ID HPV39 STANDARD; ds-DNA; VRL; 7833 bp. XX DE Human papillomavirus type 39 (HPV-39), complete genome. XX AC M62849 M38185 XX DT 06-MAR-1991 XX OS Human papillomavirus type 39 DNA isolated from a penile Bowenoid OS papule biopsy. OC Human papillomavirus type 39 OC Viridae; ds-DNA nonenveloped viruses; Papovaviridae; OC Papillomavirus. XX RN [1] RP 1-7833 RA Volpers,C. and Streeck,R.E.; RT "Genome organization and nucleotide sequence of human papillomavirus RT type 39"; RL Virology 181, 419-423 (1991). XX XX In developing countries, cancer of the cervix is responsible for XX 24% of all cancers in women. In these areas, it is the most XX frequent female malignancy. In developed countries, it ranks XX behind cancers of the breast, lung, uterus, and ovaries and XX accounts for 7% of all female cancers. HPV-39 is most often found XX in lesions of the genital mucosa which may have a risk for XX malignant progression. Estimates indicate that HPV-39 and other XX less studied HPV types (-31, -33, -35, -45, -51, -52, and -56) have XX been recovered from about 15% of all invasive cervical cancers. In XX a recent study of 365 female HPV positive patients, HPV-39 DNA was XX detected in 3.9% of the tissue samples. XX XX The 7833 bp genome of HPV-39 was first recovered and cloned from XX biopsy samples of penile Bowenoid papules, which contained the XX viral DNA in episomal form. Its genome contains an E7 ORF which is XX located immediately upstream of E1, which is common among all XX genital papillomaviruses. Also seen in this genome is a absence of XX an initiation codon for E4, characteristic of types 16, 31, and 33. XX Unusually, a large ORF of 1.3 kb has been found on the XX complementary strand of DNA. This ORF contains an initiation XX codon, a potential splice acceptor site close to the 5' end, and a XX polyadenylation signal at the 3' end. Further upstream of this XX large ORF is a smaller ORf preceeded by a TATA box and a NF-1 XX binding site. XX XX The noncoding region of HPV-39 contains several features common XX among other papillomavirus types. It contains three complete and XX two degenerate versions of a PV-specific palindrome, which is XX speculated to be an E2 activator and/or repressor binding site. XX Possible promoter elements which have been identified include two XX TATA boxes, a conserved AAAGGGAGTA promoter element which is XX upstream of a 12 bp palindrome tandem repeat, and an enhancer core XX sequence. Various transcription factor binding sites are also XX present. These include four possible sites for nuclear factor 1 XX (NF-1), two possible sites for activator protein 1 (AP-1), and a XX motif for a recently postulated papillomavirus enhancer associated XX factor (PVF). A glucocorticoid response element (GRE) is found XX resembling those found in other types. In addition, a GRE is found XX in the L1 ORF with no equivalent in other types. XX XX The E6 and E7 ORFs of HPV-39 contain four copies and one copy XX respectively of the well-conserved cysteine doublet (Cys-X-X-Cys) XX motif. These motifs may be involved in the formation of zinc XX finger like structures. The author points out that mutational XX analysis of the HPV-16 ORF has shown that one copy of this motif is XX sufficient for transformation. In addition, the E7 ORF of HPV-39 XX contains a putative cell division motif found in genital HPVs XX associated with malignancy, SV40 large T antigen, adenovirus E1A, XX and the myc protein. XX XX FT KEY Location/Qualifiers FT CDS <3393..3677 FT /note="E4 ORF from bp 3393 to 3677" FT /gene="E4" FT /note="putative" FT /codon_start=1 FT 5'UTR join(7161..7833,1..106) FT /standard_name="LCR" FT promoter 33..42 FT /note="putative" FT protein_bind 43..54 FT /function="gene transcription" FT /bound_moiety="E2" FT /note="putative" FT protein_bind 59..70 FT /function="gene transcription" FT /bound_moiety="E2" FT /note="putative" FT TATA_signal 74..80 FT /note="putative" FT CDS 107..583 FT /note="E6 ORF from bp 44 to 583" FT /product="transforming protein" FT /gene="E6" FT /note="putative" FT /codon_start=1 FT CDS 592..921 FT /note="E7 ORF from bp 493 to 921" FT /product="transforming protein" FT /gene="E7" FT /note="putative" FT /codon_start=1 FT CDS 928..2871 FT /note="E1 ORF from bp 922 to 2871" FT /product="replication protein" FT /gene="E1" FT /note="putative" FT /codon_start=1 FT CDS 2798..3910 FT /note="E2 ORF from bp 2780 to 3910" FT /product="regulatory protein" FT /gene="E2" FT /note="putative" FT /codon_start=1 FT CDS 3958..4176 FT /note="E5 ORF from bp 3958 to 4176" FT /gene="E5" FT /note="putative" FT /codon_start=1 FT polyA_signal 4243..4248 FT CDS 4250..5662 FT /note="L2 ORF from bp 4172 to 5662" FT /product="minor capsid protein" FT /gene="L2" FT /note="putative" FT /codon_start=1 FT CDS 5643..7160 FT /note="L1 ORF from bp 5610 to 7160" FT /product="major capsid protein" FT /gene="L1" FT /note="putative" FT /codon_start=1 FT protein_bind 6367..6381 FT /bound_moiety="hormone receptor" FT /standard_name="glucocorticoid responsive element" FT /note="putative" FT polyA_signal 7261..7266 FT protein_bind 7425..7439 FT /bound_moiety="hormone receptor" FT /standard_name="glucocorticoid responsive element" FT /note="putative" FT protein_bind 7456..7467 FT /function="gene transcription" FT /bound_moiety="E2" FT /note="putative" FT protein_bind 7798..7809 FT /function="gene transcription" FT /bound_moiety="E2" FT /note="putative" FT source 1..7833 FT /organism="Human papillomavirus type 39" FT /sequenced_mol="DNA" XX SQ SEQUENCE 7833 bp; 2426 a; 1485 c; 1660 g; 2262 t; cttataacat tttataagta tcttgtttaa aaaaagggag taaccgaaaa cggtcaggac 60 cgaaatcggt ggatataaaa cgcagtcaca gtttctgtcc ataccgatgg cgcgatttca 120 caatcctgca gaacggccat acaaattgcc agacctgtgc acaacgctgg acaccacctt 180 gcaggacatt acaatagcct gtgtctattg cagacgacca ctacagcaaa ccgaggtata 240 tgaatttgca tttagtgatt tatatgtagt atatagggac ggggaaccac tagctgcatg 300 ccaatcatgt ataaaatttt atgctaaaat acgggagcta cgatattact cggactcggt 360 gtatgcaact acattagaaa atataactaa tacaaagtta tataatttat taataaggtg 420 catgtgttgt ctgaaaccgc tgtgtccagc agaaaaatta agacacctaa atagcaaacg 480 aagatttcat aaaatagcag gaagctatac aggacagtgt cgacggtgct ggaccacaaa 540 acgggaggac cgcagactaa cacgaagaga aacccaagta taacatcaga tatgcgtgga 600 ccaaagccca ccttgcagga aattgtatta gatttatgtc cttacaatga aatacagccg 660 gttgaccttg tatgtcacga gcaattagga gagtcagagg atgaaataga tgaacccgac 720 catgcagtta atcaccaaca tcaactacta gccagacggg atgaaccaca gcgtcacaca 780 atacagtgtt cgtgttgtaa gtgtaacaac acactgcagc tggtagtaga agcctcacgg 840 gatactctgc gacaactaca gcagctgttt atggactcac taggatttgt gtgtccgtgg 900 tgtgcaactg caaaccagta acctgctatg gccaatcgtg aaggtacaga cggggatggg 960 tcgggatgta acggatggtt tctagtacag gcaatagtag ataaacaaac aggcgacaca 1020 gtgtcggagg atgaggatga aaatgcaaca gatacaggtt cagacctggc agactttatt 1080 gatgattcca cagatatttg tgtacaggca gagcgtgaga cagcacaggt acttttacat 1140 atgcaagagg cccaaaggga tgcacaagca gtgcgtgcct taaaacgaaa gtatacagac 1200 agcagtggcg acactagacc gtatggaaaa aaagtaggca ggaataccag gggaacacta 1260 caggaaattt cattaaatgt aagcagtacg caggcaacac aaacggtgta ttccgtgcca 1320 gacagcggat atggcaatat ggaagtggaa acagctgaag tggaggaggt aactgtagca 1380 actaatacaa atggggatgc tgaaggggaa catggcggca gtgtacggga ggagtgcagt 1440 agtgtggata gtgctataga tagtgaaaac caggatccca aatctccaac tgcacaaatt 1500 aaattattgt tacaatccaa taacaaaaag gctgcaatgc taacacaatt taaagaaaca 1560 tatggactat cctttactga cctggtacgt acgtttaaaa gtgataaaac aacatgtaca 1620 gactgggtgg cagccatatt tggagtacat ccaactattg cagaaggatt taaaacatta 1680 atcaacaaat atgccttata tacacatata caaagcttag acacaaaaca aggagtacta 1740 attttaatgc taataagata tacatgtgga aaaaataggg ttactgtagg aaagggatta 1800 agtacattgt tacatgttcc agaaagttgt atgcttctgg agcctcctaa actgcgcagc 1860 cctgtagcag cactatattg gtatcgcaca ggtatatcca atattagtgt ggtaacaggg 1920 gatacgccag aatggataca acgattaact gttatacaac atggaataga tgatagtgta 1980 tttgacctat cggacatggt acaatgggca tttgacaatg aatatactga tgaaagtgac 2040 atagcattta attatgcaat gttagcagat tgtaacagta atgctgcagc ctttttaaaa 2100 agtaactgcc aggcaaaata tgtaaaagat tgtgcaacaa tgtgtaaaca ttacaagcga 2160 gcacaaaaaa ggcaaatgtc catgtctcaa tggataaaat ttaggtgtag taaatgtgat 2220 gaaggcgggg actggagacc catagtacaa ttcttaagat atcaaggaat agaatttata 2280 tcctttttat gtgcattaaa ggaattttta aagggtactc ccaaaaaaaa ctgtatagtt 2340 atatatggac ctgcgaatac aggaaagtca catttttgta tgagccttat gcatttttta 2400 cagggcacag ttatttcata tgtaaactcc accagccact tttggctaga accacttgca 2460 gatgcaaaac tagcaatgtt agatgatgca accggtacct gctggtcata tttcgataat 2520 tatatgagaa atgcattaga tgggtatgca ataagtttag ataggaaata taaaagttta 2580 ctacaaatga aatgtccacc attattaata acctccaata ccaatcctgt ggaagacgat 2640 aggtggccat atttacgtag taggctaaca gtgtttaaat ttcctaatgc atttccattt 2700 gaccaaaaca ggaatccagt gtacacaatc aatgataaaa actggaaatg tttttttgaa 2760 aagacttggt gcagattaga cttgcagcag gacgaggatg aaggagacaa tgatgaaaac 2820 actttcacaa cgtttaaatg tgttacagga caaaatacta gaatactatg aacaagacag 2880 taaatcaata tatgatcaaa ttaattattg gaaatgtgtg cgaatggaaa atgcaatatt 2940 ttatgcagca cgagaacgtg gcatgcatac tattgaccac caggtggtgc caaccataaa 3000 catttcaaaa tgtaaagcat atcaagctat tgaactgcag atggcactag aaagtgttgc 3060 acaaactgaa tacaatacag aggagtggac attaaaagac actagtaatg aactgtggca 3120 tacacagcca aaacaatgtt ttaaaaaaca aggaactaca gtggaggtgt ggtatgatgg 3180 ggacaaatgt aatgctatga actatgtatt atggggtgct atatattata aaaataatat 3240 agacatatgg tgtaaaacag aagggtgtgt ggactattgg ggtatatatt atatgaacga 3300 gcacctaaaa gtatactatg aagtgtttat tcaagatgcg gaaaggtatg ggactagtgg 3360 caaatgggaa gtgcattata atggcaacat aattcattgt cctgactcta tgtgcagtac 3420 cagtgacgga tcggtaccca ctactgaact tactaccgaa ttatcaaaca ccaccgcgac 3480 ccattccacc gcaacaaccc catgcaccca aaaaacaatc ccgccgccgt ctcgaaagcg 3540 acctcgacag tgtgcagtca cagagcccac tgagcccgac ggagtgtccc tggaccatct 3600 taacaaccca ctccacagta acagtacagg ccacaacaca agacggtacc tcagttgtgg 3660 taacactacg cctataatac atttaaaagg tgacaaaaat ggtttaaaat gtttaagata 3720 tagactacaa aaatatgaca cattgtttga aaatatttca tgtacctggc attggatacg 3780 gggtaaggga accaaaaacg ctggcatatt aactgttaca tatgccacag agtcacaacg 3840 ccaaaaattt ttggacactg ttaaaatacc ttctagtgta catgtttcat tgggttacat 3900 gacattgtaa agtatactat ggatattgtg tatgtatatt gtatacatac tacatagatg 3960 atattattgg tatttttggt gtggtttggt gtgtgtatat atatatgttg caatgtcccg 4020 cttttgccgt ctgtgcatgt gtgtgcgtat gtgtggataa ttgtgtttgt gtttattctt 4080 atacgtacca caccattgga ggtgtttttt gtatatttac tattttttgt attgcccatg 4140 tggttgttgc atagactggc aatggatatg atatagtact gtatatgtat gtgcattgtg 4200 cataactact gtacatagct ttttatattt ttttttgtta ctaataaaca tggtttccca 4260 ccgtgctgcc aggcgtaagc gtgcatctgc aactgaccta tatagaacct gtaaacaatc 4320 gggtacctgt ccaccagacg ttgttgataa agttgagggt actacacttg ctgacaaaat 4380 tttacagtgg actagtttag gtatattttt gggtgggtta ggcataggca caggtactgg 4440 tactggggga cgcacaggat atatacccct ggggggtagg cctaatactg ttgtagatgt 4500 gtctcctgca cgtccacctg tagttattga acctgttggt ccttctgagc catctattgt 4560 gcaattggtg gaggactcaa gtgttataac ctctggaaca ccagtaccaa catttacagg 4620 cacctctgga tttgaaatta cttcttcttc tactactacg cctgcggtat tggatattac 4680 accctcctct gggtctgtac aaataacctc tactagttat actaaccctg cctttacgga 4740 tccttcctta attgaggttc cccaaacagg tgaaacctcg ggtaatatat ttgtcagtac 4800 ccctacatca ggtacacatg gctatgagga aatacctatg gaagtgtttg ccacacatgg 4860 cacaggtacc gaacctatta gcagcacacc tacacctgga atcagtcgtg tggcaggacc 4920 acgtttatat agtagagcac atcagcaggt tcgtgttagt aattttgatt ttgtaactca 4980 cccttcatca tttgtaacat ttgataatcc tgcttttgag cctgttgata ctacattaac 5040 atatgaagct gctgacatag ctccagatcc ggattttctg gacattgttc gtttacatag 5100 gcctgcctta acctcgcgta aaggaacagt aaggtttagt aggcttggca aaaaggctac 5160 catggttacc cggcgtggca cacaaattgg agcgcaagta cattattacc atgacattag 5220 tagtattgct cctgctgaaa gcattgaatt acagccccta gttcacgctg agccctctga 5280 tgcttcagat gcattatttg atatatatgc tgatgtggac aataacacat atttagatac 5340 tgcatttaat aatacaaggg attcgggcac tacatataac acaggctcac taccttctgt 5400 ggcttcttca gcatctacta aatatgccaa tacaactatt ccttttagta cctcatggaa 5460 tatgcctgta aatactggtc ctgatattgc tttaccaagt actactccac agttgccatt 5520 ggtgccttct ggaccaatag acacaacata tgcaataacc attcagggtt ccaattatta 5580 tttgttgcca ttattgtatt ttttcctaaa aaaacgtaaa cgtattccct attttttttc 5640 agatggctat gtggcggtct agtgacagca tggtgtattt gcctccacct tctgtggcga 5700 aggttgtcaa tactgatgat tatgttacac gcacaggcat atattattat gctggcagct 5760 ctagattatt aacagtagga catccatatt ttaaagtggg tatgaatggt ggtcgcaagc 5820 aggacattcc aaaggtgtct gcatatcaat atagggtatt tcgcgtgaca ttgcccgatc 5880 ctaataaatt cagtattcca gatgcatcct tatataatcc agaaacacaa cgtttagtat 5940 gggcttgtgt aggggtggag gtgggcaggg gccagccatt gggtgttggt attagtggac 6000 acccattata taatagacag gatgatactg aaaactcacc attttcatca accaccaata 6060 aggacagtag ggataatgtg tctgtggatt ataaacagac acagttgtgc attataggct 6120 gtgttcccgc cattggggag cactggggta agggaaaggc atgcaagccc aataatgtat 6180 ctacggggga ctgtcctcct ttggaactag taaacacccc tattgaggat ggtgatatga 6240 ttgatactgg ctatggagct atggactttg gtgcattgca ggaaaccaaa agtgaggtgc 6300 ctttagatat ttgtcaatcc atttgtaaat atcctgatta tttgcaaatg tctgcagatg 6360 tgtatgggga cagtatgttc ttctgtttac gtagggaaca actgtttgca agacattttt 6420 ggaatcgtgg tggtatggtg ggtgacgcca ttcctgccca attgtatatt aagggcacag 6480 atatacgtgc aaaccccggt agttctgtat actgcccctc tcccagcggt tccatggtaa 6540 cctctgattc ccagttattt aataagcctt attggctaca taaggcccag ggccacaaca 6600 atggtatatg ttggcataat caattatttc ttactgttgt ggacactacc cgtagtacca 6660 actttacatt atctacctct atagagtctt ccataccttc tacatatgat ccttctaagt 6720 ttaaggaata taccaggcac gtggaggagt atgatttaca atttatattt caactgtgta 6780 ctgtcacatt aacaactgat gttatgtctt atattcacac tatgaattcc tctatattgg 6840 acaattggaa ttttgctgta gctcctccac catctgccag tttggtagac acttacagat 6900 acctacagtc tgcagccatt acatgtcaaa aggatgctcc agcacctgaa aagaaagatc 6960 catatgacgg tctaaagttt tggaatgttg acttaaggga aaagtttagt ttggaacttg 7020 atcaattccc tttgggacgt aaatttttgt tgcaggccag ggtccgcagg cgccctacta 7080 taggtccccg aaagcggcct gctgcatcca cttcctcgtc ctcagctact aaacacaaac 7140 gtaaacgtgt gtctaaataa tgcatgtgta tgccttgtta tgtgtgtgta tgttgtttgt 7200 ttccttatgt gttgagtgta tatgtgtatg tttgtaggta tgtgtgtata tgtttttgtt 7260 aataaagtat gtatgacagt ttcatgtgtg attgcacacc ctgtgactaa cagtgtattt 7320 gttttacata taataggtct gcaacatttc atacataatc tatatgccct accctaaggt 7380 gtgtttacta cctaatatgt aatttttaca ttgttgtatg cgtttctaca ttttatactt 7440 cgccattttg tggcgaccga agtcggtcgt gggttgagca ttttttttaa actagtggaa 7500 accacctttc tcagcaaaaa catgtcttta ccttaggttc accctgcata gttggcactg 7560 gtaacagttt tactggcgcg ccttattact catcatcctg tccaggtgca ctgcaacaat 7620 actttggcaa catccatatc tccaccctat gtaataaaac tgcttttagg catatatttt 7680 agctgttttt acttgcttaa ttaaatagtt ggcctgtata actacttttt gattcaggaa 7740 tgtgtcttac agtataagtt atacaagtga ctaatgtagc acacaatagt ttatgcaacc 7800 gaaataggtt gggcatacat acctatactt tta 7833 //