LOCUS       sequence-330524-        3112 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  ddPCR gating control for droplets containing either env+5'pol 
            targets OR env+3'pol targets.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 3112)
  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 3112)
  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_29_006
FEATURES             Location/Qualifiers
     source          1..3112
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(30..47)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(201..789)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(281..300)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(960..1751,1752..1820))
                     /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     1583..1602
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(1821..1925)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     1993..2011
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     primer_bind     complement(2049..2071)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     2171..2190
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     2384..2406
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     2398..2415
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     2399..2415
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2911..2927)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2911..2927)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(2924..2946)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    2935..2951
                     /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(2959..2965,2966..2983,2984..2989))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    3004..3025
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
ORIGIN
        1 ggtttgcgta ttgggcgctc ttccgcttcc tcgctcactg actcgctgcg ctcggtcgtt
       61 cggctgcggc gagcggtatc agctcactca aaggcggtaa tacggttatc cacagaatca
      121 ggggataacg caggaaagaa catgtgagca aaaggccagc aaaaggccag gaaccgtaaa
      181 aaggccgcgt tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat
      241 cgacgctcaa gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc
      301 cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgt cgcttaccgg atacctgtcc
      361 gcctttctcc cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt
      421 tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac
      481 cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg
      541 ccactggcag cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca
      601 gagttcttga agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc
      661 gctctgctga agccagttac cttcggaaaa agagttggta gctcttgatc cggcaaacaa
      721 accaccgctg gtagcggtgg tttttttgtt tgcaagcagc agattacgcg cagaaaaaaa
      781 ggatctcaag aagatccttt gatcttttct acggggtctg acgctcagtg gaacgaaaac
      841 tcacgttaag ggattttggt catgagatta tcaaaaagga tcttcaccta gatcctttta
      901 aattaaaaat gaagttttaa atcaatctaa agtatatatg agtaaacttg gtctgacagt
      961 taccaatgct taatcagtga ggcacctatc tcagcgatct gtctatttcg ttcatccata
     1021 gttgcctgac tccccgtcgt gtagataact acgatacggg agggcttacc atctggcccc
     1081 agtgctgcaa tgataccgcg agacccacgc tcaccggctc cagatttatc agcaataaac
     1141 cagccagccg gaagggccga gcgcagaagt ggtcctgcaa ctttatccgc ctccatccag
     1201 tctattaatt gttgccggga agctagagta agtagttcgc cagttaatag tttgcgcaac
     1261 gttgttgcca ttgctacagg catcgtggtg tcacgctcgt cgtttggtat ggcttcattc
     1321 agctccggtt cccaacgatc aaggcgagtt acatgatccc ccatgttgtg caaaaaagcg
     1381 gttagctcct tcggtcctcc gatcgttgtc agaagtaagt tggccgcagt gttatcactc
     1441 atggttatgg cagcactgca taattctctt actgtcatgc catccgtaag atgcttttct
     1501 gtgactggtg agtactcaac caagtcattc tgagaatagt gtatgcggcg accgagttgc
     1561 tcttgcccgg cgtcaatacg ggataatacc gcgccacata gcagaacttt aaaagtgctc
     1621 atcattggaa aacgttcttc ggggcgaaaa ctctcaagga tcttaccgct gttgagatcc
     1681 agttcgatgt aacccactcg tgcacccaac tgatcttcag catcttttac tttcaccagc
     1741 gtttctgggt gagcaaaaac aggaaggcaa aatgccgcaa aaaagggaat aagggcgaca
     1801 cggaaatgtt gaatactcat actctacctt tttcaatatt attgaagcat ttatcagggt
     1861 tattgtctca tgagcggata catatttgaa tgtatttaga aaaataaaca aataggggtt
     1921 ccgcgcacat ttccccgaaa agtgccacct gacgtctaag aaaccattat tatcatgaca
     1981 ttaacctata aaaataggcg tatcacgagg ccctttcgtc tcgcgcgttt cggtgatgac
     2041 ggtgaaaacc tctgacacat gcagctcccg gagacggtca cagcttgtct gtaagcggat
     2101 gccgggagca gacaagcccg tcagggcgcg tcagcgggtg ttggcgggtg tcggggctgg
     2161 cttaactatg cggcatcaga gcagattgta ctgagagtgc accaaatgcg gtgtgaaata
     2221 ccgcacagat gcgtaaggag aaaataccgc atcaggcgcc attcgccatt caggctgcgc
     2281 aactgttggg aagggcgatc ggtgcgggcc tcatcgctat tacgccagct ggcgaaaggg
     2341 ggatgtgctg caaggcgatt aagttgggta acgccagggt tttcccagtc acgacgttgt
     2401 aaaacgacgg ccagtgcaac gcgatgacga tggatagcga ttcatcgatg agctgacccg
     2461 atcgccgccg ccggagggtt gcgtttgaga cgggcgacag atccatgggg taccatgcat
     2521 tcctttagct tccctcagat cactctttgg caacgacccc tcgtcacaat aaagataggg
     2581 gggcaattaa aggaagctct attagataca ggagcagatg atacagtaat gcatttaatt
     2641 aaagagatcc actttggaaa ggaccagcaa agctcctctg gaaaggtgaa ggggcagtag
     2701 taatacaaga taatagtgac ataaaagtag tgttaattaa cctgcagggt cgactgttcc
     2761 ttgggttctt gggagcagca ggaagcacta tgggcgcagc gtcaatgacg ctgacggtac
     2821 aggccagaca attattgtct ggtatagtgc gtcgacccat ggatcagttc tggaccagcg
     2881 agctgtgctg cgactcgtgg cgtaatcatg gtcatagctg tttcctgtgt gaaattgtta
     2941 tccgctcaca attccacaca acatacgagc cggaagcata aagtgtaaag cctggggtgc
     3001 ctaatgagtg agctaactca cattaattgc gttgcgctca ctgcccgctt tccagtcggg
     3061 aaacctgtcg tgccagctgc attaatgaat cggccaacgc gcggggagag gc
//
