LOCUS       sequence-330525-        3163 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  ddPCR gating control for droplets containing either gag+5'pol 
            targets OR 3'pol+tat targets.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 3163)
  AUTHORS   Levy CN, Hughes SM, Roychoudhury P, Reeves DB, Amstuz C, Zhu H, 
            Huang ML, Wei Y, Bull ME, Cassidy NAJ, McClure J, Frenkel LM, Stone 
            M, Bakkour S, Wonderlich ER, Busch MP, Deeks SG, Schiffer JT, Coombs
            RW, Lehman DA, Jerome KR, Hladik F
  TITLE     A highly multiplexed droplet digital PCR assay to measure the intact
            HIV-1 proviral reservoir.
  JOURNAL   Cell Rep Med. 2021 Apr 12;2(4):100243. doi: 
            10.1016/j.xcrm.2021.100243. eCollection 2021 Apr 20.
  PUBMED    33948574
REFERENCE   2  (bases 1 to 3163)
  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: "Cell Rep 
            Med."; date: "2021-04-12"; volume: "2(4):100243. doi"; pages: " 
            10.1016/j.xcrm.2021.100243. eCollection 2021 Apr 20"
COMMENT     Sequence Label: Seattle_IPDA_control_6_002
FEATURES             Location/Qualifiers
     source          1..3163
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      complement(134..722)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(214..233)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(893..1684,1685..1753))
                     /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     1516..1535
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(1754..1858)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     1926..1944
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     primer_bind     complement(1982..2004)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     2104..2123
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     2317..2339
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     2331..2348
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     2332..2348
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2895..2911)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2895..2911)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(2908..2930)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    2919..2935
                     /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(2943..2949,2950..2967,2968..2973))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    2988..3009
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(3126..3143)
                     /label=L4440
                     /note="L4440 vector, forward primer"
ORIGIN
        1 ggcgagcggt atcagctcac tcaaaggcgg taatacggtt atccacagaa tcaggggata
       61 acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc caggaaccgt aaaaaggccg
      121 cgttgctggc gtttttccat aggctccgcc cccctgacga gcatcacaaa aatcgacgct
      181 caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggaa
      241 gctccctcgt gcgctctcct gttccgaccc tgtcgcttac cggatacctg tccgcctttc
      301 tcccttcggg aagcgtggcg ctttctcata gctcacgctg taggtatctc agttcggtgt
      361 aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg
      421 ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta tcgccactgg
      481 cagcagccac tggtaacagg attagcagag cgaggtatgt aggcggtgct acagagttct
      541 tgaagtggtg gcctaactac ggctacacta gaagaacagt atttggtatc tgcgctctgc
      601 tgaagccagt taccttcgga aaaagagttg gtagctcttg atccggcaaa caaaccaccg
      661 ctggtagcgg tggttttttt gtttgcaagc agcagattac gcgcagaaaa aaaggatctc
      721 aagaagatcc tttgatcttt tctacggggt ctgacgctca gtggaacgaa aactcacgtt
      781 aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac ctagatcctt ttaaattaaa
      841 aatgaagttt taaatcaatc taaagtatat atgagtaaac ttggtctgac agttaccaat
      901 gcttaatcag tgaggcacct atctcagcga tctgtctatt tcgttcatcc atagttgcct
      961 gactccccgt cgtgtagata actacgatac gggagggctt accatctggc cccagtgctg
     1021 caatgatacc gcgagaccca cgctcaccgg ctccagattt atcagcaata aaccagccag
     1081 ccggaagggc cgagcgcaga agtggtcctg caactttatc cgcctccatc cagtctatta
     1141 attgttgccg ggaagctaga gtaagtagtt cgccagttaa tagtttgcgc aacgttgttg
     1201 ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg tatggcttca ttcagctccg
     1261 gttcccaacg atcaaggcga gttacatgat cccccatgtt gtgcaaaaaa gcggttagct
     1321 ccttcggtcc tccgatcgtt gtcagaagta agttggccgc agtgttatca ctcatggtta
     1381 tggcagcact gcataattct cttactgtca tgccatccgt aagatgcttt tctgtgactg
     1441 gtgagtactc aaccaagtca ttctgagaat agtgtatgcg gcgaccgagt tgctcttgcc
     1501 cggcgtcaat acgggataat accgcgccac atagcagaac tttaaaagtg ctcatcattg
     1561 gaaaacgttc ttcggggcga aaactctcaa ggatcttacc gctgttgaga tccagttcga
     1621 tgtaacccac tcgtgcaccc aactgatctt cagcatcttt tactttcacc agcgtttctg
     1681 ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg aataagggcg acacggaaat
     1741 gttgaatact catactctac ctttttcaat attattgaag catttatcag ggttattgtc
     1801 tcatgagcgg atacatattt gaatgtattt agaaaaataa acaaataggg gttccgcgca
     1861 catttccccg aaaagtgcca cctgacgtct aagaaaccat tattatcatg acattaacct
     1921 ataaaaatag gcgtatcacg aggccctttc gtctcgcgcg tttcggtgat gacggtgaaa
     1981 acctctgaca catgcagctc ccggagacgg tcacagcttg tctgtaagcg gatgccggga
     2041 gcagacaagc ccgtcagggc gcgtcagcgg gtgttggcgg gtgtcggggc tggcttaact
     2101 atgcggcatc agagcagatt gtactgagag tgcaccaaat gcggtgtgaa ataccgcaca
     2161 gatgcgtaag gagaaaatac cgcatcaggc gccattcgcc attcaggctg cgcaactgtt
     2221 gggaagggcg atcggtgcgg gcctcatcgc tattacgcca gctggcgaaa gggggatgtg
     2281 ctgcaaggcg attaagttgg gtaacgccag ggttttccca gtcacgacgt tgtaaaacga
     2341 cggccagtgc aacgcgatga cgatggatag cgattcatcg atgagctgac ccgatcgccg
     2401 ccgccggagg gttgcgtttg agacgggcga cagatccatg gggtaccgac tagcggaggc
     2461 tagaaggaga gagatgggtg cgagagcgtc agtattaagc gggggagaat tagggtacca
     2521 tgcattcctt tagcttccct cagatcactc tttggcaacg acccctcgtc acaataaaga
     2581 taggggggca attaaaggaa gctctattag atacaggagc agatgataca gtaatgcatt
     2641 taattaaaga gatccacttt ggaaaggacc agcaaagctc ctctggaaag gtgaaggggc
     2701 agtagtaata caagataata gtgacataaa agtagtgtta attaacctgc aggtttgttt
     2761 cataacaaaa ggcttaggca tctcctatgg caggaagaag cggagacagc gacgaagagc
     2821 tcctcacctg cagggtcgac ccatggatca gttctggacc agcgagctgt gctgcgactc
     2881 gtggcgtaat catggtcata gctgtttcct gtgtgaaatt gttatccgct cacaattcca
     2941 cacaacatac gagccggaag cataaagtgt aaagcctggg gtgcctaatg agtgagctaa
     3001 ctcacattaa ttgcgttgcg ctcactgccc gctttccagt cgggaaacct gtcgtgccag
     3061 ctgcattaat gaatcggcca acgcgcgggg agaggcggtt tgcgtattgg gcgctcttcc
     3121 gcttcctcgc tcactgactc gctgcgctcg gtcgttcggc tgc
//
