ID AJ609019; SV 1; circular; genomic DNA; STD; VRL; 7141 BP. XX AC AJ609019; XX DT 25-NOV-2004 (Rel. 81, Created) DT 15-APR-2005 (Rel. 83, Last updated, Version 3) XX DE Cacao swollen shoot virus complete genome, isolate Peki XX KW aspartyl protease; capsid protein; complete genome; KW nucleic acid-binding protein; ORF1; ORF2; ORF3; ORF4; ORFX; ORFY; KW polyprotein; reverse transcriptase; ribonuclease H. XX OS Cacao swollen shoot virus OC Viruses; Ortervirales; Caulimoviridae; Badnavirus. XX RN [1] RP 1-7141 RA Muller E.; RT ; RL Submitted (25-NOV-2003) to the INSDC. RL Muller E., CIRAD, UMR BGPI TA 41/K, Campus International de Baillarguet, RL 34398 Montpellier cedex 5, FRANCE. XX RN [2] RA Muller E., Sackey S.; RT "Four new full sequences of Cacao swollen shoot virus: a PCR full length RT cloning strategy and a variability analysis"; RL Unpublished. XX RN [3] RA Muller E., Sackey S.; RT "Molecular variability analysis of five new complete cacao swollen RT shootvirus genomic sequences"; RL Arch. Virol. 50(1):53-66(2005). XX DR MD5; 08f5303050e6ebc353397b33ff1b0f18. DR EuropePMC; PMC5649073; 29052506. XX FH Key Location/Qualifiers FH FT source 1..7141 FT /organism="Cacao swollen shoot virus" FT /host="Theobroma cacao" FT /isolate="Peki" FT /mol_type="genomic DNA" FT /country="Ghana:Peki" FT /db_xref="taxon:31559" FT CDS 296..727 FT /product="hypothetical protein" FT /note="ORF1" FT /db_xref="InterPro:IPR010746" FT /db_xref="UniProtKB/TrEMBL:Q5TJI7" FT /protein_id="CAE81277.1" FT /translation="MSSRWEDSIQEWYEKSHTANLEYLDLASTSKVTNNQLAHNLAVTF FT DRVNLGNRVFIKNLKQIQESILELNTRIDTVEVALRRLTKQFRENKPLSESEVKKLVEE FT IAQQPKIVEKQALEISQQLELKLEKVEKLLHKLDQWVGQ" FT CDS 724..1161 FT /product="nucleic acid-binding protein" FT /note="ORF2" FT /db_xref="UniProtKB/TrEMBL:Q5TJI6" FT /protein_id="CAE81278.1" FT /translation="MSESPSYQEALKEAEKIDPPAIGLTTSSGVTAVQGFRTVIKQNNV FT QICLLATIADKLEELVQDQKKARKDKAKEIAIPEDLITKLQGLSIREKGEAKVTRKPEP FT KGTLFGFKDPYKILAAEKAKITPKPVKEKKDESSKTATSSS" FT CDS 1127..6577 FT /product="polyprotein" FT /note="ORF3" FT /note="putative capsid protein, aspartyl protease, FT ribonuclease H and reverse transcriptase" FT /db_xref="GOA:Q5TJI5" FT /db_xref="InterPro:IPR000477" FT /db_xref="InterPro:IPR001878" FT /db_xref="InterPro:IPR002156" FT /db_xref="InterPro:IPR018061" FT /db_xref="InterPro:IPR021109" FT /db_xref="InterPro:IPR036875" FT /db_xref="InterPro:IPR041373" FT /db_xref="UniProtKB/TrEMBL:Q5TJI5" FT /protein_id="CAE81279.1" FT /translation="MSRARPQPPVPSVTSTTSEQNREGPLYEDQIRDYRRSQRRIFNLR FT RRARRLRRSMMGSRYQETLEQEIDPQTTLRLSMQERARLVPAEVLYRSRRDTVHHRVYT FT HRSEESVLCVGGNQVDRAFIQPESLEQLQRTGMSFIHIGILQVRIQILHRQEEGTMALV FT VFRDNRWSGDQSIFAQMEIDLTKGSQLVFVIPDTMMTIGDFARNVQLSILTRGYENWQN FT GEANLLITRGMTGRLSNTPNVAFAYQIASATDYLASHGVKAIAGKKMNLQHLRNQQWIL FT RPPQADITPMQPRSVETRNLVDGSISIRFHDYEAATSTSRPHYNEEDEEVESETESEIR FT EHTVAVWIGEEEVPDQTGRKKVWEESSNGNGRFFRYYTPPPTSDEQIIATGWGSDDDYD FT EIPPKWDESPDEEGSSETTWDQEEKEEEDEYDPNIYMAYLQKEENEWQEIAASLQEEME FT MEYPRRRPRTETVFSETVDYTPPGDTLMTPVGYPPASSSRSTVTTPSRPPLFEGRVTHV FT PRFLKRDDYTEWWQLPSSQGTTGALFVMPKQMGLFHEVFSRWESITKNYVAAQGFTDPT FT EKMEFMENLLGETEKLTWIQWRMNYEAEYQQLLTQADGRQGTQNILSQIKRVFSLEDPA FT SGSTRIQDAAYRDLERLTCHNIKDIVQFLNDYGRLAAKSGRLFLGTELSEKLWMKMPPE FT LGNRMKEAFQKEYSGNEVGVFPRILFAYRYLEQECKDAAFKRSLKSLSFCKDMPLTGYY FT DKTPKYGMRKSKTYKGKPHASHARIEKRKHLIRNKKCKCYLCGDEGHFARECPNNKRDV FT KRVAIFEGINLPEGFDIVSVEEGEDDSDAIYSISENENGEELDAEVVQEKVFMMREEDQ FT SYWLGKTNHWTAMVRVSSQQYHCLHQWEHNKEITVVAHINCHFCKQPTQLRSRIHCSTC FT KLTSCFMCAPIYCNITVQQQPKPPTPFNTNTLLQQQAAYIQWLEGENQRLTEAVEFYKK FT EAADLRLEKELEKDRKDLEPKIQDRGKKVQILDPEAGPSDDEQTAYLEEDTVSRIIGHT FT VEEQQEVKKPVKRGNMLYNLDVVLLIPEVGRPIKVKAILDTGATTCCININSVPKTAIE FT QNTFLVQFRGINSTQSVDKKLKYGRMTISNHQFRIPYCYAFPLSLGDGIEMILGCNFIR FT GMYGGLRIEGHTITFYKNVTTIQTRLAAVMVGGTTTSELGEEGTEPIFEIEEETEEFDS FT EVHQQIMSHVAAQAQQQKLDPKLQQLMERLKDQGFIGENPMQHWAKNKILCRLDIKNPD FT LIIEDKPIKHLTPAMEKQFQKHVKALLDIGVIRPSKSKHRTTAFIVESGTVIDPVTKKT FT IHGKERMVFNYKRLNDNTEKDQYSLPGIQTILKRVGNKKIFSKFDLKSGFHQVAMAKES FT IPWTAFWVPQGLYEWLVMPFGLKNAPAVFQRKMDQCFKGTEEFIAVYIDDILVFSETMA FT EHTKHIGIMLTICQENGLVLSPNKICLAQREIEFLGTIISQGQMKLQPHIIKKIVNKAD FT MELETTKGLRSFLGLLNYARIYIPNLGKKLSPLYAKTSPTGEKKFNRQDWHLIKEIKNM FT VQKLPNLAIPPARCCIIIESDGCMEGWGAVCKWKLAKEDSRTTEKICAYASGKFGIIKS FT TIDAEIFALIKALESFKIFYLDKKHLVARTDCQAIVTFYNKTSTHKPSRIRWITFSDYI FT TGLGVQVTIEHINGKENQLADTLSRLVYTTWNQSQAHLSEEEEPEKSPHLSLAVLAIPI FT AWPMTAFYSRRRTPLLKGGSPWQQNKPSQHSCIASKSKQPEKHSWPYETYRTYCTPSET FT T" FT CDS 2310..2582 FT /product="hypothetical protein" FT /note="ORFX" FT /db_xref="UniProtKB/TrEMBL:Q5TJI4" FT /protein_id="CAE81280.1" FT /translation="MMIMMKSLQNGMKVLMKKDQVRQLGIRKKKKKKTNMIPTSIWPIY FT KRKKMSGKKSPPVYKKKWKWNIHGGGHGRRQYSLKQLTIHHLVTH" FT CDS 4212..4499 FT /product="hypothetical protein" FT /note="ORF4" FT /db_xref="UniProtKB/TrEMBL:Q5TJI3" FT /protein_id="CAE81281.1" FT /translation="MMNKQRILRKIPLAELSAILWKSNKRSKNQSKGGTCYTTSTWFYL FT SLKLEDLSRLKLSLIQAQLPVASTSTLFPRQQLNRTLFWFNSEALIPRNQ" FT CDS 6307..6702 FT /product="hypothetical protein" FT /note="ORFY" FT /db_xref="UniProtKB/TrEMBL:Q5TJI2" FT /protein_id="CAE81282.1" FT /translation="MEPVPSSPVGGRRAGEISTSQLSGVSYPYSLAYDGLLQQKKNAIT FT QGRLTLATEQAISAQLYRIEEQAARKALMALRDLQDVLHSKRDYLTATATRDNWASDRL FT PAAQQDSAALDQHADVINAIIERAVQP" XX SQ Sequence 7141 BP; 2414 A; 1542 C; 1598 G; 1587 T; 0 other; tggtatcaaa gcttggtttt agcaatggtc atgtccggct aagttagtca gtctaggttc 60 agggaaagag tgaggtaacc gttaggcgtc aaaatactgt tccaaaatac tattcaccaa 120 atcactaggg gtatcctgtt tatgtgaaaa agacgtaacc cagacgaaaa gtacccacga 180 agggggaaaa cttggggaaa aggtgatcag taaacagaaa acaaactatt cctcgtatgc 240 tctacggttg cagccacggc tgatcctccg tatcagaaaa ggaaaagttt ggtgtatgtc 300 tagccgatgg gaagatagta tccaggaatg gtatgagaag tctcacactg ccaaccttga 360 gtaccttgac ctggcctcta ccagtaaagt gaccaacaac caactagctc ataacctcgc 420 agtaaccttt gatagagtca acttaggaaa ccgagtcttc attaaaaacc ttaaacaaat 480 tcaagagtct atcctagaac taaataccag aattgacact gtagaagtag ccttgagaag 540 gctaaccaag cagttccgag aaaacaaacc actgtctgaa tctgaagtaa agaaactagt 600 ggaagagata gcccagcaac ccaaaattgt tgagaaacag gcactggaaa tttctcaaca 660 gttagaactc aaactagaaa aagtggaaaa gcttctacac aagcttgacc agtgggttgg 720 tcaatgagtg aaagcccctc ttaccaagaa gcacttaagg aagctgaaaa gatcgaccct 780 ccagcgattg gactaaccac atccagtgga gtaactgcgg tccaaggctt caggactgtc 840 atcaaacaaa acaacgtcca gatttgccta cttgcgacta tagcagacaa acttgaagaa 900 ctggtgcaag atcagaagaa agcaagaaaa gacaaggcca aggagattgc tattcctgag 960 gatcttatca caaaactcca aggattatcc atccgggaga aaggtgaagc aaaggtcaca 1020 agaaaaccag agccaaaagg aacactgttt ggattcaaag atccttacaa aattttggca 1080 gcagaaaagg ctaagatcac accaaagcct gtaaaagaaa agaaagatga gtcgagcaag 1140 accgcaacct ccagttccta gtgtgacatc taccactagt gaacagaaca gagaagggcc 1200 tctttatgag gatcaaatca gagattacag aaggagtcag aggaggatct tcaacctaag 1260 aaggagagcc agaaggttga gaagatcaat gatggggtct agataccagg agaccctaga 1320 acaagaaatt gatccacaga caacactgag gttgtccatg caagaaagag cgcgattagt 1380 accagctgaa gtactgtaca gatcacgacg agacactgtt caccacaggg tctacaccca 1440 tcgctctgaa gaatccgtcc tatgtgttgg cggaaatcaa gttgacaggg ccttcattca 1500 gcccgaaagt ttagagcaac ttcagaggac tggaatgtcc ttcattcaca taggaatcct 1560 gcaagttagg attcaaatcc tgcatcgtca agaagaaggt accatggctt tagttgtctt 1620 ccgtgacaac agatggtctg gggaccagtc tatcttcgca caaatggaga tagatctaac 1680 taaaggcagc cagttggtat ttgtcatacc agataccatg atgacgatcg gagattttgc 1740 ccggaacgta caactatcaa tcctcacacg aggatatgag aattggcaaa atggagaagc 1800 caacctttta atcacacgtg gcatgacggg acgactatcc aacacaccta atgtcgcctt 1860 tgcctaccaa attgccagcg cgacagatta tctggcaagc cacggagtaa aagccatcgc 1920 agggaaaaag atgaacttac aacacctgcg aaatcaacag tggattctac gaccaccgca 1980 agctgacatc acaccgatgc aaccaagatc ggtagaaacc aggaacctgg tagatggcag 2040 catttccatc agattccatg attatgaggc agccacctca acatcaagac cccattacaa 2100 cgaagaagat gaagaagtgg agtctgaaac agaatctgaa ataagagaac acactgtagc 2160 agtctggatt ggggaagaag aagttccaga ccaaacagga agaaagaaag tatgggaaga 2220 atctagtaat ggaaatggaa ggttcttccg gtactacact cctccaccaa catctgatga 2280 acaaatcata gccactggtt ggggaagtga tgatgattat gatgaaatcc ctccaaaatg 2340 ggatgaaagt cctgatgaag aaggatcaag tgagacaact tgggatcagg aagaaaaaga 2400 agaagaagac gaatatgatc ccaacatcta tatggcctat ttacaaaagg aagaaaatga 2460 gtggcaagaa atcgccgcca gtttacaaga agaaatggaa atggaatatc cacggcggag 2520 gccacggacg gagacagtat tctctgaaac agttgactat acaccacctg gtgacacact 2580 gatgacacct gtcggatatc caccggcctc gtcatcaaga tcaacagtca caacaccaag 2640 taggccccct ttatttgaag gaagggttac acacgtgcca agattcttaa aacgggatga 2700 ctacacagaa tggtggcaac taccatcatc ccaaggcaca actggggcac tatttgtgat 2760 gcccaaacaa atgggcctat ttcatgaggt cttctccaga tgggagtcca tcaccaaaaa 2820 ctatgttgcg gcccaaggtt tcacggaccc aacagaaaag atggagttca tggaaaattt 2880 acttggagaa acagaaaaac taacctggat ccaatggaga atgaattatg aggctgagta 2940 ccagcagctg ttaacccaag ctgatggacg gcaagggacc cagaatatct tgtcccaaat 3000 taagagagtc ttctctctag aagaccccgc ctcaggatct acgaggatac aagatgctgc 3060 atacagagac cttgaaagat taacctgcca caacataaaa gatatcgttc agttcctgaa 3120 tgattatggg cggttagcag caaaaagtgg gcgactgttt ctaggaacag agctcagtga 3180 aaaattatgg atgaagatgc caccagaact agggaatcgc atgaaggaag catttcaaaa 3240 ggaatactca ggcaatgaag taggagtctt cccgcgtatc ttgttcgcgt acagatactt 3300 agaacaagaa tgcaaagatg cagcttttaa gcgcagcctg aaatcgttga gtttctgtaa 3360 ggacatgccg ttgacaggtt actatgataa aacacccaaa tacggcatga ggaagtcaaa 3420 aacttacaaa ggaaagccac acgcatcaca tgcaagaata gaaaagagaa agcacttaat 3480 caggaataaa aagtgcaagt gctatctgtg tggagatgaa ggacattttg ccagagaatg 3540 ccctaataac aaaagagatg tcaagagagt agccattttt gaaggcatca atcttcctga 3600 gggtttcgac attgtctcag tagaagaagg ggaagatgac tcagatgcta tttatagcat 3660 atctgagaat gaaaatgggg aagaacttga cgcagaagta gtccaagaga aggtcttcat 3720 gatgcgagaa gaggaccaat cctactggct aggaaaaaca aatcactgga cagcaatggt 3780 acgagtcagc agccaacagt atcattgctt gcaccaatgg gagcacaaca aggagatcac 3840 ggtggtggcc cacatcaact gccacttctg taagcagcct actcaactga ggagtcgaat 3900 acactgttcc acgtgtaaac tcaccagctg cttcatgtgt gcccctatct actgcaatat 3960 aacggtccaa cagcagccta aaccgcctac gccattcaac accaacacct tgctccaaca 4020 acaagcggcg tatatccaat ggttagaagg agaaaaccag cggttaacag aggcagttga 4080 attttataaa aaggaagctg cagatctaag gctcgaaaaa gaattggaaa aagatagaaa 4140 agatttagag ccaaagatac aagacagggg gaagaaggtt caaattcttg atccagaagc 4200 aggaccctct gatgatgaac aaacagcgta tcttgaggaa gataccgtta gccgaattat 4260 cggccatact gtggaagagc aacaagaggt caaaaaacca gtcaaaaggg ggaacatgtt 4320 atacaacctc gacgtggttt tacttatccc tgaagttgga agacctatca aggttaaagc 4380 tatccttgat acaggcgcaa ctacctgttg catcaacatc aactctgttc ccaagacagc 4440 aattgaacag aacacttttt tggttcaatt cagaggcatt aattccacgc aatcagtaga 4500 taaaaagcta aaatacgggc ggatgactat tagcaaccac cagttccgga tcccgtactg 4560 ttatgccttt cctctatctc ttggagacgg aatagaaatg atcctcgggt gtaacttcat 4620 ccgtgggatg tatggcggtt tgaggattga aggtcacaca atcaccttct acaaaaacgt 4680 caccactatt caaacccgcc ttgctgctgt aatggttggt ggtacaacca cttctgagtt 4740 gggggaggaa ggtactgaac ccatttttga aattgaagaa gaaacagaag agtttgactc 4800 agaagtccat caacaaatta tgagtcatgt tgcagcccaa gcccaacaac aaaaattaga 4860 cccaaaactc caacaactaa tggaacggtt aaaggatcag ggctttattg gggaaaatcc 4920 gatgcaacat tgggctaaaa acaagatcct gtgtagattg gatatcaaga atccagacct 4980 tatcatagaa gacaagccca ttaaacactt aacaccggct atggagaagc agttccagaa 5040 gcatgtcaaa gctctcctgg acattggtgt tatcaggcct agtaagtcaa aacacaggac 5100 tacggccttc atagtagaat caggcactgt tattgatcca gtaacaaaga agaccataca 5160 cggcaaagaa agaatggtct ttaactacaa acgcctgaat gacaatacgg agaaggatca 5220 atactcgcta cctggtatac agaccatcct gaagcgagta ggcaacaaaa agattttcag 5280 caagttcgat ttaaaatcgg gcttccatca ggttgccatg gcaaaagagt ccatcccttg 5340 gactgctttt tgggtaccgc agggcctata cgagtggtta gttatgccct ttgggctcaa 5400 aaacgctcct gcagtatttc aaagaaaaat ggaccaatgt ttcaaaggca cagaagaatt 5460 catagctgtg tatattgatg acatcttggt cttcagcgag actatggcgg aacacaccaa 5520 gcatattgga atcatgctaa caatctgcca agaaaatggg ctggtcctaa gcccaaataa 5580 aatatgtctt gctcaacgag agattgaatt tttgggcaca atcatctctc aaggtcaaat 5640 gaagcttcag cctcatatca taaagaagat agtcaacaag gcagatatgg agctcgaaac 5700 aactaaaggc ctaagatcat ttttgggcct cctgaactat gcccgaatct acatacccaa 5760 tctggggaag aagctaagtc cactatatgc caaaaccagt cccaccggag aaaagaagtt 5820 taatcgacag gattggcatt tgataaagga gattaaaaat atggtccaaa agctcccaaa 5880 cctcgctatc ccaccagcaa gatgctgtat tatcatagaa agcgatggtt gcatggaagg 5940 atggggggcc gtatgcaagt ggaaattagc aaaagaagat tcccgcacta ctgaaaagat 6000 atgtgcctac gctagtggaa aattcggcat aatcaagtcc acaattgacg ccgagatttt 6060 cgcactcata aaagcattag aatcttttaa aatcttctat ctggacaaaa aacatttggt 6120 ggcgcgtact gactgtcagg cgatagtgac gttttataac aagacaagca ctcacaagcc 6180 ttctcgtata cgttggatca ccttttccga ctatataacg gggttaggag ttcaagttac 6240 tatcgaacac ataaacggaa aggagaacca gttagcagat acactaagca gactagtgta 6300 caccacatgg aaccagtccc aagctcacct gtcggaggaa gaagagccgg agaaatctcc 6360 acatctcagc ttagcggtgt tagctatccc tatagcttgg cctatgacgg ccttctacag 6420 cagaagaaga acgccattac tcaagggagg ctcaccttgg caacagaaca agccatctca 6480 gcacagctgt atcgcatcga agagcaagca gccagaaaag cactcatggc cctacgagac 6540 ctacaggacg tactgcactc caagcgagac tacttgactg cgactgccac acgtgacaac 6600 tgggccagtg atagactgcc agctgcccaa caagattcag ccgccctcga ccaacatgct 6660 gacgtgatta acgccattat cgaaagggct gtccaaccct agtttggacg atagtgtgta 6720 ataattaagt gtgctttact ttccagctgt ccaaccctag tttggacgat agtgtgtaat 6780 aattaagtgt gctttacttt ccagctgtcc aactctagtt tggacgatag tgtgtaataa 6840 ttaagtatgc tttactttcc agctgtaact cattatagag tagacatagt gattgacgat 6900 ggggcccgaa gagcacccgg attactactc taccatctat aaatgggagt gtgtaaggct 6960 tagccatcaa ggaggaagag atatccatcc tgattctaag cattctagag cttgtaagtt 7020 tttaagagaa ataaagaatc ttcttagtga ttatttcttt gtttcccctg ggaaaatttt 7080 aaacagtttc tgttattctg tttaatcctg ttccacgttt catttcctct gcaagcctac 7140 t 7141 //