LOCUS       sequence-339547-        4019 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  PCR template for reporter gene with mouse Rhodopsin promoter with 
            DsRed.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 4019)
  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 4019)
  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: pJK01_Rho_minprox_DsREd
FEATURES             Location/Qualifiers
     source          1..4019
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     regulatory      267..276
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             273..950
                     /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(453..473)
                     /label=DsRed1-N
                     /note="DsRed1, reverse primer"
     primer_bind     865..888
                     /label=DsRed1-C
                     /note="DsRed1, forward primer"
     primer_bind     complement(1055..1074)
                     /label=Bglob-pA-R
                     /note="Rabbit beta-globin polyA region, reverse primer"
     polyA_signal    1120..1175
                     /label=beta-globin poly(A) signal
                     /note="rabbit beta-globin polyadenylation signal (Gil and 
                     Proudfoot, 1987)"
     primer_bind     complement(1174..1193)
                     /label=rbglobpA-R
                     /note="Rabbit beta-globin polyA, reverse primer. Also 
                     called rb-glob-pA-term-R"
     primer_bind     complement(1536..1552)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1536..1552)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(1549..1571)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    1560..1576
                     /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(1584..1590,1591..1608,1609..1614))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1629..1650
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        1709..1904
                     /label=SV40 promoter
                     /note="SV40 early promoter"
     rep_origin      1755..1890
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    1910..2044
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(1947..1966)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2001..2020
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(2112..2129)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2283..2871)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(2363..2382)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(3042..3833,3834..3902))
                     /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     3665..3684
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(3903..4007)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 aaaagtgcca cctgggtcga cgatatctct agaatgtcac cttggcccct ctgcaagcca
       61 attaggcccc ggtggcagca gtgggattag cgttagtatg atatctcgcg gatgctgaat
      121 cagcctctgg cttagggaga gaaggtcact ttataagggt ctgggggggg tcagtgcctg
      181 gagttgcgct gtgggagccg tcagaggctg agctcgccaa gcagccttgg tctctgtcgg
      241 taccgcgggc ccgggatcca ccggtcgcca ccatggcctc ctccgagaac gtcatcaccg
      301 agttcatgcg cttcaaggtg cgcatggagg gcaccgtgaa cggccacgag ttcgagatcg
      361 agggcgaggg cgagggccgc ccctacgagg gccacaacac cgtgaagctg aaggtgacca
      421 agggcggccc cctgcccttc gcctgggaca tcctgtcccc ccagttccag tacggctcca
      481 aggtgtacgt gaagcacccc gccgacatcc ccgactacaa gaagctgtcc ttccccgagg
      541 gcttcaagtg ggagcgcgtg atgaacttcg aggacggcgg cgtggcgacc gtgacccagg
      601 actcctccct gcaggacggc tgcttcatct acaaggtgaa gttcatcggc gtgaacttcc
      661 cctccgacgg ccccgtgatg cagaagaaga ccatgggctg ggaggcctcc accgagcgcc
      721 tgtacccccg cgacggcgtg ctgaagggcg agacccacaa ggccctgaag ctgaaggacg
      781 gcggccacta cctggtggag ttcaagtcca tctacatggc caagaagccc gtgcagctgc
      841 ccggctacta ctacgtggac gccaagctgg acatcacctc ccacaacgag gactacacca
      901 tcgtggagca gtacgagcgc accgagggcc gccaccacct gttcctgtag cggccgttac
      961 tcgagatcga tggccgcact cctcaggtgc aggctgccta tcagaaggtg gtggctggtg
     1021 tggccaatgc cctggctcac aaataccact gagatctttt tccctctgcc aaaaattatg
     1081 gggacatcat gaagcccctt gagcatctga cttctggcta ataaaggaaa tttattttca
     1141 ttgcaatagt gtgttggaat tttttgtgtc tctcactcgg aaggacatat gggagggcaa
     1201 atcatttaaa acatcagaat gagtatttgg tttagagttt ggcaacatat gcccatatgc
     1261 tggctgccat gaacaaaggt tggctataaa gaggtcatca gtatatgaaa cagccccctg
     1321 ctgtccattc cttattccat agaaaagcct tgacttgagg ttagattttt tttatatttt
     1381 gttttgtgtt atttttttct ttaacatccc taaaattttc cttacatgtt ttactagcca
     1441 gatttttcct cctctcctga ctactcccag tcatagctgt ccctcttctc ttatggagat
     1501 ccctcgacct gcagcccaag cttggcgtaa tcatggtcat agctgtttcc tgtgtgaaat
     1561 tgttatccgc tcacaattcc acacaacata cgagccggaa gcataaagtg taaagcctgg
     1621 ggtgcctaat gagtgagcta actcacatta attgcgttgc gctcactgcc cgctttccag
     1681 tcgggaaacc tgtcgtgcca gcggatccgc atctcaatta gtcagcaacc atagtcccgc
     1741 ccctaactcc gcccatcccg cccctaactc cgcccagttc cgcccattct ccgccccatg
     1801 gctgactaat tttttttatt tatgcagagg ccgaggccgc ctcggcctct gagctattcc
     1861 agaagtagtg aggaggcttt tttggaggcc taggcttttg caaaaagcta acttgtttat
     1921 tgcagcttat aatggttaca aataaagcaa tagcatcaca aatttcacaa ataaagcatt
     1981 tttttcactg cattctagtt gtggtttgtc caaactcatc aatgtatctt atcatgtctg
     2041 gatccgctgc attaatgaat cggccaacgc gcggggagag gcggtttgcg tattgggcgc
     2101 tcttccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta
     2161 tcagctcact caaaggcggt aatacggtta tccacagaat caggggataa cgcaggaaag
     2221 aacatgtgag caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg
     2281 tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg
     2341 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg
     2401 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga
     2461 agcgtggcgc tttctcatag ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc
     2521 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
     2581 aactatcgtc ttgagtccaa cccggtaaga cacgacttat cgccactggc agcagccact
     2641 ggtaacagga ttagcagagc gaggtatgta ggcggtgcta cagagttctt gaagtggtgg
     2701 cctaactacg gctacactag aagaacagta tttggtatct gcgctctgct gaagccagtt
     2761 accttcggaa aaagagttgg tagctcttga tccggcaaac aaaccaccgc tggtagcggt
     2821 ggtttttttg tttgcaagca gcagattacg cgcagaaaaa aaggatctca agaagatcct
     2881 ttgatctttt ctacggggtc tgacgctcag tggaacgaaa actcacgtta agggattttg
     2941 gtcatgagat tatcaaaaag gatcttcacc tagatccttt taaattaaaa atgaagtttt
     3001 aaatcaatct aaagtatata tgagtaaact tggtctgaca gttaccaatg cttaatcagt
     3061 gaggcaccta tctcagcgat ctgtctattt cgttcatcca tagttgcctg actccccgtc
     3121 gtgtagataa ctacgatacg gtagggctta ccatctggcc ccagtgctgc aatgataccg
     3181 cgagacccac gctcaccggc tccagattta tcagcaataa accagccagc cggaagggcc
     3241 gagcgcagaa gtggtcctgc aactttatcc gcctccatcc agtctattaa ttgttgccgg
     3301 gaagctagag taagtagttc gccagttaat agtttgcgca acgttgttgc cattgctaca
     3361 ggcatcgtgg tgtcacgctc gtcgtttggt atggcttcat tcagctccgg ttcccaacga
     3421 tcaaggcgag ttacatgatc ccccatgttg tgcaaaaaag cggttagctc cttcggtcct
     3481 ccgatcgttg tcagaagtaa gttggccgca gtgttatcac tcatggttat ggcagcactg
     3541 cataattctc ttactgtcat gccatccgta agatgctttt ctgtgactgg tgagtactca
     3601 accaagtcat tctgagaata gtgtatgcgg cgaccgagtt gctcttgccc ggcgtcaata
     3661 cgggataata ccgcgccaca tagcagaact ttaaaagtgc tcatcattgg aaaacgttct
     3721 tcggggcgaa aactctcaag gatcttaccg ctgttgagat ccagttcgat gtaacccact
     3781 cgtgcaccca actgatcttc agcatctttt actttcacca gcgtttctgg gtgagcaaaa
     3841 acaggaaggc aaaatgccgc aaaaaaggga ataagggcga cacggaaatg ttgaatactc
     3901 atactcttcc tttttcaata ttattgaagc atttatcagg gttattgtct catgagcgga
     3961 tacatatttg aatgtattta gaaaaataaa caaatagggg ttccgcgcac atttccccg
//
