LOCUS       sequence-330499-        2951 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  ddPCR gating control for droplets containing gat and tat targets.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 2951)
  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 2951)
  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_17_005
FEATURES             Location/Qualifiers
     source          1..2951
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     protein_bind    115..136
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(151..156,157..174,175..181)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    189..205
                     /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     194..216
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     213..229
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     213..229
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(564..581)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(564..580)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(573..595)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     complement(789..808)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     908..930
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(968..986)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        1054..1158
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(1159..1227,1228..2019)
                     /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(1377..1396)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      2190..2778
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     2679..2698
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     2932..2949
                     /label=L4440
                     /note="L4440 vector, forward primer"
ORIGIN
        1 agcggaagag cgcccaatac gcaaaccgcc tctccccgcg cgttggccga ttcattaatg
       61 cagctggcac gacaggtttc ccgactggaa agcgggcagt gagcgcaacg caattaatgt
      121 gagttagctc actcattagg caccccaggc tttacacttt atgcttccgg ctcgtatgtt
      181 gtgtggaatt gtgagcggat aacaatttca cacaggaaac agctatgacc atgattacgc
      241 cacgagtcgc agcacagctc gctggtccag aactgatcca tgggtcgacc ctgcaggtga
      301 ggagctcttc gtcgctgtct ccgcttcttc ctgccatagg agatgcctaa gccttttgtt
      361 atgaaacaaa cctgcaggtt aattaaatgc atggtaccct aattctcccc cgcttaatac
      421 tgacgctctc gcacccatct ctctccttct agcctccgct agtcggtacc ccatggatct
      481 gtcgcccgtc tcaaacgcaa ccctccggcg gcggcgatcg ggtcagctca tcgatgaatc
      541 gctatccatc gtcatcgcgt tgcactggcc gtcgttttac aacgtcgtga ctgggaaaac
      601 cctggcgtta cccaacttaa tcgccttgca gcacatcccc ctttcgccag ctggcgtaat
      661 agcgatgagg cccgcaccga tcgcccttcc caacagttgc gcagcctgaa tggcgaatgg
      721 cgcctgatgc ggtattttct ccttacgcat ctgtgcggta tttcacaccg catttggtgc
      781 actctcagta caatctgctc tgatgccgca tagttaagcc agccccgaca cccgccaaca
      841 cccgctgacg cgccctgacg ggcttgtctg ctcccggcat ccgcttacag acaagctgtg
      901 accgtctccg ggagctgcat gtgtcagagg ttttcaccgt catcaccgaa acgcgcgaga
      961 cgaaagggcc tcgtgatacg cctattttta taggttaatg tcatgataat aatggtttct
     1021 tagacgtcag gtggcacttt tcggggaaat gtgcgcggaa cccctatttg tttatttttc
     1081 taaatacatt caaatatgta tccgctcatg agacaataac cctgataaat gcttcaataa
     1141 tattgaaaaa ggtagagtat gagtattcaa catttccgtg tcgcccttat tccctttttt
     1201 gcggcatttt gccttcctgt ttttgctcac ccagaaacgc tggtgaaagt aaaagatgct
     1261 gaagatcagt tgggtgcacg agtgggttac atcgaactgg atctcaacag cggtaagatc
     1321 cttgagagtt ttcgccccga agaacgtttt ccaatgatga gcacttttaa agttctgcta
     1381 tgtggcgcgg tattatcccg tattgacgcc gggcaagagc aactcggtcg ccgcatacac
     1441 tattctcaga atgacttggt tgagtactca ccagtcacag aaaagcatct tacggatggc
     1501 atgacagtaa gagaattatg cagtgctgcc ataaccatga gtgataacac tgcggccaac
     1561 ttacttctga caacgatcgg aggaccgaag gagctaaccg cttttttgca caacatgggg
     1621 gatcatgtaa ctcgccttga tcgttgggaa ccggagctga atgaagccat accaaacgac
     1681 gagcgtgaca ccacgatgcc tgtagcaatg gcaacaacgt tgcgcaaact attaactggc
     1741 gaactactta ctctagcttc ccggcaacaa ttaatagact ggatggaggc ggataaagtt
     1801 gcaggaccac ttctgcgctc ggcccttccg gctggctggt ttattgctga taaatctgga
     1861 gccggtgagc gtgggtctcg cggtatcatt gcagcactgg ggccagatgg taagccctcc
     1921 cgtatcgtag ttatctacac gacggggagt caggcaacta tggatgaacg aaatagacag
     1981 atcgctgaga taggtgcctc actgattaag cattggtaac tgtcagacca agtttactca
     2041 tatatacttt agattgattt aaaacttcat ttttaattta aaaggatcta ggtgaagatc
     2101 ctttttgata atctcatgac caaaatccct taacgtgagt tttcgttcca ctgagcgtca
     2161 gaccccgtag aaaagatcaa aggatcttct tgagatcctt tttttctgcg cgtaatctgc
     2221 tgcttgcaaa caaaaaaacc accgctacca gcggtggttt gtttgccgga tcaagagcta
     2281 ccaactcttt ttccgaaggt aactggcttc agcagagcgc agataccaaa tactgttctt
     2341 ctagtgtagc cgtagttagg ccaccacttc aagaactctg tagcaccgcc tacatacctc
     2401 gctctgctaa tcctgttacc agtggctgct gccagtggcg ataagtcgtg tcttaccggg
     2461 ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg
     2521 tgcacacagc ccagcttgga gcgaacgacc tacaccgaac tgagatacct acagcgtgag
     2581 ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcgac
     2641 agggtcggaa caggagagcg cacgagggag cttccagggg gaaacgcctg gtatctttat
     2701 agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg
     2761 gggcggagcc tatggaaaaa cgccagcaac gcggcctttt tacggttcct ggccttttgc
     2821 tggccttttg ctcacatgtt ctttcctgcg ttatcccctg attctgtgga taaccgtatt
     2881 accgcctttg agtgagctga taccgctcgc cgcagccgaa cgaccgagcg cagcgagtca
     2941 gtgagcgagg a
//
