LOCUS NC_004750 5677 bp ss-RNA linear VRL 12-NOV-2015 DEFINITION Barley yellow dwarf virus - PAV, complete genome. ACCESSION NC_004750 VERSION NC_004750.1 DBSOURCE BioProject accession PRJNA15196 KEYWORDS RefSeq; coat protein; genome; RNA polymerase; unidentified reading; frame. 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 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) PUBMED 3399386 REFERENCE 2 (bases 1 to 5677) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (28-APR-2003) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA REFERENCE 3 (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 VALIDATED REFSEQ: This record has undergone validation or preliminary 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. COMPLETENESS: full length. FEATURES Location/Qualifiers source 1..5677 /mol_type="genomic RNA" /db_xref="taxon:12040" /country="Australia" /organism="Barley yellow dwarf virus-PAV" gene 142..2744 /locus_tag="BYDVPAVgp1" /db_xref="GeneID:1492003" CDS join(142..1155,1155..2744) /locus_tag="BYDVPAVgp1" /db_xref="UniProtKB/Swiss-Prot:P09505" /db_xref="GeneID:1492003" /codon_start=1 /protein_id="NP_840014.2" /translation="MFFEILIGASAKAVKDFISHCYSRLKSIYYSFKRWLMEISGQFK AHDAFVNMCFGHMADIEDFEAELAEEFAEREDEVEEARSLLKLLVAQKSKSGVTEAWT DFFTKSRGGVYAPLSCEPTRQELEVKSEKLERLLEEQHQFEVRAAKKYIKEKGRGFIN CWNDLRSRLRLVKDVKDEAKDNARAAAKIGAEMFAPVDVQDLYSFTEVKKVETGLMKE VVKEKNGEEEKHLEPIMEEVRSIKDTAEARDAASTWITETVKLKNATLNADELSLATI ARYVENVGDKFKLDIASKTYLKQVASMSVPIPTNKDIKLKMVLQSPEARARRERMDVL DSVGFLEGLCTASGFESPFPILGLPEIAVTDGARLRKVSSNIRYLSQTHLGLVYKAPN ASLHNALVAVERRVFTVGKGDKAIYPPRPEHDIFTDTMDYFQKSIIEEVGYCKTYPAQ LLANSYSAGKRAMYHKAIASLKTVPYHQKDANVQAFLKKEKHWMTKDIAPRLICPRSK RYNIILGTRLKFNEKKIMHAIDSVFGSPTVLSGYDNFKQGRIIAKKWQKFACPVAIGV DASRFDQHVSEQALKWEHGIYNGIFGDSEMALALEHQITNNIKMFVEDKMLRFKVRGH RMSGDINTSMGNKLIMCGMMHAYLKKLGVEAELCNNGDDCVIITDRANEKLFDGMYDH FLQYGFNMVTEKPVYELEQLEFCQSKPVSINGKYRMVRRPDSIGKDSTTLLSMLNQSD VKSYMSAVAQCGLVLNAGVPILESFYKCLYRSSGYKKVSEEFIKNVISYGTDERLQGR RTYNETPITNHSRMSYWESFGVDPKIQQIVERYYDGLTVSAQLQSVKVTTPHLQSILL SIPENHSQNEY" /product="RNA-dependent RNA polymerase P1-P2 fusion protein" /note="low-abundance product derived from -1 ribosomal frameshift" gene 142..1161 /locus_tag="BYDVPAVgp2" /db_xref="GeneID:1492001" CDS 142..1161 /locus_tag="BYDVPAVgp2" /db_xref="GeneID:1492001" /codon_start=1 /protein_id="NP_840067.1" /translation="MFFEILIGASAKAVKDFISHCYSRLKSIYYSFKRWLMEISGQFK AHDAFVNMCFGHMADIEDFEAELAEEFAEREDEVEEARSLLKLLVAQKSKSGVTEAWT DFFTKSRGGVYAPLSCEPTRQELEVKSEKLERLLEEQHQFEVRAAKKYIKEKGRGFIN CWNDLRSRLRLVKDVKDEAKDNARAAAKIGAEMFAPVDVQDLYSFTEVKKVETGLMKE VVKEKNGEEEKHLEPIMEEVRSIKDTAEARDAASTWITETVKLKNATLNADELSLATI ARYVENVGDKFKLDIASKTYLKQVASMSVPIPTNKDIKLKMVLQSPEARARRERMDVL DSVGF" /product="RNA-dependent RNA polymerase P1" gene 2734..2877 /locus_tag="BYDVPAVgp8" /db_xref="GeneID:26196460" /gene="ORF3a" CDS 2734..2877 /locus_tag="BYDVPAVgp8" /protein_id="YP_009179361.1" /gene="ORF3a" /note="p3a; essential for viral movement; Non-AUG initiation (ACG initiation); non-AUG codon is translated by initiator-tRNA-Met giving N-terminal Met. ORF3a in Luteovirus and Polerovirus genera was predicted by statistical analysis of sequence variation in large set of aligned sequences. Functional analysis of protein 3a was conducted with Turnip yellows virus. ORF3a was translated in vitro, and confirmed by immunological assay in infected protoplasts and in agroinoculated plants. Mutations that prevent expression of protein 3a prevent virus systemic infection (long-distance movement in plants). PMID 25946037" /db_xref="GeneID:26196460" /codon_start=1 /inference="non-experimental evidence, no additional details recorded" /translation="MNINYQILAGFGIGFIVSIPCTLALAYFIYNKVSDTTREVVNEF SRS" /product="protein 3a" /transl_except=(pos:2734..2736,aa:Met) gene 2858..4813 /locus_tag="BYDVPAVgp3" /db_xref="GeneID:1492000" CDS 2858..4813 /locus_tag="BYDVPAVgp3" /protein_id="NP_840017.2" /note="translated from subgenomic RNA1 as a fusion protein via read-through of the coat protein (P3) stop codon" /db_xref="UniProtKB/Swiss-Prot:P09516" /db_xref="GeneID:1492000" /codon_start=1 /product="aphid transmission protein P5" /translation="MNSVGRRGPRRANQNGTRRRRRRTVRPVVVVQPNRAGPRRRNGR RKGRGGANFVFRPTGGTEVFVFSVDNLKANSSGAIKFGPSLSQCPALSDGILKSYHRY KITSIRVEFKSHASANTAGAIFIELDTACKQSALGSYINSFTISKTASKTFRSEAING KEFQESTIDQFWMLYKANGTTTDTAGQFIITMSVSLMTAKXVDSSTPEPKPAPEPTPT PQPTPAPQPTPEPTPAPVPKRFFEYIGTPTGTISTRENTDSISVSKLGGQSMQYIENE KCETKVIDSFWSTNNNVSAQAAFVYPVPEGSYSVNISCEGFQSVDHIGGNEDGYWIGL IAYSNSSGDNWGVGNYKGCSFKNFLATNTWRPGHKDLKLTDCQFTDGQIVERDAVMSF HVEATGKDASFYLMAPKTMKTDKYNYVVSYGGYTNKRMEFGTISVTCDESDVEAERIT RHAETPIRSKHILVSERYAEPLPTIVNQGLCDVKTPEQEQTLVDEDDRQTVSTESDIA LLEYEAATAEIPDAEEDVLPSKEQLSSKPMDTSGNIIPKPKEPEVLGTYQGQNIYPED VPPMARQKLREAANAPSTLLYERRTPKKSGNFLSRLVEANRSPTTPTAPSVSTTSNMT REQLREYTRIRNSSGITAAKAYKAQFQ" /transl_except=(pos:3458..3460,aa:OTHER) gene 2858..3460 /locus_tag="BYDVPAVgp4" /db_xref="GeneID:1491998" CDS 2858..3460 /locus_tag="BYDVPAVgp4" /db_xref="UniProtKB/Swiss-Prot:P09510" /db_xref="GeneID:1491998" /codon_start=1 /protein_id="NP_840015.1" /translation="MNSVGRRGPRRANQNGTRRRRRRTVRPVVVVQPNRAGPRRRNGR RKGRGGANFVFRPTGGTEVFVFSVDNLKANSSGAIKFGPSLSQCPALSDGILKSYHRY KITSIRVEFKSHASANTAGAIFIELDTACKQSALGSYINSFTISKTASKTFRSEAING KEFQESTIDQFWMLYKANGTTTDTAGQFIITMSVSLMTAK" /product="coat protein P3" gene 2901..3362 /locus_tag="BYDVPAVgp5" /db_xref="GeneID:1491997" CDS 2901..3362 /locus_tag="BYDVPAVgp5" /db_xref="UniProtKB/Swiss-Prot:P09513" /db_xref="GeneID:1491997" /codon_start=1 /protein_id="NP_840016.1" /translation="MAQEGGAVEQFGQWLWSNPIEQDPDDEMVDAREEEGQILYLDQQ AGLRYSYSQLTTLKPTPPGQSNSAPVYRNAQRFQTEYSSPTIVTRSQVSELSLSHTRP PIRQALSLLSSTPRASNQPWVATLIPSPSARPPPRPSGQRQLMGRNSRNQR" /product="putative movement protein P4" misc_feature 4621..5160 /note="highly variable region" gene 4920..5111 /locus_tag="BYDVPAVgp6" /db_xref="GeneID:1492002" CDS 4920..5111 /locus_tag="BYDVPAVgp6" /db_xref="UniProtKB/Swiss-Prot:P09517" /db_xref="GeneID:1492002" /codon_start=1 /protein_id="NP_840018.1" /translation="MEDLHVIAVCILALTVLSGVGAVLSCCRWCCSNPFPPSLSSVQA KDSRSVRETIKNIEGASAQ" /product="P6 protein" /note="translated from subgenomic RNA2" gene 5309..5476 /locus_tag="BYDVPAVgp7" /db_xref="GeneID:1491999" CDS 5309..5476 /locus_tag="BYDVPAVgp7" /db_xref="UniProtKB/Swiss-Prot:P09518" /db_xref="GeneID:1491999" /codon_start=1 /protein_id="NP_840019.1" /translation="MYTRSSGLKTLKLDDLVQVVKLTRVDTPHPAQHVGIPTIRNVGL LEPLPVMQGRV" /product="hypothetical protein" 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 //