LOCUS       sequence-269279-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Scrambled shRNA (negative control) inserted into the PLKO.1 plasmid 
            (CCTAAGGTTAAGTCGCCCTCG).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7084)
  AUTHORS   Fischer JW, Busa VF, Shao Y, Leung AKL
  TITLE     Structure-Mediated RNA Decay by UPF1 and G3BP1.
  JOURNAL   Mol Cell. 2020 Apr 2;78(1):70-84.e6. doi: 
            10.1016/j.molcel.2020.01.021. Epub 2020 Feb 3.
  PUBMED    32017897
REFERENCE   2  (bases 1 to 7084)
  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.molcel.2020.01.021"; journalName: "Mol Cell"; date: 
            "2020-04-2- 2"; volume: "78"; issue: "1"; pages: "70-84.e6"
COMMENT     Sequence Label: PLKO.1-Scrambled
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             122..166
                     /codon_start=1
                     /product="antigenic peptide corresponding to amino acids 
                     655 to 669 of the HIV envelope protein gp41 (Lutje Hulsik 
                     et al., 2013)"
                     /label=gp41 peptide
                     /note="recognized by the 2H10 single-chain llama nanobody"
                     /translation="KNEQELLELDKWASL"
     promoter        464..712
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     464..484
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     635..654
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    809..926
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        975..1485
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1404..1422
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1507..2106
                     /codon_start=1
                     /gene="pac from Streptomyces alboniger"
                     /product="puromycin N-acetyltransferase"
                     /label=PuroR
                     /note="confers resistance to puromycin"
                     /translation="MTEYKPTVRLATRDDVPRAVRTLAAAFADYPATRHTVDPDRHIER
                     VTELQELFLTRVGLDIGKVWVADDGAAVAVWTTPESVEAGAVFAEIGPRMAELSGSRLA
                     AQQQMEGLLAPHRPKEPAWFLATVGVSPDHQGKGLGSAVVLPGVEAAERAGVPAFLETS
                     APRNLPFYERLGFTVTADVEVPEGPRTWCMTRKPGA"
     primer_bind     complement(1507..1526)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     2003..2023
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             2234..2467
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2539..2660
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2576..2595)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2630..2649
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2700..2835
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2855..2874)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(2856..2874)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2884..2901)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2884..2900)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2893..2915)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3042..3497
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3129..3148)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3339..3360
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3523..3627
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3628..3696,3697..4488)
                     /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(3846..3865)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4659..5247
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5148..5167
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5401..5418
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5535..5556
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5571..5576,5577..5594,5595..5601)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5609..5625
                     /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     5614..5636
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5633..5649
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5633..5649
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5668..5688
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5670..5688
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5716..5942
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             5943..6123
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6170..6295
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6788..7021
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
ORIGIN
        1 gagtaataaa tctctggaac agatttggaa tcacacgacc tggatggagt gggacagaga
       61 aattaacaat tacacaagct taatacactc cttaattgaa gaatcgcaaa accagcaaga
      121 aaagaatgaa caagaattat tggaattaga taaatgggca agtttgtgga attggtttaa
      181 cataacaaat tggctgtggt atataaaatt attcataatg atagtaggag gcttggtagg
      241 tttaagaata gtttttgctg tactttctat agtgaataga gttaggcagg gatattcacc
      301 attatcgttt cagacccacc tcccaacccc gaggggaccc gacaggcccg aaggaataga
      361 agaagaaggt ggagagagag acagagacag atccattcga ttagtgaacg gatctcgacg
      421 gtatcgatca cgagactagc ctcgagcggc cgcccccttc accgagggcc tatttcccat
      481 gattccttca tatttgcata tacgatacaa ggctgttaga gagataattg gaattaattt
      541 gactgtaaac acaaagatat tagtacaaaa tacgtgacgt agaaagtaat aatttcttgg
      601 gtagtttgca gttttaaaat tatgttttaa aatggactat catatgctta ccgtaacttg
      661 aaagtatttc gatttcttgg ctttatatat cttgtggaaa ggacgaaaca ccggcctaag
      721 gttaagtcgc cctcgctcga gcgagggcga cttaacctta ggtttttgaa ttctcgacct
      781 cgagacaaat ggcagtattc atccacaatt ttaaaagaaa aggggggatt ggggggtaca
      841 gtgcagggga aagaatagta gacataatag caacagacat acaaactaaa gaattacaaa
      901 aacaaattac aaaaattcaa aattttcggg tttattacag ggacagcaga gatccacttt
      961 ggccgcggct cgagggggtt ggggttgcgc cttttccaag gcagccctgg gtttgcgcag
     1021 ggacgcggct gctctgggcg tggttccggg aaacgcagcg gcgccgaccc tgggtctcgc
     1081 acattcttca cgtccgttcg cagcgtcacc cggatcttcg ccgctaccct tgtgggcccc
     1141 ccggcgacgc ttcctgctcc gcccctaagt cgggaaggtt ccttgcggtt cgcggcgtgc
     1201 cggacgtgac aaacggaagc cgcacgtctc actagtaccc tcgcagacgg acagcgccag
     1261 ggagcaatgg cagcgcgccg accgcgatgg gctgtggcca atagcggctg ctcagcaggg
     1321 cgcgccgaga gcagcggccg ggaaggggcg gtgcgggagg cggggtgtgg ggcggtagtg
     1381 tgggccctgt tcctgcccgc gcggtgttcc gcattctgca agcctccgga gcgcacgtcg
     1441 gcagtcggct ccctcgttga ccgaatcacc gacctctctc cccaggggga tccaccggag
     1501 cttaccatga ccgagtacaa gcccacggtg cgcctcgcca cccgcgacga cgtccccagg
     1561 gccgtacgca ccctcgccgc cgcgttcgcc gactaccccg ccacgcgcca caccgtcgat
     1621 ccggaccgcc acatcgagcg ggtcaccgag ctgcaagaac tcttcctcac gcgcgtcggg
     1681 ctcgacatcg gcaaggtgtg ggtcgcggac gacggcgccg cggtggcggt ctggaccacg
     1741 ccggagagcg tcgaagcggg ggcggtgttc gccgagatcg gcccgcgcat ggccgagttg
     1801 agcggttccc ggctggccgc gcagcaacag atggaaggcc tcctggcgcc gcaccggccc
     1861 aaggagcccg cgtggttcct ggccaccgtc ggcgtctcgc ccgaccacca gggcaagggt
     1921 ctgggcagcg ccgtcgtgct ccccggagtg gaggcggccg agcgcgccgg ggtgcccgcc
     1981 ttcctggaga cctccgcgcc ccgcaacctc cccttctacg agcggctcgg cttcaccgtc
     2041 accgccgacg tcgaggtgcc cgaaggaccg cgcacctggt gcatgacccg caagcccggt
     2101 gcctgacgcc cgccccacga cccgcagcgc ccgaccgaaa ggagcgcacg accccatgca
     2161 tcggtacctt taagaccaat gacttacaag gcagctgtag atcttagcca ctttttaaaa
     2221 gaaaaggggg gactggaagg gctaattcac tcccaacgaa gacaagatct gctttttgct
     2281 tgtactgggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctaactaggg
     2341 aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt
     2401 ctgttgtgtg actctggtaa ctagagatcc ctcagaccct tttagtcagt gtggaaaatc
     2461 tctagcagta gtagttcatg tcatcttatt attcagtatt tataacttgc aaagaaatga
     2521 atatcagaga gtgagaggaa cttgtttatt gcagcttata atggttacaa ataaagcaat
     2581 agcatcacaa atttcacaaa taaagcattt ttttcactgc attctagttg tggtttgtcc
     2641 aaactcatca atgtatctta tcatgtctgg ctctagctat cccgccccta actccgccca
     2701 tcccgcccct aactccgccc agttccgccc attctccgcc ccatggctga ctaatttttt
     2761 ttatttatgc agaggccgag gccgcctcgg cctctgagct attccagaag tagtgaggag
     2821 gcttttttgg aggcctaggg acgtacccaa ttcgccctat agtgagtcgt attacgcgcg
     2881 ctcactggcc gtcgttttac aacgtcgtga ctgggaaaac cctggcgtta cccaacttaa
     2941 tcgccttgca gcacatcccc ctttcgccag ctggcgtaat agcgaagagg cccgcaccga
     3001 tcgcccttcc caacagttgc gcagcctgaa tggcgaatgg gacgcgccct gtagcggcgc
     3061 attaagcgcg gcgggtgtgg tggttacgcg cagcgtgacc gctacacttg ccagcgccct
     3121 agcgcccgct cctttcgctt tcttcccttc ctttctcgcc acgttcgccg gctttccccg
     3181 tcaagctcta aatcgggggc tccctttagg gttccgattt agtgctttac ggcacctcga
     3241 ccccaaaaaa cttgattagg gtgatggttc acgtagtggg ccatcgccct gatagacggt
     3301 ttttcgccct ttgacgttgg agtccacgtt ctttaatagt ggactcttgt tccaaactgg
     3361 aacaacactc aaccctatct cggtctattc ttttgattta taagggattt tgccgatttc
     3421 ggcctattgg ttaaaaaatg agctgattta acaaaaattt aacgcgaatt ttaacaaaat
     3481 attaacgctt acaatttagg tggcactttt cggggaaatg tgcgcggaac ccctatttgt
     3541 ttatttttct aaatacattc aaatatgtat ccgctcatga gacaataacc ctgataaatg
     3601 cttcaataat attgaaaaag gaagagtatg agtattcaac atttccgtgt cgcccttatt
     3661 cccttttttg cggcattttg ccttcctgtt tttgctcacc cagaaacgct ggtgaaagta
     3721 aaagatgctg aagatcagtt gggtgcacga gtgggttaca tcgaactgga tctcaacagc
     3781 ggtaagatcc ttgagagttt tcgccccgaa gaacgttttc caatgatgag cacttttaaa
     3841 gttctgctat gtggcgcggt attatcccgt attgacgccg ggcaagagca actcggtcgc
     3901 cgcatacact attctcagaa tgacttggtt gagtactcac cagtcacaga aaagcatctt
     3961 acggatggca tgacagtaag agaattatgc agtgctgcca taaccatgag tgataacact
     4021 gcggccaact tacttctgac aacgatcgga ggaccgaagg agctaaccgc ttttttgcac
     4081 aacatggggg atcatgtaac tcgccttgat cgttgggaac cggagctgaa tgaagccata
     4141 ccaaacgacg agcgtgacac cacgatgcct gtagcaatgg caacaacgtt gcgcaaacta
     4201 ttaactggcg aactacttac tctagcttcc cggcaacaat taatagactg gatggaggcg
     4261 gataaagttg caggaccact tctgcgctcg gcccttccgg ctggctggtt tattgctgat
     4321 aaatctggag ccggtgagcg tgggtctcgc ggtatcattg cagcactggg gccagatggt
     4381 aagccctccc gtatcgtagt tatctacacg acggggagtc aggcaactat ggatgaacga
     4441 aatagacaga tcgctgagat aggtgcctca ctgattaagc attggtaact gtcagaccaa
     4501 gtttactcat atatacttta gattgattta aaacttcatt tttaatttaa aaggatctag
     4561 gtgaagatcc tttttgataa tctcatgacc aaaatccctt aacgtgagtt ttcgttccac
     4621 tgagcgtcag accccgtaga aaagatcaaa ggatcttctt gagatccttt ttttctgcgc
     4681 gtaatctgct gcttgcaaac aaaaaaacca ccgctaccag cggtggtttg tttgccggat
     4741 caagagctac caactctttt tccgaaggta actggcttca gcagagcgca gataccaaat
     4801 actgttcttc tagtgtagcc gtagttaggc caccacttca agaactctgt agcaccgcct
     4861 acatacctcg ctctgctaat cctgttacca gtggctgctg ccagtggcga taagtcgtgt
     4921 cttaccgggt tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg
     4981 gggggttcgt gcacacagcc cagcttggag cgaacgacct acaccgaact gagataccta
     5041 cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg
     5101 gtaagcggca gggtcggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg
     5161 tatctttata gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc
     5221 tcgtcagggg ggcggagcct atggaaaaac gccagcaacg cggccttttt acggttcctg
     5281 gccttttgct ggccttttgc tcacatgttc tttcctgcgt tatcccctga ttctgtggat
     5341 aaccgtatta ccgcctttga gtgagctgat accgctcgcc gcagccgaac gaccgagcgc
     5401 agcgagtcag tgagcgagga agcggaagag cgcccaatac gcaaaccgcc tctccccgcg
     5461 cgttggccga ttcattaatg cagctggcac gacaggtttc ccgactggaa agcgggcagt
     5521 gagcgcaacg caattaatgt gagttagctc actcattagg caccccaggc tttacacttt
     5581 atgcttccgg ctcgtatgtt gtgtggaatt gtgagcggat aacaatttca cacaggaaac
     5641 agctatgacc atgattacgc caagcgcgca attaaccctc actaaaggga acaaaagctg
     5701 gagctgcaag cttaatgtag tcttatgcaa tactcttgta gtcttgcaac atggtaacga
     5761 tgagttagca acatgcctta caaggagaga aaaagcaccg tgcatgccga ttggtggaag
     5821 taaggtggta cgatcgtgcc ttattaggaa ggcaacagac gggtctgaca tggattggac
     5881 gaaccactga attgccgcat tgcagagata ttgtatttaa gtgcctagct cgatacataa
     5941 acgggtctct ctggttagac cagatctgag cctgggagct ctctggctaa ctagggaacc
     6001 cactgcttaa gcctcaataa agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt
     6061 tgtgtgactc tggtaactag agatccctca gaccctttta gtcagtgtgg aaaatctcta
     6121 gcagtggcgc ccgaacaggg acttgaaagc gaaagggaaa ccagaggagc tctctcgacg
     6181 caggactcgg cttgctgaag cgcgcacggc aagaggcgag gggcggcgac tggtgagtac
     6241 gccaaaaatt ttgactagcg gaggctagaa ggagagagat gggtgcgaga gcgtcagtat
     6301 taagcggggg agaattagat cgcgatggga aaaaattcgg ttaaggccag ggggaaagaa
     6361 aaaatataaa ttaaaacata tagtatgggc aagcagggag ctagaacgat tcgcagttaa
     6421 tcctggcctg ttagaaacat cagaaggctg tagacaaata ctgggacagc tacaaccatc
     6481 ccttcagaca ggatcagaag aacttagatc attatataat acagtagcaa ccctctattg
     6541 tgtgcatcaa aggatagaga taaaagacac caaggaagct ttagacaaga tagaggaaga
     6601 gcaaaacaaa agtaagacca ccgcacagca agcggccgct gatcttcaga cctggaggag
     6661 gagatatgag ggacaattgg agaagtgaat tatataaata taaagtagta aaaattgaac
     6721 cattaggagt agcacccacc aaggcaaaga gaagagtggt gcagagagaa aaaagagcag
     6781 tgggaatagg agctttgttc cttgggttct tgggagcagc aggaagcact atgggcgcag
     6841 cgtcaatgac gctgacggta caggccagac aattattgtc tggtatagtg cagcagcaga
     6901 acaatttgct gagggctatt gaggcgcaac agcatctgtt gcaactcaca gtctggggca
     6961 tcaagcagct ccaggcaaga atcctggctg tggaaagata cctaaaggat caacagctcc
     7021 tggggatttg gggttgctct ggaaaactca tttgcaccac tgctgtgcct tggaatgcta
     7081 gttg
//
