LOCUS NC_021481 5736 bp RNA linear VRL 09-DEC-2015 DEFINITION Barley yellow dwarf virus Ker-II isolate K439, complete genome. ACCESSION NC_021481 VERSION NC_021481.1 DBSOURCE BioProject accession PRJNA208540 KEYWORDS RefSeq. SOURCE Barley yellow dwarf virus-kerII ORGANISM Barley yellow dwarf virus-kerII Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Luteoviridae; Luteovirus. REFERENCE 1 (bases 1 to 5736) AUTHORS Svanella-Dumas,L., Candresse,T., Hulle,M. and Marais,A. TITLE Distribution of Barley yellow dwarf virus-PAV in the Sub-Antarctic Kerguelen Islands and Characterization of Two New Luteovirus Species JOURNAL PLoS ONE 8 (6), E67231 (2013) PUBMED 23825645 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 5736) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (17-JUN-2013) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA REFERENCE 3 (bases 1 to 5736) AUTHORS Svanella-Dumas,L., Candresse,T., Hulle,M. and Marais,A. TITLE Direct Submission JOURNAL Submitted (01-FEB-2013) UMR 1332 Biologie du Fruit et Pathologie, INRA, 71 Avenue Edouard Bourleaux, Villenave d'Ornon Cedex, CS 20032 33883, France COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence is identical to KC571999. ##Assembly-Data-START## Assembly Method :: Mega v. 5.02 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END## COMPLETENESS: full length. FEATURES Location/Qualifiers source 1..5736 /mol_type="genomic RNA" /country="France: Kerguelen Islands TC13" /collection_date="2009" /host="Poa cookii" /PCR_primers="fwd_seq: agtgaagattgacc, rev_seq: gctcttgtgtccaccttac" /db_xref="taxon:1304863" /isolate="K439" /organism="Barley yellow dwarf virus-kerII" 5'UTR 1..154 gene 155..2757 /locus_tag="M525_gp1" /db_xref="GeneID:15842604" /gene="ORF1" CDS join(155..1171,1171..2757) /locus_tag="M525_gp1" /protein_id="YP_008083724.1" /gene="ORF1" /note="RdRp" /db_xref="GeneID:15842604" /ribosomal_slippage /codon_start=1 /translation="MVFFELLIGASVKAVKDFISHCYSRLKSIYYSLKRWLWELQGKF KAHDAFVNMCYGHMSDIEDFEIPLAGEFEVREGDLEIARAKLALLIAQHSDIGVTEAY GKYASLTGSIPVPEDYKPSVKELGSAADSVESLISEHLQAAREASKIYIKEKGVGFIN SFNSLKARFKHVKEQTLLFKHNEEAASKIKQQLFAVENIDELHNFTEVTQEENGLKKT IIKEVNGEEQYFEMPIKVDVRRIKDTPVDREKAATWIRAYIKAKNSSLTADELSFATI PKYIENLAAKHDLSAESRTYLTKCALIMVPLPTSEEIAIKMTVQSPAARSRREQIEIL DARGFLDGLCSETGFESPFSELGLPEISVTDGARIRKQSSKIHFLSQTSLGLVFQAPN ASLHNALVAVERRVFTVGKGNEITLPPRPELDIFTESMKYFSDEIVNQVGCCKVFSPE FLAFSYSSGKRSQYLKAIESLKMKPYEEKDSHVTAFLKKEKHWMTKPIAPRLICPRTK RYNIILGTHLKFNEKKIMHAIDCVFGSPTVLSGFDSFQQGKVIARKWRKFSNPVAIGV DASRFDQHVSEQALMWEHSIYNDIFNDPFLKTALSHQLNNNILMFVDDKMLRFKVKGH RMSGDINTSMGNKLIMCGMMHAYFKSLNVDAELCNNGDDCVIICERKDEAKFAGMYDF FLKYGFNLVTEHPVYELEKLEFCQSRPVCVNGKYRMVRRPDCISKDSHTLLSMLGQED VKSYMSAVAQCGLVLNSGVPILESFYECLYRSSGYKKVSEEYIKNVISYGTEERLQGR RARQIEPITLGTRLSYWETFGVDPRTQEIVERYFNSLTISTQLQRVKVTTPHMQSILL SIPEKNPPATQ" /product="RNA-dependent RNA polymerase P1-P2 fusion" CDS 155..1174 /locus_tag="M525_gp1" /protein_id="YP_008083725.1" /gene="ORF1" /db_xref="GeneID:15842604" /codon_start=1 /product="RNA-dependent RNA polymerase P1" /translation="MVFFELLIGASVKAVKDFISHCYSRLKSIYYSLKRWLWELQGKF KAHDAFVNMCYGHMSDIEDFEIPLAGEFEVREGDLEIARAKLALLIAQHSDIGVTEAY GKYASLTGSIPVPEDYKPSVKELGSAADSVESLISEHLQAAREASKIYIKEKGVGFIN SFNSLKARFKHVKEQTLLFKHNEEAASKIKQQLFAVENIDELHNFTEVTQEENGLKKT IIKEVNGEEQYFEMPIKVDVRRIKDTPVDREKAATWIRAYIKAKNSSLTADELSFATI PKYIENLAAKHDLSAESRTYLTKCALIMVPLPTSEEIAIKMTVQSPAARSRREQIEIL DARGF" gene 2754..2891 /locus_tag="M525_gp5" /db_xref="GeneID:26386275" /gene="ORF3a" CDS 2754..2891 /locus_tag="M525_gp5" /protein_id="YP_009186824.1" /gene="ORF3a" /note="p3a; essential for viral movement; Non-AUG initiation (AUA 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:26386275" /codon_start=1 /inference="non-experimental evidence, no additional details recorded" /translation="MDFHFLTGLGIGFILAIPCTLALTYFIYNKVSDTTREVVNEFSR P" /product="protein 3a" /transl_except=(pos:2754..2756,aa:Met) gene 2872..4875 /locus_tag="M525_gp2" /db_xref="GeneID:15842601" /gene="ORF3" CDS 2872..4875 /locus_tag="M525_gp2" /protein_id="YP_008083726.1" /gene="ORF3" /note="created by ribosomal read-through of the ORF3 stop codon" /db_xref="GeneID:15842601" /codon_start=1 /translation="MNSVGRRRASKNVRARSNRTVRPVVVVRTNPNGRRRRAPRRPRR GRANPILGPAGRSEVFVFSINDIKANSSGVIKFGPDLSQCPALSSGILKSYHRYKISN VKIEFKSHASSTTVGAMFIELDTACTQSTLGSYINSFTLSKSGTKTFNAQQIAGKEFR ETSVNQFYLLFKANGVTSDTAGQFIITLRVSNMTPKXVDSSTPGPGPKPKPDPTPTPA PEPKTPKRFFEFIGTPSGVIQTRESSDSISVSKLGDQTFQKIENEKSNDVFLSSYWQY SNSVYAQAAFVIPIYQGSYSVNISCEGMQSVDHIGGEQDGYWIGLIAYSNSTDDVWGV GNYQGCTITKYLVTNSWRPGHQDLKLNDCAFDKGQIVERDAVLSFHVEAVGDNPSFYL LAPKTQKTDKYNYVVSYGGYTNKKMEFGTIAITCDESDVEALRNARHANYPIKENHQE LYHGSGTLLPAYSPDRVEVYPDITSSERTVQPRPSEEPKFRDIQNQEELSSLFDLYDL ATSEIPDAREDVLPTKQEMSKKPIDSLGTEIPRPRSMSPEYPRPRSRSPEYPRPRSRS PEPIGTYHGQNIYDDDVPKQVAERLREAAELPSTMLYNRKPKNRNSSFLSRFIEQNKS PDATAPSEATTSRMTRDQLKEYTRVRNQYGLTAAKQYKASLGQ" /product="aphid transmission protein P5" /transl_except=(pos:3460..3462,aa:OTHER) CDS 2872..3462 /locus_tag="M525_gp2" /protein_id="YP_008083727.1" /gene="ORF3" /db_xref="GeneID:15842601" /codon_start=1 /product="coat protein P3" /translation="MNSVGRRRASKNVRARSNRTVRPVVVVRTNPNGRRRRAPRRPRR GRANPILGPAGRSEVFVFSINDIKANSSGVIKFGPDLSQCPALSSGILKSYHRYKISN VKIEFKSHASSTTVGAMFIELDTACTQSTLGSYINSFTLSKSGTKTFNAQQIAGKEFR ETSVNQFYLLFKANGVTSDTAGQFIITLRVSNMTPK" gene 2906..3364 /locus_tag="M525_gp3" /db_xref="GeneID:15842602" /gene="ORF4" CDS 2906..3364 /locus_tag="M525_gp3" /protein_id="YP_008083728.1" /gene="ORF4" /db_xref="GeneID:15842602" /codon_start=1 /product="movement protein P4" /translation="MSEPGAIEQFGQWLWSGPIQMDEDVEPLDAQEEEGQILYLDQQA GLRYSYSQSTILKPIPQGSSNSAPIFHNVQRFQAEYLSPTTVTRSQMSRSSLSHTRPP LQSALCLLNSTPRAHNQPWVATLTHSPSPSQEPKRLMPSKSLAKSSGRRR" gene 5005..5115 /locus_tag="M525_gp4" /db_xref="GeneID:15842603" /gene="ORF6" CDS 5005..5115 /locus_tag="M525_gp4" /protein_id="YP_008083729.1" /gene="ORF6" /db_xref="GeneID:15842603" /codon_start=1 /product="P6" /translation="MGGLEVIAVCMIAIVFLQAVGTIVNMCICVGAIAAA" 3'UTR 5113..5736 ORIGIN 1 agtgaagatt gacccctcac caaagttctc ttgtgctaga gagacacggc tcaccctttt 61 tgtcttaggg aagtcgtttg caaaggtcac agcgtcgcct gactcgccgc tgccacccca 121 cctatacatc cccccccccc tttccatcgt agatatggtg ttctttgagc tcctgattgg 181 agctagcgtc aaagccgtaa aggatttcat ctcccactgc tacagccgcc taaagagtat 241 ttattactct ttgaaacggt ggctatggga gctacagggc aaattcaagg cccatgacgc 301 ctttgtcaac atgtgctatg ggcacatgtc tgacattgaa gatttcgaga tcccccttgc 361 tggtgagttc gaagtcaggg agggcgatct ggagatcgcg agagcaaagc tggcgctact 421 gattgcgcag cactccgaca tcggggtaac cgaggcgtac gggaaatacg ctagtcttac 481 tgggagcata cctgtaccag aggactataa accaagcgtc aaagaactag gttccgcggc 541 tgatagtgtg gaatcactaa tatccgagca cctgcaagcc gccagagaag cttccaaaat 601 ctacatcaaa gagaaaggtg taggttttat caattctttc aattcactca aagctcgatt 661 caagcatgta aaagagcaaa cacttctgtt caagcacaat gaggaagcag caagcaagat 721 caaacagcaa ctttttgctg tggaaaatat tgatgagctg cataacttta cagaagtcac 781 tcaagaggaa aatggcctaa agaaaaccat tatcaaggag gttaatggcg aggagcaata 841 cttcgaaatg cctattaaag ttgacgtccg cagaatcaaa gatactcctg ttgacaggga 901 gaaagccgct acttggatta gggcctacat caaggccaag aattcaagtt taactgccga 961 cgaactctca ttcgccacca tccccaaata cattgaaaat cttgcggcca aacatgactt 1021 gtctgctgaa agtcgcacgt accttaccaa gtgcgctttg ataatggtcc ccctgcctac 1081 aagcgaggaa atcgcaatca aaatgaccgt tcaatcccct gctgctcgtt ctagacgcga 1141 gcagatagaa attcttgacg ctaggggttt ttagatgggc tctgttccga gacaggtttt 1201 gaaagcccct tttctgaact tggcttacct gaaatctcgg tcacagatgg agcccgtatt 1261 cgtaaacagt ctagtaaaat tcatttccta tcgcaaacta gtttaggatt agttttccaa 1321 gcccccaatg ccagcctaca taatgcactc gtagccgttg aaaggagagt tttcaccgtt 1381 ggaaaaggaa atgaaataac actccccccg agaccagaac ttgacatttt cactgaatca 1441 atgaaatact tctcggacga aattgtaaat caagtggggt gttgtaaggt tttctctcct 1501 gagtttctcg ctttcagtta ctcttccgga aaaaggtcac aatatcttaa ggcaatagaa 1561 tcccttaaaa tgaaaccata tgaagaaaag gattctcatg taactgcctt cctcaagaaa 1621 gaaaaacatt ggatgaccaa gcccattgcc cccagactca tatgccccag aaccaagcga 1681 tacaatatta ttctgggaac ccacctcaag tttaacgaaa agaagatcat gcacgctatt 1741 gattgtgtgt ttggatcccc cacagtactc tcaggtttcg actcatttca acaaggaaag 1801 gtcatagcca gaaagtggcg aaaattttct aatcctgttg ctatcggagt cgatgccagt 1861 cgttttgatc agcacgtatc agaacaggct ctaatgtggg aacatagcat ctacaacgat 1921 atattcaatg atccgtttct caaaacggca ctgtcacatc aactgaacaa taatatattg 1981 atgtttgtag atgacaagat gttgaggttt aaagtcaagg gacaccgtat gtccggtgat 2041 ataaacacaa gcatggggaa taagctcatt atgtgtggca tgatgcatgc ttatttcaaa 2101 tcactaaatg tcgacgcaga actttgtaat aacggagacg attgtgtcat tatttgcgaa 2161 aggaaagacg aagccaaatt tgctggcatg tacgacttct ttctcaagta tggattcaat 2221 ctggttactg aacaccccgt ttatgaactt gaaaagctag agttctgcca atcgagacct 2281 gtttgtgtaa atggaaagta tagaatggta cgcagacctg attgtatatc aaaagacagc 2341 cataccttgt tgagtatgct cggccaagag gacgtcaagt cctatatgtc ggccgttgct 2401 cagtgtggtc tagtcttgaa ttctggcgtt ccgattctcg aaagcttcta cgagtgcctg 2461 taccgaagta gcggttataa gaaagtatct gaggagtaca tcaaaaacgt catatcctat 2521 ggtacggagg aaaggcttca gggtagacgt gcccgccaaa tcgagcctat taccctaggg 2581 acaagactca gttactggga aacatttgga gttgatccaa ggacacaaga aattgttgag 2641 aggtacttca acagtctaac gatcagtact cagctccaaa gagtgaaggt gacaactcca 2701 cacatgcaat caatccttct ctcaatccca gagaaaaatc cacccgctac acaatagatt 2761 ttcacttcct aactggctta ggaataggtt tcattttagc aattccctgt acattagctc 2821 tcacttactt catttacaat aaagtttcag acaccactag agaggtggtg aatgaattca 2881 gtaggccgta gaagagcaag caagaatgtc agagccagga gcaatagaac agttcggcca 2941 gtggttgtgg tccggaccaa tccaaatgga cgaagacgtc gagcccctcg acgcccaaga 3001 agaggaaggg caaatcctat acttggacca gcaggcaggt ctgaggtatt cgtattctca 3061 atcaacgata ttaaagccaa ttcctcaggg gtcatcaaat tcggccccga tctttcacaa 3121 tgtccagcgc tttcaagcgg aatacttaag tcctaccacc gttacaagat ctcaaatgtc 3181 aagatcgagt ttaagtcaca cgcgtcctcc actacagtcg gcgctatgtt tattgaactc 3241 gacaccgcgt gcacacaatc aaccttgggt agctacatta actcattcac cctctccaag 3301 tcaggaacca aaacgtttaa tgcccagcaa atcgctggca aagagttcag ggagacgtcg 3361 gtaaatcagt tttatttatt gttcaaagct aacggtgtta catctgacac tgcaggacaa 3421 ttcattatca ccttgcgggt ttcaaacatg actcccaaat aggtagactc ctcaacacca 3481 ggacccggcc caaagccaaa accagacccc acaccaaccc cagcccctga gcctaaaacc 3541 cccaagagat ttttcgagtt tatcggaaca ccttctgggg taatccaaac cagggaatca 3601 tcggacagca tttctgtgtc caagctggga gatcagacat tccaaaagat cgagaatgag 3661 aagtcaaatg acgtctttct ctcttcttac tggcaataca gtaacagtgt ttacgcccaa 3721 gctgcctttg taattccaat ttaccaaggt agctacagcg ttaacatttc atgtgaagga 3781 atgcaatctg tagatcacat aggaggggaa caagatggtt attggatagg tttgatagcc 3841 tactccaatt cgacagacga tgtctggggc gtcgggaatt accaaggatg cacaatcacg 3901 aaatacctcg tcaccaattc ttggagacca ggccatcaag acttaaaact caatgattgt 3961 gcgttcgaca aaggccaaat cgtagaaaga gacgcagtct tatcgttcca tgtagaagct 4021 gttggtgaca accccagttt ctacttacta gcaccaaaaa cgcaaaagac tgacaagtac 4081 aactatgttg tctcctacgg tggctacacc aacaagaaaa tggaatttgg aacaatagcc 4141 attacttgtg atgaatctga tgttgaggca ctccgcaatg caagacatgc aaactacccc 4201 atcaaggaaa accaccaaga attatatcat ggttcgggta ctttgctacc tgcctactcg 4261 cctgatagag tagaagtcta tcctgatatc actagctctg agcgaacggt tcaaccccgt 4321 cctagtgaag aacccaaatt tcgagatatc caaaatcagg aagaactttc aagtctattt 4381 gacttgtacg atctcgccac ctctgaaata cccgacgcaa gggaagatgt tttaccaacc 4441 aagcaagaaa tgagcaaaaa gccaattgac agcttgggca ctgaaattcc acgccctagg 4501 tctatgtccc cagagtatcc acgaccacgg tcacgctctc cggagtatcc ccgacctcgg 4561 tcacgatccc ctgaacccat aggaacctac catggccaaa acatctatga cgatgacgtc 4621 cccaaacaag tggctgagag gcttagagaa gccgctgaat tgccttctac tatgctctat 4681 aaccgaaaac ccaaaaacag aaattctagt tttctttccc gtttcattga acaaaataaa 4741 tcaccagatg ccaccgcccc ttccgaggct accacctcgc gaatgacccg agatcagctg 4801 aaagaataca ctcgtgttag gaatcagtat ggtctcaccg ctgctaagca atacaaagct 4861 tcacttggac agtgaaggtg aaagactgca ctctttcaca ccacctacca ctggcaaaag 4921 acggatcctg ggaaacaggc agtgcttagg cacgtaagct cggggatact agtcatatcc 4981 cgccgcatca cttttgtctg gccgatgggt gggctggagg tcattgctgt ctgtatgata 5041 gcaattgtgt tccttcaagc agtcggtacc attgtaaata tgtgcatctg tgtcggcgcc 5101 attgctgccg cataaaccaa aatgccattg cactgtgagc aacggcacac aaaaacaaag 5161 acgggagctc ttagctcagg aaagaggtca atcacctcat gacaggctgg tctaggtgga 5221 cttgaataac ccaccgcaag acaactggaa acccaccaga gaacaaataa ggtagcttgc 5281 ttctgagcta ttcactgccc cagtaacgtc tgggtaaaca aaacttcaca ccaccccgat 5341 gagaagaggg gagagtgtgc ggggttaggg atcccgtgat ataccctaga tcgtcgtggc 5401 ttgaggacgt taaaacgcaa cgaccttatt aagtcgttaa actgatagtc atctcccgag 5461 tgatgacccc tacccatgac ttataggaac gatacgaaac gttctactac ccgatgccgg 5521 aaccccctcg cggtcggcct ggatgagaaa ccaggattac atccggtagt tggctcgaat 5581 ggccatagca caagtcaggt actagggaaa aatactttgg aagcgagccc atgcgggcct 5641 ccgagttgcc agccggcaag acaactcgtg agtatcttca ctggtaacag tgaaggggtc 5701 cgacatattg acaggtggct cttgtgtcca ccttac //