Path: utzoo!utgpu!news-server.csri.toronto.edu!bonnie.concordia.ca!uunet!bionet!will From: GenBank-Updates@genbank.bio.net Newsgroups: bionet.molbio.genbank.updates Subject: Human lymphadenopathy virus (MAL isolate), complete genome. Message-ID: Date: 28 May 91 18:42:32 GMT Sender: will@genbank.bio.net Distribution: bionet Lines: 223 Approved: lear@genbank.bio.net Checksum: 54234 15 LOCUS HIVVMALCG 9229 bp ss-mRNA VRL 28-MAY-1991 DEFINITION Human lymphadenopathy virus (MAL isolate), complete genome. ACCESSION X04415 KEYWORDS acquired immune deficiency syndrome; env gene; gag gene; genome; long terminal repeat; pol gene; polyprotein; provirus; reverse transcriptase. SOURCE Human immunodeficiency virus type 1 RNA. ORGANISM Human immunodeficiency virus type 1 Viridae; ss-RNA enveloped viruses; Positive strand RNA virus; Retroviridae; Lentivirinae. REFERENCE 1 (bases 1 to 9229) AUTHORS Alizon,M., Wain-Hobson,S., Montagnier,L. and Sonigo,P. TITLE Genetic variability of the AIDS virus: Nucleotide sequence analysis of two isolates from African patients JOURNAL Cell 46, 63-74 (1986) STANDARD full automatic COMMENT SWISS-PROT; P04583; ENV$HIV1M. SWISS-PROT; P04588; POL$HIV1M. SWISS-PROT; P04594; GAG$HIV1M. SWISS-PROT; P04599; VIF$HIV1M. SWISS-PROT; P04603; NEF$HIV1M. SWISS-PROT; P04613; TAT$HIV1M. SWISS-PROT; P04622; REV$HIV1M. SWISS-PROT; P05924; VPU$HIV1M. SWISS-PROT; P05955; VPR$HIV1M. Acquired immune deficiency syndrome (AIDS) is caused by a retrovirus known by several different names, probably representing two separate strains: human T-cell lymphotropic virus-III (HTLV-III) and lymphadenopathy-associated virus (LAV) are thought to be one strain, and AIDS-associated retrovirus type 2 (ARV-2) the other. All three viruses, whose sequences do not differ by more than about 6%, are believed to belong to the retroviral subfamily Lentiviridae, or "slow" viruses. For the details of the annotation and for other pertinent references, see the HIV reference entry. From EMBL entry HIVMALCG; dated 18-DEC-1990. FEATURES Location/Qualifiers CDS join(5405..5619,7959..8007) /product="tat protein" /codon_start=5405 repeat_region 1..177 /note="5' LTR" repeat_region 1..96 /note="R repeat 5' copy" misc_feature 179..196 /note="primer (Lys-tRNA) binding site" CDS 350..1867 /product="gag polyprotein" /codon_start=350 CDS 1963..4671 /product="pol polyprotein (NH2-terminus uncertain; AA at 1963)" /codon_start=1963 CDS 4616..5194 /product="sor 23K protein" /codon_start=4616 CDS 5134..5424 /note="urfC" /codon_start=5134 CDS 5799..8378 /product="envelope polyprotein precursor" /codon_start=5799 CDS 8380..9009 /product="27K protein" /codon_start=8380 repeat_region 8678..9229 /note="3' LTR" repeat_region 9134..9229 /note="R repeat 3' copy" BASE COUNT 3355 a 1627 c 2204 g 2043 t ORIGIN 1 ggtctctctt gttagaccag gtcgagcccg ggagctctct ggctagcaag gaacccactg 61 cttaagcctc aataaagctt gccttgagtg cctcaagcag tgtgtgccca tctgttgtgt 121 gactctggta actagagatc cctcagacca ctctagacgg tgtaaaaatc tctagcagtg 181 gcgcccgaac agggacttta aagtgaaagt aacagggact cgaaagcgga agttccagag 241 aagttctctc gacgcaggac tcggcttgct gaggtgcaca cagcaagagg cgagagcggc 301 gactggtgag tacgccaatt tttgactagc ggaggctaga aggagagaga tgggtgcgag 361 agcgtcagta ttaagcgggg gaaaattaga tgcatgggag aaaattcggt taaggccagg 421 gggaaagaaa aaatatagac tgaaacattt agtatgggca agcagggagc tggaaagatt 481 cgcacttaac cctggccttt tagaaacagg agaaggatgt caacaaataa tggaacagct 541 acaatcaact ctcaagacag gatcagaaga aattaaatca ttatataata cagtagcaac 601 cctctattgt gtacatcaaa ggatagatgt aaaagacacc aaggaagcgc tagataaaat 661 agaggaaata caaaataaga gcaggcaaaa gacacagcag gcagcagctg cacagcaggc 721 agcagctgcc acaaaaaaca gcagcagtgt cagtcaaaat taccccatag tgcaaaatgc 781 acaagggcaa atgatacatc aggccatatc acctaggact ttgaatgcat gggtgaaagt 841 aatagaagaa aaggctttca gcccagaagt gatacccatg ttctcagcat tatcagaggg 901 ggccacccca caagatttaa atatgatgct gaacatagtt ggaggacacc aggcagctat 961 gcaaatgtta aaagatacca tcaatgagga agctgcagac tgggacaggg tacatccagt 1021 acatgcaggg cctattcccc caggccagat gagagaacca agaggaagtg acatagcagg 1081 aactactagt acccttcaag aacaaatagg atggatgaca agcaacccac ctatcccagt 1141 gggagacatc tataaaagat ggataatcct gggattaaat aaaatagtaa gaatgtatag 1201 ccctgtcagc attttggaca taagacaagg gccaaaggaa ccttttagag actatgtaga 1261 taggttcttt aaaactctca gagctgagca agctacacag gaggtaaaaa attggatgac 1321 agaaaccttg ctggtccaaa atgcgaatcc agactgtaag accattttaa aagcattagg 1381 accaggggct acattagaag aaatgatgac agcatgccag ggagtgggag gacccagtca 1441 taaagcaaga gttttggctg aggcaatgag ccaagcaaca aattcaactg ctgccataat 1501 gatgcagaga ggtaatttta agggccagaa aagaattaag tgtttcaact gtggcaaaga 1561 aggacaccta gccagaaatt gcagggcccc taggaaaaag ggctgttgga aatgtgggaa 1621 ggaaggacac caaatgaaag actgcactga gagacaggct aattttttag ggaaaatttg 1681 gccttcccac aagggaaggc cagggaattt ccttcagagc agaccagagc caacagcccc 1741 accagcagag agcttcgggt ttggggagga gataaaaccc tctcagaaac aggagcagaa 1801 agacaaggaa ttgtatcctt tagcttccct caaatcactc tttggcaacg accagttgtc 1861 acagtaagag taggaggaca gctaaaagaa gctctattag acacaggagc agatgataca 1921 gtattagaag aaataaattt gccaggaaaa tggaaaccaa aaatgatagg gggaattgga 1981 ggttttatca aagtaagaca gtatgatcaa atacttatag aaatttgtgg aaaaaaggct 2041 ataggtacaa tattggtagg acctacacct gtcaacataa ttggacgaaa tatgttgact 2101 cagattggtt gtactttaaa ttttccaatt agtcctattg agactgtacc agtaaaatta 2161 aagccaggga tggatggccc aagggttaaa caatggccat tgacagaaga aaaaataaaa 2221 gcattaacag aaatttgtaa agatatggaa aaggaaggaa aaattttaaa aattgggcct 2281 gaaaatccat acaatactcc agtatttgcc ataaagaaaa aagacagcac taaatggaga 2341 aaattagtga atttcagaga gcttaataaa agaactcaag atttttggga agttcaatta 2401 ggaataccac atcctgctgg gttgaaaaag aaaaaatcag tcacagtatt ggatgtgggg 2461 gatgcatatt tttcagtccc tttagatgaa gatttcagga agtatactgc attcactata 2521 cccagtatta ataatgagac accagggatt agatatcagt acaatgtgct accacaggga 2581 tggaaaggat caccagcaat attccagagt agcatgacaa aaatcttaga accctttaga 2641 acaaaaaatc cagaaatagt catataccaa tacatggatg atttgtatgt agggtctgat 2701 ttagaaatag gacaacatag aacaaaaata gaggaactaa gagaacatct attgaaatgg 2761 ggatttacca caccagacaa aaagcatcag aaagaacccc catttctttg gatggggtat 2821 gaactccacc ctgacaaatg gacagtgcag cctatacaac tgccagacaa ggaaagctgg 2881 actgtcaatg atatacagaa attggtggga aaactaaatt gggcaagtca gatttatcca 2941 ggaattaaag taaagcaatt atgtaaactc cttaggggag caaaagcact aacagacata 3001 gtaccattaa ctgcagaggc agaattagaa ttggcagaga acagggaaat tctaaaagaa 3061 ccagtgcatg gggtatatta tgacccatca aaagacttaa tagcagaaat acagaagcag 3121 gggcaaggtc aatggacata tcaaatatac caagagcaat ataaaaatct gaaaacaggg 3181 aagtatgcaa gaataaagtc tgcccacact aatgatgtaa aacaattaac agaagcagtg 3241 caaaagatag cccaagaaag catagtaata tggggaaaaa ctcctaaatt tagactaccc 3301 atacaaaaag aaacatggga ggcatggtgg acagaatatt ggcaagccac ctggatccct 3361 gaatgggagt ttgtcaatac tcctccccta gtaaaactat ggtaccagtt agaaacagaa 3421 cccatagtag gagcagaaac tttctatgta gatggggcag ctaatagaga aactaaaaag 3481 ggaaaagcag gatatgttac tgacagagga agacaaaagg ttgtctcctt aactgaaaca 3541 acaaatcaga agactgaatt acaagcaatc cacttagctt tacaggattc aggatcagaa 3601 gtaaacatag taacagactc acagtatgca ttagggatta ttcaagcaca accagataaa 3661 agtgaatcag agattgttaa tcaaataata gagcaattaa tacagaagga caaggtctac 3721 ctgtcatggg taccagcaca caaagggatt ggaggaaatg aacaagtaga taaattagtc 3781 agcagtggaa tcagaaaggt actattttta gatgggatag ataaggctca agaagaacat 3841 gaaaaatatc acagcaattg gagagcaatg gctagtgact ttaatctacc acctatagta 3901 gcgaaggaaa tagtagccag ctgtgataaa tgtcaactaa aaggggaagc catgcatgga 3961 caagtagact gtagtccagg gatatggcaa ttagattgca cacatctaga aggaaaaata 4021 atcatagtag cagtccatgt agccagtgga tatatagaag cagaagttat cccagcagaa 4081 acaggacagg agacagcata ctttatacta aaattagcag gaagatggcc agtaaaagta 4141 gtacacacag acaatggcag caatttcacc agtgctgcag ttaaagcagc ctgttggtgg 4201 gcaaatatca aacaggaatt tggaattccc tacaaccccc aaagtcaagg agtagtggaa 4261 tctatgaata aggaattaaa gaaaatcata gggcaggtaa gagagcaagc tgaacacctt 4321 aagacagcag tacaaatggc agtgttcatt cacaatttta aaagaaaagg ggggattggg 4381 gggtacagtg caggggaaag aataatagac atgatagcaa cagacataca aactaaagaa 4441 ttacaaaaac aaattacaaa aattcaaaat tttcgggttt attacaggga caacagagac 4501 ccaatttgga aaggaccagc aaaactactc tggaaaggtg aaggggcagt agtaatacag 4561 gacaatagtg atataaaggt agtaccaaga agaaaagcaa aaatcattag ggattatgga 4621 aaacagatgg caggtgatga ttgtgtggca ggtggacagg atgaggatta gaacatggca 4681 cagtttagta aaacatcata tgtatgtctc aaagaaagct aaaaattggt tttatagaca 4741 tcactatgaa agcaggcatc caaaagtaag ttcagaagta cacatcccac taggggatgc 4801 tagattagta gtaagaacat attggggtct gcaaacagga gaaaaagact ggcacttggg 4861 tcatggggtc tccatagaat ggaggcagaa aagatatagc acacaactag atcctgacct 4921 agcagaccaa ctgattcatc tgtactattt tgattgtttt tcagaatctg ccataagaca 4981 agccatatta ggacatatag ttagtcctag gtgtgattat caagcaggac ataacaaggt 5041 aggatcttta cagtatttgg cactaacagc attaatagca ccaaaaaaga caaggccacc 5101 tttgcctagt gttaggaagc taacagaaga tagatggaac aagccccagc agaccaaggg 5161 ccacagaggg agccacacaa tgaatggaca ttagaacttt tagaggagct taagcaagaa 5221 gctgtcagac actttcctag gatatggctc catagtttag gacaacatat ctatgaaact 5281 tatggggata cctgggaagg agttgaagct ataataagaa gtctgcaaca actgctgttt 5341 attcatttca gaattgggtg tcaacatagc agaataggca ttactcgaca gagaagagca 5401 agaaatggat ccagtagatc ctaacttaga gccctggaac catccaggga gtcagcctag 5461 gacgccttgt aataagtgtt attgtaaaaa gtgctgctat cattgccaaa tgtgcttcat 5521 aacgaaaggc ttaggcatct cctatggcag gaagaagcgg agacagcgac gaagacctcc 5581 tcagggcaat caggctcatc aagatcctct accagagcag taagtagtat atgtaataca 5641 acctttagtg atattagcaa tagtagcatt agtagtaacg ctaataatag caatagttgt 5701 gtggaccata gtatttatag aaattaggaa aataagaaga caaaggaaaa tagacaggtt 5761 gattgataga ataagagaaa gagcagaaga tagtggcaat gagagtgagg gagatacaga 5821 ggaattatca aaactggtgg agatggggca tgatgctcct tgggatgttg atgacctgta 5881 gtattgcaga agatttgtgg gttacagttt attatggggt acctgtgtgg aaagaagcaa 5941 ccactactct attttgtgca tcagatgcta aatcatatga aacagaagta cataacatct 6001 gggctacaca tgcctgtgta cccacggacc ccaacccaca agaaatagaa ctggaaaatg 6061 tcacagaagg gtttaacatg tggaaaaata acatggtgga gcagatgcat gaggatataa 6121 tcagtttatg ggatcaaagc ctaaaaccat gtgtaaagct aaccccactc tgtgtcactt 6181 taaactgcac taatgtgaat gggactgctg tgaatgggac taatgctggg agtaatagga 6241 ctaatgcaga attgaaaatg gaaattggag aagtgaaaaa ctgctctttc aatataaccc 6301 cagtaggaag tgataaaagg caagaatatg caacttttta taaccttgat ctagtacaaa 6361 tagatgatag tgataatagt agttataggc taataaattg taatacctca gtaattacac 6421 aggcttgtcc aaaggtaacc tttgatccaa ttcccataca ttattgtgcc ccagctggtt 6481 ttgcaattct aaagtgtaat gataagaagt tcaatggaac ggaaatatgt aaaaatgtca 6541 gtacagtaca atgtacacat ggaattaagc cagtggtgtc aactcaactg ctgttaaatg 6601 gcagtctagc agaagaagag ataatgatta gatctgaaaa tctcacagac aatactaaaa 6661 acataatagt acagcttaat gaaactgtaa caattaattg tacaaggcct ggaaacaata 6721 caagaagagg gatacatttc ggcccagggc aagcactcta tacaacaggg atagtaggag 6781 atataagaag agcatattgt actattaatg aaacagaatg ggataaaact ttacaacagg 6841 tagctgtaaa actaggaagc cttcttaaca aaacaaaaat aatttttaat tcatcctcag 6901 gaggggaccc agaaattaca acacacagtt ttaattgtag aggggaattt ttctactgta 6961 atacatcaaa actgtttaat agtacatggc agaataatgg tgcaagacta agtaatagca 7021 cagagtcaac tggtagtatc acactcccat gcagaataaa acaaattata aatatgtggc 7081 agaaaacagg aaaagctatg tatgcccctc ccatcgcagg agtcatcaac tgtttatcaa 7141 atattacagg gctgatatta acaagagatg gtggaaatag tagtgacaat agtgacaatg 7201 agaccttaag acctggagga ggagatatga gggacaattg gataagtgaa ttatataaat 7261 ataaagtagt aagaattgaa cccctaggag tagcacccac caaggcaaag agaagagtgg 7321 tggaaagaga aaaaagagca ataggactag gagccatgtt ccttgggttc ttgggagcag 7381 caggaagcac gatgggcgca gcgtcactaa cgctgacggt acaggccaga cagttactgt 7441 ctggtatagt gcaacagcaa aacaatttgc tgagggctat agaggcgcaa cagcatctgt 7501 tgcaactcac ggtctggggc attaaacagc tccaggcaag agtcctggct gtggaaagat 7561 acctacagga tcaacggctc ctaggaatgt ggggttgctc tggaaaacac atttgcacca 7621 catttgtgcc ttggaactct agttggagta atagatctct agatgacatt tggaataata 7681 tgacctggat gcagtgggaa aaagaaatta gcaattacac aggcataata tacaacttaa 7741 ttgaagaatc gcaaatccag caagaaaaga atgaaaagga attattggaa ttggacaagt 7801 gggcaagttt gtggaattgg tttagcatat caaaatggct gtggtatata agaatattca 7861 taatagtagt aggaggctta ataggtttaa gaataatttt tgctgtgctt tctttagtaa 7921 atagagttag gcagggatac tcacctctgt cgttgcagac cctcctccca acaccgaggg 7981 gaccacccga caggcccgaa ggaatagaag aagaaggtgg agagcaaggc agaggcagat 8041 caattcgatt ggtgaacgga ttctcagcac ttatctggga cgacctgagg aacctgtgcc 8101 tcttcagtta ccaccgcttg agagacttac tcttaattgc aacgaggatt gtggaacttc 8161 tgggacgcag ggggtgggaa gccctcaaat atctgtggaa tctcctgcaa tattggggtc 8221 aggaactgaa gaatagtgct attagcttgc ttaataccac agcaatagca gtagctgaat 8281 gcacagatag ggttatagaa ataggacaaa gatttggtag agctattctc cacataccta 8341 gaagaattag acagggcttc gaaagggctt tgctataaca tgggtggcaa gtggtcaaaa 8401 agtagcatag taggatggcc taagattagg gaaagaataa gacgaactcc cccaacagaa 8461 acaggagtag gagcagtatc tcaagatgca gtatctcaag atttagataa atgtggagca 8521 gccgcaagca gcagtccagc agctaataat gctagttgtg aaccaccaga agaagaggag 8581 gaggtaggct ttccagtccg tcctcaggta cctttaagac caatgactta taaaggagct 8641 tttgatctca gccacttttt aaaagaaaag gggggactgg atgggttagt ttggtcccca 8701 aaaagacaag aaatccttga tctgtgggtc taccacacac aaggctactt ccctgattgg 8761 cagaattaca caccagggcc agggattaga ttcccactga ccttcggatg gtgctttaag 8821 ttagtaccaa tgagtccaga ggaagtagag gaggccaatg aaggagagaa caactgtctg 8881 ttacacccta ttagccaaca tggaatggag gacgcagaaa gagaagtgct aaaatggaag 8941 tttgacagca gcctagcact aagacacaga gccagagaac aacatccgga gtactacaaa 9001 gactgctgac acagaagttg ctgacagggg actttccgct ggggactttc caggggaggc 9061 gtaacttggg cgggaccggg gagtggctaa ccctcagatg ctgcatataa gcagctgctt 9121 ttcgcctgta ctgggtctct cttgttagac caggtcgagc ccgggagctc tctggctagc 9181 aaggaaccca ctgcttaagc ctcaataaag cttgccttga gtgcctcaa //