LOCUS       sequence-330515-        2900 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  ddPCR gating control for droplets containing the env target.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 2900)
  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 2900)
  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_14_004
FEATURES             Location/Qualifiers
     source          1..2900
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     132..151
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     385..402
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    519..540
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(555..560,561..578,579..585)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    593..609
                     /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     598..620
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     617..633
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     617..633
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(917..934)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(917..933)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(926..948)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     complement(1142..1161)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     1261..1283
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(1321..1339)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        1407..1511
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(1512..1580,1581..2372)
                     /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     complement(1730..1749)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      join(2543..2900,1..231)
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
ORIGIN
        1 acctacaccg aactgagata cctacagcgt gagctatgag aaagcgccac gcttcccgaa
       61 gggagaaagg cggacaggta tccggtaagc gacagggtcg gaacaggaga gcgcacgagg
      121 gagcttccag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg ccacctctga
      181 cttgagcgtc gatttttgtg atgctcgtca ggggggcgga gcctatggaa aaacgccagc
      241 aacgcggcct ttttacggtt cctggccttt tgctggcctt ttgctcacat gttctttcct
      301 gcgttatccc ctgattctgt ggataaccgt attaccgcct ttgagtgagc tgataccgct
      361 cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga agagcgccca
      421 atacgcaaac cgcctctccc cgcgcgttgg ccgattcatt aatgcagctg gcacgacagg
      481 tttcccgact ggaaagcggg cagtgagcgc aacgcaatta atgtgagtta gctcactcat
      541 taggcacccc aggctttaca ctttatgctt ccggctcgta tgttgtgtgg aattgtgagc
      601 ggataacaat ttcacacagg aaacagctat gaccatgatt acgccacgag tcgcagcaca
      661 gctcgctggt ccagaactga tccatgggtc gacgcactat accagacaat aattgtctgg
      721 cctgtaccgt cagcgtcatt gacgctgcgc ccatagtgct tcctgctgct cccaagaacc
      781 caaggaacag tcgaccctgc aggttaatta aatgcatggt accccatgga tctgtcgccc
      841 gtctcaaacg caaccctccg gcggcggcga tcgggtcagc tcatcgatga atcgctatcc
      901 atcgtcatcg cgttgcactg gccgtcgttt tacaacgtcg tgactgggaa aaccctggcg
      961 ttacccaact taatcgcctt gcagcacatc cccctttcgc cagctggcgt aatagcgatg
     1021 aggcccgcac cgatcgccct tcccaacagt tgcgcagcct gaatggcgaa tggcgcctga
     1081 tgcggtattt tctccttacg catctgtgcg gtatttcaca ccgcatttgg tgcactctca
     1141 gtacaatctg ctctgatgcc gcatagttaa gccagccccg acacccgcca acacccgctg
     1201 acgcgccctg acgggcttgt ctgctcccgg catccgctta cagacaagct gtgaccgtct
     1261 ccgggagctg catgtgtcag aggttttcac cgtcatcacc gaaacgcgcg agacgaaagg
     1321 gcctcgtgat acgcctattt ttataggtta atgtcatgat aataatggtt tcttagacgt
     1381 caggtggcac ttttcgggga aatgtgcgcg gaacccctat ttgtttattt ttctaaatac
     1441 attcaaatat gtatccgctc atgagacaat aaccctgata aatgcttcaa taatattgaa
     1501 aaaggtagag tatgagtatt caacatttcc gtgtcgccct tattcccttt tttgcggcat
     1561 tttgccttcc tgtttttgct cacccagaaa cgctggtgaa agtaaaagat gctgaagatc
     1621 agttgggtgc acgagtgggt tacatcgaac tggatctcaa cagcggtaag atccttgaga
     1681 gttttcgccc cgaagaacgt tttccaatga tgagcacttt taaagttctg ctatgtggcg
     1741 cggtattatc ccgtattgac gccgggcaag agcaactcgg tcgccgcata cactattctc
     1801 agaatgactt ggttgagtac tcaccagtca cagaaaagca tcttacggat ggcatgacag
     1861 taagagaatt atgcagtgct gccataacca tgagtgataa cactgcggcc aacttacttc
     1921 tgacaacgat cggaggaccg aaggagctaa ccgctttttt gcacaacatg ggggatcatg
     1981 taactcgcct tgatcgttgg gaaccggagc tgaatgaagc cataccaaac gacgagcgtg
     2041 acaccacgat gcctgtagca atggcaacaa cgttgcgcaa actattaact ggcgaactac
     2101 ttactctagc ttcccggcaa caattaatag actggatgga ggcggataaa gttgcaggac
     2161 cacttctgcg ctcggccctt ccggctggct ggtttattgc tgataaatct ggagccggtg
     2221 agcgtgggtc tcgcggtatc attgcagcac tggggccaga tggtaagccc tcccgtatcg
     2281 tagttatcta cacgacgggg agtcaggcaa ctatggatga acgaaataga cagatcgctg
     2341 agataggtgc ctcactgatt aagcattggt aactgtcaga ccaagtttac tcatatatac
     2401 tttagattga tttaaaactt catttttaat ttaaaaggat ctaggtgaag atcctttttg
     2461 ataatctcat gaccaaaatc ccttaacgtg agttttcgtt ccactgagcg tcagaccccg
     2521 tagaaaagat caaaggatct tcttgagatc ctttttttct gcgcgtaatc tgctgcttgc
     2581 aaacaaaaaa accaccgcta ccagcggtgg tttgtttgcc ggatcaagag ctaccaactc
     2641 tttttccgaa ggtaactggc ttcagcagag cgcagatacc aaatactgtt cttctagtgt
     2701 agccgtagtt aggccaccac ttcaagaact ctgtagcacc gcctacatac ctcgctctgc
     2761 taatcctgtt accagtggct gctgccagtg gcgataagtc gtgtcttacc gggttggact
     2821 caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac
     2881 agcccagctt ggagcgaacg
//
