LOCUS       sequence-336488-        3928 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Vector backbone used to clone MPRA libraries.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 3928)
  AUTHORS   White MA, Myers CA, Corbo JC, Cohen BA
  TITLE     Massively parallel in vivo enhancer assay reveals that highly local 
            features determine the cis-regulatory function of ChIP-seq peaks.
  JOURNAL   Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11952-7. doi: 
            10.1073/pnas.1307449110. Epub 2013 Jul 1.
  PUBMED    23818646
REFERENCE   2  (bases 1 to 3928)
  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"; doi: 
            "10.1073/pnas.1307449110"; journalName: "Proc Natl Acad Sci U S A"; 
            date: "2013-07-16- 16"; volume: "110"; issue: "29"; pages: "11952-7"
COMMENT     Sequence Label: pJK03_Rho_basal_DsRed
FEATURES             Location/Qualifiers
     source          1..3928
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     regulatory      164..173
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             170..847
                     /codon_start=1
                     /product="improved tetrameric variant of DsRed fluorescent 
                     protein"
                     /label=DsRed2
                     /note="mammalian codon-optimized"
                     /translation="MASSENVITEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVK
                     LKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGV
                     ATVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGETHK
                     ALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDAKLDITSHNEDYTIVEQYERTEGRHH
                     LFL"
     primer_bind     complement(350..370)
                     /label=DsRed1-N
                     /note="DsRed1, reverse primer"
     primer_bind     762..785
                     /label=DsRed1-C
                     /note="DsRed1, forward primer"
     primer_bind     complement(952..971)
                     /label=Bglob-pA-R
                     /note="Rabbit beta-globin polyA region, reverse primer"
     polyA_signal    1017..1072
                     /label=beta-globin poly(A) signal
                     /note="rabbit beta-globin polyadenylation signal (Gil and 
                     Proudfoot, 1987)"
     primer_bind     complement(1071..1090)
                     /label=rbglobpA-R
                     /note="Rabbit beta-globin polyA, reverse primer. Also 
                     called rb-glob-pA-term-R"
     primer_bind     complement(1431..1447)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1431..1447)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(1444..1466)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    1455..1471
                     /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(1479..1485,1486..1503,1504..1509))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1524..1545
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        1604..1799
                     /label=SV40 promoter
                     /note="SV40 early promoter"
     rep_origin      1650..1785
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    1805..1939
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(1842..1861)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     1896..1915
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(2007..2024)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2178..2766)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(2258..2277)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2937..3728,3729..3797))
                     /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     3560..3579
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(3798..3902)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 gtcgagatat ctctagaggt accgaattcg attcagccgg gagcttaggg aggggaggtc
       61 acttcataag ggcttggggg gggagttgga gccacgagtc gtccagccgg agccccgtgt
      121 ggctgagctc cggcctcaga agcatccccg ggatccaccg gtcgccacca tggcctcctc
      181 cgagaacgtc atcaccgagt tcatgcgctt caaggtgcgc atggagggca ccgtgaacgg
      241 ccacgagttc gagatcgagg gcgagggcga gggccgcccc tacgagggcc acaacaccgt
      301 gaagctgaag gtgaccaagg gcggccccct gcccttcgcc tgggacatcc tgtcccccca
      361 gttccagtac ggctccaagg tgtacgtgaa gcaccccgcc gacatccccg actacaagaa
      421 gctgtccttc cccgagggct tcaagtggga gcgcgtgatg aacttcgagg acggcggcgt
      481 ggcgaccgtg acccaggact cctccctgca ggacggctgc ttcatctaca aggtgaagtt
      541 catcggcgtg aacttcccct ccgacggccc cgtgatgcag aagaagacca tgggctggga
      601 ggcctccacc gagcgcctgt acccccgcga cggcgtgctg aagggcgaga cccacaaggc
      661 cctgaagctg aaggacggcg gccactacct ggtggagttc aagtccatct acatggccaa
      721 gaagcccgtg cagctgcccg gctactacta cgtggacgcc aagctggaca tcacctccca
      781 caacgaggac tacaccatcg tggagcagta cgagcgcacc gagggccgcc accacctgtt
      841 cctgtagcgg ccgttactcg agatcgatgg ccgcactcct caggtgcagg ctgcctatca
      901 gaaggtggtg gctggtgtgg ccaatgccct ggctcacaaa taccactgag atctttttcc
      961 ctctgccaaa aattatgggg acatcatgaa gccccttgag catctgactt ctggctaata
     1021 aaggaaattt attttcattg caatagtgtg ttggaatttt ttgtgtctct cactcggaag
     1081 gacatatggg agggcaaatc atttaaaaca tcagaatgag tatttggttt agagtttggc
     1141 aacatatgcc atatgctggc tgccatgaac aaaggtggct ataaagaggt catcagtata
     1201 tgaaacagcc ccctgctgtc cattccttat tccatagaaa agccttgact tgaggttaga
     1261 ttttttttat attttgtttt gtgttatttt tttctttaac atccctaaaa ttttccttac
     1321 atgttttact agccagattt ttcctcctct cctgactact cccagtcata gctgtccctc
     1381 ttctcttatg aagatccctc gacctgcagc ccaagcttgg cgtaatcatg gtcatagctg
     1441 tttcctgtgt gaaattgtta tccgctcaca attccacaca acatacgagc cggaagcata
     1501 aagtgtaaag cctggggtgc ctaatgagtg agctaactca cattaattgc gttgcgctca
     1561 ctgcccgctt tccagtcggg aaacctgtcg tgccagcgga tccgcatctc aattagtcag
     1621 caaccatagt cccgccccta actccgccca tcccgcccct aactccgccc agttccgccc
     1681 attctccgcc ccatggctga ctaatttttt ttatttatgc agaggccgag gccgcctcgg
     1741 cctctgagct attccagaag tagtgaggag gcttttttgg aggcctaggc ttttgcaaaa
     1801 agctaacttg tttattgcag cttataatgg ttacaaataa agcaatagca tcacaaattt
     1861 cacaaataaa gcattttttt cactgcattc tagttgtggt ttgtccaaac tcatcaatgt
     1921 atcttatcat gtctggatcc gctgcattaa tgaatcggcc aacgcgcggg gagaggcggt
     1981 ttgcgtattg ggcgctcttc cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg
     2041 ctgcggcgag cggtatcagc tcactcaaag gcggtaatac ggttatccac agaatcaggg
     2101 gataacgcag gaaagaacat gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag
     2161 gccgcgttgc tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaatcga
     2221 cgctcaagtc agaggtggcg aaacccgaca ggactataaa gataccaggc gtttccccct
     2281 ggaagctccc tcgtgcgctc tcctgttccg accctgccgc ttaccggata cctgtccgcc
     2341 tttctccctt cgggaagcgt ggcgctttct caatgctcac gctgtaggta tctcagttcg
     2401 gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac cccccgttca gcccgaccgc
     2461 tgcgccttat ccggtaacta tcgtcttgag tccaacccgg taagacacga cttatcgcca
     2521 ctggcagcag ccactggtaa caggattagc agagcgaggt atgtaggcgg tgctacagag
     2581 ttcttgaagt ggtggcctaa ctacggctac actagaagga cagtatttgg tatctgcgct
     2641 ctgctgaagc cagttacctt cggaaaaaga gttggtagct cttgatccgg caaacaaacc
     2701 accgctggta gcggtggttt ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga
     2761 tctcaagaag atcctttgat cttttctacg gggtctgacg ctcagtggaa cgaaaactca
     2821 cgttaaggga ttttggtcat gagattatca aaaaggatct tcacctagat ccttttaaat
     2881 taaaaatgaa gttttaaatc aatctaaagt atatatgagt aaacttggtc tgacagttac
     2941 caatgcttaa tcagtgaggc acctatctca gcgatctgtc tatttcgttc atccatagtt
     3001 gcctgactcc ccgtcgtgta gataactacg atacgggagg gcttaccatc tggccccagt
     3061 gctgcaatga taccgcgaga cccacgctca ccggctccag atttatcagc aataaaccag
     3121 ccagccggaa gggccgagcg cagaagtggt cctgcaactt tatccgcctc catccagtct
     3181 attaattgtt gccgggaagc tagagtaagt agttcgccag ttaatagttt gcgcaacgtt
     3241 gttgccattg ctacaggcat cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc
     3301 tccggttccc aacgatcaag gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt
     3361 agctccttcg gtcctccgat cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg
     3421 gttatggcag cactgcataa ttctcttact gtcatgccat ccgtaagatg cttttctgtg
     3481 actggtgagt actcaaccaa gtcattctga gaatagtgta tgcggcgacc gagttgctct
     3541 tgcccggcgt caatacggga taataccgcg ccacatagca gaactttaaa agtgctcatc
     3601 attggaaaac gttcttcggg gcgaaaactc tcaaggatct taccgctgtt gagatccagt
     3661 tcgatgtaac ccactcgtgc acccaactga tcttcagcat cttttacttt caccagcgtt
     3721 tctgggtgag caaaaacagg aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg
     3781 aaatgttgaa tactcatact cttccttttt caatattatt gaagcattta tcagggttat
     3841 tgtctcatga gcggatacat atttgaatgt atttagaaaa ataaacaaat aggggttccg
     3901 cgcacatttc cccgaaaagt gccacctg
//
