ID J04357; SV 1; linear; genomic RNA; STD; VRL; 3890 BP. XX AC J04357; M24621; XX DT 02-FEB-1990 (Rel. 22, Created) DT 23-JUN-2016 (Rel. 129, Last updated, Version 9) XX DE Red clover necrotic mosaic virus RNA-1, complete sequence. XX KW . XX OS Red clover necrotic mosaic virus OC Viruses; Riboviria; Tombusviridae; Regressovirinae; Dianthovirus. XX RN [1] RP 1-3890 RX DOI; 10.1016/0042-6822(89)90624-7. RX PUBMED; 2763465. RA Xiong Z., Lommel S.A.; RT "The complete nucleotide sequence and genome organization of red clover RT necrotic mosaic virus RNA-1"; RL Virology 171(2):543-554(1989). XX RN [2] RP 1-3890 RX DOI; 10.1006/viro.1993.1117. RX PUBMED; 8438566. RA Xiong Z., Kim K.H., Kendall T.L., Lommel S.A.; RT "Synthesis of the putative red clover necrotic mosaic virus RNA polymerase RT by ribosomal frameshifting in vitro"; RL Virology 193(1):213-221(1993). XX RN [3] RP 1-3890 RA Xiong Z., Lommel S.A.; RT ; RL Submitted (15-MAY-1989) to the INSDC. RL Department of Plant Pathology, North Carolina State University, Raleigh, NC RL 27695-7616, USA XX RN [4] RC Amino acid sequence updated by submitter RP 1-3890 RA Xiong Z., Lommel S.A.; RT ; RL Submitted (11-MAY-2015) to the INSDC. RL Department of Plant Pathology, North Carolina State University, Raleigh, NC RL 27695-7616, USA XX DR MD5; 8525a2ea7ceb763f84792fee2a9da1e0. DR EuropePMC; PMC112128; 10864632. DR EuropePMC; PMC1421387; 16524473. DR EuropePMC; PMC6299227; 30563900. DR RFAM; RF01453; RCNMV_TE_DR1. DR RFAM; RF01454; RCNMV_5UTR. XX FH Key Location/Qualifiers FH FT source 1..3890 FT /organism="Red clover necrotic mosaic virus" FT /segment="RNA-1" FT /strain="Australia" FT /mol_type="genomic RNA" FT /db_xref="taxon:12267" FT CDS join(124..831,831..2426) FT /codon_start=1 FT /ribosomal_slippage FT /product="88 kDa protein" FT /note="putative RNA polymerase; -1 ribosome frameshifting" FT /db_xref="GOA:P22956" FT /db_xref="InterPro:IPR002166" FT /db_xref="InterPro:IPR007094" FT /db_xref="UniProtKB/Swiss-Prot:P22956" FT /protein_id="AAB02540.2" FT /translation="MGFINLSLFDVDKLMVWVSKFNPGKILSAICNLGIDCWNRFRKWF FT FGLNFDAHMWAVDAFIPLMPHYTEQMERVVDDFCSETPESKLEDCLELDTSVNEFFDEE FT VYKKDEEGVMKLQRSAARKHIKRVRPGMMQAAIKAVETRIRNRHTIFGDDMGKVDEAAV FT RATASDICGEFKINEHHTNALVYAAAYLAMTPDQRSIDSVKLAYNPKSQARRTLVSAIR FT ENKAVAGFKSLEDFLGGPLSFPVEDAPYPILGIPEIRVAEKRASRVMKSKRVVGLPAVS FT AGLKVCVHQTSLHNMIVSLERRVFRVKNSAGELVVPPKPIQNAFDSISYFREEWLRKLS FT HKGQILKSSLADVVACYSSEKRKLYQKAADSLEKKPVQWRDSKVQAFIKVEKLECDTKD FT PVPRTIQPRSKRYNLAIGQYLRLNEKKMLDSIDDVFKEKTVLSGLDNRAQGRAIAHKWR FT KYQNPIGIGLDASRFDQHCSVDALKFEQTFYKACFPGDQQLETLLKWQLSNTGSALLPT FT GELVRYRTKGCRMSGDINTGLGNKILMCSMVHAFLKETGVRASLANNGDDCVLFCEKGD FT YEQINRNLEQWFLCRGFEMTVEKPVDVLEKVAFCRSQPVCIATQWAMVRQLGSLSRDCF FT STQDWLNPKTFKDAMNALGQCNGIINDGVPIHMAQAKLMHRIGGNRKFNLDALHKQMEY FT SWRDRLGKRTNLLWSEVEDATRLSYFRAFGIEPYIQRIVEEYFSQVEITCEGRSTNVLP FT THYSRIHKDLIKAR" FT CDS 124..834 FT /codon_start=1 FT /product="27 kDa protein" FT /note="putative" FT /db_xref="GOA:P22956" FT /db_xref="InterPro:IPR002166" FT /db_xref="InterPro:IPR007094" FT /db_xref="UniProtKB/Swiss-Prot:P22956" FT /protein_id="AAB02539.1" FT /translation="MGFINLSLFDVDKLMVWVSKFNPGKILSAICNLGIDCWNRFRKWF FT FGLNFDAHMWAVDAFIPLMPHYTEQMERVVDDFCSETPESKLEDCLELDTSVNEFFDEE FT VYKKDEEGVMKLQRSAARKHIKRVRPGMMQAAIKAVETRIRNRHTIFGDDMGKVDEAAV FT RATASDICGEFKINEHHTNALVYAAAYLAMTPDQRSIDSVKLAYNPKSQARRTLVSAIR FT ENKAVAGFKSLEDF" FT misc_feature 821..841 FT /note="frameshifting region; putative" FT CDS 927..2426 FT /codon_start=1 FT /product="57 kDa protein" FT /note="putative" FT /db_xref="GOA:P22956" FT /db_xref="InterPro:IPR002166" FT /db_xref="InterPro:IPR007094" FT /db_xref="UniProtKB/Swiss-Prot:P22956" FT /protein_id="AAB02541.1" FT /translation="MKSKRVVGLPAVSAGLKVCVHQTSLHNMIVSLERRVFRVKNSAGE FT LVVPPKPIQNAFDSISYFREEWLRKLSHKGQILKSSLADVVACYSSEKRKLYQKAADSL FT EKKPVQWRDSKVQAFIKVEKLECDTKDPVPRTIQPRSKRYNLAIGQYLRLNEKKMLDSI FT DDVFKEKTVLSGLDNRAQGRAIAHKWRKYQNPIGIGLDASRFDQHCSVDALKFEQTFYK FT ACFPGDQQLETLLKWQLSNTGSALLPTGELVRYRTKGCRMSGDINTGLGNKILMCSMVH FT AFLKETGVRASLANNGDDCVLFCEKGDYEQINRNLEQWFLCRGFEMTVEKPVDVLEKVA FT FCRSQPVCIATQWAMVRQLGSLSRDCFSTQDWLNPKTFKDAMNALGQCNGIINDGVPIH FT MAQAKLMHRIGGNRKFNLDALHKQMEYSWRDRLGKRTNLLWSEVEDATRLSYFRAFGIE FT PYIQRIVEEYFSQVEITCEGRSTNVLPTHYSRIHKDLIKAR" FT CDS 2428..3447 FT /codon_start=1 FT /product="37 kDa capsid protein" FT /note="putative" FT /db_xref="GOA:P22955" FT /db_xref="InterPro:IPR000937" FT /db_xref="InterPro:IPR029053" FT /db_xref="UniProtKB/Swiss-Prot:P22955" FT /protein_id="AAB02542.1" FT /translation="MSSKAPKKSKQRSQPRNRTPNTSVKTVAIPFAKTQIIKTVNPPPK FT PARGILHTQLVMSVVGSVQMRTNNGKSNQRFRLNPSNPALFPTLAYEAANYDMYRLKKL FT TLRYVPLVTVQNSGRVAMIWDPDSQDSAPQSRQEISAYSRSVSTAVYEKCSLTIPADNQ FT WRFVADNTTVDRKLVDFGQLLFVTHSGSDGIETGDIFLDCEVEFKGPQPTASIVQKTVI FT DLGGTLTSFEGPSYLMPPDAFITSSSFGLFVDVAGTYLLTLVVTCSTTGSVTVGGNSTL FT VGDGRAAYGSSNYIASIVFTSSGVLSTTPSVQFSGSSGVSRVQMNICRCKQGNTFILG" FT regulatory 3862..3890 FT /note="stem-loop structure" FT /regulatory_class="other" XX SQ Sequence 3890 BP; 1122 A; 857 C; 946 G; 965 T; 0 other; gacaaacgtt ttaccggttt gtaaatagga gcacacaagc tcgctagtcg cccccttcgt 60 atcggggatc tagagattaa acggtatacc tgtcatttta aatttctact tttcgtacca 120 gtcatgggtt ttataaatct ttcgcttttt gatgtggata aattaatggt gtgggtgagt 180 aaattcaatc caggcaaaat cctgtctgca atctgcaact tgggtataga ctgttggaat 240 cgctttcgca agtggttctt tggtctcaac tttgatgcac atatgtgggc ggtggatgcc 300 ttcattccac tcatgccaca ttacacggag cagatggaac gtgtagtcga cgacttctgc 360 agcgaaaccc cagaatccaa attagaagac tgtctggaac tggacacctc agtaaatgaa 420 ttcttcgatg aagaggtgta caagaaggat gaggaaggcg tgatgaaact ccaaaggagc 480 gctgccagga aacacattaa acgtgtgcgc ccaggcatga tgcaagcggc cattaaggct 540 gtagaaacga ggatcagaaa tcgccatacc atctttggag atgacatggg aaaggtagac 600 gaagctgcag ttagagcaac tgccagtgac atatgtggtg agttcaagat caacgaacac 660 cacaccaatg cattggtgta tgccgcagca taccttgcca tgacaccaga ccagaggtct 720 atcgacagcg tcaagctcgc ctacaatcct aagagtcaag ccagaaggac tttggtttca 780 gccattcgtg agaacaaggc tgttgccggg ttcaaatccc ttgaggattt ttaggcggcc 840 cactcagctt tccggttgaa gatgccccat atcctatttt aggcatcccg gaaatcaggg 900 tagctgagaa gcgggccagt agagtcatga aaagtaagag agtcgtaggg ttacctgctg 960 ttagtgcagg tttgaaggtt tgcgtccatc aaacctccct acataatatg atagttagtc 1020 tcgaacgcag ggtttttcgt gtgaagaact ctgcaggaga gttagtagta cctcccaaac 1080 ctatccaaaa tgcatttgac tccatttcct atttccgtga agaatggttg aggaaattgt 1140 ctcacaaggg tcaaattctc aagtcctctt tggcggatgt tgtggcgtgt tactcttctg 1200 aaaagaggaa gttataccaa aaagcagcag actccttaga gaagaaacct gtgcaatgga 1260 gagactccaa ggtacaagca ttcatcaaag ttgaaaagct tgagtgtgac accaaggatc 1320 ccgtacctcg tacgattcaa cctcgatcca agaggtacaa cctagcaata ggccagtatc 1380 tcagattaaa tgaaaagaag atgttggatt ccatagacga cgttttcaaa gagaagactg 1440 tcttatcagg tttggacaac agggctcaag ggagagccat cgcccacaag tggcgtaaat 1500 accagaaccc aatagggatc gggctggatg catcgagatt cgatcaacat tgcagcgtcg 1560 atgccctcaa attcgagcaa actttctata aagcgtgctt tcctggggat caacagttgg 1620 aaacattatt gaaatggcaa ttatccaata ctggatcggc tttgttacca actggagaac 1680 tggttagata tcgtaccaaa gggtgtcgca tgagcggcga tataaacaca ggccttggga 1740 acaaaattct catgtgcagc atggtacacg cattcttgaa agagacggga gtgcgagctt 1800 cgttggccaa caatggtgac gattgtgtcc tcttctgtga gaagggagat tatgagcaga 1860 taaaccgcaa tcttgagcaa tggttcctgt gcaggggttt cgaaatgacc gtcgaaaaac 1920 ctgtcgatgt actcgagaag gtggcgtttt gtcgtagtca accggtttgc attgccacgc 1980 aatgggctat ggtaaggcaa ttgggaagtt tgtcgagaga ctgcttttca acacaggatt 2040 ggttaaaccc aaagacattc aaagatgcaa tgaatgcgct aggtcaatgt aacgggatca 2100 tcaatgatgg agttccaata catatggcac aagcaaaact aatgcataga atcggtggaa 2160 accgtaagtt caatctagat gcgcttcata aacaaatgga gtacagctgg agagatcgtc 2220 tcggtaagag aacgaatctt ttgtggagtg aggtagagga tgctacaaga ttgtcgtact 2280 ttagagcatt cggaatagaa ccttacattc aaagaatagt ggaggagtac ttctcacagg 2340 tggaaatcac ttgtgagggg cgatcaacaa acgtattacc tacacactac tctagaatcc 2400 acaaagatct aatcaaagcc cgataaaatg tcttcaaaag ctcccaagaa atccaaacaa 2460 cggtcccagc ccaggaaccg gaccccaaat accagtgtaa agactgtagc catccccttt 2520 gccaagacgc aaataatcaa gactgtgaat cctccaccga aaccagcaag aggtatattg 2580 catacccagt tagttatgag tgtggttgga tcagttcaaa tgcgtacaaa taatggcaaa 2640 tccaaccaaa ggttcagatt aaaccctagc aatcctgctc ttttccccac tctagcatat 2700 gaagctgcaa attatgacat gtatcgctta aagaagctga cactccgtta cgtcccactc 2760 gttaccgtgc aaaattccgg gcgagttgca atgatctggg atcccgactc gcaagactcg 2820 gccccacaat ccagacagga gatatcagcc tattcccgat cagtctcgac tgccgtgtac 2880 gagaaatgct cgttgacgat tccggcggat aatcaatggc gcttcgttgc agataacacc 2940 acagtggaca gaaagctcgt cgattttggc cagcttttgt tcgttacaca ctctggtagt 3000 gatggaatag aaacagggga catattctta gattgtgaag tcgagttcaa aggaccccaa 3060 ccaaccgcaa gcatcgtaca gaaaactgta attgatctcg gtgggacact cacttctttc 3120 gaagggccat cttatctgat gcctccggat gcctttatta ccagttctag tttcggcctg 3180 tttgttgacg tcgcagggac ctatctgctt acactagtgg tgacttgttc gaccactggt 3240 agcgtcacag taggaggaaa ttcaactctg gttggcgacg gtagggcggc atacggtagt 3300 agcaattaca ttgcttctat agtattcact agttcgggtg tgttatcgac cacccctagt 3360 gtgcagtttt caggttcctc tggagtatca cgcgtgcaaa tgaacatctg cagatgtaaa 3420 caggggaaca ctttcatact tggttaattg gttcttttaa gtgtagcctc cacccgagtt 3480 gcaagagggg aacacgcagt ctcgccgacc ctgttggcaa acagtaaaat tgcaaaaaat 3540 agagtgctag gagtagttcc cgtacccgcg ggagcaagac cctactacag tagacgaacc 3600 ggcatcggac cctgggaaac aggtacctag cgtattaata ggtcgctaga aatcgggcgg 3660 gcttcacctt cgggtaaccc gccgtcgaga gggaaaacct ctgtgtggtt gtgcgcacgt 3720 cgttgtcgga agactctcac tgttgtagtt atttcctttt tcttttaggt aggagcactt 3780 gctcagaggg cgcatacctc tggtaaaaca aaattggccc ctgagagtag aaaactcagg 3840 ttaataaaac aggagaatat ttacctagtc gtataacggc taggtacccc 3890 //