LOCUS       Exported                7682 bp ds-DNA     circular SYN 04-FEB-2014
DEFINITION  synthetic circular DNA
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7682)
  AUTHORS   UNKNOWN
  TITLE     Direct Submission
  JOURNAL   Exported Monday, Apr 22, 2019 from SnapGene Viewer 4.3.6
            https://www.snapgene.com
COMMENT     cloned by Tyler Longmire by taking EF1aL-GFP cutting notI/BamH1 and 
            cloning in CMV-CGA-Luciferase from G Murphy248|CGA-luciferase insert
            cut NotI/BamH1 for cloning into the lenti BB.248|sequenced perfect. 
            note : luciferase is preceded by a 5 codon leader 
            sequence,248|detailed in Murphy G, Mulligan RC, Nature Medicine 
            2006..248|5/16/07 clone 4 sequencing perfect including junctions and
            entire insert.248|248|248|248|
FEATURES             Location/Qualifiers
     source          1..7682
                     /organism="synthetic DNA construct"
                     /mol_type="other DNA"
     LTR             1..636
                     /gene="LTR"
                     /label=5' LTR
                     /note="Long Terminal Repeat"
     misc_feature    1..454
                     /label=HIV U3
                     /note="Full Length HIV U3"
     primer_bind     complement(158..179)
                     /label=pHAGE-A0050-8050
     primer_bind     401..421
                     /label=pHAGE-S501-1000
     misc_feature    455..551
                     /label=HIV R
                     /note="HIV Repeat Region"
     polyA_site      550
                     /label=pA Site
                     /note="Exact base to which Poly-A is added"
     5'UTR           551..635
                     /note="HIV 5' UTR"
     misc_feature    552..636
                     /label=HIV U5
                     /note="HIV U5"
     polyA_signal    570..577
                     /label=G-T cluster
                     /note="GT Cluster shown to be necessary for Poly-A site 
                     activity by Cullen in J Virol. 1989 January; 63(1):421-424"
     misc_feature    636..658
                     /label=PBS-K
                     /note="tRNA binding site for Lysine tRNA"
     misc_feature    637..1155
                     /gene="psi"
                     /label=PSI
                     /note="PSI Packaging Sequence"
     primer_bind     complement(667..690)
                     /label=pHAGE-A0550-0050
     misc_feature    697..806
                     /label=HIV-PSI
     stem_loop       697..731
                     /label=SL-1
                     /note="PSI Stem loop 1"
     stem_loop       736..754
                     /label=SL-2
                     /note="PSI Stem loop 2"
     misc_feature    744..745
                     /label=5' SD 289
                     /note="Major 5' Splice Donor 289"
     stem_loop       766..779
                     /label=SL-3
                     /note="PSI Stem Loop 3"
     CDS             790..1144
                     /label=HIV gag
                     /note="HIV gag sequence from 336bp to 688bp (Clone to PvuII
                     site in HIV and filled in ClaI digest to take gag CDS out 
                     of frame)"
     stem_loop       793..806
                     /label=SL-4
                     /note="PSI Stem Loop 4"
     misc_feature    807..1144
                     /label=HR-ePSI
                     /note="HIV gag sequence 351bp to 688bp"
     misc_feature    833..834
                     /label=Fill-in
                     /note="Filled in Cla Site from original HIV genome to 
                     disrupt gag polyprotein ORF"
     misc_feature    853..855
                     /label=Stop Codon
                     /note="Stop codon in gag put in frame by ClaI fill in"
     primer_bind     898..919
                     /label=pHAGE-S1001-1500
     CDS             1156..2013
                     /label=env
                     /note="HIV env sequence from bp7168 to 8025 (contains RRE) 
                     Cloned from BglII to BamHI out of HIV"
     primer_bind     complement(1166..1189)
                     /label=pHAGE-A1050-0550
     misc_feature    1245..1593
                     /label=RRE
                     /note="Rev Responsive Element according to Belasco in 
                     Molecular Cell, Vol. 7, 603-614, March, 2001"
     misc_feature    1303..1536
                     /gene="rre"
                     /label=RRE
                     /note="Rev Responsive Element"
     misc_feature    1357
                     /label=RRE Mutation
                     /note="This G is a C in the WT HIV-1 genome"
     primer_bind     1391..1417
                     /label=pHAGE-S1501-2000
     primer_bind     complement(1650..1678)
                     /label=pHAGE-A1550-1050
     primer_bind     1898..1922
                     /label=pHAGE-S2001-2500
     misc_feature    1911..1912
                     /label=SA 7925
     misc_feature    2014..2027
                     /label=Junk
                     /note="Linker Junk Sequence probably left over from 
                     cloning"
     misc_feature    2034..2211
                     /gene="cppt"
                     /label=HIV cpPu (Trip)
                     /note="Central Poly Purine Track"
     primer_bind     complement(2084..2112)
                     /label=pHAGE-A2050-1550
     misc_feature    2188..2189
                     /label=SA 4459
     misc_feature    2218..3402
                     /label=Human EF1a Promoter
                     /note="Human Elongation Factor 1 alpha promoter"
     intron          2454..3045
                     /note="Human EF1a Intron"
     misc_feature    2531
                     /label=EF1a Mutation
                     /note="Missing GCCC according to Genbank and Celera 
                     sequences"
     misc_feature    3412..4116
                     /label=mcherry
     misc_feature    4123..4714
                     /gene="WPRE"
                     /label=WPRE
                     /note="Woodchuck Hepatitis Virus Posttranscriptional 
                     Regulatory Element"
     primer_bind     complement(4151..4185)
                     /label=pHAGE 3' CDS
     primer_bind     complement(4229..4252)
                     /label=pHAGE-A3550-3050
     primer_bind     4382..4402
                     /label=pHAGE-S4001-4500
     LTR             4719..5040
                     /label=3' LTR
     misc_feature    4719..4820
                     /label=HIV nef
                     /note="HIV nef"
     misc_feature    4769..4783
                     /label=HIV PPT
                     /note="PolyPurine Tract"
     misc_feature    4786..4822
                     /label=dU3
                     /note="1st Half of deleted U3"
     misc_feature    4842..4860
                     /label=dU3
                     /note="2nd Half of deleted U3"
     misc_feature    4861..4957
                     /label=HIV R
     misc_feature    4958..5040
                     /label=HIV U5
                     /note="HIV U5"
     primer_bind     5072..5094
                     /label=pHAGE-S6001-6500
     promoter        5243..5277
                     /label=P-Bla
                     /note="Beta Lactamase Promoter"
     CDS             5296..6135
                     /gene="AMPr"
                     /label=AMPr
                     /note="Ampicillin Resistance Gene"
     primer_bind     complement(5345..5368)
                     /label=pHAGE-A6050-5550
     primer_bind     5545..5569
                     /label=pHAGE-S6501-7000
     primer_bind     complement(5814..5837)
                     /label=pHAGE-A6550-6050
     primer_bind     6065..6089
                     /label=pHAGE-S7001-7500
     primer_bind     complement(6325..6346)
                     /label=pHAGE-A7050-6550
     rep_origin      6364..6897
                     /gene="ORI"
                     /label=ORI
                     /note="Bacterial Origin of Replication"
     primer_bind     6569..6593
                     /label=pHAGE-S7501-8000
     primer_bind     complement(6836..6857)
                     /label=pHAGE-A7550-7050
     primer_bind     7072..7091
                     /label=pHAGE-S8001-8500
     misc_feature    7134..7257
                     /gene="SV40 ori"
                     /label=SV40 ori
     primer_bind     complement(7312..7338)
                     /label=pHAGE-A8050-7550
     primer_bind     7577..7605
                     /label=pHAGE-S1-500
ORIGIN
        1 tggaagggct aattcactcc caaagaagac aagatatcct tgatctgtgg atctaccaca
       61 cacaaggcta cttccctgat tagcagaact acacaccagg gccaggggtc agatatccac
      121 tgacctttgg atggtgctac aagctagtac cagttgagcc agataaggta gaagaggcca
      181 ataaaggaga gaacaccagc ttgttacacc ctgtgagcct gcatgggatg gatgacccgg
      241 agagagaagt gttagagtgg aggtttgaca gccgcctagc atttcatcac gtggcccgag
      301 agctgcatcc ggagtacttc aagaactgct gatatcgagc ttgctacaag ggactttccg
      361 ctggggactt tccagggagg cgtggcctgg gcgggactgg ggagtggcga gccctcagat
      421 cctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga
      481 gcctgggagc tctctggcta actagggaac ccactgctta agcctcaata aagcttgcct
      541 tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta gagatccctc
      601 agaccctttt agtcagtgtg gaaaatctct agcagtggcg cccgaacagg gacttgaaag
      661 cgaaagggaa accagaggag ctctctcgac gcaggactcg gcttgctgaa gcgcgcacgg
      721 caagaggcga ggggcggcga ctggtgagta cgccaaaaat tttgactagc ggaggctaga
      781 aggagagaga tgggtgcgag agcgtcagta ttaagcgggg gagaattaga tcgcgatggg
      841 aaaaaattcg gttaaggcca gggggaaaga aaaaatataa attaaaacat atagtatggg
      901 caagcaggga gctagaacga ttcgcagtta atcctggcct gttagaaaca tcagaaggct
      961 gtagacaaat actgggacag ctacaaccat cccttcagac aggatcagaa gaacttagat
     1021 cattatataa tacagtagca accctctatt gtgtgcatca aaggatagag ataaaagaca
     1081 ccaaggaagc tttagacaag atagaggaag agcaaaacaa aagtaagacc accgcacagc
     1141 aagcggccgg ccgctgatct tcagacctgg aggaggagat atgagggaca attggagaag
     1201 tgaattatat aaatataaag tagtaaaaat tgaaccatta ggagtagcac ccaccaaggc
     1261 aaagagaaga gtggtgcaga gagaaaaaag agcagtggga ataggagctt tgttccttgg
     1321 gttcttggga gcagcaggaa gcactatggg cgcagcgtca atgacgctga cggtacaggc
     1381 cagacaatta ttgtctggta tagtgcagca gcagaacaat ttgctgaggg ctattgaggc
     1441 gcaacagcat ctgttgcaac tcacagtctg gggcatcaag cagctccagg caagaatcct
     1501 ggctgtggaa agatacctaa aggatcaaca gctcctgggg atttggggtt gctctggaaa
     1561 actcatttgc accactgctg tgccttggaa tgctagttgg agtaataaat ctctggaaca
     1621 gatttggaat cacacgacct ggatggagtg ggacagagaa attaacaatt acacaagctt
     1681 aatacactcc ttaattgaag aatcgcaaaa ccagcaagaa aagaatgaac aagaattatt
     1741 ggaattagat aaatgggcaa gtttgtggaa ttggtttaac ataacaaatt ggctgtggta
     1801 tataaaatta ttcataatga tagtaggagg cttggtaggt ttaagaatag tttttgctgt
     1861 actttctata gtgaatagag ttaggcaggg atattcacca ttatcgtttc agacccacct
     1921 cccaaccccg aggggacccg acaggcccga aggaatagaa gaagaaggtg gagagagaga
     1981 cagagacaga tccattcgat tagtgaacgg atctcgacgg tatcgccgaa ttcacaaatg
     2041 gcagtattca tccacaattt taaaagaaaa ggggggattg gggggtacag tgcaggggaa
     2101 agaatagtag acataatagc aacagacata caaactaaag aattacaaaa acaaattaca
     2161 aaaattcaaa attttcgggt ttattacagg gacagcagag atccagtttg gactagtcgt
     2221 gaggctccgg tgcccgtcag tgggcagagc gcacatcgcc cacagtcccc gagaagttgg
     2281 ggggaggggt cggcaattga accggtgcct agagaaggtg gcgcggggta aactgggaaa
     2341 gtgatgtcgt gtactggctc cgcctttttc ccgagggtgg gggagaaccg tatataagtg
     2401 cagtagtcgc cgtgaacgtt ctttttcgca acgggtttgc cgccagaaca caggtaagtg
     2461 ccgtgtgtgg ttcccgcggg cctggcctct ttacgggtta tggcccttgc gtgccttgaa
     2521 ttacttccac ctggctgcag tacgtgattc ttgatcccga gcttcgggtt ggaagtgggt
     2581 gggagagttc gaggccttgc gcttaaggag ccccttcgcc tcgtgcttga gttgaggcct
     2641 ggcctgggcg ctggggccgc cgcgtgcgaa tctggtggca ccttcgcgcc tgtctcgctg
     2701 ctttcgataa gtctctagcc atttaaaatt tttgatgacc tgctgcgacg ctttttttct
     2761 ggcaagatag tcttgtaaat gcgggccaag atctgcacac tggtatttcg gtttttgggg
     2821 ccgcgggcgg cgacggggcc cgtgcgtccc agcgcacatg ttcggcgagg cggggcctgc
     2881 gagcgcggcc accgagaatc ggacgggggt agtctcaagc tggccggcct gctctggtgc
     2941 ctggcctcgc gccgccgtgt atcgccccgc cctgggcggc aaggctggcc cggtcggcac
     3001 cagttgcgtg agcggaaaga tggccgcttc ccggccctgc tgcagggagc tcaaaatgga
     3061 ggacgcggcg ctcgggagag cgggcgggtg agtcacccac acaaaggaaa agggcctttc
     3121 cgtcctcagc cgtcgcttca tgtgactcca cggagtaccg ggcgccgtcc aggcacctcg
     3181 attagttctc gagcttttgg agtacgtcgt ctttaggttg gggggagggg ttttatgcga
     3241 tggagtttcc ccacactgag tgggtggaga ctgaagttag gccagcttgg cacttgatgt
     3301 aattctcctt ggaatttgcc ctttttgagt ttggatcttg gttcattctc aagcctcaga
     3361 cagtggttca aagttttttt cttccatttc aggtgtcgtg aagcggccgc cgtgagcaag
     3421 ggcgaggagg ataacatggc catcatcaag gagttcatgc gcttcaaggt gcacatggag
     3481 ggctccgtga acggccacga gttcgagatc gagggcgagg gcgagggccg cccctacgag
     3541 ggcacccaga ccgccaagct gaaggtgacc aagggtggcc ccctgccctt cgcctgggac
     3601 atcctgtccc ctcagttcat gtacggctcc aaggcctacg tgaagcaccc cgccgacatc
     3661 cccgactact tgaagctgtc cttccccgag ggcttcaagt gggagcgcgt gatgaacttc
     3721 gaggacggcg gcgtggtgac cgtgacccag gactcctccc tgcaggacgg cgagttcatc
     3781 tacaaggtga agctgcgcgg caccaacttc ccctccgacg gccccgtaat gcagaagaag
     3841 accatgggct gggaggcctc ctccgagcgg atgtaccccg aggacggcgc cctgaagggc
     3901 gagatcaagc agaggctgaa gctgaaggac ggcggccact acgacgctga ggtcaagacc
     3961 acctacaagg ccaagaagcc cgtgcagctg cccggcgcct acaacgtcaa catcaagttg
     4021 gacatcacct cccacaacga ggactacacc atcgtggaac agtacgaacg cgccgagggc
     4081 cgccactcca ccggcggcat ggacgagctg tacaagggat cctaatcaac ctctggatta
     4141 caaaatttgt gaaagattga ctggtattct taactatgtt gctcctttta cgctatgtgg
     4201 atacgctgct ttaatgcctt tgtatcatgc tattgcttcc cgtatggctt tcattttctc
     4261 ctccttgtat aaatcctggt tgctgtctct ttatgaggag ttgtggcccg ttgtcaggca
     4321 acgtggcgtg gtgtgcactg tgtttgctga cgcaaccccc actggttggg gcattgccac
     4381 cacctgtcag ctcctttccg ggactttcgc tttccccctc cctattgcca cggcggaact
     4441 catcgccgcc tgccttgccc gctgctggac aggggctcgg ctgttgggca ctgacaattc
     4501 cgtggtgttg tcggggaaat catcgtcctt tccttggctg ctcgcctgtg ttgccacctg
     4561 gattctgcgc gggacgtcct tctgctacgt cccttcggcc ctcaatccag cggaccttcc
     4621 ttcccgcggc ctgctgccgg ctctgcggcc tcttccgcgt cttcgccttc gccctcagac
     4681 gagtcggatc tccctttggg ccgcctcccc gcctggtacc tttaagacca atgacttaca
     4741 aggcagctgt agatcttagc cactttttaa aagaaaaggg gggactggaa gggctaattc
     4801 actcccaacg aagacaagat cacctgcagg acaggcgcgc cctgcttttt gcttgtactg
     4861 ggtctctctg gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac
     4921 tgcttaagcc tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt
     4981 gtgactctgg taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca
     5041 cccgggcgat taaggaaagg gctagatcat tcttgaagac gaaagggcct cgtgatacgc
     5101 ctatttttat aggttaatgt catgataata atggtttctt agacgtcagg tggcactttt
     5161 cggggaaatg tgcgcggaac ccctatttgt ttatttttct aaatacattc aaatatgtat
     5221 ccgctcatga gacaataacc ctgataaatg cttcaataat attgaaaaag gaagagtatg
     5281 agtattcaac atttccgtgt cgcccttatt cccttttttg cggcattttg ccttcctgtt
     5341 tttgctcacc cagaaacgct ggtgaaagta aaagatgctg aagatcagtt gggtgcacga
     5401 gtgggttaca tcgaactgga tctcaacagc ggtaagatcc ttgagagttt tcgccccgaa
     5461 gaacgttttc caatgatgag cacttttaaa gttctgctat gtggcgcggt attatcccgt
     5521 gttgacgccg ggcaagagca actcggtcgc cgcatacact attctcagaa tgacttggtt
     5581 gagtactcac cagtcacaga aaagcatctt acggatggca tgacagtaag agaattatgc
     5641 agtgctgcca taaccatgag tgataacact gcggccaact tacttctgac aacgatcgga
     5701 ggaccgaagg agctaaccgc ttttttgcac aacatggggg atcatgtaac tcgccttgat
     5761 cgttgggaac cggagctgaa tgaagccata ccaaacgacg agcgtgacac cacgatgcct
     5821 gtagcaatgg caacaacgtt gcgcaaacta ttaactggcg aactacttac tctagcttcc
     5881 cggcaacaat taatagactg gatggaggcg gataaagttg caggaccact tctgcgctcg
     5941 gcccttccgg ctggctggtt tattgctgat aaatctggag ccggtgagcg tgggtctcgc
     6001 ggtatcattg cagcactggg gccagatggt aagccctccc gtatcgtagt tatctacacg
     6061 acggggagtc aggcaactat ggatgaacga aatagacaga tcgctgagat aggtgcctca
     6121 ctgattaagc attggtaact gtcagaccaa gtttactcat atatacttta gattgattta
     6181 aaacttcatt tttaatttaa aaggatctag gtgaagatcc tttttgataa tctcatgacc
     6241 aaaatccctt aacgtgagtt ttcgttccac tgagcgtcag accccgtaga aaagatcaaa
     6301 ggatcttctt gagatccttt ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca
     6361 ccgctaccag cggtggtttg tttgccggat caagagctac caactctttt tccgaaggta
     6421 actggcttca gcagagcgca gataccaaat actgttcttc tagtgtagcc gtagttaggc
     6481 caccacttca agaactctgt agcaccgcct acatacctcg ctctgctaat cctgttacca
     6541 gtggctgctg ccagtggcga taagtcgtgt cttaccgggt tggactcaag acgatagtta
     6601 ccggataagg cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag
     6661 cgaacgacct acaccgaact gagataccta cagcgtgagc tatgagaaag cgccacgctt
     6721 cccgaaggga gaaaggcgga caggtatccg gtaagcggca gggtcggaac aggagagcgc
     6781 acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac
     6841 ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac
     6901 gccagcaacg cggccttttt acggttcctg gccttttgct ggccttttgc tcacatgttc
     6961 tttcctgcgt tatcccctga ttctgtggat aaccgtatta ccgcctttga gtgagctgat
     7021 accgctcgcc gcagccgaac gaccgagcgc agcgagtcag tgagcgagga agcggaagag
     7081 cgcccaatac gcaaaccgcc tctccccgcg cgttggccga ttcattaatg cagcaagctc
     7141 atggctgact aatttttttt atttatgcag aggccgaggc cgcctcggcc tctgagctat
     7201 tccagaagta gtgaggaggc ttttttggag gcctaggctt ttgcaaaaag ctccccgtgg
     7261 cacgacaggt ttcccgactg gaaagcgggc agtgagcgca acgcaattaa tgtgagttag
     7321 ctcactcatt aggcacccca ggctttacac tttatgcttc cggctcgtat gttgtgtgga
     7381 attgtgagcg gataacaatt tcacacagga aacagctatg acatgattac gaatttcaca
     7441 aataaagcat ttttttcact gcattctagt tgtggtttgt ccaaactcat caatgtatct
     7501 tatcatgtct ggatcaactg gataactcaa gctaaccaaa atcatcccaa acttcccacc
     7561 ccatacccta ttaccactgc caattacctg tggtttcatt tactctaaac ctgtgattcc
     7621 tctgaattat tttcatttta aagaaattgt atttgttaaa tatgtactac aaacttagta
     7681 gt
//
