LOCUS       sequence-318868-        7050 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Lentiviral negative control vector containing scramble shRNA.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7050)
  AUTHORS   Roman-Fernandez A, Roignot J, Sandilands E, Nacke M, Mansour MA, 
            McGarry L, Shanks E, Mostov KE, Bryant DM
  TITLE     The phospholipid PI(3,4)P2 is an apical identity determinant.
  JOURNAL   Nat Commun. 2018 Nov 28;9(1):5041. doi: 10.1038/s41467-018-07464-8.
  PUBMED    30487552
REFERENCE   2  (bases 1 to 7050)
  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: "Nat 
            Commun."; date: "2018-11-28"; volume: "9(1):5041. doi"; pages: " 
            10.1038/s41467-018-07464-8"
COMMENT     Sequence Label: pLKO.1 Puro shRNA Scramble
FEATURES             Location/Qualifiers
     source          1..7050
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        243..491
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     243..263
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     414..433
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    554..671
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        720..1230
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1149..1167
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1252..1851
                     /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(1252..1271)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     1748..1768
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             1979..2212
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2284..2405
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2321..2340)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2375..2394
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2445..2580
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2600..2619)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(2601..2619)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2629..2646)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2629..2645)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2638..2660)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      2787..3242
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2874..2893)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3084..3105
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3268..3372
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3373..3441,3442..4233)
                     /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(3591..3610)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4404..4992
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     4893..4912
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5146..5163
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5280..5301
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5316..5321,5322..5339,5340..5346)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5354..5370
                     /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     5359..5381
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5378..5394
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5378..5394
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5413..5433
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5415..5433
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5461..5687
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             5688..5868
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    5915..6040
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6533..6766
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             6951..6995
                     /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"
ORIGIN
        1 tagtaggagg cttggtaggt ttaagaatag tttttgctgt actttctata gtgaatagag
       61 ttaggcaggg atattcacca ttatcgtttc agacccacct cccaaccccg aggggacccg
      121 acaggcccga aggaatagaa gaagaaggtg gagagagaga cagagacaga tccattcgat
      181 tagtgaacgg atctcgacgg tatcgatcac gagactagcc tcgagcggcc gcccccttca
      241 ccgagggcct atttcccatg attccttcat atttgcatat acgatacaag gctgttagag
      301 agataattgg aattaatttg actgtaaaca caaagatatt agtacaaaat acgtgacgta
      361 gaaagtaata atttcttggg tagtttgcag ttttaaaatt atgttttaaa atggactatc
      421 atatgcttac cgtaacttga aagtatttcg atttcttggc tttatatatc ttgtggaaag
      481 gacgaaacac cggtccgcag gtatgcacgc gtgaattctc gacctcgaga caaatggcag
      541 tattcatcca caattttaaa agaaaagggg ggattggggg gtacagtgca ggggaaagaa
      601 tagtagacat aatagcaaca gacatacaaa ctaaagaatt acaaaaacaa attacaaaaa
      661 ttcaaaattt tcgggtttat tacagggaca gcagagatcc actttggccg cggctcgagg
      721 gggttggggt tgcgcctttt ccaaggcagc cctgggtttg cgcagggacg cggctgctct
      781 gggcgtggtt ccgggaaacg cagcggcgcc gaccctgggt ctcgcacatt cttcacgtcc
      841 gttcgcagcg tcacccggat cttcgccgct acccttgtgg gccccccggc gacgcttcct
      901 gctccgcccc taagtcggga aggttccttg cggttcgcgg cgtgccggac gtgacaaacg
      961 gaagccgcac gtctcactag taccctcgca gacggacagc gccagggagc aatggcagcg
     1021 cgccgaccgc gatgggctgt ggccaatagc ggctgctcag cagggcgcgc cgagagcagc
     1081 ggccgggaag gggcggtgcg ggaggcgggg tgtggggcgg tagtgtgggc cctgttcctg
     1141 cccgcgcggt gttccgcatt ctgcaagcct ccggagcgca cgtcggcagt cggctccctc
     1201 gttgaccgaa tcaccgacct ctctccccag ggggatccac cggagcttac catgaccgag
     1261 tacaagccca cggtgcgcct cgccacccgc gacgacgtcc ccagggccgt acgcaccctc
     1321 gccgccgcgt tcgccgacta ccccgccacg cgccacaccg tcgatccgga ccgccacatc
     1381 gagcgggtca ccgagctgca agaactcttc ctcacgcgcg tcgggctcga catcggcaag
     1441 gtgtgggtcg cggacgacgg cgccgcggtg gcggtctgga ccacgccgga gagcgtcgaa
     1501 gcgggggcgg tgttcgccga gatcggcccg cgcatggccg agttgagcgg ttcccggctg
     1561 gccgcgcagc aacagatgga aggcctcctg gcgccgcacc ggcccaagga gcccgcgtgg
     1621 ttcctggcca ccgtcggcgt ctcgcccgac caccagggca agggtctggg cagcgccgtc
     1681 gtgctccccg gagtggaggc ggccgagcgc gccggggtgc ccgccttcct ggagacctcc
     1741 gcgccccgca acctcccctt ctacgagcgg ctcggcttca ccgtcaccgc cgacgtcgag
     1801 gtgcccgaag gaccgcgcac ctggtgcatg acccgcaagc ccggtgcctg acgcccgccc
     1861 cacgacccgc agcgcccgac cgaaaggagc gcacgacccc atgcatcggt acctttaaga
     1921 ccaatgactt acaaggcagc tgtagatctt agccactttt taaaagaaaa ggggggactg
     1981 gaagggctaa ttcactccca acgaagacaa gatctgcttt ttgcttgtac tgggtctctc
     2041 tggttagacc agatctgagc ctgggagctc tctggctaac tagggaaccc actgcttaag
     2101 cctcaataaa gcttgccttg agtgcttcaa gtagtgtgtg cccgtctgtt gtgtgactct
     2161 ggtaactaga gatccctcag acccttttag tcagtgtgga aaatctctag cagtagtagt
     2221 tcatgtcatc ttattattca gtatttataa cttgcaaaga aatgaatatc agagagtgag
     2281 aggaacttgt ttattgcagc ttataatggt tacaaataaa gcaatagcat cacaaatttc
     2341 acaaataaag catttttttc actgcattct agttgtggtt tgtccaaact catcaatgta
     2401 tcttatcatg tctggctcta gctatcccgc ccctaactcc gcccatcccg cccctaactc
     2461 cgcccagttc cgcccattct ccgccccatg gctgactaat tttttttatt tatgcagagg
     2521 ccgaggccgc ctcggcctct gagctattcc agaagtagtg aggaggcttt tttggaggcc
     2581 tagggacgta cccaattcgc cctatagtga gtcgtattac gcgcgctcac tggccgtcgt
     2641 tttacaacgt cgtgactggg aaaaccctgg cgttacccaa cttaatcgcc ttgcagcaca
     2701 tccccctttc gccagctggc gtaatagcga agaggcccgc accgatcgcc cttcccaaca
     2761 gttgcgcagc ctgaatggcg aatgggacgc gccctgtagc ggcgcattaa gcgcggcggg
     2821 tgtggtggtt acgcgcagcg tgaccgctac acttgccagc gccctagcgc ccgctccttt
     2881 cgctttcttc ccttcctttc tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg
     2941 ggggctccct ttagggttcc gatttagtgc tttacggcac ctcgacccca aaaaacttga
     3001 ttagggtgat ggttcacgta gtgggccatc gccctgatag acggtttttc gccctttgac
     3061 gttggagtcc acgttcttta atagtggact cttgttccaa actggaacaa cactcaaccc
     3121 tatctcggtc tattcttttg atttataagg gattttgccg atttcggcct attggttaaa
     3181 aaatgagctg atttaacaaa aatttaacgc gaattttaac aaaatattaa cgcttacaat
     3241 ttaggtggca cttttcgggg aaatgtgcgc ggaaccccta tttgtttatt tttctaaata
     3301 cattcaaata tgtatccgct catgagacaa taaccctgat aaatgcttca ataatattga
     3361 aaaaggaaga gtatgagtat tcaacatttc cgtgtcgccc ttattccctt ttttgcggca
     3421 ttttgccttc ctgtttttgc tcacccagaa acgctggtga aagtaaaaga tgctgaagat
     3481 cagttgggtg cacgagtggg ttacatcgaa ctggatctca acagcggtaa gatccttgag
     3541 agttttcgcc ccgaagaacg ttttccaatg atgagcactt ttaaagttct gctatgtggc
     3601 gcggtattat cccgtattga cgccgggcaa gagcaactcg gtcgccgcat acactattct
     3661 cagaatgact tggttgagta ctcaccagtc acagaaaagc atcttacgga tggcatgaca
     3721 gtaagagaat tatgcagtgc tgccataacc atgagtgata acactgcggc caacttactt
     3781 ctgacaacga tcggaggacc gaaggagcta accgcttttt tgcacaacat gggggatcat
     3841 gtaactcgcc ttgatcgttg ggaaccggag ctgaatgaag ccataccaaa cgacgagcgt
     3901 gacaccacga tgcctgtagc aatggcaaca acgttgcgca aactattaac tggcgaacta
     3961 cttactctag cttcccggca acaattaata gactggatgg aggcggataa agttgcagga
     4021 ccacttctgc gctcggccct tccggctggc tggtttattg ctgataaatc tggagccggt
     4081 gagcgtgggt ctcgcggtat cattgcagca ctggggccag atggtaagcc ctcccgtatc
     4141 gtagttatct acacgacggg gagtcaggca actatggatg aacgaaatag acagatcgct
     4201 gagataggtg cctcactgat taagcattgg taactgtcag accaagttta ctcatatata
     4261 ctttagattg atttaaaact tcatttttaa tttaaaagga tctaggtgaa gatccttttt
     4321 gataatctca tgaccaaaat cccttaacgt gagttttcgt tccactgagc gtcagacccc
     4381 gtagaaaaga tcaaaggatc ttcttgagat cctttttttc tgcgcgtaat ctgctgcttg
     4441 caaacaaaaa aaccaccgct accagcggtg gtttgtttgc cggatcaaga gctaccaact
     4501 ctttttccga aggtaactgg cttcagcaga gcgcagatac caaatactgt tcttctagtg
     4561 tagccgtagt taggccacca cttcaagaac tctgtagcac cgcctacata cctcgctctg
     4621 ctaatcctgt taccagtggc tgctgccagt ggcgataagt cgtgtcttac cgggttggac
     4681 tcaagacgat agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca
     4741 cagcccagct tggagcgaac gacctacacc gaactgagat acctacagcg tgagctatga
     4801 gaaagcgcca cgcttcccga agggagaaag gcggacaggt atccggtaag cggcagggtc
     4861 ggaacaggag agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct
     4921 gtcgggtttc gccacctctg acttgagcgt cgatttttgt gatgctcgtc aggggggcgg
     4981 agcctatgga aaaacgccag caacgcggcc tttttacggt tcctggcctt ttgctggcct
     5041 tttgctcaca tgttctttcc tgcgttatcc cctgattctg tggataaccg tattaccgcc
     5101 tttgagtgag ctgataccgc tcgccgcagc cgaacgaccg agcgcagcga gtcagtgagc
     5161 gaggaagcgg aagagcgccc aatacgcaaa ccgcctctcc ccgcgcgttg gccgattcat
     5221 taatgcagct ggcacgacag gtttcccgac tggaaagcgg gcagtgagcg caacgcaatt
     5281 aatgtgagtt agctcactca ttaggcaccc caggctttac actttatgct tccggctcgt
     5341 atgttgtgtg gaattgtgag cggataacaa tttcacacag gaaacagcta tgaccatgat
     5401 tacgccaagc gcgcaattaa ccctcactaa agggaacaaa agctggagct gcaagcttaa
     5461 tgtagtctta tgcaatactc ttgtagtctt gcaacatggt aacgatgagt tagcaacatg
     5521 ccttacaagg agagaaaaag caccgtgcat gccgattggt ggaagtaagg tggtacgatc
     5581 gtgccttatt aggaaggcaa cagacgggtc tgacatggat tggacgaacc actgaattgc
     5641 cgcattgcag agatattgta tttaagtgcc tagctcgata cataaacggg tctctctggt
     5701 tagaccagat ctgagcctgg gagctctctg gctaactagg gaacccactg cttaagcctc
     5761 aataaagctt gccttgagtg cttcaagtag tgtgtgcccg tctgttgtgt gactctggta
     5821 actagagatc cctcagaccc ttttagtcag tgtggaaaat ctctagcagt ggcgcccgaa
     5881 cagggacttg aaagcgaaag ggaaaccaga ggagctctct cgacgcagga ctcggcttgc
     5941 tgaagcgcgc acggcaagag gcgaggggcg gcgactggtg agtacgccaa aaattttgac
     6001 tagcggaggc tagaaggaga gagatgggtg cgagagcgtc agtattaagc gggggagaat
     6061 tagatcgcga tgggaaaaaa ttcggttaag gccaggggga aagaaaaaat ataaattaaa
     6121 acatatagta tgggcaagca gggagctaga acgattcgca gttaatcctg gcctgttaga
     6181 aacatcagaa ggctgtagac aaatactggg acagctacaa ccatcccttc agacaggatc
     6241 agaagaactt agatcattat ataatacagt agcaaccctc tattgtgtgc atcaaaggat
     6301 agagataaaa gacaccaagg aagctttaga caagatagag gaagagcaaa acaaaagtaa
     6361 gaccaccgca cagcaagcgg ccgctgatct tcagacctgg aggaggagat atgagggaca
     6421 attggagaag tgaattatat aaatataaag tagtaaaaat tgaaccatta ggagtagcac
     6481 ccaccaaggc aaagagaaga gtggtgcaga gagaaaaaag agcagtggga ataggagctt
     6541 tgttccttgg gttcttggga gcagcaggaa gcactatggg cgcagcgtca atgacgctga
     6601 cggtacaggc cagacaatta ttgtctggta tagtgcagca gcagaacaat ttgctgaggg
     6661 ctattgaggc gcaacagcat ctgttgcaac tcacagtctg gggcatcaag cagctccagg
     6721 caagaatcct ggctgtggaa agatacctaa aggatcaaca gctcctgggg atttggggtt
     6781 gctctggaaa actcatttgc accactgctg tgccttggaa tgctagttgg agtaataaat
     6841 ctctggaaca gatttggaat cacacgacct ggatggagtg ggacagagaa attaacaatt
     6901 acacaagctt aatacactcc ttaattgaag aatcgcaaaa ccagcaagaa aagaatgaac
     6961 aagaattatt ggaattagat aaatgggcaa gtttgtggaa ttggtttaac ataacaaatt
     7021 ggctgtggta tataaaatta ttcataatga
//
