LOCUS       sequence-100392-        8658 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Backbone for lentiviral transduction of Massively Parallel Reporter 
            Assay (MPRA) libraries.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8658)
  TITLE     Mikkelsen Lab MPRA plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 8658)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Dec 15, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: 
            "Unpublished"
COMMENT     Sequence Label: pMPRAlenti1
FEATURES             Location/Qualifiers
     source          1..8658
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     LTR             1..634
                     /label=3' LTR
                     /note="3' long terminal repeat (LTR) from HIV-1"
     misc_feature    681..806
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1303..1536
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1721..1765
                     /codon_start=1
                     /product="antigenic peptide corresponding to amino acids 
                     655 to 669 of the HIV envelope protein gp41 (Lutje Hulsik 
                     et al., 2013)"
                     /label=gp41 peptide
                     /note="recognized by the 2H10 single-chain llama nanobody"
                     /translation="KNEQELLELDKWASL"
     misc_feature    2028..2143
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1 (lacking the first T)"
     protein_bind    2224..2348
                     /gene="mutant version of attR"
                     /label=attR1
                     /bound_moiety="LR Clonase(TM)"
                     /note="recombination site for the Gateway(R) LR reaction"
     promoter        join(2373..2378,2379..2396,2397..2403)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             2457..3116
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(2523..2542)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             3458..3763
                     /codon_start=1
                     /gene="ccdB"
                     /product="CcdB, a bacterial toxin that poisons DNA gyrase"
                     /label=ccdB
                     /note="Plasmids containing the ccdB gene cannot be 
                     propagated in standard E. coli strains."
                     /translation="MQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDK
                     VSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI"
     primer_bind     3642..3661
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     protein_bind    complement(3804..3928)
                     /gene="mutant version of attR"
                     /label=attR2
                     /bound_moiety="LR Clonase(TM)"
                     /note="recombination site for the Gateway(R) LR reaction"
     CDS             4215..4613
                     /codon_start=1
                     /gene="Aspergillus terreus BSD"
                     /product="blasticidin S deaminase"
                     /label=BSD
                     /note="confers resistance to blasticidin"
                     /translation="MAKPLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTG
                     VNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGI
                     KAIVKDSDGQPTAVGIRELLPSGYVWEG"
     misc_feature    4627..5215
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(4680..4700)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(5098..5109)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             5422..6055
                     /label=3' LTR
                     /note="3' long terminal repeat (LTR) from HIV-1"
     primer_bind     complement(6183..6199)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(6183..6199)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(6196..6218)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    6207..6223
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     promoter        complement(join(6231..6237,6238..6255,6256..6261))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6276..6297
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(6414..6431)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(6585..7173)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(6665..6684)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(7344..8135,8136..8204))
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     7967..7986
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(8205..8309)
                     /gene="bla"
                     /label=AmpR promoter
     polyA_signal    8357..8491
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(8394..8413)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     8448..8467
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
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 tatcgccttt aaaagaaaag
     2041 gggggattgg ggggtacagt gcaggggaaa gaatagtaga cataatagca acagacatac
     2101 aaactaaaga attacaaaaa caaattacaa aaattcaaaa ttttcgggtt tattacaggg
     2161 acagcagaga tccagtttat cgatggccta actggccagt gtggtggaat tctgcagata
     2221 tcaacaagtt tgtacaaaaa agctgaacga gaaacgtaaa atgatataaa tatcaatata
     2281 ttaaattaga ttttgcataa aaaacagact acataatact gtaaaacaca acatatccag
     2341 tcactatggc ggccgcatta ggcaccccag gctttacact ttatgcttcc ggctcgtata
     2401 atgtgtggat tttgagttag gatccggcga gattttcagg agctaaggaa gctaaaatgg
     2461 agaaaaaaat cactggatat accaccgttg atatatccca atggcatcgt aaagaacatt
     2521 ttgaggcatt tcagtcagtt gctcaatgta cctataacca gaccgttcag ctggatatta
     2581 cggccttttt aaagaccgta aagaaaaata agcacaagtt ttatccggcc tttattcaca
     2641 ttcttgcccg cctgatgaat gctcatccgg aattccgtat ggcaatgaaa gacggtgagc
     2701 tggtgatatg ggatagtgtt cacccttgtt acaccgtttt ccatgagcaa actgaaacgt
     2761 tttcatcgct ctggagtgaa taccacgacg atttccggca gtttctacac atatattcgc
     2821 aagatgtggc gtgttacggt gaaaacctgg cctatttccc taaagggttt attgagaata
     2881 tgtttttcgt ctcagccaat ccctgggtga gtttcaccag ttttgattta aacgtggcca
     2941 atatggacaa cttcttcgcc cccgttttca ccatgggcaa atattatacg caaggcgaca
     3001 aggtgctgat gccgctggcg attcaggttc atcatgccgt ctgtgatggc ttccatgtcg
     3061 gcagaatgct taatgaatta caacagtact gcgatgagtg gcagggcggg gcgtaaagat
     3121 ctggatccgg cttactaaaa gccagataac agtatgcgta tttgcgcgct gatttttgcg
     3181 gtataagaat atatactgat atgtataccc gaagtatgtc aaaaagaggt gtgctatgaa
     3241 gcagcgtatt acagtgacag ttgacagcga cagctatcag ttgctcaagg catatatgat
     3301 gtcaatatct ccggtctggt aagcacaacc atgcagaatg aagcccgtcg tctgcgtgcc
     3361 gaacgctgga aagcggaaaa tcaggaaggg atggctgagg tcgcccggtt tattgaaatg
     3421 aacggctctt ttgctgacga gaacagggac tggtgaaatg cagtttaagg tttacaccta
     3481 taaaagagag agccgttatc gtctgtttgt ggatgtacag agtgatatta ttgacacgcc
     3541 cgggcgacgg atggtgatcc ccctggccag tgcacgtctg ctgtcagata aagtctcccg
     3601 tgaactttac ccggtggtgc atatcgggga tgaaagctgg cgcatgatga ccaccgatat
     3661 ggccagtgtg ccggtctccg ttatcgggga agaagtggct gatctcagcc accgcgaaaa
     3721 tgacatcaaa aacgccatta acctgatgtt ctggggaata taaatgtcag gctccgttat
     3781 acacagccag tctgcaggtc gaccatagtg actggatatg ttgtgtttta cagtattatg
     3841 tagtctgttt tttatgcaaa atctaattta atatattgat atttatatca ttttacgttt
     3901 ctcgttcagc tttcttgtac aaagtggttg gcctcggcgg ccaagctagt cggggcggcc
     3961 ggccgcttcg agcagacatt aattaaaagg atctgcgatc gctccggtgc ccgtcagtgg
     4021 gcagagcgca catcgcccac agtccccgag aagttggggg gaggggtcgg caattgaacc
     4081 ggtgcctaga gaaggtggcg cggggtaaac tgggaaagtg atgtcgtgta ctggctccgc
     4141 ctttttcccg agggtggggg agaaccgtat ataagtgcag tagtcgccgt gaacgttctt
     4201 tttcgcaagt taacatggcc aagcctttgt ctcaagaaga atccaccctc attgaaagag
     4261 caacggctac aatcaacagc atccccatct ctgaagacta cagcgtcgcc agcgcagctc
     4321 tctctagcga cggccgcatc ttcactggtg tcaatgtata tcattttact gggggacctt
     4381 gtgcagaact cgtggtgctg ggcactgctg ctgctgcggc agctggcaac ctgacttgta
     4441 tcgtcgcgat cggaaatgag aacaggggca tcttgagccc ctgcggacgg tgccgacagg
     4501 tgcttctcga tctgcatcct gggatcaaag ccatagtgaa ggacagtgat ggacagccga
     4561 cggcagttgg gattcgtgaa ttgctgccct ctggttatgt gtgggagggc taaacgcgtc
     4621 tggaacaatc aacctctgga ttacaaaatt tgtgaaagat tgactggtat tcttaactat
     4681 gttgctcctt ttacgctatg tggatacgct gctttaatgc ctttgtatca tgctattgct
     4741 tcccgtatgg ctttcatttt ctcctccttg tataaatcct ggttgctgtc tctttatgag
     4801 gagttgtggc ccgttgtcag gcaacgtggc gtggtgtgca ctgtgtttgc tgacgcaacc
     4861 cccactggtt ggggcattgc caccacctgt cagctccttt ccgggacttt cgctttcccc
     4921 ctccctattg ccacggcgga actcatcgcc gcctgccttg cccgctgctg gacaggggct
     4981 cggctgttgg gcactgacaa ttccgtggtg ttgtcgggga agctgacgtc ctttccatgg
     5041 ctgctcgcct gtgttgccac ctggattctg cgcgggacgt ccttctgcta cgtcccttcg
     5101 gccctcaatc cagcggacct tccttcccgc ggcctgctgc cggctctgcg gcctcttccg
     5161 cgtcttcgcc ttcgccctca gacgagtcgg atctcccttt gggccgcctc cccgcctgga
     5221 attaattctg cagtcgagac ctagaaaaac atggagcaat cacaagtagc aatacagcag
     5281 ctaccaatgc tgattgtgcc tggctagaag cacaagagga ggaggaggtg ggttttccag
     5341 tcacacctca ggtaccttta agaccaatga cttacaaggc agctgtagat cttagccact
     5401 ttttaaaaga aaagagggga ctggaagggc taattcactc ccaacgaaga caagatatcc
     5461 ttgatctgtg gatctaccac acacaaggct acttccctga ttagcagaac tacacaccag
     5521 ggccaggggt cagatatcca ctgacctttg gatggtgcta caagctagta ccagttgagc
     5581 cagataaggt agaagaggcc aataaaggag agaacaccag cttgttacac cctgtgagcc
     5641 tgcatgggat ggatgacccg gagagagaag tgttagagtg gaggtttgac agccgcctag
     5701 catttcatca cgtggcccga gagctgcatc cggagtactt caagaactgc tgatatcgag
     5761 cttgctacaa gggactttcc gctggggact ttccagggag gcgtggcctg ggcgggactg
     5821 gggagtggcg agccctcaga tcctgcatat aagcagctgc tttttgcctg tactgggtct
     5881 ctctggttag accagatctg agcctgggag ctctctggct aactagggaa cccactgctt
     5941 aagcctcaat aaagcttgcc ttgagtgctt caagtagtgt gtgcccgtct gttgtgtgac
     6001 tctggtaact agagatccct cagacccttt tagtcagtgt ggaaaatctc tagcagtagt
     6061 agttcatgtc atcttattat tcagtattta taacttgcaa agaaatgaat atcagagagt
     6121 gagaggcctt gacattgcta gcgtttaccg tcgacctcta gctagagctt ggcgtaatca
     6181 tggtcatagc tgtttcctgt gtgaaattgt tatccgctca caattccaca caacatacga
     6241 gccggaagca taaagtgtaa agcctggggt gcctaatgag tgagctaact cacattaatt
     6301 gcgttgcgct cactgcccgc tttccagtcg ggaaacctgt cgtgccagct gcattaatga
     6361 atcggccaac gcgcggggag aggcggtttg cgtattgggc gctcttccgc ttcctcgctc
     6421 actgactcgc tgcgctcggt cgttcggctg cggcgagcgg tatcagctca ctcaaaggcg
     6481 gtaatacggt tatccacaga atcaggggat aacgcaggaa agaacatgtg agcaaaaggc
     6541 cagcaaaagg ccaggaaccg taaaaaggcc gcgttgctgg cgtttttcca taggctccgc
     6601 ccccctgacg agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga
     6661 ctataaagat accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc
     6721 ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat
     6781 agctcacgct gtaggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg
     6841 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
     6901 aacccggtaa gacacgactt atcgccactg gcagcagcca ctggtaacag gattagcaga
     6961 gcgaggtatg taggcggtgc tacagagttc ttgaagtggt ggcctaacta cggctacact
     7021 agaagaacag tatttggtat ctgcgctctg ctgaagccag ttaccttcgg aaaaagagtt
     7081 ggtagctctt gatccggcaa acaaaccacc gctggtagcg gtggtttttt tgtttgcaag
     7141 cagcagatta cgcgcagaaa aaaaggatct caagaagatc ctttgatctt ttctacgggg
     7201 tctgacgctc agtggaacga aaactcacgt taagggattt tggtcatgag attatcaaaa
     7261 aggatcttca cctagatcct tttaaattaa aaatgaagtt ttaaatcaat ctaaagtata
     7321 tatgagtaaa cttggtctga cagttaccaa tgcttaatca gtgaggcacc tatctcagcg
     7381 atctgtctat ttcgttcatc catagttgcc tgactccccg tcgtgtagat aactacgata
     7441 cgggagggct taccatctgg ccccagtgct gcaatgatac cgcgagaccc acgctcaccg
     7501 gctccagatt tatcagcaat aaaccagcca gccggaaggg ccgagcgcag aagtggtcct
     7561 gcaactttat ccgcctccat ccagtctatt aattgttgcc gggaagctag agtaagtagt
     7621 tcgccagtta atagtttgcg caacgttgtt gccattgcta caggcatcgt ggtgtcacgc
     7681 tcgtcgtttg gtatggcttc attcagctcc ggttcccaac gatcaaggcg agttacatga
     7741 tcccccatgt tgtgcaaaaa agcggttagc tccttcggtc ctccgatcgt tgtcagaagt
     7801 aagttggccg cagtgttatc actcatggtt atggcagcac tgcataattc tcttactgtc
     7861 atgccatccg taagatgctt ttctgtgact ggtgagtact caaccaagtc attctgagaa
     7921 tagtgtatgc ggcgaccgag ttgctcttgc ccggcgtcaa tacgggataa taccgcgcca
     7981 catagcagaa ctttaaaagt gctcatcatt ggaaaacgtt cttcggggcg aaaactctca
     8041 aggatcttac cgctgttgag atccagttcg atgtaaccca ctcgtgcacc caactgatct
     8101 tcagcatctt ttactttcac cagcgtttct gggtgagcaa aaacaggaag gcaaaatgcc
     8161 gcaaaaaagg gaataagggc gacacggaaa tgttgaatac tcatactctt cctttttcaa
     8221 tattattgaa gcatttatca gggttattgt ctcatgagcg gatacatatt tgaatgtatt
     8281 tagaaaaata aacaaatagg ggttccgcgc acatttcccc gaaaagtgcc acctgacgtc
     8341 gacggatcgg gagatcaact tgtttattgc agcttataat ggttacaaat aaagcaatag
     8401 catcacaaat ttcacaaata aagcattttt ttcactgcat tctagttgtg gtttgtccaa
     8461 actcatcaat gtatcttatc atgtctggat caactggata actcaagcta accaaaatca
     8521 tcccaaactt cccaccccat accctattac cactgccaat tacctgtggt ttcatttact
     8581 ctaaacctgt gattcctctg aattattttc attttaaaga aattgtattt gttaaatatg
     8641 tactacaaac ttagtagt
//
