LOCUS pOME0246P 6161 bp DNA linear VRL 27-AUG-2012 DEFINITION T61 Human herpesvirus 8 strain JSC-1 clone BAC16, complete genome. ACCESSION GQ994935 VERSION GQ994935.1 GI:261853473 KEYWORDS . SOURCE Human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus) ORGANISM Human herpesvirus 8 Viruses; dsDNA viruses, no RNA stage; Herpesvirales; Herpesviridae; Gammaherpesvirinae; Rhadinovirus. REFERENCE 1 (bases 1 to 138146) AUTHORS Brulois,K.F., Chang,H., Lee,A.S., Ensser,A., Wong,L.Y., Toth,Z., Lee,S.H., Lee,H.R., Myoung,J., Ganem,D., Oh,T.K., Kim,J.F., Gao,S.J. and Jung,J.U. TITLE Construction and manipulation of a new Kaposi's sarcoma-associated herpesvirus Bacterial artificial chromosome clone JOURNAL J. Virol. 86 (18), 9708-9720 (2012) PUBMED 22740391 REFERENCE 2 (bases 1 to 138146) AUTHORS Brulois,K., Lee,A. and Chang,H. TITLE Direct Submission JOURNAL Submitted (21-SEP-2009) Molecular Microbiology and Immunology, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, USA FEATURES Location/Qualifiers misc_RNA 1..6161 /note="corresp. to 5' end ID'd by 2005 Taylor et al. (Chang/Moore lab)" /note="corresp. to PAN RNA 3' end ID'd by KSHV 2.0" /note="corresp. pos." /label="K4.5 (T6.1) - Chang/Moore lab 2005/2011, Ganem lab 2014" Site 1..6 /site_type="restriction site" /label=KpnI repeat_region <1..705 /rpt_family="LIR1" /rpt_type=inverted source <1..>6161 /organism="Human herpesvirus 8" /mol_type="genomic DNA" /strain="JSC-1" /db_xref="taxon:37296" /clone="BAC16" /note="infectious BAC clone harboring full-length KSHV genome; derived from rKSHV.219, KSHV-infected JSC1 primary effusion lymphoma cell line" Site 1..6 /site_type="mutagenized site" /label="5' RE site" misc_RNA 557..1860 /note="5' end approx." /note="corresp. pos." /label="K4.7 (T1.5) - Chang/Moore lab 2011" misc_RNA 640..1859 /label="K4.7 (T1.5) - Ganem lab 2014" misc_RNA 656..1860 /note="corresp. pos." /label="K4.7 (T1.5) - Yuan lab 2004" repeat_region 707..1146 /note="22 copies" /rpt_family="DR1" /rpt_type=direct repeat_region 1160..1314 /note="5 copies" /rpt_family="DR2" /rpt_type=direct polyA_signal 1519..1524 /label="PAS K4.7(T1.5) - Schifano guess" polyA_site 1534 /note="corresp. pos." /label="TTS K4.7(T1.5) - Zheng lab 2013" polyA_site 1610 /note="not confirmed by 3' RACE, corresp. pos." /label="TTS K4.7(T1.5) - Zheng lab 2013" misc_RNA 1780..6161 /note="5' end not determine, est. based on Fig. 2" /label="K4.5 (T6.1, as-K5-K6) - Ganem lab 2014" polyA_signal 1839..1844 /label="PAS K4.7(T1.5) - Schifano guess" polyA_site 1859 /note="corresp. pos." /label="TTS K4.7(T1.5) - Zheng lab 2013" polyA_site complement(1956) /note="corresp. pos." /label="TTS K5 - Yamanishi lab 2000" polyA_site complement(1963) /note="corresp. pos." /label="TTS K5 - Gao lab 2014" polyA_site complement(1965) /note="corresp. pos." /label="TTS K5 - Zheng lab 2013" polyA_signal complement(1987..1992) /note="corresp. pos." /label="PAS K5 - Gao lab 2014" CDS complement(2128..2898) /codon_start=1 /product="K5" /protein_id="ACY00410.1" /db_xref="GI:261853488" /translation="MASKDVEEGVEGPICWICREEVGNEGIHPCACTGELDVVHPQCL STWLTVSRNTACQMCRVIYRTRTQWRSRLNLWPEMERQEIFELFLLMSVVVAGLVGVA LCTWTLLVILTAPAGTFSPGAVLGFLCFFGFYQIFIVFAFGGICRVSGTVRALYAANN TRVTVLPYRRPRRPTANEDNIELTVLVGPAGGTDEEPTDESSEGDVASGDKERDGSSG DEPDGGPNDRAGLRGTARTDLCAPTKKPVRKNHPKNNG" polyA_site complement(3307) /note="corresp. pos." /label="TTS K6 - Zheng lab 2013" polyA_site complement(3310) /note="corresp. pos." /label="TTS K6 - Gao lab 2014" polyA_signal complement(3330..3335) /note="corresp. pos." /label="PAS K6 - Gao lab 2014" CDS complement(3552..3839) /codon_start=1 /product="K6" /protein_id="ACY00411.1" /db_xref="GI:261853489" /translation="MAPVHVLCCVSVLLATFYLTPTESAGSLVSYTPNSCCYGFQQHP PPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIA" polyA_signal complement(4877..4882) /label="PAS K7.3(anti-PAN lncRNA) - Schifano guess" misc_RNA complement(4878..6138) /note="5' end approx." /note="corresp. pos." /label="K7.3 (anti-PAN lncRNA) - Chang/Moore lab 2011" CDS 5037..5417 /codon_start=1 /product="K7" /protein_id="ACY00412.1" /db_xref="GI:261853490" /translation="MGTLEIKGASLSQFSTGTAQSPWLPLHLWILCSLLAFLPLLVFI GAADCGLIASLLAIYPSWLSARFSVLLFPHWPESCSTKNTARSGALHKPAEQKLRFAQ KPCHGNYTVTPCGLLHWIQSPGQL" misc_RNA 5076..>6161 /note="corresp. pos." /label="PAN RNA - Zheng lab 2013" misc_RNA 5081..6161 /note="from 2014 Arias et al. (Ganem lab) KSHV 2.0" /label="PAN RNA - Ganem lab 2014" misc_RNA 5082..>6161 /note="corresp. pos." /label="PAN RNA - NC_009333 genome annotation" polyA_site 5340 /note="corresp. pos." /label="TTS K4.5(T6.1)-PAN - Zheng lab 2013" polyA_site 5692 /note="corresp. pos." /label="TTS K4.5(T6.1)-PAN-K7 - Zheng lab 2013" polyA_signal 6134..6139 /note="corresp. pos." /label="PAS K4.5-PAN-K7 - Gao lab 2014" polyA_site 6154 /note="corresp. pos." /label="TTS K4.5(T6.1)-PAN-K7 - Zheng lab 2013" Site 6156..6161 /site_type="restriction site" /label=EcoRI Site 6156..6161 /site_type="mutagenized site" /label="3' RE site" ORIGIN 1 ggtaccAATC CTAGCGCAGC TGAGTCATCG CAGCCCCTAT TCCAGTAGGT ATACCCAGCT 61 GGGTAATCCA GTAGGTATAC CCAGGTGGGT GAACCCAGCT GGGTATACCC AGCTGCAATT 121 CTATAATTAA ACAAGGTAGA AACCAACGGG GTCCTCAGGT GGTATTTCCG GAAGCATTAC 181 CAAATAAGGC AACCTCAGCT GGGAATACCA GCGGACTACC CCCAACTGTA TTCAACCCTC 241 CTTTGTTTTC CGGAAGTATA TCCATTTATG GAAATCAGCT GGGTCACTCT ACTGGGTTAT 301 TCTTTATAAT AGGGCCCGAT GAGTCATGGG GTTGGGATTT TTCTACTAGG TCGTTTCGGT 361 GGATGGGTGC CAGGATTATA GGGGCCCTGT CCACGGGGTT GTTCGGTGGC GGGGGGGGGG 421 GGGCTAGTGA GTCACGGGCC TGGAATCTCG CCTCTGGGTG GTTTCGGTAG ATGGGGGCCG 481 GGAGGATGGG GCCCCGCCCA CCGCTGGCGC GCCCCAGAAC ATGGGTGGCT AACGCCTACA 541 TGGGCAGCTT GTCCTACGGT TACGCCCATT TGAGACGGGT TAACCAACTG TTACACCCCT 601 TCGCCGGGAA CGCTATAAAA ACGAGGGACA GCAGCCCCCC TCGCGCACTG CGCGCGCGGC 661 GGCACGTGGG ACGGATCTCT TGGATTTACC CGTAACGAGG AGCGGCGCAC CCCAGGAGCC 721 CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC 781 CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC 841 CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC 901 CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC 961 CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC 1021 CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC 1081 CCGGCAGGAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC CCGGCAGCAC CCCAGGAGCC 1141 CCGGCAGCAC CCCACCCCCC CCCCGGAGGG GGATCCCGGC GCGCCACCCT CCCCCGGAGG 1201 GGGATCCCGG CGCGCCACCC TCCCCCGGAG GGGGATCCCG GCGCGCCACC CTCCCCCGGA 1261 GGGGGATCCC GGCGCGCCAC CCTCCCCCGG AGGGGGATCC CGGCGCGCCA CCCTCCCCGG 1321 CAACAACCTG TTGCCATGTA TGGCGATTTG TATCAGTCAC AAGCACACAA CCCCTGCTAG 1381 TATTAATGGT GTTTAAAACG TTCTACACGT ACGGCGGACC GCATCCGTCG CAAGCACGCG 1441 CATATAACCC CCAAATGCAC CATGATGAGA AGCACAGCCA CGCGTCAAAA AACTTTAAAA 1501 ACATCGTTAT CCAATATCAT TAAAAACCAC ACCGAAATTT ACACAGGTAG CACGTCACCG 1561 TGTTAGTGTC ACCCACTGTA CACAAGGCGT GTCGTATATG TAGTATAGGT ATTTGATGAG 1621 GCGGAAGCAT ATCCCGCTTC CAGCGAACGG AAATAAGAAT CATCCGTTCC AGCATTTATT 1681 CAAAGGGGGC ACAGAGGATT CACATTGTTT AGAGAGAGTT TTTCTTAGTC ACCATTCCAT 1741 ACTTGGGCAG TATTGGCCTA CGATTTGGGC GACGTTTCAG GCTGGTCTAT TCTCCGTCCA 1801 CTTTTCCCCG GCTATTCTGT CCCAGCATAG GCTCTTGAAA TAAACAATGT TTACCGAGTA 1861 AAAGGTTCCA CTCACCCTCA TTTGTCGTTG CACCCATCCC CCCTTTGCTT AATCACCCGA 1921 AAACTAGAGG ACACGGATGG AAAACATATC GCACGCGGGT TGTTTGAAAG TCAACAGCTA 1981 CTTGTTTTTA ATGAGGACAG ATTTGGGCAC AGGCCAGAGG GTAAAGCCCT ACGTGTGCGC 2041 GGGGGGGGTG TATACGCTGC GAAAACCTGC ACGGTGCATA ACACCCAGGG CGTCACGTCA 2101 CATATCTCTG TGCACCCAAG TGGTTGTTCA ACCGTTGTTT TTTGGATGAT TTTTCCGCAC 2161 CGGCTTTTTT GTGGGCGCGC ATAGGTCGGT ACGCGCTGTC CCCCTAAGTC CCGCACGGTC 2221 GTTCGGGCCC CCGTCCGGCT CGTCTCCGGA TGAACCGTCA CGTTCTTTGT CTCCAGAGGC 2281 GACGTCTCCT TCAGATGACT CGTCCGTGGG CTCCTCGTCC GTCCCGCCCG CGGGTCCGAC 2341 AAGGACCGTC AATTCGATGT TATCTTCGTT CGCGGTTGGC CGGCGCGGCC GTCGGTATGG 2401 CAGTACGGTC ACCCGGGTGT TATTTGCCGC GTATAATGCC CTCACAGTGC CACTTACGCG 2461 GCATATGCCG CCAAATGCAA ACACAATAAA TATTTGGTAA AACCCAAAGA AGCAGAGAAA 2521 ACCGAGCACG GCCCCGGGGG AGAATGTTCC CGCAGGAGCA GTTAGGATGA CCAGGAGCGT 2581 CCAGGTGCAC AACGCCACGC CGACAAGCCC AGCCACCACC ACAGACATCA GCAAAAACAG 2641 TTCAAAAATT TCTTGGCGCT CCATCTCCGG CCACAGGTTA AGGCGACTAC GCCACTGCGT 2701 GCGCGTGCGG TATATAACGC GACACATTTG ACAGGCCGTG TTTCGAGACA CTGTTAGCCA 2761 AGTGCTTAAA CACTGCGGGT GGACGACATC CAGCTCTCCG GTACAGGCGC AGGGGTGTAT 2821 GCCCTCGTTC CCCACCTCTT CCCTACATAT CCAGCAGATG GGTCCCTCTA CACCCTCTTC 2881 TACGTCCTTG GACGCCATCT CTGCAGCTGG GGTGGAAGTC TGAAAAAGGG AAAGGGGAGG 2941 TGAGCAGAGT GCCCAGTTAG TCTCCGACCC GCCGTCCGCC CTACTGTCGC TATCCCGCCT 3001 TGACAGATGT CTAACATATT CACGGACGCC ACATGTGTGT CTATTTTCCT ACATCCAGGC 3061 TTTCCCTGGA AAACTGTCAC AACCCACCCT GCTTTAGCTC TACATCTGTA TTTTTGTTTA 3121 CGCACAGGAT CAACGCTTCG TGCCCGTCCA CCCCCGCGCT CTCCGCCTGT GTTTGGAGGT 3181 TTTATGAGTG GTTAGTTCTA GGCAGCTCCG GACAAGTTGT CCAAAACACG GCGCGCCCCG 3241 CCCTTCCTTC CCTCCGGATC CGCCCACACC GGACCTATGA AATAAGGGAC ACGCGTCATC 3301 ACTAGTTATG AGAGAAAAAC CACAACAGCT TTATTGGAAA ACACCTGAGT GGATCCCCCA 3361 CCCCCCGCGT ACGACAGGCG TTTCTGTGGT GCGCTTCTGG GAAAAACGTT TTTCCCCCAT 3421 TTCTTCCTCG ACAGGTCTTC TAAGGTAGAT AAATCCCCCC CCTTTGCGCG TCTCCTAGAA 3481 TGGCCTAGGC GCACGATGGC GTTGTCGCCT CGAGCAGTTG GGCCGCAGTG ATATCTTCAA 3541 CTTTCGACCG TCTAAGCTAT GGCAGGCAGC CGCTGCATCA GCTGCCTAAC CCAGTTTTTG 3601 GAAGGGTCTG CGCAGATCTG ACGCCCTCGC TTGGTCAGCA AAATAACTCC GGGTTTTGGG 3661 CACGCTGGGG ACGTGGGATA CCACTCTTTT AGAATTTGGA CGGGCGGTGG GTGCTGCTGG 3721 AACCCGTAGC AGCAGCTATT AGGCGTGTAC GACACGAGTG ACCCCGCGCT TTCTGTGGGC 3781 GTCAGGTAAA ACGTGGCAAG CAGTACGCTA ACGCAGCATA AAACGTGGAC GGGGGCCATC 3841 TGGAGGTGCC AAGTTCGCAA CAGTCTAAAG AAAACCGTAA AGGCTATTTG GGGTTTCTGT 3901 TCTGTCAGAT GTAACGCCGA GTTCCTTATA TGCTTACCTG ATTCTGGTCT CACCTGTTTA 3961 TTTATAGTGG CGTATGCTAA CCGCCAGCTT ACATGCGGGA TAAGTTGGCC TAACTCACCA 4021 AAAACGGGTT GCAGACAAAA GTGATTGTTG GGGCGCTTAC TTAGAAGGTG TGAGGGTTTC 4081 TAAGAAACCC CGCCAACGCC CGGAAACCGC ATGCGTTCCA GTCGGTGCGG CCTGCGCCGG 4141 CGTCGCTGTG GCGCCTTTGT GGGCTTTGAG TTCTGTCATT AAGCCAGGTT TCCATTGCCA 4201 CCCGGGCGAA AACAAGCCGG GTAGTTTCAG GGGTCATCTG GCGATCAGTG TACCATATTC 4261 CCACGACCCA TCAACACCGC TGCTTGAGGC GTGTCTCTGT ATGTGTCACC GGAGACTGCA 4321 TGTATCGTGC ATATCTGTAT TGTGCGCTTG CGCGGAGACA ACATACCGAC GACCAAGTCA 4381 GGGGTCACCT CCAGTGCACG CCGCTAGGTG GGACCGTGGG CGAGCCGAAA TAATTATATA 4441 TTTTTTTGGC ACGGTTGTGA GCAACGCCAT CGTGAGTTGG TTAATACCCT CTAAACGCAT 4501 AGTCTTTTTT TATTTGTCAA CCAACCAGTC AATCACCTGT CATCGCCGCT CAGAAGCACA 4561 CGTCTTCGGC CAATGCCGTG TTGGCGGGTT TGACCACGGT TACTGATAGG TAGACGAGTC 4621 CGACAATCAC ACACGTCCGC CAGCGATTTG CAGCGCAGCT AAAATCGCGT GGCCGGGTTG 4681 GTAGAAGCAA ATTATCCAAT GGTCGTGTTT GGGTTTGTTT TGGGGTTATC TACATATTAT 4741 ATTCCTTATC CCGACTGGTT GCGGAAGTAT TCGCAGCTTG GCTACTCTGC TCGATTACCC 4801 CGTGAATAAC TGGGCGGGGG GTGACCCAAC ATAGTGATTC GGTAGATTTG GGGGACTGGA 4861 TGAACATTAA TGAAAGTTTA TTAATGTTCA TCCGTATTGT GTATATGTAA TTTGGTTTCC 4921 ATATTTGGTA GGAGTATGGA GTTTTCTTAT GGATTATTAA GGGTCAGCTT GAAGGATGAT 4981 GTTAATGACA TAAAGGGGCG TGGCTTCCAA AAATGGGTGG CTAACCTGTC CAAAATATGG 5041 GAACACTGGA GATAAAAGGG GCCAGCTTGA GTCAGTTTAG CACTGGGACT GCCCAGTCAC 5101 CTTGGCTGCC GCTTCACCTA TGGATTTTGT GCTCGCTGCT TGCCTTCTTG CCGCTTCTGG 5161 TTTTCATTGG TGCCGCCGAT TGTGGGTTGA TTGCGTCGCT TTTGGCAATA TACCCATCCT 5221 GGCTTTCGGC TAGGTTTTCC GTCCTACTTT TCCCACATTG GCCTGAGAGC TGTAGTACAA 5281 AAAACACCGC GCGGTCTGGA GCTCTCCATA AGCCCGCAGA ACAAAAGCTG CGATTTGCCC 5341 AAAAACCTTG CCATGGCAAC TATACAGTCA CCCCTTGCGG GTTATTGCAT TGGATTCAAT 5401 CTCCAGGCCA GTTGTAGCCC CCTTTTATGA TATGCGAGGA TACTTAACGT GTCTGAATGT 5461 GGAATATAAT GTGAAAGGAA AGCAGCGCCC ACTGGTGTAT CAGAACAGTG GTGCACTACC 5521 TATCTGCTCA TTCGTTGTTT CGGTTCTGTG TTTGTCTGAT TCTTAGATAG TGTTGAGGTA 5581 ATTCTAGAAA GCGGATTGAG TGTAAATCGG GCCACTTTGC CCTAAATGTG ACAATCTGGA 5641 TGTGTATCTT ATTGGTGCGT TGTGAAGCAT TTTAAAATGC GTTTTAGATT GTATCAGGCT 5701 AGTGCTGTAA TGGTGTGTTT ATTTTTCCAG TGTAAGCAAG TCGATTTGAA TGACATAGGC 5761 GACAAAGTGA GGTGGCATTT GTCAGAAGTT TCAAAGTCGT GTAAGAACAT TGGACTAAAG 5821 TGGTGTGCGG CAGCTGGGAG CGCTCTTTCA ATGTTAATGT TTTAATGTGT ATGTTGTGTT 5881 GGAAGTTCCA GGCTAATATT TGATGTTTTG CTAGGTTGAC TAACGATGTT TTCTTGTAGG 5941 TGAAAGCGTT GTGTAACAAT GATAACGGTG TTTTGGCTGG GTTTTTCCTT GTTCGCACCG 6001 GACACCTCCA GTGACCAGAC GGCAAGGTTT TTATCCCAGT GTATATTGGA AAAACATGTT 6061 ATACTTTTGA CAATTTAACG TGCCTAGAGC TCAAATTAAA CTAATACCAT AACGTAATGC 6121 AACTTACAAC ATAAATAAAG GTCAATGTTT AATCCgaatt c //