LOCUS       sequence-275613-        4077 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  This plasmid is used to generate the unique standard curve required 
            to quantify the capture of genomic signature using DTECT.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 4077)
  AUTHORS   Billon P, Nambiar TS, Hayward SB, Zafra MP, Schatoff EM, Oshima K, 
            Dunbar A, Breinig M, Park YC, Ryu HS, Tschaharganeh DF, Levine RL, 
            Baer R, Ferrando A, Dow LE, Ciccia A
  TITLE     Detection of Marker-Free Precision Genome Editing and Genetic 
            Variation through the Capture of Genomic Signatures.
  JOURNAL   Cell Rep. 2020 Mar 10;30(10):3280-3295.e6. doi: 
            10.1016/j.celrep.2020.02.068.
  PUBMED    32160537
REFERENCE   2  (bases 1 to 4077)
  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: 
            "10.1016/j.celrep.2020.02"; journalName: "Cell Rep"; date: 
            "2020-03-10- 10"; volume: "30"; issue: "10"; pages: "3280-3295.e6"
COMMENT     Sequence Label: DTECT - Plasmid for Standard Curve
FEATURES             Location/Qualifiers
     source          1..4077
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     protein_bind    25..46
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(61..66,67..84,85..91)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    99..115
                     /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)."
     primer_bind     104..126
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     123..139
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     123..139
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     promoter        160..178
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(367..386)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(368..386)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(393..410)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(393..409)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(402..424)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     CDS             547..849
                     /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="QFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKV
                     SRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI"
     primer_bind     728..747
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     CDS             1198..1992
                     /codon_start=1
                     /product="aminoglycoside phosphotransferase"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     CDS             1198..1992
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(1252..1271)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     1862..1881
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     CDS             complement(join(2242..3033,3034..3102))
                     /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     2865..2884
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      3226..3814
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     3715..3734
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     3968..3985
                     /label=L4440
                     /note="L4440 vector, forward primer"
ORIGIN
        1 agcgggcagt gagcgcaacg caattaatgt gagttagctc actcattagg caccccaggc
       61 tttacacttt atgcttccgg ctcgtatgtt gtgtggaatt gtgagcggat aacaatttca
      121 cacaggaaac agctatgacc atgattacgc caagctcaga attaaccctc actaaaggga
      181 ctagtcctgc aggtttaaac gaattcgccc ttcgggtacc gagctcgaat tcttagaaga
      241 gagacagaat gcttcttacc cgtgccccag cgaagttttt cattcacttc agcttcttcc
      301 ctgaaatcag gacgggtctc gtgaggaatt ggcaagggcg aattcgcggc cgctaaattc
      361 aattcgccct atagtgagtc gtattacaat tcactggccg tcgttttaca acgtcgtgac
      421 tgggaaaacc ctggcgttac ccaacttaat cgccttgcag cacatccccc tttcgccagc
      481 tggcgtaata gcgaagaggc ccgcaccgat cgcccttccc aacagttgcg cagcctatac
      541 gtacggcagt ttaaggttta cacctataaa agagagagcc gttatcgtct gtttgtggat
      601 gtacagagtg atattattga cacgccgggg cgacggatgg tgatccccct ggccagtgca
      661 cgtctgctgt cagataaagt ctcccgtgaa ctttacccgg tggtgcatat cggggatgaa
      721 agctggcgca tgatgaccac cgatatggcc agtgtgccgg tctccgttat cggggaagaa
      781 gtggctgatc tcagccaccg cgaaaatgac atcaaaaacg ccattaacct gatgttctgg
      841 ggaatataaa tgtcaggcat gagattatca aaaaggatct tcacctagat ccttttcacg
      901 tagaaagcca gtccgcagaa acggtgctga ccccggatga atgtcagcta ctgggctatc
      961 tggacaaggg aaaacgcaag cgcaaagaga aagcaggtag cttgcagtgg gcttacatgg
     1021 cgatagctag actgggcggt tttatggaca gcaagcgaac cggaattgcc agctggggcg
     1081 ccctctggta aggttgggaa gccctgcaaa gtaaactgga tggctttctt gccgccaagg
     1141 atctgatggc gcaggggatc aagctctgat caagagacag gatgaggatc gtttcgcatg
     1201 attgaacaag atggattgca cgcaggttct ccggccgctt gggtggagag gctattcggc
     1261 tatgactggg cacaacagac aatcggctgc tctgatgccg ccgtgttccg gctgtcagcg
     1321 caggggcgcc cggttctttt tgtcaagacc gacctgtccg gtgccctgaa tgaactgcaa
     1381 gacgaggcag cgcggctatc gtggctggcc acgacgggcg ttccttgcgc agctgtgctc
     1441 gacgttgtca ctgaagcggg aagggactgg ctgctattgg gcgaagtgcc ggggcaggat
     1501 ctcctgtcat ctcaccttgc tcctgccgag aaagtatcca tcatggctga tgcaatgcgg
     1561 cggctgcata cgcttgatcc ggctacctgc ccattcgacc accaagcgaa acatcgcatc
     1621 gagcgagcac gtactcggat ggaagccggt cttgtcgatc aggatgatct ggacgaagag
     1681 catcaggggc tcgcgccagc cgaactgttc gccaggctca aggcgagcat gcccgacggc
     1741 gaggatctcg tcgtgaccca tggcgatgcc tgcttgccga atatcatggt ggaaaatggc
     1801 cgcttttctg gattcatcga ctgtggccgg ctgggtgtgg cggaccgcta tcaggacata
     1861 gcgttggcta cccgtgatat tgctgaagag cttggcggcg aatgggctga ccgcttcctc
     1921 gtgctttacg gtatcgccgc tcccgattcg cagcgcatcg ccttctatcg ccttcttgac
     1981 gagttcttct gaattattaa cgcttacaat ttcctgatgc ggtattttct ccttacgcat
     2041 ctgtgcggta tttcacaccg catcaggtgg cacttttcgg ggaaatgtgc gcggaacccc
     2101 tatttgttta tttttctaaa tacattcaaa tatgtatccg ctcatgagat tatcaaaaag
     2161 gatcttcacc tagatccttt taaattaaaa atgaagtttt aaatcaatct aaagtatata
     2221 tgagtaaact tggtctgaca gttaccaatg cttaatcagt gaggcaccta tctcagcgat
     2281 ctgtctattt cgttcatcca tagttgcctg actccccgtc gtgtagataa ctacgatacg
     2341 ggagggctta ccatctggcc ccagtgctgc aatgataccg cgagacccac gctcaccggc
     2401 tccagattta tcagcaataa accagccagc cggaagggcc gagcgcagaa gtggtcctgc
     2461 aactttatcc gcctccatcc agtctattaa ttgttgccgg gaagctagag taagtagttc
     2521 gccagttaat agtttgcgca acgttgttgc cattgctaca ggcatcgtgg tgtcacgctc
     2581 gtcgtttggt atggcttcat tcagctccgg ttcccaacga tcaaggcgag ttacatgatc
     2641 ccccatgttg tgcaaaaaag cggttagctc cttcggtcct ccgatcgttg tcagaagtaa
     2701 gttggccgca gtgttatcac tcatggttat ggcagcactg cataattctc ttactgtcat
     2761 gccatccgta agatgctttt ctgtgactgg tgagtactca accaagtcat tctgagaata
     2821 gtgtatgcgg cgaccgagtt gctcttgccc ggcgtcaata cgggataata ccgcgccaca
     2881 tagcagaact ttaaaagtgc tcatcattgg aaaacgttct tcggggcgaa aactctcaag
     2941 gatcttaccg ctgttgagat ccagttcgat gtaacccact cgtgcaccca actgatcttc
     3001 agcatctttt actttcacca gcgtttctgg gtgagcaaaa acaggaaggc aaaatgccgc
     3061 aaaaaaggga ataagggcga cacggaaatg ttgaatactc atactcttcc tttttcaata
     3121 ttattgaagc atttatcagg gttattgtct catgaccaaa atcccttaac gtgagttttc
     3181 gttccactga gcgtcagacc ccgtagaaaa gatcaaagga tcttcttgag atcctttttt
     3241 tctgcgcgta atctgctgct tgcaaacaaa aaaaccaccg ctaccagcgg tggtttgttt
     3301 gccggatcaa gagctaccaa ctctttttcc gaaggtaact ggcttcagca gagcgcagat
     3361 accaaatact gttcttctag tgtagccgta gttaggccac cacttcaaga actctgtagc
     3421 accgcctaca tacctcgctc tgctaatcct gttaccagtg gctgctgcca gtggcgataa
     3481 gtcgtgtctt accgggttgg actcaagacg atagttaccg gataaggcgc agcggtcggg
     3541 ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca ccgaactgag
     3601 atacctacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa aggcggacag
     3661 gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagcttc cagggggaaa
     3721 cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc gtcgattttt
     3781 gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc agcaacgcgg cctttttacg
     3841 gttcctggcc ttttgctggc cttttgctca catgttcttt cctgcgttat cccctgattc
     3901 tgtggataac cgtattaccg cctttgagtg agctgatacc gctcgccgca gccgaacgac
     3961 cgagcgcagc gagtcagtga gcgaggaagc ggaagagcgc ccaatacgca aaccgcctct
     4021 ccccgcgcgt tggccgattc attaatgcag ctggcacgac aggtttcccg actggaa
//
