaaagcgca 4801 atttcagtga agattaacac cactaacaca agccgaatcc tgggaaacag gcagaactta 4861 ggttcgtaag ctcgggtaat tggaaggtgg gctgtcaacc caccaccatc ttaccgccgc 4921 attgccttgt gtttggccga tggacgatct ccatgtcatc gctgtttgta tgcttgccat 4981 gaccactttc acagcagtgg gagttgtgct tggttgctgc attggttgta tagaagccct 5041 ctgtggcagt aaacgctaaa catgtatctc ggtctgtgcg agatgcaact caaaaacaag 5101 tagggagctt gggctcagtg agaggattaa cgaccctcag taaaggctgg tcctggtgga 5161 catgaataac ccgctatagg acgaagtgga agccaaccac tgatcaaata tggcagcttg 5221 cttatgagct gtacactgcc ccagaggata ctgggtaaac aaatctatcc acccaactcg 5281 atgaaatgag agtggaggtg gcggggtggg tgaccccgtg atgtacaccc gagcgtcagg 5341 attgaagacg tcataaaact caacgagatg agcaacactc gttaaaagtt ccccggctga 5401 tacacccagt cggcccgacc cgtaggcata ccctcgatac gaaacgaggg ttcctaggag 5461 ccaccacctg tgatgcaagg tggggtaaga gtcttagcaa gctctgtacc tgggaatgga 5521 cataaaccat agcaatccta cggcatccgg ggcgcgagct ttccgcacta ggtgaagcgt 5581 gccactggcc tgttgcaagc aatctagctc tgcttgcaac agtatccctt agaagcaatt 5641 cttcgggggg actggattct aactgccggc actcgaaaga gaagcccggc atccc //