LOCUS       NC_004750               5677 bp ss-RNA     linear   VRL 12-JAN-2004
DEFINITION  Barley yellow dwarf virus - PAV, complete genome.
ACCESSION   NC_004750
VERSION     NC_004750.1  GI:30146774
KEYWORDS    coat protein; genome; RNA polymerase; unidentified reading frame.
SOURCE      Barley yellow dwarf virus - PAV
  ORGANISM  Barley yellow dwarf virus - PAV
            Viruses; ssRNA positive-strand viruses, no DNA stage; Luteoviridae;
            Luteovirus.
REFERENCE   1
  AUTHORS   Miller,W.A., Waterhouse,P.M. and Gerlach,W.L.
  TITLE     Sequence and organization of barley yellow dwarf virus genomic RNA
  JOURNAL   Nucleic Acids Res. 16 (13), 6097-6111 (1988)
  MEDLINE   88289355
   PUBMED   3399386
REFERENCE   2  (bases 1 to 5677)
  AUTHORS   Miller,W.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-MAY-1988) Miller W.A., CSIRO, Division of Plant
            Industry, GPO Box 1600, Canberra A.C.T. 2601, Australia
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from X07653.
            Authors suggest the occurence of
            a 99K 'transframe' protein, a fusion of the preceding 39K protein
            and the 50K. The 'stop' is read through by a translational frame
            shift.
FEATURES             Location/Qualifiers
     source          1..5677
                     /organism="Barley yellow dwarf virus - PAV"
                     /mol_type="genomic RNA"
                     /db_xref="taxon:12040"
                     /country="Australia"
     gene            142..2744
                     /locus_tag="BYDVPAVgp1"
                     /db_xref="GeneID:1492003"
     CDS             join(142..1155,1155..2744)
                     /locus_tag="BYDVPAVgp1"
                     /note="low-abundance product derived from -1 ribosomal
                     frameshift"
                     /codon_start=1
                     /product="RNA-dependent RNA polymerase P1-P2 fusion
                     protein"
                     /protein_id="NP_840014.2"
                     /db_xref="GI:30187599"
                     /db_xref="Swiss-Prot:P09505"
                     /db_xref="GeneID:1492003"
                     /translation="MFFEILIGASAKAVKDFISHCYSRLKSIYYSFKRWLMEISGQFK
                     AHDAFVNMCFGHMADIEDFEAELAEEFAEREDEVEEARSLLKLLVAQKSKSGVTEAWT
                     DFFTKSRGGVYAPLSCEPTRQELEVKSEKLERLLEEQHQFEVRAAKKYIKEKGRGFIN
                     CWNDLRSRLRLVKDVKDEAKDNARAAAKIGAEMFAPVDVQDLYSFTEVKKVETGLMKE
                     VVKEKNGEEEKHLEPIMEEVRSIKDTAEARDAASTWITETVKLKNATLNADELSLATI
                     ARYVENVGDKFKLDIASKTYLKQVASMSVPIPTNKDIKLKMVLQSPEARARRERMDVL
                     DSVGFLEGLCTASGFESPFPILGLPEIAVTDGARLRKVSSNIRYLSQTHLGLVYKAPN
                     ASLHNALVAVERRVFTVGKGDKAIYPPRPEHDIFTDTMDYFQKSIIEEVGYCKTYPAQ
                     LLANSYSAGKRAMYHKAIASLKTVPYHQKDANVQAFLKKEKHWMTKDIAPRLICPRSK
                     RYNIILGTRLKFNEKKIMHAIDSVFGSPTVLSGYDNFKQGRIIAKKWQKFACPVAIGV
                     DASRFDQHVSEQALKWEHGIYNGIFGDSEMALALEHQITNNIKMFVEDKMLRFKVRGH
                     RMSGDINTSMGNKLIMCGMMHAYLKKLGVEAELCNNGDDCVIITDRANEKLFDGMYDH
                     FLQYGFNMVTEKPVYELEQLEFCQSKPVSINGKYRMVRRPDSIGKDSTTLLSMLNQSD
                     VKSYMSAVAQCGLVLNAGVPILESFYKCLYRSSGYKKVSEEFIKNVISYGTDERLQGR
                     RTYNETPITNHSRMSYWESFGVDPKIQQIVERYYDGLTVSAQLQSVKVTTPHLQSILL
                     SIPENHSQNEY"
     gene            142..1161
                     /locus_tag="BYDVPAVgp2"
                     /db_xref="GeneID:1492001"
     CDS             142..1161
                     /locus_tag="BYDVPAVgp2"
                     /codon_start=1
                     /product="RNA-dependent RNA polymerase P1"
                     /protein_id="NP_840067.1"
                     /db_xref="GI:30187600"
                     /db_xref="GeneID:1492001"
                     /translation="MFFEILIGASAKAVKDFISHCYSRLKSIYYSFKRWLMEISGQFK
                     AHDAFVNMCFGHMADIEDFEAELAEEFAEREDEVEEARSLLKLLVAQKSKSGVTEAWT
                     DFFTKSRGGVYAPLSCEPTRQELEVKSEKLERLLEEQHQFEVRAAKKYIKEKGRGFIN
                     CWNDLRSRLRLVKDVKDEAKDNARAAAKIGAEMFAPVDVQDLYSFTEVKKVETGLMKE
                     VVKEKNGEEEKHLEPIMEEVRSIKDTAEARDAASTWITETVKLKNATLNADELSLATI
                     ARYVENVGDKFKLDIASKTYLKQVASMSVPIPTNKDIKLKMVLQSPEARARRERMDVL
                     DSVGF"
     gene            2858..4813
                     /locus_tag="BYDVPAVgp3"
                     /db_xref="GeneID:1492000"
     CDS             2858..4813
                     /locus_tag="BYDVPAVgp3"
                     /note="translated from subgenomic RNA1 as a fusion protein
                     via read-through of the coat protein (P3) stop codon"
                     /codon_start=1
                     /transl_except=(pos:3458..3460,aa:OTHER)
                     /product="aphid transmission protein P5"
                     /protein_id="NP_840017.2"
                     /db_xref="GI:30187598"
                     /db_xref="Swiss-Prot:P09516"
                     /db_xref="GeneID:1492000"
                     /translation="MNSVGRRGPRRANQNGTRRRRRRTVRPVVVVQPNRAGPRRRNGR
                     RKGRGGANFVFRPTGGTEVFVFSVDNLKANSSGAIKFGPSLSQCPALSDGILKSYHRY
                     KITSIRVEFKSHASANTAGAIFIELDTACKQSALGSYINSFTISKTASKTFRSEAING
                     KEFQESTIDQFWMLYKANGTTTDTAGQFIITMSVSLMTAKXVDSSTPEPKPAPEPTPT
                     PQPTPAPQPTPEPTPAPVPKRFFEYIGTPTGTISTRENTDSISVSKLGGQSMQYIENE
                     KCETKVIDSFWSTNNNVSAQAAFVYPVPEGSYSVNISCEGFQSVDHIGGNEDGYWIGL
                     IAYSNSSGDNWGVGNYKGCSFKNFLATNTWRPGHKDLKLTDCQFTDGQIVERDAVMSF
                     HVEATGKDASFYLMAPKTMKTDKYNYVVSYGGYTNKRMEFGTISVTCDESDVEAERIT
                     RHAETPIRSKHILVSERYAEPLPTIVNQGLCDVKTPEQEQTLVDEDDRQTVSTESDIA
                     LLEYEAATAEIPDAEEDVLPSKEQLSSKPMDTSGNIIPKPKEPEVLGTYQGQNIYPED
                     VPPMARQKLREAANAPSTLLYERRTPKKSGNFLSRLVEANRSPTTPTAPSVSTTSNMT
                     REQLREYTRIRNSSGITAAKAYKAQFQ"
     gene            2858..3460
                     /locus_tag="BYDVPAVgp4"
                     /db_xref="GeneID:1491998"
     CDS             2858..3460
                     /locus_tag="BYDVPAVgp4"
                     /codon_start=1
                     /product="coat protein P3"
                     /protein_id="NP_840015.1"
                     /db_xref="GI:30146775"
                     /db_xref="Swiss-Prot:P09510"
                     /db_xref="GeneID:1491998"
                     /translation="MNSVGRRGPRRANQNGTRRRRRRTVRPVVVVQPNRAGPRRRNGR
                     RKGRGGANFVFRPTGGTEVFVFSVDNLKANSSGAIKFGPSLSQCPALSDGILKSYHRY
                     KITSIRVEFKSHASANTAGAIFIELDTACKQSALGSYINSFTISKTASKTFRSEAING
                     KEFQESTIDQFWMLYKANGTTTDTAGQFIITMSVSLMTAK"
     gene            2901..3362
                     /locus_tag="BYDVPAVgp5"
                     /db_xref="GeneID:1491997"
     CDS             2901..3362
                     /locus_tag="BYDVPAVgp5"
                     /codon_start=1
                     /product="putative movement protein P4"
                     /protein_id="NP_840016.1"
                     /db_xref="GI:30146776"
                     /db_xref="Swiss-Prot:P09513"
                     /db_xref="GeneID:1491997"
                     /translation="MAQEGGAVEQFGQWLWSNPIEQDPDDEMVDAREEEGQILYLDQQ
                     AGLRYSYSQLTTLKPTPPGQSNSAPVYRNAQRFQTEYSSPTIVTRSQVSELSLSHTRP
                     PIRQALSLLSSTPRASNQPWVATLIPSPSARPPPRPSGQRQLMGRNSRNQR"
     misc_feature    4621..5160
                     /note="highly variable region"
     gene            4920..5111
                     /locus_tag="BYDVPAVgp6"
                     /db_xref="GeneID:1492002"
     CDS             4920..5111
                     /locus_tag="BYDVPAVgp6"
                     /note="translated from subgenomic RNA2"
                     /codon_start=1
                     /product="P6 protein"
                     /protein_id="NP_840018.1"
                     /db_xref="GI:30146778"
                     /db_xref="Swiss-Prot:P09517"
                     /db_xref="GeneID:1492002"
                     /translation="MEDLHVIAVCILALTVLSGVGAVLSCCRWCCSNPFPPSLSSVQA
                     KDSRSVRETIKNIEGASAQ"
     gene            5309..5476
                     /locus_tag="BYDVPAVgp7"
                     /db_xref="GeneID:1491999"
     CDS             5309..5476
                     /locus_tag="BYDVPAVgp7"
                     /codon_start=1
                     /product="hypothetical protein"
                     /protein_id="NP_840019.1"
                     /db_xref="GI:30146779"
                     /db_xref="Swiss-Prot:P09518"
                     /db_xref="GeneID:1491999"
                     /translation="MYTRSSGLKTLKLDDLVQVVKLTRVDTPHPAQHVGIPTIRNVGL
                     LEPLPVMQGRV"
ORIGIN      
        1 ngtgaagatt gaccatctca caaaagctgt tacgtgcttg taacacacta cgcgcccgtt
       61 ttgtattcgg gaagtagttg cgaaaacggt ccccttattg cctgacaagc taagggccac
      121 ccttctttcc ccaccgccat catgtttttc gaaatactaa taggtgctag cgccaaggcg
      181 gtcaaagact tcattagcca ttgctattct agattgaaat ctatatacta ttctttcaag
      241 cgatggctaa tggagatatc agggcaattt aaggcccacg acgcctttgt caacatgtgc
      301 tttgggcaca tggctgacat tgaggacttc gaggcggaac tcgctgagga gttcgccgag
      361 agggaggatg aggtggaaga ggcgaggagc ctcttgaaac tgctggtcgc ccaaaaatct
      421 aaatctgggg tgaccgaggc ttggaccgac ttttttacaa agtcgagagg tggtgtttac
      481 gcaccacttt cctgcgagcc taccaggcag gagctagaag tcaagagtga gaaactcgag
      541 cgacttctag aagagcagca ccaatttgag gtgcgagcgg ccaagaaata catcaaggaa
      601 aagggccgcg gcttcatcaa ctgctggaac gacttgcgga gtcgtctcag gttggtgaag
      661 gacgtcaagg acgaggcgaa ggacaacgcc agagctgctg ccaagattgg agcagaaatg
      721 ttcgcccctg ttgacgtgca ggacctctac agtttcacgg aggtcaagaa ggtggagacc
      781 ggcctcatga aggaggtcgt gaaagagaaa aacggcgaag aagagaaaca cctcgaaccc
      841 atcatggaag aggtgaggtc catcaaggac accgccgaag ccagggacgc cgcctccact
      901 tggataacag agacagttaa gctgaagaac gcaacgctta acgcagatga actgtctctt
      961 gccaccatcg cccgctacgt tgaaaacgta ggggacaagt tcaaactcga cattgctagt
     1021 aaaacatatc taaagcaagt cgcatcgatg tctgtaccaa ttccaaccaa caaagacatc
     1081 aaattgaaga tggtgctaca gagtcctgaa gcacgtgcca ggcgggaacg catggacgtg
     1141 cttgactctg tgggttttta gaggggctct gtaccgcctc tggttttgag agcccattcc
     1201 ctattctcgg gctgccagag attgcggtca cagacggagc ccggctccgc aaggttagta
     1261 gcaatattag ataccttagc caaacccatc taggtcttgt atataaggca ccaaatgcct
     1321 ccctgcacaa cgcgcttgtg gcagtggaga gaagagtttt tacagtagga aagggggaca
     1381 aggcaatcta ccccccccgc cctgagcatg acattttcac tgatacgatg gattactttc
     1441 aaaaatccat tatagaagag gtgggatact gtaaaacata tccagcgcaa ctcctggcta
     1501 atagctatag cgcaggaaag agggccatgt atcacaaagc cattgcatcc ttgaaaactg
     1561 tcccatatca tcagaaggat gccaatgtgc aagctttcct gaagaaggaa aaacattgga
     1621 tgaccaagga catcgccccc cgattgattt gcccccgcag caagcggtat aatatcatcc
     1681 taggaactcg tttgaaattc aacgagaaga agatcatgca cgccatcgat agtgtgtttg
     1741 gatcccccac tgtgctttct ggttatgaca acttcaaaca aggaagaatc atagccaaaa
     1801 agtggcaaaa gtttgcatgc cccgtcgcca tcggcgtgga tgctagccgc tttgaccaac
     1861 atgtgtcaga gcaggcgctt aagtgggaac acgggatata caatggaatc ttcggagaca
     1921 gcgaaatggc tcttgcactt gaacaccaaa tcaccaacaa catcaagatg tttgttgaag
     1981 acaaaatgct taggttcaag gtaagaggcc acagaatgtc cggtgacatt aataccagca
     2041 tgggaaataa gctcataatg tgcggcatga tgcacgcata tcttaagaag ctgggtgttg
     2101 aagctgaact atgtaataac ggagacgact gtgtcatcat cactgataga gccaatgaga
     2161 agctctttga tggcatgtac gaccatttcc tccagtatgg cttcaacatg gtgaccgaaa
     2221 aaccagttta cgaactggaa caattggagt tttgccagtc aaaaccggtc tctattaatg
     2281 gaaagtatag aatggtcaga aggcccgata gcataggcaa agatagcaca acactactga
     2341 gcatgctcaa tcaatccgac gtcaagagct acatgtcggc tgtcgctcag tgtggtttgg
     2401 tgctcaacgc tggagtaccc atacttgaaa gtttctataa atgcctatat aggagctcgg
     2461 ggtacaaaaa agtgagtgag gaatttatta aaaacgtcat atcgtatgga acagatgaga
     2521 gactacaagg tagacgtacc tataatgaaa cacctatcac aaaccacagt agaatgtcct
     2581 actgggaatc attcggagtt gaccctaaga tacagcaaat cgtcgagagg tactacgacg
     2641 gtcttacggt aagtgcccaa ctccagagtg tgaaggtgac gactccacat ctgcaatcaa
     2701 tactgctttc cataccggaa aaccactcac aaaacgaata ttaattacca aatcttagct
     2761 gggtttggga tagggtttat agttagtata ccctgtacat tagctctcgc gtactttatt
     2821 tacaataaag tttcagacac cactagagag gtggtgaatg aattcagtag gtcgtagagg
     2881 acctagacgc gcaaatcaaa atggcacaag aaggaggcgc cgtagaacag ttcggccagt
     2941 ggttgtggtc caacccaatc gagcaggacc cagacgacga aatggtcgac gcaagggaag
     3001 aggaggggca aattttgtat ttagaccaac aggcgggact gaggtattcg tattctcagt
     3061 tgacaacctt aaagccaact cctccggggc aatcaaattc ggccccagtc tatcgcaatg
     3121 cccagcgctt tcagacggaa tactcaagtc ctaccatcgt tacaagatca caagtatccg
     3181 agttgagttt aagtcacacg cgtccgccaa tacggcaggc gctatcttta ttgagctcga
     3241 caccgcgtgc aagcaatcag ccctgggtag ctacattaat tccttcacca tcagcaagac
     3301 cgcctccaag accttccggt cagaggcaat taatgggaag gaattccagg aatcaacgat
     3361 agaccaattt tggatgctct acaaggccaa tggaactacc actgacacgg caggacaatt
     3421 tatcattacg atgagtgtca gtttgatgac ggccaaatag gtagactcct caacaccgga
     3481 accaaaacct gcaccggaac caacaccaac cccccagcca acgccggctc cacagcccac
     3541 acctgaacca actcctgcac ctgtccccaa aagattcttc gagtatatcg gaactcctac
     3601 cggtacaatc tcgactagag agaacactga cagtatatct gtcagcaagc tcggtggaca
     3661 gtcgatgcag tacattgaga atgagaaatg tgaaacgaaa gtcatcgatt ccttttggag
     3721 cactaacaac aacgtttctg cgcaagcagc tttcgtttat ccagtgccag agggatcata
     3781 cagcgttaac atttcgtgcg aaggcttcca gtcagttgac cacatcggtg gcaacgagga
     3841 cggctattgg attggtttaa ttgcctactc caattcgtct ggcgataatt ggggagttgg
     3901 caattacaaa gggtgcagtt ttaagaattt cttggcaacc aacacttgga gaccaggcca
     3961 caaagatctc aagttgactg attgccagtt cacagatgga caaatagttg aaagggacgc
     4021 cgtgatgtct ttccacgtag aagcaacagg caaggatgcc agcttctacc tcatggctcc
     4081 caaaacaatg aaaactgaca aatacaacta tgttgtctca tatggagggt acacaaacaa
     4141 gcgaatggaa ttcggtacca tatctgtgac atgtgatgaa tccgatgttg aggcagaacg
     4201 aataacaagg cacgctgaaa cgcccatacg ttctaaacat attcttgttt ctgagcggta
     4261 tgcggaacca ttgcccacca tagtcaacca aggcttgtgt gatgtgaaaa ctcccgagca
     4321 agaacaaaca ctggtggatg aagatgacag acaaactgtt tctactgaat ctgatatagc
     4381 actcctggag tatgaggctg caacagctga gattccggat gctgaagagg acgttttgcc
     4441 ctccaaggaa cagttgtctt caaaaccaat ggatacgtct ggcaatataa taccaaaacc
     4501 caaggaacct gaagtacttg ggacatacca aggacagaac atttatcctg aagacgtacc
     4561 tccaatggcg cggcagaaat tgagagaagc cgcgaatgcg ccttccacgc tactctatga
     4621 aagaagaacc ccaaagaaga gtggcaactt tttatccaga cttgtagaag cgaataggtc
     4681 ccctactact cccactgccc catccgtgtc aactacttca aacatgacaa gggagcagct
     4741 ccgggagtac actaggatta gaaattccag cggaatcaca gcagcaaagg cgtacaaggc
     4801 gcaattccag tgaagacaac accactagca caaatcggat cctgggaaac aggcagaact
     4861 tcggttcgta agctcgggta ggccgtcaac ctaccgccgt atcgtattgt gtttggccga
     4921 tggaggatct tcacgttatc gccgtttgta ttcttgcttt gactgtgctc tctggggtag
     4981 gcgctgtttt gagttgctgc cgttggtgct gcagcaatcc ttttcctccc tccctctctt
     5041 ctgttcaagc aaaagactct cgatctgtgc gagagacaat caaaaatatc gagggagctt
     5101 cggctcagtg aggggattaa cgacccccag taatggccgg tcctggcgga cataaataac
     5161 ccgctatagg acgaagtggt agccaccact gatcaaatgg caaacatgct tctgtgttgt
     5221 acactgcccc ggagcctacc gggtcaacaa ggctatccca ccaacccgat gaaatgaggg
     5281 tggagtgagc ggagtgggtg acttcgtgat gtacacccga tcgtcaggat tgaagacgtt
     5341 aaaactcgac gacctggtac aagtcgttaa actgactcgg gtggatacac cacacccggc
     5401 ccagcatgtt ggcataccca cgatacgaaa cgtgggtctc ttggagccac tacctgtgat
     5461 gcaaggtagg gtatgagtct tagcaagctc tgagccagga gatggacata aaccatagca
     5521 atccaacgtg taaccgcaat ggggcaaaca acaggtgaac cgtgtccacg ggcctggtta
     5581 ccgaaaggaa agccagtatc caacacagca atgtgttggg ggtcacacct tcggggtact
     5641 cttaacgctg acactcgaaa gagcagttcg gcaaccc
//
