LOCUS NC_036580 3453 bp RNA linear VRL 13-JAN-2018 DEFINITION Allium cepa amalgavirus 1 strain AcAV1-OH1, complete genome. ACCESSION NC_036580 VERSION NC_036580.1 DBLINK BioProject: PRJNA429843 KEYWORDS RefSeq. SOURCE Allium cepa amalgavirus 1 ORGANISM Allium cepa amalgavirus 1 Viruses; dsRNA viruses; Amalgaviridae; unclassified Amalgaviridae. REFERENCE 1 (bases 1 to 3453) AUTHORS Nibert,M.L., Pyle,J.D. and Firth,A.E. TITLE A +1 ribosomal frameshifting motif prevalent among plant amalgaviruses JOURNAL Virology 498, 201-208 (2016) PUBMED 27596539 REFERENCE 2 (bases 1 to 3453) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (12-JAN-2018) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA REFERENCE 3 (bases 1 to 3453) AUTHORS Nibert,M.L., Pyle,J.D. and Firth,A.E. TITLE Direct Submission JOURNAL Submitted (04-APR-2017) Department of Microbiology & Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to BK010347. ##Assembly-Data-START## Assembly Method :: Newbler v. 2.5.3 Sequencing Technology :: 454 ##Assembly-Data-END## COMPLETENESS: full length. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-3453 GAAO01011981.1 1-3453 FEATURES Location/Qualifiers source 1..3453 /organism="Allium cepa amalgavirus 1" /mol_type="genomic RNA" /strain="AcAV1-OH1" /db_xref="taxon:2058778" 5'UTR 1..148 gene 149..3323 /gene="ORF1+ORF2" /locus_tag="C1180_gp1" /db_xref="GeneID:35381322" CDS join(149..982,984..3323) /gene="ORF1+ORF2" /locus_tag="C1180_gp1" /ribosomal_slippage /note="RNA-dependent RNA polymerase encoded by ORF2 region" /codon_start=1 /product="ORF1+2p" /protein_id="YP_009447919.1" /db_xref="GeneID:35381322" /translation="MSAEDFTPRTGLVDTELLVDPAAELEELHDALMPLEVLNINVKA FTRANIFALRMTVPQYIKEVRVLQNLQDVQLIRKVWTEAISHKCATLPDEADAGVCLS FARWLKRGVGAKVLSDAQHLIKLQKRAVGSVEPKVLAFVQLLDQQIADMHAERKKIQA EGQAKIDELRREIQRVEREYDEKAKASSKRFKPARKYVPPTKAKIDEECWNAYLNKVQ KSGKTAPEWNAVLQEQANTMYQQLYLTQHKQDFCGLESNQIPLKVWADSKLKELADNH EFVASARPSESWVSRVESHLHRLPLPQRVFQANNVPVGPVSQLVMNQSRNMALRTLLN PQLLTWKSQIGMRKKPPLQKANESRSSKIDLLLRNPRILVLRKPERGPLGGIPTARSK FEAMVRKVIGGGEMLNWSIDSNMYRGGGNFTDALTLLADARYDAPEMFLSDYLSIEKA RSLLCLPSDLKVPCHRNCVSVNNFNNEATAGPFFRAHGIRNKYGMRLQLEDFAWECYN AYVDSGGNPSMLPYISSRVGFRTKLVSTTEAFAKMKDNKPIGRCVMMLDAIEQMFSTP LYNVLSKTTAAQRFDIKSGFRNTIVRASSDWAKFWEEVKAAKVIVELDWKKFDRERPT EDLEFIIQVIISCFKPTDERERLFLRGYGIMLRRCLIDRYFITDDGGVFKIDGMVPSG SLWTGWVDTALNILYLQSVMISLGLVSTAVSPKCAGDDNLTLFWKDFDDKRLLSIKTR LNAWFRAGIDDEDFFIHRPPYHVTREQATFPPGTDLTKGTSRKLKDAIWIPIDGEPII DQAQGLSHRWQYVFRGKPKFLSAYWLEDGRPIRPTHVNAEKLLFPEGIHKDIEQYESA VLSMIVDNPYNHHNVNHCMHRFIICEQVKRQSAAGIDPVDILWFSRIRPGNPDVVPYP MVASWRRCEGYVDLEQLPFISDYVKDLKEFVAGVTSLYARDSIGGLDAWRFTEIIRGE TDLGTGQFGNDIDVWIHWLHHHPLTKYLKPIKRHRQPPLSVMPDKELHGRIEEALQVY RDIRGTTTNASAEAFSLFLSNVIKHQG" gene 149..1324 /gene="ORF1" /locus_tag="C1180_gp2" /db_xref="GeneID:35381321" CDS 149..1324 /gene="ORF1" /locus_tag="C1180_gp2" /codon_start=1 /product="ORF1p" /protein_id="YP_009447920.1" /db_xref="GeneID:35381321" /translation="MSAEDFTPRTGLVDTELLVDPAAELEELHDALMPLEVLNINVKA FTRANIFALRMTVPQYIKEVRVLQNLQDVQLIRKVWTEAISHKCATLPDEADAGVCLS FARWLKRGVGAKVLSDAQHLIKLQKRAVGSVEPKVLAFVQLLDQQIADMHAERKKIQA EGQAKIDELRREIQRVEREYDEKAKASSKRFKPARKYVPPTKAKIDEECWNAYLNKVQ KSGKTAPEWNAVLQEQANTMYQQLYLTQHKQDFCGLESNQIPLKVWADSKLKELADNH EFRRVRETQRILGLASGVPSSPSASASKSLSGKQRSGGPSQSAGDEPVEEHGSSNSAK PAAPDMEITDRDEEKTSSSKGKRKQKLKDRLAAKKSKDLSAKKTRKGTIRRDPHRKK" regulatory 980..985 /regulatory_class="other" /gene="ORF1" /locus_tag="C1180_gp2" /note="+1 ribosomal frameshifting motif" 3'UTR 3324..3453 ORIGIN 1 gggtataaat aaaattctta ttcgtaggac ctcattatac ttgccttctc agttacctgc 61 tcgtgctacc gctttaactg cttgctcggt gtgttctgtt ctctgcttct tggttggtta 121 aattttactt caatttctgc aatccaatat gtctgccgaa gattttaccc ccaggaccgg 181 cttagttgat acggagttgt tagtcgatcc cgccgctgaa cttgaggagt tgcatgatgc 241 actcatgcca cttgaagtcc ttaacatcaa tgttaaggcc ttcacacgtg ctaacatctt 301 cgccctccga atgaccgttc cgcaatatat taaggaggtg cgtgtacttc aaaatctgca 361 agatgtgcag cttattcgca aagtctggac tgaggccatc agccacaaat gcgctacctt 421 gccagatgaa gctgatgctg gcgtttgtct cagctttgcg cgttggttga agcgtggtgt 481 gggtgccaaa gtgttatctg atgctcagca tcttatcaaa ttacagaaac gtgctgttgg 541 gagcgttgag cctaaagttt tggcatttgt ccagctgctt gaccagcaaa tcgctgatat 601 gcatgctgaa cgtaaaaaga ttcaggccga aggtcaggct aaaattgatg agttacgtcg 661 tgaaatccag agggttgaaa gggagtacga tgaaaaagct aaggcctcat cgaagcgctt 721 taagcctgct aggaagtatg tgcccccgac aaaagcaaaa atcgatgaag aatgttggaa 781 tgcttatctc aataaagtgc aaaagagtgg caaaactgct cctgaatgga atgctgtcct 841 acaggaacag gctaatacca tgtatcagca gctatatctc acacagcata aacaggactt 901 ctgtggcctt gagtctaatc agataccact caaggtatgg gccgactcta agttgaagga 961 attggcagat aatcatgagt ttcgtcgcgt ccgcgagacc cagcgaatct tgggtctcgc 1021 gagtggagtc ccatcttcac cgtctgcctc tgcctcaaag agtctttcag gcaaacaacg 1081 ttccggtggg cccagtcagt cagctggtga tgaaccagtc gaggaacatg gctcttcgaa 1141 ctctgctaaa cccgcagctc ctgacatgga aatcacagat agggatgagg aaaaaacctc 1201 ctcttcaaaa ggcaaacgaa agcagaagct caaagatcga cttgctgcta agaaatccaa 1261 ggatcttagt gctaagaaaa ccagaaaggg gaccattagg agggatcccc accgcaagaa 1321 gtaaatttga ggcaatggtc aggaaggtga ttggtggcgg agagatgctg aactggtcta 1381 tcgattccaa tatgtatcgg ggaggcggca atttcactga tgcactcaca ttattggctg 1441 atgcaagata tgatgcacct gaaatgtttc tgtccgatta tctttcgatc gagaaagccc 1501 gttcacttct ctgtttacct tctgacctta aagtgccgtg ccaccgtaat tgtgtgtctg 1561 taaataattt caataacgaa gctacagctg gaccgttctt ccgtgcccat ggcattagga 1621 ataaatatgg catgcggttg cagctagagg attttgcatg ggaatgttac aatgcatatg 1681 ttgatagtgg tggtaatccg agtatgctgc catatatctc atcaagagtc ggatttcgca 1741 ctaaattggt ttcaaccacc gaagcctttg ccaaaatgaa agacaataaa ccaatcgggc 1801 gttgtgttat gatgttggat gcgatcgagc agatgttttc tacgccatta tataatgtac 1861 tttctaagac cacagcggca cagcgttttg acataaaatc gggcttccgt aacaccatcg 1921 tgagagcatc ctccgactgg gctaaatttt gggaggaagt caaggctgct aaggttattg 1981 ttgaactgga ttggaagaag tttgatcgtg aacgtccaac tgaggatctt gagtttatta 2041 tccaagttat aatctcatgt ttcaagccca cagatgaacg ggaacggctc ttcctgagag 2101 gttatggcat tatgctcagg cgctgtctta ttgatagata tttcataacg gatgacggtg 2161 gcgttttcaa gatagatggt atggtaccta gtggttcact ctggacagga tgggttgata 2221 ctgcattgaa tatattatat ctgcaatccg tcatgatatc actcggtctt gtcagcacag 2281 cagtctcacc caaatgcgct ggggatgata atttgacgtt attctggaag gattttgatg 2341 ataaacgctt gctaagcatt aaaacgcgtc taaatgcatg gttccgcgct ggtattgatg 2401 atgaagattt cttcattcat agaccaccgt atcatgttac tagagaacaa gcaacttttc 2461 ccccgggcac tgatttgacc aaaggaactt caagaaagtt aaaggatgca atatggatac 2521 ctattgatgg tgagcctatc attgatcaag cacaaggttt atctcataga tggcaatatg 2581 tattccgggg caagccgaag tttctctcgg cgtattggct ggaagatggt cgtccaatca 2641 gaccaaccca cgtcaatgcc gaaaagcttc tatttcctga gggcatacat aaagacatcg 2701 aacaatatga atctgccgtg ttatcgatga tcgttgataa tccatataat catcataatg 2761 taaatcattg tatgcatcgc tttattatat gtgaacaggt aaaaagacag tcggccgccg 2821 ggattgatcc agttgacatc ttatggtttt cgcgcatacg acctggtaac cctgatgttg 2881 taccgtaccc tatggtagca tcttggcggc gttgtgaagg atacgttgat ctggagcaac 2941 tgccattcat cagtgattat gttaaagacc ttaaagagtt tgttgctggc gtcacttctc 3001 tctatgcacg tgattcaatc ggcggacttg acgcttggcg tttcactgaa ataatacgtg 3061 gtgaaactga tcttggcact gggcagttcg gaaacgatat agatgtatgg atacactggt 3121 tgcatcatca tccattaact aaatacctca agccaatcaa gcgacatcgt cagccaccac 3181 tctcagttat gccggacaag gagctgcatg gaagaatcga ggaagcactt caagtctaca 3241 gggacattcg cggcaccacc accaatgcct ctgctgaagc tttttcttta tttttatcca 3301 atgtaattaa acatcaaggc taggacccga acgttatgta gcgttcgcag acaccagcct 3361 tctactatgt tttctttcta ttgtaactga ttattatata gtatatacgt ggactaccta 3421 cggtataggt ccatgtccaa aaacacacac aaa //