ID AJ609020; SV 1; circular; genomic DNA; STD; VRL; 7006 BP. XX AC AJ609020; XX DT 25-NOV-2004 (Rel. 81, Created) DT 22-JAN-2005 (Rel. 82, Last updated, Version 2) XX DE Cacao swollen shoot virus complete genome, isolate N1A XX KW ORF1; ORF2; ORF3; ORFX; ORFY; polyprotein; capsid protein; ribonuclease H; KW complete genome; aspartyl protease; reverse transcriptase; KW nucleic acid-binding protein. XX OS Cacao swollen shoot virus OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes; OC Ortervirales; Caulimoviridae; Badnavirus. XX RN [1] RP 1-7006 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new full sequences of Cacao swollen shoot virus: a PCR full length RT cloning strategy and a variability analysis"; RL Unpublished.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; efbb91fb66940272c199486c717fafa3. DR EuropePMC; PMC5649073; 29052506. XX FH Key Location/Qualifiers FH FT source 1..7006 FT /organism="Cacao swollen shoot virus" FT /host="Theobroma cacao" FT /isolate="N1A" FT /mol_type="genomic DNA" FT /country="Ghana" FT /db_xref="taxon:31559" FT CDS 284..715 FT /product="hypothetical protein" FT /note="ORF1" FT /db_xref="InterPro:IPR010746" FT /db_xref="UniProtKB/TrEMBL:Q5TJI1" FT /protein_id="CAE81283.1" FT /translation="MSSRWENSIQEWYEKSHTANLEYLDLASTSKVTNNQLAHNLAVTF FT DRINLGNRVFIKNLKQIQESILELNTRIDTVEVALRRLTKQFRENKPLSESEVKRLVEE FT IARQPKIVEKQALEISQQLELKLEKVEKLLHKLDQWVGQ" FT CDS 712..1149 FT /product="nucleic acid-binding protein" FT /note="ORF2" FT /db_xref="UniProtKB/TrEMBL:Q5TJI0" FT /protein_id="CAE81284.1" FT /translation="MSESPSYQEALKEAEKIDPPAIGLTTSSGVTAVQGFRTVIKQNNV FT QICLLAAIADKLEELVQDQKKARKDKAKEVAIPEDLITKLQGLSIQEKGEAKVTRKPEP FT RGTLFGFKDPYKILAAEKAKIIPKPVKEKKDESSKTATLSS" FT CDS 1345..6657 FT /product="polyprotein" FT /note="ORF3" FT /note="putative capsid protein, aspartyl protease, FT ribonuclease H and reverse transcriptase" FT /db_xref="GOA:Q5TJH9" 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:Q5TJH9" FT /protein_id="CAE81285.1" FT /translation="MQERARLVPAEVLYRSRRDTVHHRVYTHRSEESVLCVGGNQVDRA FT FIQPESLEQLQRTGMSFIQIGILQVRIQILHRQEEGTMALVVFRDNRWSGDQSIFAQME FT IDLTKGSQLVFVIPDTMMTIGDFARNVQLSILTRGYENWQNGEANLLITRGMTGRLSNT FT PNVAFAYQIASATDYLASHGVKAIAGKKMNLQHLRNQQWILRPPQADITPMQPRSVETR FT NLVDGSISIRFHDYEAATSTSRPHYNEEDEEVESETESEIREHTVAVWIGEEEVPDQTG FT RKKVWEESSNGNGRFFRYYTTPPTSDEQIIATGWGSDDNYDDEIPPKWDESPDEEGSSK FT TIWDQEEEEEEDEYDPNIYMAYLQKEEDEWQEIAASLQEEMEMEYPRRRPQTETVFSET FT VDYTPPGDTLMTPVGYPPASSSRSTVTTPSRPPLFEGRVTHVPRFLKRDDYTEWWQLPS FT SQGTTGALFVMPKQMGLFHDVFSRWESITKNYVAAQGFTDPTEKMEFMENLLGETEKLT FT WIQWRMNYEAEYQQLLTQADGRQGTQNILSQIKRVFSLEDPASGSTRIQDAAYRDLERL FT TCHNIKDIVQFLNDYGRLAAKSGRLFLGTELSEKLWMKMPPELGNRMKEAFQKEYSGNE FT VGVFPRILFAYRYLEQECKDAAFKRSLKSLSFCKDMPLTGYYDKTPKYGMRKSKTYKGK FT PHASHARVEKRKHLIRNKKCKCYLCGDEGHFARECPNNKRDVKRVAIFEGINLPEGFDI FT VSVEEGEDDSDAIYSISENENEEELDAEVVQEKVFMMREEDQSYWLGKTNHWTAMVRVS FT SQQYYCLHQWEHNKEITVVAHINCHFCKQLTQLRSRIHCPTCKLTSCFMCAPIYCNIKV FT QQQPKPPTPFNINTLLQQQAAYIQWLEGENQRLTEAVEFYRKEASDLRLEKELEKDRKD FT LEPKIQDRGKKVQILDPEAVPSDDEQTAYLKEDTVSRIIGHTVEEQQEVKKPVKRGNML FT YNLDVVLLIPEVGRPIKVKAILDTGATTCCININSVPKTAIEQNTFLVQFRGINSTQSV FT DKKLKYGRMTISNHQFRIPYCYAFPLSLGDGIEMILGCNFIRGMYGGLRIEGHTITFYK FT NVTTIQTRLAAVMVGGTTTSELGEEGTEPIFETEEETEEFDSEVHQQIVSHVAAQAQQQ FT ELDPKLQQLMERLKDQGFIGENPMQHWAKNKILCRLDIKNPDLIIEDKPIKHLTPAMEK FT QFQKHVKALLDIGVIRPSKSKHRTTAFIVESGTVIDPVTKKTIHGKERMVFNYKRLNDN FT TEKDQYSLPGIQTILKRVGNKKIFSKFDLKSGFHQVAMAKESIPWTAFWVPQGLYEWLV FT MPFGLKNAPAVFQRKMDQCFKGTEEFIAVYIDDILVFSETMAEHTKHIGIMLTICQENG FT LVLSPNKICLAQREIEFLGTIISQGQMKLQPHIIKKIVNKADMELETTKGLRSFLGLLN FT YARIYIPNLGKKLSPLYAKTSPTGEKKFNRQDWHLIKEIKNMVQRLPNLAIPPARCCII FT IESDGCMEGWGAVCKWKLAKEDSRTTEKVCAYASGKFGIIKSTIDAEIFALIKALESFK FT IFYLDKKHLVVRTDCQAIVTFYNKTSTHKPSRIRWITFSDYITGLGVQVTIEHINGKEN FT QLADTLSRLVYTTWSQSQAHLPEEEEPEKSPHLSLAVLATPMAWPMTAFYSKRRTPLIT FT GDSPWQQNKPSQDSSIASKSKQPEKHSWPYETYRAYCTSSETIWPQLPHMTTGPVIDCQ FT LPNKIQPPSTNMLA" FT CDS 2297..2572 FT /product="hypothetical protein" FT /note="ORFX" FT /db_xref="UniProtKB/TrEMBL:Q5TJH8" FT /protein_id="CAE81286.1" FT /translation="MIIMMMKSLQNGMKVLMKKDQVRQFGIRKKKKKKMNMIPTSIWLI FT YKRKKMSGKKSPPVYKKKWKWNIHGGGHRLRQYSLKQLTIHRLVTH" FT CDS 6297..6692 FT /product="hypothetical protein" FT /note="ORFY" FT /db_xref="UniProtKB/TrEMBL:Q5TJH7" FT /protein_id="CAE81287.1" FT /translation="MEPVPSSPAGGRRAGEVPTSQLSGVSYPYGLAYDGLLQQKEDAIN FT HGRLTLATEQAISRQLYRIEEQAARKALMALRDLQGVLHFKRDYLAATATHDNWASDRL FT PAAQQDSAALDQHAGVINAIIERTVQP" XX SQ Sequence 7006 BP; 2386 A; 1518 C; 1565 G; 1537 T; 0 other; tggtatcaga gcttggtttt agcaatggtc atgtccggct aagttagtca gtctaggttc 60 agggaaagag tgaggtaacc gttaggcgtc aaaatactgt tccagaatac tattcaccaa 120 atcactaggg tatcctgttt atgtgaaaaa gacgtaaccc agacgaaaag tacccatgag 180 ggggaaaact tggggaaaag gtgatcagta aacagaaaaa actatgcctt gtatgctcta 240 cggttgcagc cacggctgat cctccgtatc agaaatttgg catatgtcta gcagatggga 300 aaatagtatc caggaatggt atgagaagtc tcacactgcc aaccttgagt accttgacct 360 agcctctacc agtaaagtga ccaacaacca actagctcat aacctcgcag taacctttga 420 tagaatcaac ttaggaaacc gagtcttcat taaaaacctt aaacagattc aagagtctat 480 cctagaacta aataccagaa ttgacactgt agaagtagcc ttgagaaggc taaccaagca 540 gttccgagaa aacaaaccac tgtctgaatc tgaagtaaag agactagtgg aagagatagc 600 ccggcaaccc aaaattgttg agaagcaggc actggaaata tctcaacaat tagaactcaa 660 actagaaaaa gtggaaaagc ttctacacaa gcttgaccag tgggttggtc aatgagtgaa 720 agcccctctt accaagaagc acttaaagaa gctgaaaaga tcgaccctcc agcgattgga 780 ctaaccacat ccagtggagt gactgcggtc caaggcttca ggaccgtcat caaacaaaac 840 aacgtccaga tttgcctact tgcggctata gctgacaaac ttgaagaact ggtgcaagat 900 cagaagaaag caagaaaaga caaggctaag gaggttgcca ttcctgagga tcttatcaca 960 aaactccaag gattatccat ccaggagaaa ggtgaagcaa aagtcacaag gaaaccagag 1020 ccaagaggaa cactgtttgg attcaaagat ccttacaaaa ttttggcagc agaaaaggct 1080 aagatcatac caaagcctgt aaaagaaaag aaagatgagt cgagcaagac cgcaaccctc 1140 agttcctagt gtggcatcta ccactagtga acagaacaga gaagggcctc tttatgagga 1200 tcaaatcaga gactacagaa ggagtcagag aaggatcttc aacctaagaa ggaatgctag 1260 gaggttgaga agatcaatga tggggtctag ataccaggag accctagaca agaaattgat 1320 ccacaggcaa cactgaggtt gtccatgcaa gaaagagcgc gattagtacc agctgaagta 1380 ctgtacagat cacgacgaga cactgttcac cacagggtct acacccatcg ctctgaagaa 1440 tccgttctat gtgtcggcgg aaatcaagtt gacagggcct ttattcagcc tgaaagttta 1500 gaacaacttc agaggactgg aatgtctttt attcaaatag gaatcctgca agttaggatt 1560 caaatcctgc atcggcaaga agaaggtacc atggctttag ttgtcttccg tgacaacaga 1620 tggtctggag accagtctat cttcgcacaa atggagatag atttaactaa aggcagccag 1680 ttggtatttg tcataccaga taccatgatg acgatcggag attttgcccg gaacgtacaa 1740 ctatcaatcc tcacacgagg atatgagaat tggcaaaatg gagaagccaa tctgttaatc 1800 acacgtggca tgactggacg actatccaac acacctaatg tcgcctttgc ctaccaaatt 1860 gccagcgcga cagattatct ggcaagccac ggagtaaaag ccatcgcagg aaaaaagatg 1920 aacttacaac acctgcgaaa ccaacagtgg attttacgac caccgcaagc tgacatcaca 1980 ccgatgcaac caagatcggt agaaaccagg aacctggtag atggcagcat ttccatcaga 2040 ttccatgatt atgaggcagc cacctcaaca tcaagacccc attacaacga agaagatgaa 2100 gaagtggagt ctgaaacaga atctgaaata agagaacaca ctgtagcagt ctggattggg 2160 gaagaagaag ttccagacca aacaggaaga aagaaagtat gggaagaatc cagtaatgga 2220 aatggaaggt tcttccggta ctacactact ccaccaacat ctgatgaaca aatcatagcc 2280 actggttggg gaagtgatga taattatgat gatgaaatcc ctccaaaatg ggatgaaagt 2340 cctgatgaag aaggatcaag taagacaatt tgggatcagg aagaagaaga agaagaagat 2400 gaatatgatc ccaacatcta tatggcttat ttacaaaagg aagaagatga gtggcaagaa 2460 atcgccgcca gtctacaaga agaaatggaa atggaatatc cacggcggag gccacagact 2520 gagacagtat tctctgaaac agttgactat acaccgcctg gtgacacact gatgacacct 2580 gtcggatatc caccggcctc gtcatcaaga tcaacagtca caacaccaag taggccccct 2640 ttattcgaag gaagagttac acacgtgcca agattcttaa aacgagatga ctacacagaa 2700 tggtggcaac taccatcatc ccaaggcaca actggggcat tatttgtgat gcccaaacaa 2760 atgggcctat ttcatgatgt cttctccaga tgggagtcca tcaccaaaaa ctatgttgcg 2820 gcccaaggtt tcacggaccc aacagaaaag atggagttca tggaaaactt acttggagaa 2880 acagaaaaac taacatggat ccaatggaga atgaattatg aggctgagta ccagcagctg 2940 ttaacccaag ctgatggacg gcaagggacc cagaatatct tgtcccaaat taagagagtc 3000 ttctctctag aagaccccgc ctcaggatcc acaaggatac aagatgctgc atacagagac 3060 cttgaaagat taacctgcca caacataaaa gatattgttc agttcctgaa tgattatggg 3120 cggttagcag caaaaagtgg gcgactgttt ttaggaacag agctcagtga aaaactatgg 3180 atgaagatgc caccagaact agggaatcgc atgaaggaag catttcaaaa ggaatactca 3240 ggcaatgaag taggagtctt cccgcgtatc ttgttcgcgt acagatactt agaacaagaa 3300 tgcaaagacg cagcgtttaa gcgcagcctg aaatcgttga gcttctgcaa ggacatgccg 3360 ttgacaggtt actatgataa aacacccaag tacggcatga ggaagtcaaa aacttacaaa 3420 ggaaagccac acgcatcaca cgcaagagta gaaaagagaa agcacttaat caggaataaa 3480 aagtgcaagt gttatctgtg tggagatgaa ggacatttcg ccagagaatg ccctaataac 3540 aaaagagatg tcaagagagt ggccattttt gaaggcatca atcttcctga gggtttcgac 3600 atcgtctcag tagaagaagg ggaagatgac tcagatgcta tttatagcat atctgaaaat 3660 gaaaatgagg aagaacttga cgcagaagta gtccaagaga aagtcttcat gatgcgagaa 3720 gaggaccaat cctactggtt aggaaaaaca aatcactgga cagcaatggt acgagtcagc 3780 agccaacagt attattgcct gcaccaatgg gagcacaaca aggagattac ggtggtggcc 3840 cacatcaatt gccacttctg taaacagctc actcaactga ggagtcgaat acactgtccc 3900 acgtgtaaac tcaccagctg cttcatgtgt gcccctatct actgcaatat aaaggtccaa 3960 cagcagccta aaccgcctac gccattcaac atcaacactc tgctccaaca acaagcggcg 4020 tatatccaat ggttagaagg agaaaaccag cggttaacag aggcagttga attttataga 4080 aaggaagctt cagatctaag gctcgagaaa gaattggaaa aagatagaaa agatctagag 4140 ccaaaaatac aagacagagg gaagaaggtt caaattcttg atccagaagc agtaccctct 4200 gatgatgaac aaacagcgta tcttaaggaa gataccgtta gccgaattat cggccatact 4260 gtggaagagc aacaagaggt taaaaaacca gtaaaaaggg ggaacatgtt atacaacctc 4320 gacgtggttt tacttatccc tgaagttgga agacctatca aggttaaagc tatccttgat 4380 accggcgcaa ctacctgttg catcaacatc aactctgttc ccaagacagc aattgaacag 4440 aacacttttc tggttcaatt cagaggcatc aattccacgc aatcagtaga taaaaagcta 4500 aaatacgggc ggatgactat tagcaaccac cagttccgga tcccgtactg ttatgccttt 4560 cctctatctc ttggagacgg aatagaaatg atcctcggat gtaacttcat ccgtgggatg 4620 tatggcggtt tgaggattga aggtcacaca atcaccttct acaaaaacgt caccactatt 4680 caaacccgcc ttgctgctgt aatggttggt ggtacaacca cttctgagtt gggggaggaa 4740 ggtactgaac ccatttttga aactgaagaa gaaacagaag agtttgactc agaagtccat 4800 caacaaattg tgagtcatgt tgcagcccaa gcccaacaac aagaactaga cccaaagctc 4860 caacaactaa tggaacggtt aaaggatcag ggctttattg gggaaaatcc gatgcaacat 4920 tgggctaaaa acaagatcct gtgtagattg gatatcaaga atccagacct tatcatagaa 4980 gacaagccca ttaaacactt aacaccggct atggagaagc agttccagaa gcatgtcaaa 5040 gctctcctgg acattggtgt tatcaggcct agtaagtcaa aacatagaac tacggccttc 5100 atagtagaat caggcactgt tattgatcca gtaacaaaga agaccataca cggcaaagaa 5160 agaatggtct ttaactacaa acgcctgaac gacaatacgg agaaggatca atactcgcta 5220 cctggtatac agaccatcct gaagcgagta ggcaacaaaa agattttcag caagttcgat 5280 ttaaaatcgg gcttccatca ggttgccatg gcaaaagagt ccatcccttg gactgctttc 5340 tgggtaccgc agggcctata cgagtggtta gttatgccct ttgggctcaa aaacgctcct 5400 gcagtatttc aaagaaaaat ggatcaatgt ttcaaaggca cagaagaatt catagctgtg 5460 tatattgatg acatcttggt cttcagcgag actatggcgg aacacaccaa gcatattgga 5520 atcatgctaa caatctgcca agaaaacggg ctggtcctaa gcccaaataa aatatgtctt 5580 gctcaacgag agattgaatt tttgggcaca atcatctctc aaggtcagat gaagcttcag 5640 cctcatatca taaaaaagat agtcaacaag gcagatatgg agctcgaaac aactaagggc 5700 ctaagatcat ttttgggcct cctgaactat gcccgaatct acatacccaa tctggggaag 5760 aaactaagtc cactatatgc caaaaccagt cccaccggag aaaagaagtt taatcgacag 5820 gattggcatc tgataaagga gattaaaaat atggtccaaa ggctcccaaa cctcgctatc 5880 ccaccagcaa gatgctgcat tatcatagaa agcgatggtt gtatggaagg atggggggcc 5940 gtatgcaagt ggaaattagc aaaagaagat tcccgcacaa ctgaaaaggt atgtgcctac 6000 gctagtggaa aattcggcat aatcaagtcc acaattgacg ccgagatttt cgcactcata 6060 aaagcactgg aatctttcaa aatcttctat ctggacaaaa aacatttggt ggtgcgtact 6120 gactgtcagg cgatagtgac gttttataac aaaacaagca ctcacaagcc ttctcgtata 6180 cgttggatca ccttttccga ctatataacg gggttaggag ttcaagttac tatcgaacac 6240 ataaacggaa aggagaacca gttagcagat acactaagca gactagtata caccacatgg 6300 agccagtccc aagctcacct gccggaggaa gaagagccgg agaagtcccc acatctcagc 6360 ttagcggtgt tagctacccc tatggcttgg cctatgacgg ccttctacag caaaaggagg 6420 acgccattaa tcacgggaga ctcaccctgg caacagaaca agccatctca agacagctct 6480 atcgcatcga agagcaagca gccagaaaag cactcatggc cctacgagac ctacagggcg 6540 tactgcactt caagcgagac tatttggccg caactgccac acatgacaac tgggccagtg 6600 atagactgcc agctgcccaa caagattcag ccgccctcga ccaacatgct ggcgtgatta 6660 acgccattat tgaaaggact gtccaaccct agtttggacg atagtgtgca ataattaatt 6720 gtgcttttac tttccagctg taactcatta tagagtagac atagtaattg acgatggggc 6780 ccgaggagca cccggattac tactctacca tctataaatg agagtatgta aggcttagcc 6840 atcagagagg aaaacatatc catcctgatt ctaagcattc tagagcttgt aagtttttaa 6900 gagaaataaa gaatcttctt agtgattatt tctttgtttc ccctgggaaa aatttaaaca 6960 gtttctgtta ttctgtttaa tcccgttcca cgttaccgtt catact 7006 //