LOCUS       NC_003369               5964 bp ss-RNA     linear   VRL 13-JAN-2004
DEFINITION  Bean leafroll virus, complete genome.
ACCESSION   NC_003369
VERSION     NC_003369.1  GI:18314284
KEYWORDS    .
SOURCE      Bean leafroll virus
  ORGANISM  Bean leafroll virus
            Viruses; ssRNA positive-strand viruses, no DNA stage; Luteoviridae;
            Luteovirus.
REFERENCE   1  (bases 1 to 5964)
  AUTHORS   Domier,L.L., McCoppin,N.K., Larsen,R.C. and D'Arcy,C.J.
  TITLE     Nucleotide sequence shows that Bean leafroll virus has a
            Luteovirus-like genome organization
  JOURNAL   J. Gen. Virol. 83 (Pt 7), 1791-1798 (2002)
   PUBMED   12075101
REFERENCE   2  (bases 1 to 5964)
  AUTHORS   Domier,L.L., McCoppin,N.K. and Larsen,R.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-OCT-2001) Dept. Crop Sciences, University of
            Illinois, USDA-ARS, 1102 S. Goodwin Ave., Urbana, IL 61801, USA
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AF441393.
FEATURES             Location/Qualifiers
     source          1..5964
                     /organism="Bean leafroll virus"
                     /mol_type="genomic RNA"
                     /db_xref="taxon:12041"
     gene            179..2883
                     /locus_tag="BLRVgp1"
                     /db_xref="GeneID:932045"
     CDS             join(179..1278,1278..2883)
                     /locus_tag="BLRVgp1"
                     /note="ORFs 1+2; low-abundance product derived from  -1
                     ribosomal frameshift during translation of ORF1"
                     /codon_start=1
                     /exception="ribosomal slippage"
                     /product="RNA-dependent RNA polymerase P1-P2 fusion"
                     /protein_id="NP_563609.1"
                     /db_xref="GI:18314286"
                     /db_xref="GeneID:932045"
                     /translation="MFNFDSLITASSRVVKDFIHFCYNRARSVYCALKRWLWELQGKF
                     DAHNAFVDLCYDAMYGIEKFEEELAEEYTLAESEVALAECHYRYLVSNGAPLTHWPVP
                     CPPPGAHRSIDDYEDSVDEAGAFEEVIPSVPKPEPIPSKDGKKDHSKSNPFRVKAFIN
                     LVKAKEVLQATEQKIKVVYEEEIGESPFGRWFNTLPSRMHYIKRALKKRAVNAKRAKH
                     VTSMMKEVNVIPDFVACCEVVQVPTGEMIPPKKNEHGEDVGEPTPKTKMVRRVLPECA
                     AEARSYIRQHIRNNNMRLIDGTDVAHATINRYALKFCEELDLDLPSTTMLVDYAMTMV
                     PLPLKNDIERAKIVHSPNARRIRDELDCLTSSVFLEGLCSDSGFESPFSILGLPEIVV
                     RSGAIPRKSRSKINFLSQFTLGLDYQCPNPSLHNALVAVERRVFTVGKGNEVVRPYSP
                     LQGQFEKMNYFRDAIVKDVGCPKTYTPEQLAATFKSGKRSLYNTAVLSLKRKAVEKQD
                     SFVTAFLKMEKHMMCKKIAPRLICPRNKRYNVELGRRLKFSEKKFMHAIDNVFKSPTV
                     LSGYDSFKVGRIIADKWGRFKRPVAIGVDASRFDQHVSKQALEWEHSIYNGCFRDKQL
                     EELLKWQTENKVMLFVEDKILKFKVSGHRMSGDINTSMGNKLIMCGMMHNYFRELGVE
                     AELCNNGDDCVIICERKNEKRFSDMHRWFKEYGFDMQIEKPVYKLTELEFCQSKPVKI
                     NGFYRMVRKPQSISKDAHSLISMASAEDVKTFMSATAQCGLILNSGVPVLEAFHNCLY
                     KASGYKHVSQELIDKVVSFGTQDKLGLRKERVEEPVTMENRLSYWESFGVDPQTQVLV
                     ERYFNNLQVSIEPRGVKRLTPLLDAKLLNIDIPARCSVSLPTILQ"
     gene            179..1285
                     /locus_tag="BLRVgp2"
                     /db_xref="GeneID:932047"
     CDS             179..1285
                     /locus_tag="BLRVgp2"
                     /note="ORF1"
                     /codon_start=1
                     /product="RNA-dependent RNA polymerase P1"
                     /protein_id="NP_563610.1"
                     /db_xref="GI:18314285"
                     /db_xref="GeneID:932047"
                     /translation="MFNFDSLITASSRVVKDFIHFCYNRARSVYCALKRWLWELQGKF
                     DAHNAFVDLCYDAMYGIEKFEEELAEEYTLAESEVALAECHYRYLVSNGAPLTHWPVP
                     CPPPGAHRSIDDYEDSVDEAGAFEEVIPSVPKPEPIPSKDGKKDHSKSNPFRVKAFIN
                     LVKAKEVLQATEQKIKVVYEEEIGESPFGRWFNTLPSRMHYIKRALKKRAVNAKRAKH
                     VTSMMKEVNVIPDFVACCEVVQVPTGEMIPPKKNEHGEDVGEPTPKTKMVRRVLPECA
                     AEARSYIRQHIRNNNMRLIDGTDVAHATINRYALKFCEELDLDLPSTTMLVDYAMTMV
                     PLPLKNDIERAKIVHSPNARRIRDELDCLTSSVF"
     gene            3093..5261
                     /locus_tag="BLRVgp3"
                     /db_xref="GeneID:932046"
     CDS             3093..5261
                     /locus_tag="BLRVgp3"
                     /note="ORFs3+5; 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 and/or
                     aphid transmission"
                     /codon_start=1
                     /transl_except=(pos:3681..3683,aa:OTHER)
                     /product="coat P3 and systemic movement/aphid
                     transmission P5 fusion protein"
                     /protein_id="NP_563611.1"
                     /db_xref="GI:18314289"
                     /db_xref="GeneID:932046"
                     /translation="MVARGKRVVVRQLQTRARRRLPVVLATAPVRPQRKRRQRGRNNK
                     SRGGNGFARRSSQVHEFVFSKDNLNGNSKGSITFGPSLSECKPLADGILKAYHEYNIT
                     NVELAYITEASSTSSGSIAYELDPHLKNTTIQSKINKFSITKSEKKKFSRKAINGQAW
                     HDTSEDQFRILYEGNGDAKIAGSFRVTIKVLTQNPKXVDGEPDPPGPGPDPPPPTPAP
                     TPQPQPTPKHERFIVYTGVPESRISAQSTDDSISVYSLQNQRLRYIEDENANWTNIEA
                     RWYSNNNVKATPMFIFPVPQGKWSVEISTEGYQPTSSTTDPNNGKCDGLIAYSDDDKT
                     DVWNVGVQKNITLSNNKADNTWKYGHPDLEINNCKFNNRQVLERDAYISFHVETTGPN
                     ASFFLVAPPVQKTARYNYAVSYGAWTDRMLEFGSVTVALDEHLEGGNSSRYIRRSPRP
                     GHLESTRTYDLHLLPHMDDLIAANTTAVVDGYGSSISIDRQVLVAVDNHIVDSGDETD
                     DLPGYSSSSSEAPKLPAVNQTKLPPKGFLSRLRESEIEEIADKPTEITTPEVRQLADA
                     THQPFAAGMYNDAFERLSINEKKRNFDSVKDDIAEIERTLPKEEYRVPKLPRIKPASE
                     VDNDHYGESQQTLAEIERRNVWASKDDAVAVESPPPGYPLGPIEARELMPVEWSRPDY
                     EPPKPKKSLFGRLKSQAKVEANPSSPRNDIRRSSFSSFRR"
     gene            3093..3683
                     /locus_tag="BLRVgp4"
                     /db_xref="GeneID:932044"
     CDS             3093..3683
                     /locus_tag="BLRVgp4"
                     /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_563612.1"
                     /db_xref="GI:18314287"
                     /db_xref="GeneID:932044"
                     /translation="MVARGKRVVVRQLQTRARRRLPVVLATAPVRPQRKRRQRGRNNK
                     SRGGNGFARRSSQVHEFVFSKDNLNGNSKGSITFGPSLSECKPLADGILKAYHEYNIT
                     NVELAYITEASSTSSGSIAYELDPHLKNTTIQSKINKFSITKSEKKKFSRKAINGQAW
                     HDTSEDQFRILYEGNGDAKIAGSFRVTIKVLTQNPK"
     gene            3238..3666
                     /locus_tag="BLRVgp5"
                     /db_xref="GeneID:932048"
     CDS             3238..3666
                     /locus_tag="BLRVgp5"
                     /note="ORF4"
                     /codon_start=1
                     /product="movement protein P4"
                     /protein_id="NP_563613.1"
                     /db_xref="GI:18314288"
                     /db_xref="GeneID:932048"
                     /translation="MDLPEDQARFTNSYSLRTTSMETPREVSRSGRLYQSASRSQMAY
                     SRPTMSIISRTSSWRTSPRPLPPPQVPSLMNSILTSRTQQSSPKLTNSASPSLRRKSS
                     LGRLSMDRHGTTLQRTNSGFSMKETETPRLLDRSESLSRY"
ORIGIN      
        1 ggtaaagttg acacctttac aagagcaggt tttacaagtt gactacttgt gtattggaaa
       61 cctcactgcc caacgcctcc gtatcgcgat tgcagtttac attagtgtct tttaaatgtt
      121 taacctcact gcccaacgcc tccgtaycgc gattgcagtt tgtattagtr tcttttaaat
      181 gtttaatttt gatagcttga tcaccgcgtc ttcgcgggtg gtcaaagatt ttattcattt
      241 ttgttacaat agggcaaggt cagtatactg tgcccttaaa cgctggctgt gggagctgca
      301 gggaaaattt gatgcacata atgcgtttgt tgatctctgc tacgatgcca tgtatggcat
      361 tgaaaaattt gaggaggagc tagccgagga atataccctg gctgaatctg aagtcgccct
      421 agctgagtgc cattataggt acttggttag caatggtgct cccctcaccc actggccggt
      481 accttgcccg cctcctggtg ctcatcgttc catagatgac tatgaagatt ctgtggacga
      541 ggctggggca tttgaggaag tgattccctc tgtgcctaaa cctgaaccta tcccttctaa
      601 ggatgggaag aaggaccact ctaaaagtaa tccttttagg gttaaagctt tcattaacct
      661 cgtgaaagca aaagaggttc tacaggccac tgaacaaaaa attaaggtgg tctatgagga
      721 agagattgga gagagcccct ttggaaggtg gtttaatact ctcccgtccc gcatgcatta
      781 catcaagcgt gcgctgaaga aacgtgctgt caacgcaaag agagcaaagc acgtaacaag
      841 catgatgaag gaagtcaacg tgattcctga cttcgtcgca tgctgtgaag tcgtccaggt
      901 acctactggc gaaatgatac ccccaaagaa aaatgaacat ggggaagatg ttggcgaacc
      961 cactcccaaa acaaaaatgg tgagaagggt actccccgaa tgtgcagctg aagcgcgttc
     1021 gtacataagg cagcatatcc gtaataacaa catgcgcctt attgacggca ctgacgtggc
     1081 ccacgctacc ataaataggt atgcgttaaa gttctgcgag gaacttgatc tggatctacc
     1141 aagcacaact atgctggttg attatgccat gactatggtc ccccttcccc tcaaaaatga
     1201 cattgagagg gcgaagatag ttcactcacc taatgctaga cgcattagag atgagttgga
     1261 ctgtctcacc tcatcggttt tttagagggg ctctgctccg actctggttt tgaatccccc
     1321 ttttctattt tgggattacc agagatcgtg gtgcgtagcg gggctatccc taggaagagt
     1381 cgtagtaaga ttaattttct tagtcagttt accctaggcc tagattacca gtgtcctaat
     1441 cccagcttgc acaatgcact ggtcgcagtt gaacgtcgag tgttcactgt aggaaaagga
     1501 aatgaggtgg tgcgtcctta ctctcccctt cagggtcagt ttgaaaagat gaactacttt
     1561 agagatgcta ttgttaagga tgttggatgt ccaaagacat acacaccaga acaacttgct
     1621 gccactttca aatctgggaa gaggtcgctg tacaacacag cggttctctc cttgaagagg
     1681 aaagctgttg agaagcaaga ttcgtttgtt acagcatttt tgaagatgga aaaacatatg
     1741 atgtgtaaga agatcgcacc cagacttatc tgcccccgaa ataaacggta caatgttgaa
     1801 ttagggcggc ggcttaaatt ctctgagaag aaatttatgc acgcaataga taatgtcttt
     1861 aaatccccca ccgttctcag cggttatgat agtttcaaag tgggaaggat tatagccgat
     1921 aaatggggca ggtttaagcg ccccgtagcc attggtgttg atgccagtcg ctttgaccaa
     1981 catgtcagca agcaggccct agaatgggaa cactctattt ataatgggtg ttttcgagac
     2041 aaacaactag aggaactctt gaaatggcaa acagaaaaca aagttatgct gtttgttgaa
     2101 gataagatat tgaagttcaa agtgtctgga cacagaatgt caggagacat caacacatca
     2161 atgggcaaca aattgatcat gtgcgggatg atgcacaatt acttcagaga gcttggtgta
     2221 gaagctgagc tatgcaacaa tggagatgat tgtgtcatta tctgtgagcg aaaaaacgag
     2281 aaaagattct cagatatgca cagatggttt aaggaatatg gcttcgatat gcagatagag
     2341 aaacccgttt acaaactaac ggagttagaa ttttgccaat ccaaaccggt caagatcaac
     2401 ggcttttaca gaatggtgcg taaaccacag tctatttcaa aggacgcaca ttctctcatt
     2461 tccatggcat cagctgaaga tgtcaagacc ttcatgagtg ctactgctca atgcgggtta
     2521 attttaaata gtggagtacc cgtgttggaa gcatttcata attgcctata caaagcttcc
     2581 gggtacaaac atgtttcgca ggaactaatc gacaaggtag tctcctttgg cacgcaagac
     2641 aaactcgggc tcaggaaaga gcgagttgaa gagccagtaa ctatggaaaa taggttgagt
     2701 tactgggagt cttttggggt tgacccgcaa actcaggtcc ttgttgaacg atacttcaac
     2761 aatttgcagg ttagcatcga gccccgtggc gtaaagagat tgacgccttt acttgacgcg
     2821 aaacttttaa acatagacat ccctgctaga tgctctgtgt ccttacccac tattctgcag
     2881 tagattatat tatattatta gtagctatta ttatattagt agttctcaac ctcttgctta
     2941 gctattgcct gagaagagaa gaataggttc cttcgattac aagttcttag ctgcgtttgt
     3001 gttgggcttt gtatccaaca ttccagttac agcattggga atctatattg tttaccaacg
     3061 gattctaaaa gagatcagag aaataatcaa cgatggtcgc tagaggaaaa cgagttgtcg
     3121 ttcgacaatt acagacccgc gcaaggagac gtttaccagt cgttctggct acggcccctg
     3181 tgcgaccaca acgaaaacga cgacaacgag gacgaaataa caaatctcga ggaggaaatg
     3241 gatttgcccg aagatcaagc caggttcacg aattcgtatt ctctaaggac aacctcaatg
     3301 gaaactccaa gggaagtatc acgttcgggc cgtctctatc agagtgcaag ccgctcgcag
     3361 atggcatact caaggcctac catgagtata atatcacgaa cgtcgagctg gcgtacatca
     3421 ccgaggcctc ttccacctcc tcaggttcca tcgcttatga actcgatcct cacctcaaga
     3481 acacaacaat ccagtccaaa attaacaaat tcagcatcac caagtctgag aagaaaaagt
     3541 tctctcggaa ggctatcaat ggacaggcat ggcacgacac ttcagaggac caattcagga
     3601 ttctctatga aggaaacgga gacgccaaga ttgctggatc gttcagagtc actatcaagg
     3661 tattaactca gaatccaaaa taggtagacg gagaaccgga tcctccgggc cctggcccag
     3721 atccaccacc accaacacct gcaccaacac cacaaccaca gccaacgccg aagcacgaaa
     3781 gattcatcgt ttatactggc gtacccgagt cccgcattag tgcgcaatca acggatgatt
     3841 caatctccgt ttattctttg caaaatcaaa gattgcgata catcgaggac gaaaatgcga
     3901 actggacgaa tattgaagcc aggtggtact ctaacaacaa tgttaaagcc accccgatgt
     3961 ttatttttcc agttcctcaa ggcaagtggt cggttgagat atctactgaa gggtaccaac
     4021 caacgtcaag cacaacagac cctaataatg ggaaatgcga tggattgatc gcttacagtg
     4081 atgatgacaa gacggatgtt tggaatgtag gagtgcaaaa gaacataacc cttagcaaca
     4141 acaaggccga caacacgtgg aagtatggcc acccagactt ggagattaac aactgcaagt
     4201 tcaacaatag gcaagtcctg gaacgcgatg cgtacatttc gttccatgtt gaaacaactg
     4261 ggcccaatgc ttccttcttc ttagttgcgc ctccagttca aaagactgct cggtataatt
     4321 atgccgtatc ttatggagct tggactgata ggatgctaga gtttggttct gttactgttg
     4381 cacttgatga acatttagaa ggtggtaaca gttctcgata tattaggagg tcaccaaggc
     4441 caggacacct tgagtcgaca agaacatatg atttgcactt attgcctcat atggacgatc
     4501 tcatagccgc caacactaca gctgttgtag atggctatgg gagtagtatt agtatagata
     4561 gacaagtctt agttgccgtt gacaatcata tagtagattc cggcgacgag acggatgatc
     4621 ttccaggtta ttcaagctca tcttctgaag cacctaaatt acctgccgtt aatcaaacga
     4681 agttgccacc aaaagggttt ctgtccaggt tgcgagagtc cgagatcgaa gagatagcgg
     4741 acaaaccaac cgagataaca acacctgagg ttagacaact agctgatgcc acacatcagc
     4801 cttttgccgc agggatgtac aatgacgctt ttgagcgact gtccataaat gaaaagaaac
     4861 gcaattttga ttccgtcaag gatgatattg ctgaaataga gaggacattg ccaaaagaag
     4921 agtacagggt gccaaaactg ccacgcatca agcccgcttc cgaagtggat aacgatcact
     4981 atggtgaaag tcaacaaact ttggcagaga tcgaaagacg taacgtctgg gccagtaaag
     5041 atgacgctgt tgcggttgaa tctccacccc cgggttatcc tcttgggcca attgaggcta
     5101 gggagttaat gccggttgag tggagtagac cagattatga gcccccgaaa cctaagaagt
     5161 cattgtttgg cagactcaag tcacaagcca aggtagaagc taatccttct tctcctcgca
     5221 atgacataag aagatcatct tttagtagct ttcgtagata gacatctcta gactcactga
     5281 gagccaacgc agcgccacta gtgcatcgaa tcctgggaaa caggcacgga gaacaaaatc
     5341 cggtaagctc gggaagccgt caacttccgc cgtattgatg aaaacaactt ggccgacgct
     5401 gttaataacc ttagcatctt gagttctact aaaaattaga tagttttccg cctcttccaa
     5461 aagttgccac cttttggaat gtgagataga tggagagagg ttgccttgaa taagcaactg
     5521 ttgatgtctg ctggtattga gtccaatgat caaaactcac gttgcttctg acgtatacac
     5581 tgcccctgat tcaacagggt aaacaaattt gcgccacctc gatgagatga gagtgaagcg
     5641 cggagtaaag agttgcatct acttttgtag gttgcaactc tggggagttt tgtagcaggc
     5701 caaaagccaa actagttctt cctcgtacgg aaacaaaaac aggtatgatt gttcggacat
     5761 cattggtact agttgccaat gtacagatgg tctaacagat accccccctc tgctcgggtt
     5821 taaatgtcag cgctggctct tcagcgacaa caagggggcg ttcctgcttg cctcccaatg
     5881 gatcctgcag gaacaggtct tcgaatcttt atgagatttg cggacctctt tgttgttaag
     5941 gtggcgaaag cgcccacctg cccc
//
