LOCUS       reference_p3            9047 bp    DNA              UNK 23-SEP-2015
DEFINITION  reference for patient p3, genomewide
ACCESSION   reference_p3
VERSION     reference_p3
KEYWORDS    .
SOURCE      
  ORGANISM  HIV-1
            .
FEATURES             Location/Qualifiers
     fragment        1..1798
                     /note="F1"
     fragment        1470..3343
                     /note="F2"
     fragment        3133..4660
                     /note="F3"
     fragment        4398..6041
                     /note="F4"
     fragment        5458..7444
                     /note="F5"
     fragment        7237..9047
                     /note="F6"
     RNA_structure   7198..7431
                     /note="RRE"
     RNA_structure   1..87
                     /note="LTR5'"
     RNA_structure   8527..9047
                     /note="LTR3'"
     gene            5536..5781
                     /note="vpu"
     gene            join(5305..5519,7808..7898)
                     /note="tat"
     gene            1539..4571
                     /note="pol"
     gene            4516..5094
                     /note="vif"
     gene            5699..8224
                     /note="env"
     gene            5034..5324
                     /note="vpr"
     gene            244..1767
                     /note="gag"
     gene            8226..8858
                     /note="nef"
     gene            join(5444..5519,7808..8082)
                     /note="rev"
     other           5699..5785
                     /note="env peptide"
     other           6125..6256
                     /note="V2"
     other           150..233
                     /note="psi"
     other           6815..6910
                     /note="V4"
     other           7031..7063
                     /note="V5"
     other           6086..6124
                     /note="V1"
     other           6428..6787
                     /note="V3"
     protein         244..639
                     /note="p17"
     protein         640..1332
                     /note="p24"
     protein         1333..1374
                     /note="p2"
     protein         1375..1539
                     /note="p7"
     protein         1540..1587
                     /note="p1"
     protein         1588..1767
                     /note="p6"
     protein         1728..2024
                     /note="PR"
     protein         2025..3344
                     /note="RT"
     protein         3345..3704
                     /note="p15"
     protein         3705..4571
                     /note="IN"
     protein         5786..7186
                     /note="gp120"
     protein         7187..8224
                     /note="gp41"
     other           6074..6268
                     /note="V1V2ext"
     other           6803..6922
                     /note="V4ext"
     other           7013..7078
                     /note="V5ext"
ORIGIN
        1 ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagacctt
       61 ttagtcagtg tggaaaaatc tctagcagtg gcgcccgaac agggacctga aagcgaaaga
      121 gaaaccagag gaaatctctc gacgcaggac tcggcttgct gaagcgcgca cggcaagagg
      181 cgaggggcgg cgactggtga gtacgccaac aatttttgac tagcggaggc tagaaggaga
      241 gagatgggtg cgagagcgtc agtattaagc gggggacaat tggatagatg ggaaagaatt
      301 cggttaaggc cagggggaaa gaaaaaatat cgattaaaac atatagtatg ggcaagcagg
      361 gagctagaac gattcgcagt taaccctggc ctgttagaaa catcagaagg ctgtagacaa
      421 atattggaac agctacaacc agcccttaag acaggatcag aagaacttaa gtcagtattt
      481 aatacagtag caaccctcta ttgtgtgcat caaaggatag aggtaaagga caccaaggaa
      541 gctttagata agatagagga agagcaaaac agaagtaaga aaaaagcaca gcaagcagca
      601 gctgacacag gaaacagcag tcaggtcagc caaaattacc cgatagtgca aaacctgcag
      661 gggcagatgg tacatcagcc catatcacct agaactttaa atgcatgggt gaaagtaata
      721 gaagaaaagg cttttagccc agaagtaata cccatgtttt cagcattatc agaaggagcc
      781 accccacaag atttaaacac catgctaaac acagtggggg gacatcaagc agctatgcaa
      841 atgttaaaag agaccatcaa tgaggaagct gcagaatggg atagggtgca tccagtgcag
      901 gcagggccta ttgcaccagg ccagataaga gaaccaaggg gaagtgacat agcaggaact
      961 actagtaacc ttcaggaaca aatagcatgg atgacaaata atccacctat cccagtagga
     1021 gaaatctata aaagatggat aatcttggga ttaaacaaaa tagtaaggat gtatagccct
     1081 atcagcattc tggacataag acaaggacca aaggaaccct ttagagacta tgtagaccgg
     1141 ttctataaaa ctctaagagc cgagcaagcc tcacaggaag taaaaaattg gatgacagaa
     1201 accttgctgg tccaaaatgc aaacccagat tgtaagacta ttttaaaagc attgggacca
     1261 gcagctacac tagaagaaat gatgacagca tgtcagggag taggagggcc aggccataaa
     1321 gcaagagttt tggcagaagc catgagccaa gtaacaaatt cagctaccat aatgatgcag
     1381 agaggcaact ttaaaaacca aagaaagact gttaagtgtt tcaattgtgg caaagaagga
     1441 cacatagcca gaaactgcag ggcccctagg aaaaggggct gttggaaatg tggaaaggaa
     1501 ggacaccaaa tgaaagattg tactgagaga caggctaatt ttttagggaa gctctggcct
     1561 tcccacaagg gaaggccagg gaattttctt cagagcagac cagagccaac agccccacca
     1621 gaagagagct tcaggtttgg ggaagagata acaactcccc ctcagaagca ggagcctccc
     1681 cctcagaagc aggagccgaa agacaaagaa ctgtatcctt taacttccct cagatcactc
     1741 tttggcaacg acccctcgtc acaataaagg tagggggaca actaaaggaa gctctattag
     1801 atacaggagc agatgataca gtattagaag aaatgaattt gccaggaaga tggaaaccaa
     1861 aaatgatagg gggaattgga ggttttatca aagtaagaca gtatgataat atactcatag
     1921 aaatctgtgg acataaagct ataggtacag tattagtagg acctacacct gtcaacataa
     1981 ttggaaggaa tctgttgact cagcttggtt gcactttaaa ttttcccatc agtcctattg
     2041 aaactgtacc agtaaaatta aagccgggaa tggatggccc aaaagttaaa caatggccat
     2101 tgacagaaga aaaaataaaa gcattagtag aaatttgtac agaaatggaa aaggaaggga
     2161 aaatctcaaa aattgggcct gaaaatccat acaatactcc agtatttgct ataaagaaaa
     2221 aagacagtac taaatggaga aaattagtag atttcaggga acttaataag agaacccaag
     2281 acttctggga agtgcaatta ggaataccac atcccgcagg gttaaaaaag aaaaaatcag
     2341 tgacagtact ggatgtgggt gatgcatatt tctcagttcc cttagataaa gactttagga
     2401 agtatactgc atttaccata cctagtataa acaatgagac accaggaatt agatatcaat
     2461 acaatgtgct cccacaggga tggaaaggat caccagcaat attccaaagt agcatgacaa
     2521 aaattttaga gccttttaga aaacaaaatc cagacatagt tatctatcaa tatatggatg
     2581 atttgtatgt aggatctgac ttagaaatag gacagcatag aacaaaaata gaagaactga
     2641 gacaacatct gttgaggtgg ggatttacca caccagacaa aaaacatcag aaagaacctc
     2701 cattcctctg gatgggttat gaactccatc ctgataaatg gacagtacag cctatagtgc
     2761 tgccagcaaa agacagctgg actgtcaatg acatacagaa gttagtggga aaattgaatt
     2821 gggcaagtca gatttatgct gggatcaaag taaagcaatt atgtaaactc cttaggggaa
     2881 ccaaagcact aacagaagta ataccattaa cagaagaagc agagctagag ctagcagaga
     2941 acagggaaat tctaaaagaa ccggtgcatg gggtatatta tgacccatca aaagacttaa
     3001 tagcagaact acagaagcag gggcaaggac aatggacata tcaaatttat caggagccat
     3061 ttaaaaatct gaaaacagga aaatatgcaa aaatgagggg tgcccacact aatgatgtaa
     3121 aacaattaac agaggcagtg caaaaaatag ccacagaaag catagttata tggggaaaga
     3181 ctcctaagtt taaactaccc atacaaaaag aaacatggga aacatggtgg acagagtatt
     3241 ggcaagccac ctggattcct gaatgggagt ttgtcaatac ccctccttta gtgaaattat
     3301 ggtaccagtt agaaaaagaa cccatagtag gagcagaaac tttctatgta gatggggcag
     3361 ctaacaggga gactaaatta ggaaaagcag gatatgttac tgacaaagga agacaaaagg
     3421 ttgtctccat aactgacaca acaaatcaga agactgagtt acaagcaatt catctagctt
     3481 tgcaggactc gggatcagaa gtaaatatag taacagactc acaatatgca ttaggaatca
     3541 ttcaagcaca accagataaa agtgaatcag agttagtcag tcaaataata gaggagttaa
     3601 taaaaaagga aaaagtctac ctggcatggg taccagcaca caagggaatt ggaggaaatg
     3661 aacaagtaga taaattagtc agtgctggaa tcaggaaagt actattttta gatggaatag
     3721 ataaggccca agaagaacat gagaaatatc acagtaattg gagagcaatg gctagtgatt
     3781 ttaacctgcc acctatagta gcaaaagaaa tagtagccag ctgtgataaa tgccaactaa
     3841 aaggggaagc catgcatgga caagtagatt gtagtccagg gatatggcaa ctagattgta
     3901 cacatttaga aggaaaaatt atcctggtag cagttcatgt agccagtgga tacatagaag
     3961 cagaagttat tccagcagag acagggcagg aaaccgcata ctttctctta aaattagcag
     4021 gaagatggcc agtaaaaaca atacatacag acaatggcag caatttcacc agtactgtgg
     4081 ttaaagccgc ctgttggtgg gcggggatca agcaggaatt tggtattccc tacaatcccc
     4141 aaagtcaagg agtagtagaa tctatgaata aagaattaaa gaaaattata ggccaggtaa
     4201 gagatcaggc tgaacatctt aagacagcag tacaaatggc agtattcatc cacaatttta
     4261 aaagaaaagg ggggattggg gggtacagtg caggggaaag aatagtagac ataatagcaa
     4321 cagacataca aactaaagaa ttacaaaaac aaattacaaa aattcaaaat tttcgggttt
     4381 attacaggga caacagagat cctctttgga aaggaccagc aaagcttctc tggaaaggtg
     4441 aaggggcagt agtaatacaa gataatagtg acataaaagt agtgccaaga agaaaagtaa
     4501 agatcattag ggattatgga aaacagatgg caggtgatga ttgtgtggca agtagacagg
     4561 atgaggatta gaacatggaa aagtttagta aaataccata tgcatgtttc caaaaaagct
     4621 aagggatggt tttatagaca tcactatgaa agcactcatc caaaaataag ttcagaggta
     4681 cacgtcccgc taggggacgc tagattggta ataacaacat attggggtct gcacacagga
     4741 gaaagggact ggcatctggg tcagggagtc tccatagaat ggaggaaaag gagatacagc
     4801 acacaagtag accctgacct agcagaccaa ctaatccatc tgtattactt tgattgtttt
     4861 tcagagtctg ccataagaca tgccatatta ggacatatag ttagacctta ttgtgaatat
     4921 caagcaggac ataacaaggt aggatctcta cagtacttgg cactaacagc gttaatcaca
     4981 ccaaagaaga taaagccacc tttgcctagt gttaagaaat tgacagagga tagatggaac
     5041 aagccccaga aaaccaaggg ccacagaggg agccatacaa tgaatgggca ctagaggttc
     5101 tggaggagct gaagaatgaa gctgttagac actttcctag gatatggctt catggcttag
     5161 ggcaacatat ctatgaaact tatggggata cttgggcagg agtggaagcc ataataagaa
     5221 gtctgcaaca actgctgttt attcatttca gaattgggtg tcgacatagc agaataggca
     5281 ttactccaca gaggagagca agaaatggag ccagtagatc ctagcctaga gccctggaag
     5341 catccaggaa gtcagcctaa gactgcctgt accaagtgct attgtaaaag gtgttgcttt
     5401 cattgtcaag tttgtttcat aacaaaaggc ttaggcatct actatggcag gaagaagagg
     5461 agacagcgac gaagaactcc tccagacagt cagactcatc aggtttctct atcgaagcag
     5521 taagtagtac atgtaatgca atctttacaa atagtagcaa tagtagcatt agtagtagta
     5581 ggaataatag caataattgt gtggtccata gtattcatag aatataggaa aatattaaga
     5641 caaaggaaaa tagacaggtt aattgataga atagcagaaa gagcagaaga cagtggcaat
     5701 gaaagtgaag gagatcagga agaattatca gcacttatgg agatggggca tcatgctcct
     5761 tgggatgtta atgatctgta gtcatgcaga acaattgtgg gtcacagtct attatggggt
     5821 acctgtgtgg aaagaagcaa ccaccactct attttgtgca tcagatgcta aagcatatca
     5881 taaagaagtt cataatgttt gggccacaca tgcctgtgta cccacagacc ccgacccaca
     5941 agaaatagaa ttggaaaatg tgacagaaaa ttttaacatg tggaaaaatg acatggtaga
     6001 acagatgcat gaggatataa tcagtctatg ggatcaaagc ctaaagccat gtgtaaaatt
     6061 aaccccactc tgtgttactt taaactgcac tgataagttg aatactacag gagaaataaa
     6121 aaactgctct ttcaatgtca ccacaaacat aagagataag gtgcaaaaag aatatgcatt
     6181 gttttatagg cttgatgtag taccaataga tgatgataat aataaaacta ataccagcta
     6241 taggttgata agttgtaaca cctcagtcat tacacaggcc tgtccaaaag tatcctttga
     6301 gccaattccc atacattatt gtgccccggc tggttttgcg attctaaagt gtaaagataa
     6361 gaagttcaat ggaaaaggac catgtacaaa ggtcagcaca gtacaatgta cacatggaat
     6421 taagccagta gtatcaactc aactgctgtt aaatggcagt ctagcagaag aagaggtggt
     6481 cattagatct gaaaatttca caaacaatgc taaaaccata atagtacagc tgaatgaaac
     6541 tgtagaaatt aattgtacaa gacccaataa caatacaaga aagggtatac atataggacc
     6601 agggagagca ttttatgcaa caggagaaat aataggagat ataagacaag cacattgtaa
     6661 cattagtaaa gcaaaatgga ataacacttt agaaaagata gttgaaaaac taagagaaca
     6721 atttgaaaat aaaacaatat cctttaggcc accctcagga ggggacctag aaattgtaac
     6781 acacagtttt aattgtggag gggaattctt ctattgtaat tcaacaccac tgtttaatag
     6841 tacttggaat gttactagta atggcactag ggagacagat acaggaaata acccaatcac
     6901 actccaatgc agaataaaac aaattataaa catgtggcag gaagtgggaa aagcaatgta
     6961 tgcccctccc atccaaggac aaattagatg ctcatcaaat attacagggc tgttattaac
     7021 aagagatggt ggtacagaga acgggactga gatcttcaga cctggaggag gggatatgag
     7081 agacaattgg agaagtgaat tatataaata taaagtagta aaaattgaac cattaggagt
     7141 agcacccacc aaggcaaaga gaagagtggt gcagagagaa aaaagagcag tgggaatagg
     7201 agctgtgttc cttgggttct tgggagcagc aggaagcact atgggcgcag cgtcaatgac
     7261 gctgacggta caggccagac tattattgtc tggtatagtg caacagcaga acaatttgct
     7321 gagggctatt gaggcgcaac agcatctgtt gcaactcaca gtctggggca ttaagcagct
     7381 ccaggcaaga gtcctggctg tggaaagata cctaaaggat caacagctca tggggatttg
     7441 gggatgctct ggaaaactca tctgcaccac taatgtgcct tggaatacta gttggagtaa
     7501 taaatctctg aatgtaattt gggataatat gacctggatg gattgggata gagaaattag
     7561 caattacaca agcttaatat ataccttact tgaagaatcg caaaaccaac aagaaaagaa
     7621 tgaacaagaa ttattggaat tggataagtg ggcaagtttg tggaattggt ttgacataac
     7681 aaattggctg tggtatataa agatattcat aatgatagta ggaggcttgg taggtttaag
     7741 aatagttttt actgtacttt ctatagtgaa tagagttagg cagggatatt caccattatc
     7801 gttccagacc cgcctcccag cctcgagggg acccgacagg cccgaaggaa tcgaagaaga
     7861 cggtggagag agagacagag acagatccag gcaattagtg gatggattct tagcaatttt
     7921 ctgggtcgat ctacggagcc tgtgcctctt cctctaccac cgcttgagag acttactctt
     7981 gattgtagcg aggattgtgg aacttctggg acgcaggggg tgggaagccc tcaaatactg
     8041 gtggaatctc ctacagtatt ggagtcagga actgaggaat agtgctgtta gcttgtttaa
     8101 tgccacggcc atagcagtag ctgaggggac agatagggtt atagaagtag tgcaaagagc
     8161 tggtagagct attctccaca tacctagaag aataagacag ggcgcggaaa gaattttaca
     8221 ataagatggg tggcaagtgg tcaaaacgta gtatgagtgg atggtctact gtaagggaaa
     8281 gaatgagacg agctgaacca acagctgagc cagcagcaga tggggtggga gcagtatctc
     8341 gagacctgga aaaacatgga gcaatcacaa gtggcaatac agcagctagc aatgaggatt
     8401 gtgcctggct agaagcacaa gaggacgagg aggtgggttt tccagtcaga cctcaggtac
     8461 ctttaagacc aatgacttat caggcagcta gagatcttag ccacttttta aaagaaaagg
     8521 ggggactgga agggctaatt tactcccaaa gaagacaaga tatccttgat ctgtggatct
     8581 accacacaca aggctacttc cctgattggc agaactacac accagggcca gggaccagat
     8641 atccaataac ctttggatgg tgcttcaagc tagtaccagt tgagcaagag aagatagaag
     8701 aggccaataa aggggagaat aatagcctgc tacaccctat gagccagcat gggatggatg
     8761 acccggagag agaagtgtta gagtggaggt ttgacagccg cctagcattt catcacatgg
     8821 cccgagagct gcatccagag tactaccaga actgctgata caagaactgc tgacatcgag
     8881 ttttctacaa gggactttcc gctggggact ttccagggag gtgtggccgg ggcgggacgg
     8941 gggagtggcg agccctcaga tgctgcatat aagcagctgc tttttgcctg tactgggtct
     9001 ctctggttag accagatctg agcctgggag ctctctggct aactagg
//
