Sequence of DPV Red clover necrotic mosaic virus

Red clover necrotic mosaic virus RNA-1, complete sequence.

ACC No: J04357

Dated: 2005-04-17 | Length: 3890 | CRC: 1313232103

                !!NA_SEQUENCE 1.0
ID   RNMRS1     standard; genomic RNA; VRL; 3890 BP.
XX
AC   J04357; M24621;
XX
SV   J04357.1
XX
DT   02-FEB-1990 (Rel. 22, Created)
DT   17-APR-2005 (Rel. 83, Last updated, Version 7)
XX
DE   Red clover necrotic mosaic virus RNA-1, complete sequence.
XX
KW   capsid protein; RNA polymerase.
XX
OS   Red clover necrotic mosaic virus
OC   Viruses; ssRNA positive-strand viruses, no DNA stage; Tombusviridae;
OC   Dianthovirus.
XX
RN   [1]
RP   1-3890
RX   MEDLINE; 93174929.
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   [2]
RP   1-3890
RX   MEDLINE; 89348013.
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
CC   Draft entry and computer readable copy of sequence [1] kindly
CC   provided by Z.Xiong 15-MAY-1989.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1. .3890
FT                   /chromosome="RNA-1"
FT                   /db_xref="taxon:12267"
FT                   /mol_type="genomic RNA"
FT                   /organism="Red clover necrotic mosaic virus"
FT                   /strain="Australia"
FT   CDS             join(124. .831,834. .2426)
FT                   /codon_start=1
FT                   /db_xref="GOA:P22956"
FT                   /db_xref="UniProt/Swiss-Prot:P22956"
FT                   /note="putative; -1 ribosome frameshifting"
FT                   /product="88 kDa protein"
FT                   /protein_id="AAB02540.1"
FT                   /translation="MGFINLSLFDVDKLMVWVSKFNPGKILSAICNLGIDCWNRFRKWF
FT                   FGLNFDAHMWAVDAFIPLMPHYTEQMERVVDDFCSETPESKLEDCLELDTSVNEFFDEE
FT                   VYKKDEEGVMKLQRSAARKHIKRVRPGMMQAAIKAVETRIRNRHTIFGDDMGKVDEAAV
FT                   RATASDICGEFKINEHHTNALVYAAAYLAMTPDQRSIDSVKLAYNPKSQARRTLVSAIR
FT                   ENKAVAGFKSLEDFGGPLSFPVEDAPYPILGIPEIRVAEKRASRVMKSKRVVGLPAVSA
FT                   GLKVCVHQTSLHNMIVSLERRVFRVKNSAGELVVPPKPIQNAFDSISYFREEWLRKLSH
FT                   KGQILKSSLADVVACYSSEKRKLYQKAADSLEKKPVQWRDSKVQAFIKVEKLECDTKDP
FT                   VPRTIQPRSKRYNLAIGQYLRLNEKKMLDSIDDVFKEKTVLSGLDNRAQGRAIAHKWRK
FT                   YQNPIGIGLDASRFDQHCSVDALKFEQTFYKACFPGDQQLETLLKWQLSNTGSALLPTG
FT                   ELVRYRTKGCRMSGDINTGLGNKILMCSMVHAFLKETGVRASLANNGDDCVLFCEKGDY
FT                   EQINRNLEQWFLCRGFEMTVEKPVDVLEKVAFCRSQPVCIATQWAMVRQLGSLSRDCFS
FT                   TQDWLNPKTFKDAMNALGQCNGIINDGVPIHMAQAKLMHRIGGNRKFNLDALHKQMEYS
FT                   WRDRLGKRTNLLWSEVEDATRLSYFRAFGIEPYIQRIVEEYFSQVEITCEGRSTNVLPT
FT                   HYSRIHKDLIKAR"
FT   CDS             124. .834
FT                   /codon_start=1
FT                   /db_xref="GOA:P22956"
FT                   /db_xref="UniProt/Swiss-Prot:P22956"
FT                   /note="putative"
FT                   /product="27 kDa protein"
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 (put.); putative"
FT   CDS             927. .2426
FT                   /codon_start=1
FT                   /db_xref="GOA:P22956"
FT                   /db_xref="UniProt/Swiss-Prot:P22956"
FT                   /note="57 kD protein (put.); putative"
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                   /db_xref="GOA:P22955"
FT                   /db_xref="HSSP:2TBV"
FT                   /db_xref="InterPro:IPR000937"
FT                   /db_xref="InterPro:IPR008975"
FT                   /db_xref="UniProt/Swiss-Prot:P22955"
FT                   /note="37 kD capsid protein (put.); putative"
FT                   /protein_id="AAB02542.1"
FT                   /translation="MSSKAPKKSKQRSQPRNRTPNTSVKTVAIPFAKTQIIKTVNPPPK
FT                   PARGILHTQLVMSVVGSVQMRTNNGKSNQRFRLNPSNPALFPTLAYEAANYDMYRLKKL
FT                   TLRYVPLVTVQNSGRVAMIWDPDSQDSAPQSRQEISAYSRSVSTAVYEKCSLTIPADNQ
FT                   WRFVADNTTVDRKLVDFGQLLFVTHSGSDGIETGDIFLDCEVEFKGPQPTASIVQKTVI
FT                   DLGGTLTSFEGPSYLMPPDAFITSSSFGLFVDVAGTYLLTLVVTCSTTGSVTVGGNSTL
FT                   VGDGRAAYGSSNYIASIVFTSSGVLSTTPSVQFSGSSGVSRVQMNICRCKQGNTFILG"
FT   misc_signal     3862. .3890
FT                   /note="stem-loop structure"
XX
SQ   Sequence 3890 BP; 1122 A; 857 C; 946 G; 965 T; 0 other;

   J04357  Length: 3890  May 10, 2005 10:09  Type: N  Check: 505  ..

       1  gacaaacgtt ttaccggttt gtaaatagga gcacacaagc tcgctagtcg
      51  cccccttcgt atcggggatc tagagattaa acggtatacc tgtcatttta
     101  aatttctact tttcgtacca gtcatgggtt ttataaatct ttcgcttttt
     151  gatgtggata aattaatggt gtgggtgagt aaattcaatc caggcaaaat
     201  cctgtctgca atctgcaact tgggtataga ctgttggaat cgctttcgca
     251  agtggttctt tggtctcaac tttgatgcac atatgtgggc ggtggatgcc
     301  ttcattccac tcatgccaca ttacacggag cagatggaac gtgtagtcga
     351  cgacttctgc agcgaaaccc cagaatccaa attagaagac tgtctggaac
     401  tggacacctc agtaaatgaa ttcttcgatg aagaggtgta caagaaggat
     451  gaggaaggcg tgatgaaact ccaaaggagc gctgccagga aacacattaa
     501  acgtgtgcgc ccaggcatga tgcaagcggc cattaaggct gtagaaacga
     551  ggatcagaaa tcgccatacc atctttggag atgacatggg aaaggtagac
     601  gaagctgcag ttagagcaac tgccagtgac atatgtggtg agttcaagat
     651  caacgaacac cacaccaatg cattggtgta tgccgcagca taccttgcca
     701  tgacaccaga ccagaggtct atcgacagcg tcaagctcgc ctacaatcct
     751  aagagtcaag ccagaaggac tttggtttca gccattcgtg agaacaaggc
     801  tgttgccggg ttcaaatccc ttgaggattt ttaggcggcc cactcagctt
     851  tccggttgaa gatgccccat atcctatttt aggcatcccg gaaatcaggg
     901  tagctgagaa gcgggccagt agagtcatga aaagtaagag agtcgtaggg
     951  ttacctgctg ttagtgcagg tttgaaggtt tgcgtccatc aaacctccct
    1001  acataatatg atagttagtc tcgaacgcag ggtttttcgt gtgaagaact
    1051  ctgcaggaga gttagtagta cctcccaaac ctatccaaaa tgcatttgac
    1101  tccatttcct atttccgtga agaatggttg aggaaattgt ctcacaaggg
    1151  tcaaattctc aagtcctctt tggcggatgt tgtggcgtgt tactcttctg
    1201  aaaagaggaa gttataccaa aaagcagcag actccttaga gaagaaacct
    1251  gtgcaatgga gagactccaa ggtacaagca ttcatcaaag ttgaaaagct
    1301  tgagtgtgac accaaggatc ccgtacctcg tacgattcaa cctcgatcca
    1351  agaggtacaa cctagcaata ggccagtatc tcagattaaa tgaaaagaag
    1401  atgttggatt ccatagacga cgttttcaaa gagaagactg tcttatcagg
    1451  tttggacaac agggctcaag ggagagccat cgcccacaag tggcgtaaat
    1501  accagaaccc aatagggatc gggctggatg catcgagatt cgatcaacat
    1551  tgcagcgtcg atgccctcaa attcgagcaa actttctata aagcgtgctt
    1601  tcctggggat caacagttgg aaacattatt gaaatggcaa ttatccaata
    1651  ctggatcggc tttgttacca actggagaac tggttagata tcgtaccaaa
    1701  gggtgtcgca tgagcggcga tataaacaca ggccttggga acaaaattct
    1751  catgtgcagc atggtacacg cattcttgaa agagacggga gtgcgagctt
    1801  cgttggccaa caatggtgac gattgtgtcc tcttctgtga gaagggagat
    1851  tatgagcaga taaaccgcaa tcttgagcaa tggttcctgt gcaggggttt
    1901  cgaaatgacc gtcgaaaaac ctgtcgatgt actcgagaag gtggcgtttt
    1951  gtcgtagtca accggtttgc attgccacgc aatgggctat ggtaaggcaa
    2001  ttgggaagtt tgtcgagaga ctgcttttca acacaggatt ggttaaaccc
    2051  aaagacattc aaagatgcaa tgaatgcgct aggtcaatgt aacgggatca
    2101  tcaatgatgg agttccaata catatggcac aagcaaaact aatgcataga
    2151  atcggtggaa accgtaagtt caatctagat gcgcttcata aacaaatgga
    2201  gtacagctgg agagatcgtc tcggtaagag aacgaatctt ttgtggagtg
    2251  aggtagagga tgctacaaga ttgtcgtact ttagagcatt cggaatagaa
    2301  ccttacattc aaagaatagt ggaggagtac ttctcacagg tggaaatcac
    2351  ttgtgagggg cgatcaacaa acgtattacc tacacactac tctagaatcc
    2401  acaaagatct aatcaaagcc cgataaaatg tcttcaaaag ctcccaagaa
    2451  atccaaacaa cggtcccagc ccaggaaccg gaccccaaat accagtgtaa
    2501  agactgtagc catccccttt gccaagacgc aaataatcaa gactgtgaat
    2551  cctccaccga aaccagcaag aggtatattg catacccagt tagttatgag
    2601  tgtggttgga tcagttcaaa tgcgtacaaa taatggcaaa tccaaccaaa
    2651  ggttcagatt aaaccctagc aatcctgctc ttttccccac tctagcatat
    2701  gaagctgcaa attatgacat gtatcgctta aagaagctga cactccgtta
    2751  cgtcccactc gttaccgtgc aaaattccgg gcgagttgca atgatctggg
    2801  atcccgactc gcaagactcg gccccacaat ccagacagga gatatcagcc
    2851  tattcccgat cagtctcgac tgccgtgtac gagaaatgct cgttgacgat
    2901  tccggcggat aatcaatggc gcttcgttgc agataacacc acagtggaca
    2951  gaaagctcgt cgattttggc cagcttttgt tcgttacaca ctctggtagt
    3001  gatggaatag aaacagggga catattctta gattgtgaag tcgagttcaa
    3051  aggaccccaa ccaaccgcaa gcatcgtaca gaaaactgta attgatctcg
    3101  gtgggacact cacttctttc gaagggccat cttatctgat gcctccggat
    3151  gcctttatta ccagttctag tttcggcctg tttgttgacg tcgcagggac
    3201  ctatctgctt acactagtgg tgacttgttc gaccactggt agcgtcacag
    3251  taggaggaaa ttcaactctg gttggcgacg gtagggcggc atacggtagt
    3301  agcaattaca ttgcttctat agtattcact agttcgggtg tgttatcgac
    3351  cacccctagt gtgcagtttt caggttcctc tggagtatca cgcgtgcaaa
    3401  tgaacatctg cagatgtaaa caggggaaca ctttcatact tggttaattg
    3451  gttcttttaa gtgtagcctc cacccgagtt gcaagagggg aacacgcagt
    3501  ctcgccgacc ctgttggcaa acagtaaaat tgcaaaaaat agagtgctag
    3551  gagtagttcc cgtacccgcg ggagcaagac cctactacag tagacgaacc
    3601  ggcatcggac cctgggaaac aggtacctag cgtattaata ggtcgctaga
    3651  aatcgggcgg gcttcacctt cgggtaaccc gccgtcgaga gggaaaacct
    3701  ctgtgtggtt gtgcgcacgt cgttgtcgga agactctcac tgttgtagtt
    3751  atttcctttt tcttttaggt aggagcactt gctcagaggg cgcatacctc
    3801  tggtaaaaca aaattggccc ctgagagtag aaaactcagg ttaataaaac
    3851  aggagaatat ttacctagtc gtataacggc taggtacccc