LOCUS       sequence-339548-        3931 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 3931)
  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 3931)
  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..3931
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     regulatory      157..166
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             163..840
                     /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(343..363)
                     /label=DsRed1-N
                     /note="DsRed1, reverse primer"
     primer_bind     755..778
                     /label=DsRed1-C
                     /note="DsRed1, forward primer"
     primer_bind     complement(945..964)
                     /label=Bglob-pA-R
                     /note="Rabbit beta-globin polyA region, reverse primer"
     polyA_signal    1010..1065
                     /label=beta-globin poly(A) signal
                     /note="rabbit beta-globin polyadenylation signal (Gil and 
                     Proudfoot, 1987)"
     primer_bind     complement(1064..1083)
                     /label=rbglobpA-R
                     /note="Rabbit beta-globin polyA, reverse primer. Also 
                     called rb-glob-pA-term-R"
     primer_bind     complement(1426..1442)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1426..1442)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(1439..1461)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    1450..1466
                     /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(1474..1480,1481..1498,1499..1504))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1519..1540
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        1599..1794
                     /label=SV40 promoter
                     /note="SV40 early promoter"
     rep_origin      1645..1780
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    1800..1934
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(1837..1856)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     1891..1910
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(2002..2019)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2173..2761)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(2253..2272)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2932..3723,3724..3792))
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPYRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     3555..3574
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(3793..3897)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 tatctctaga ggtaccgaat tcgattcagc cgggagctta gggaggggag gtcacttcat
       61 aagggcctgg ggggggagtt ggagccacga gtcgtccagc cggagccccg tgtggctgag
      121 ctccggcctc agaagcatcc ccgggatcca ccggtcgcca ccatggcctc ctccgagaac
      181 gtcatcaccg agttcatgcg cttcaaggtg cgcatggagg gcaccgtgaa cggccacgag
      241 ttcgagatcg agggcgaggg cgagggccgc ccctacgagg gccacaacac cgtgaagctg
      301 aaggtgacca agggcggccc cctgcccttc gcctgggaca tcctgtcccc ccagttccag
      361 tacggctcca aggtgtacgt gaagcacccc gccgacatcc ccgactacaa gaagctgtcc
      421 ttccccgagg gcttcaagtg ggagcgcgtg atgaacttcg aggacggcgg cgtggcgacc
      481 gtgacccagg actcctccct gcaggacggc tgcttcatct acaaggtgaa gttcatcggc
      541 gtgaacttcc cctccgacgg ccccgtgatg cagaagaaga ccatgggctg ggaggcctcc
      601 accgagcgcc tgtacccccg cgacggcgtg ctgaagggcg agacccacaa ggccctgaag
      661 ctgaaggacg gcggccacta cctggtggag ttcaagtcca tctacatggc caagaagccc
      721 gtgcagctgc ccggctacta ctacgtggac gccaagctgg acatcacctc ccacaacgag
      781 gactacacca tcgtggagca gtacgagcgc accgagggcc gccaccacct gttcctgtag
      841 cggccgttac tcgagatcga tggccgcact cctcaggtgc aggctgccta tcagaaggtg
      901 gtggctggtg tggccaatgc cctggctcac aaataccact gagatctttt tccctctgcc
      961 aaaaattatg gggacatcat gaagcccctt gagcatctga cttctggcta ataaaggaaa
     1021 tttattttca ttgcaatagt gtgttggaat tttttgtgtc tctcactcgg aaggacatat
     1081 gggagggcaa atcatttaaa acatcagaat gagtatttgg tttagagttt ggcaacatat
     1141 gcccatatgc tggctgccat gaacaaaggt tggctataaa gaggtcatca gtatatgaaa
     1201 cagccccctg ctgtccattc cttattccat agaaaagcct tgacttgagg ttagattttt
     1261 tttatatttt gttttgtgtt atttttttct ttaacatccc taaaattttc cttacatgtt
     1321 ttactagcca gatttttcct cctctcctga ctactcccag tcatagctgt ccctcttctc
     1381 ttatggagat ccctcgacct gcagcccaag cttggcgtaa tcatggtcat agctgtttcc
     1441 tgtgtgaaat tgttatccgc tcacaattcc acacaacata cgagccggaa gcataaagtg
     1501 taaagcctgg ggtgcctaat gagtgagcta actcacatta attgcgttgc gctcactgcc
     1561 cgctttccag tcgggaaacc tgtcgtgcca gcggatccgc atctcaatta gtcagcaacc
     1621 atagtcccgc ccctaactcc gcccatcccg cccctaactc cgcccagttc cgcccattct
     1681 ccgccccatg gctgactaat tttttttatt tatgcagagg ccgaggccgc ctcggcctct
     1741 gagctattcc agaagtagtg aggaggcttt tttggaggcc taggcttttg caaaaagcta
     1801 acttgtttat tgcagcttat aatggttaca aataaagcaa tagcatcaca aatttcacaa
     1861 ataaagcatt tttttcactg cattctagtt gtggtttgtc caaactcatc aatgtatctt
     1921 atcatgtctg gatccgctgc attaatgaat cggccaacgc gcggggagag gcggtttgcg
     1981 tattgggcgc tcttccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg
     2041 gcgagcggta tcagctcact caaaggcggt aatacggtta tccacagaat caggggataa
     2101 cgcaggaaag aacatgtgag caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc
     2161 gttgctggcg tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc
     2221 aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag
     2281 ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct
     2341 cccttcggga agcgtggcgc tttctcatag ctcacgctgt aggtatctca gttcggtgta
     2401 ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc
     2461 cttatccggt aactatcgtc ttgagtccaa cccggtaaga cacgacttat cgccactggc
     2521 agcagccact ggtaacagga ttagcagagc gaggtatgta ggcggtgcta cagagttctt
     2581 gaagtggtgg cctaactacg gctacactag aagaacagta tttggtatct gcgctctgct
     2641 gaagccagtt accttcggaa aaagagttgg tagctcttga tccggcaaac aaaccaccgc
     2701 tggtagcggt ggtttttttg tttgcaagca gcagattacg cgcagaaaaa aaggatctca
     2761 agaagatcct ttgatctttt ctacggggtc tgacgctcag tggaacgaaa actcacgtta
     2821 agggattttg gtcatgagat tatcaaaaag gatcttcacc tagatccttt taaattaaaa
     2881 atgaagtttt aaatcaatct aaagtatata tgagtaaact tggtctgaca gttaccaatg
     2941 cttaatcagt gaggcaccta tctcagcgat ctgtctattt cgttcatcca tagttgcctg
     3001 actccccgtc gtgtagataa ctacgatacg gtagggctta ccatctggcc ccagtgctgc
     3061 aatgataccg cgagacccac gctcaccggc tccagattta tcagcaataa accagccagc
     3121 cggaagggcc gagcgcagaa gtggtcctgc aactttatcc gcctccatcc agtctattaa
     3181 ttgttgccgg gaagctagag taagtagttc gccagttaat agtttgcgca acgttgttgc
     3241 cattgctaca ggcatcgtgg tgtcacgctc gtcgtttggt atggcttcat tcagctccgg
     3301 ttcccaacga tcaaggcgag ttacatgatc ccccatgttg tgcaaaaaag cggttagctc
     3361 cttcggtcct ccgatcgttg tcagaagtaa gttggccgca gtgttatcac tcatggttat
     3421 ggcagcactg cataattctc ttactgtcat gccatccgta agatgctttt ctgtgactgg
     3481 tgagtactca accaagtcat tctgagaata gtgtatgcgg cgaccgagtt gctcttgccc
     3541 ggcgtcaata cgggataata ccgcgccaca tagcagaact ttaaaagtgc tcatcattgg
     3601 aaaacgttct tcggggcgaa aactctcaag gatcttaccg ctgttgagat ccagttcgat
     3661 gtaacccact cgtgcaccca actgatcttc agcatctttt actttcacca gcgtttctgg
     3721 gtgagcaaaa acaggaaggc aaaatgccgc aaaaaaggga ataagggcga cacggaaatg
     3781 ttgaatactc atactcttcc tttttcaata ttattgaagc atttatcagg gttattgtct
     3841 catgagcgga tacatatttg aatgtattta gaaaaataaa caaatagggg ttccgcgcac
     3901 atttccccga aaagtgccac ctgggtcgag a
//
