LOCUS       pLKO.1 shSV40 neo       7623 bp    DNA     circular SYN 14-APR-2025
DEFINITION  Lentiviral shRNA vector targeting simian virus 40 T antigen 
            (SV40Tag).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7623)
  AUTHORS   Lopacinski AB, Sweatt AJ, Smolko CM, Gray-Gaillard E, Borgman CA, 
            Shah M, Janes KA
  TITLE     Modeling the complete kinetics of coxsackievirus B3 reveals human 
            determinants of host-cell feedback.
  JOURNAL   Cell Syst. 2021 Apr 21;12(4):304-323.e13. doi: 
            10.1016/j.cels.2021.02.004. Epub 2021 Mar 18.
  PUBMED    33740397
REFERENCE   2  (bases 1 to 7623)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Apr 14, 2025 from SnapGene Server 8.0.1
            //gt12365.cn
COMMENT     SGRef: number: 1; type: "Journal Article"; doi: 
            "10.1016/j.cels.2021.02.004"; journalName: "Cell Syst"; date: 
            "2021-04-21- 21"; volume: "12"; issue: "4"; pages: "304-323.e13"
COMMENT     Sequence Label: pLKO.1 shSV40 neo
FEATURES             Location/Qualifiers
     source          1..7623
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        115..363
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     115..135
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     286..305
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    460..577
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        626..1136
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1055..1073
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1509..2303
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(1563..1582)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     2173..2192
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     primer_bind     complement(2325..2341)
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2326..2342)
                     /label=pBluescriptKS
                     /note="For pBluescript vector"
     LTR             2424..2657
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2729..2850
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2766..2785)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2820..2839
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2890..3025
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(3045..3064)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(3046..3064)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(3074..3091)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(3074..3090)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3083..3105)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3232..3687
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3319..3338)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3529..3550
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3713..3817
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3818..3886,3887..4678)
                     /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(4036..4055)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4849..5437
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5338..5357
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5591..5608
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5725..5746
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5761..5766,5767..5784,5785..5791)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5799..5815
                     /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     5804..5826
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5823..5839
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5823..5839
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5858..5878
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5860..5878
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5906..6132
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             6133..6313
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6360..6485
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6978..7211
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             7396..7440
                     /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 gaaggaatag aagaagaagg tggagagaga gacagagaca gatccattcg attagtgaac
       61 ggatctcgac ggtatcgatc acgagactag cctcgagcgg ccgccccctt caccgagggc
      121 ctatttccca tgattccttc atatttgcat atacgataca aggctgttag agagataatt
      181 ggaattaatt tgactgtaaa cacaaagata ttagtacaaa atacgtgacg tagaaagtaa
      241 taatttcttg ggtagtttgc agttttaaaa ttatgtttta aaatggacta tcatatgctt
      301 accgtaactt gaaagtattt cgatttcttg gctttatata tcttgtggaa aggacgaaac
      361 accgggcata gagtgtctgc tattaactgc agttaatagc agacactcta tgctttttga
      421 attctcgacc tcgagacaaa tggcagtatt catccacaat tttaaaagaa aaggggggat
      481 tggggggtac agtgcagggg aaagaatagt agacataata gcaacagaca tacaaactaa
      541 agaattacaa aaacaaatta caaaaattca aaattttcgg gtttattaca gggacagcag
      601 agatccactt tggccgcggc tcgagggggt tggggttgcg ccttttccaa ggcagccctg
      661 ggtttgcgca gggacgcggc tgctctgggc gtggttccgg gaaacgcagc ggcgccgacc
      721 ctgggtctcg cacattcttc acgtccgttc gcagcgtcac ccggatcttc gccgctaccc
      781 ttgtgggccc cccggcgacg cttcctgctc cgcccctaag tcgggaaggt tccttgcggt
      841 tcgcggcgtg ccggacgtga caaacggaag ccgcacgtct cactagtacc ctcgcagacg
      901 gacagcgcca gggagcaatg gcagcgcgcc gaccgcgatg ggctgtggcc aatagcggct
      961 gctcagcagg gcgcgccgag agcagcggcc gggaaggggc ggtgcgggag gcggggtgtg
     1021 gggcggtagt gtgggccctg ttcctgcccg cgcggtgttc cgcattctgc aagcctccgg
     1081 agcgcacgtc ggcagtcggc tccctcgttg accgaatcac cgacctctct ccccaggggg
     1141 atccaccgga tcaagcttca cgctgccgca agcactcagg gcgcaagggc tgctaaagga
     1201 agcggaacac gtagaaagcc agtccgcaga aacggtgctg accccggatg aatgtcagct
     1261 actgggctat ctggacaagg gaaaacgcaa gcgcaaagag aaagcaggta gcttgcagtg
     1321 ggcttacatg gcgatagcta gactgggcgg ttttatggac agcaagcgaa ccggaattgc
     1381 cagctggggc gccctctggt aaggttggga agccctgcaa agtaaactgg atggctttct
     1441 tgccgccaag gatctgatgg cgcaggggat caagatctga tcaagagaca ggatgaggat
     1501 cgtttcgcat gattgaacaa gatggattgc acgcaggttc tccggccgct tgggtggaga
     1561 ggctattcgg ctatgactgg gcacaacaga caatcggctg ctctgatgcc gccgtgttcc
     1621 ggctgtcagc gcaggggcgc ccggttcttt ttgtcaagac cgacctgtcc ggtgccctga
     1681 atgaactgca ggacgaggca gcgcggctat cgtggctggc cacgacgggc gttccttgcg
     1741 cagctgtgct cgacgttgtc actgaagcgg gaagggactg gctgctattg ggcgaagtgc
     1801 cggggcagga tctcctgtca tctcaccttg ctcctgccga gaaagtatcc atcatggctg
     1861 atgcaatgcg gcggctgcat acgcttgatc cggctacctg cccattcgac caccaagcga
     1921 aacatcgcat cgagcgagca cgtactcgga tggaagccgg tcttgtcgat caggatgatc
     1981 tggacgaaga gcatcagggg ctcgcgccag ccgaactgtt cgccaggctc aaggcgcgca
     2041 tgcccgacgg cgaggatctc gtcgtgaccc atggcgatgc ctgcttgccg aatatcatgg
     2101 tggaaaatgg ccgcttttct ggattcatcg actgtggccg gctgggtgtg gcggaccgct
     2161 atcaggacat agcgttggct acccgtgata ttgctgaaga gcttggcggc gaatgggctg
     2221 accgcttcct cgtgctttac ggtatcgccg ctcccgattc gcagcgcatc gccttctatc
     2281 gccttcttga cgagttcttc tgagcgggac tctggggttc gcatcgatac cgtcgacctc
     2341 gagggggggc ccggtacctt taagaccaat gacttacaag gcagctgtag atcttagcca
     2401 ctttttaaaa gaaaaggggg gactggaagg gctaattcac tcccaacgaa gacaagatct
     2461 gctttttgct tgtactgggt ctctctggtt agaccagatc tgagcctggg agctctctgg
     2521 ctaactaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt
     2581 gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccct tttagtcagt
     2641 gtggaaaatc tctagcagta gtagttcatg tcatcttatt attcagtatt tataacttgc
     2701 aaagaaatga atatcagaga gtgagaggaa cttgtttatt gcagcttata atggttacaa
     2761 ataaagcaat agcatcacaa atttcacaaa taaagcattt ttttcactgc attctagttg
     2821 tggtttgtcc aaactcatca atgtatctta tcatgtctgg ctctagctat cccgccccta
     2881 actccgccca tcccgcccct aactccgccc agttccgccc attctccgcc ccatggctga
     2941 ctaatttttt ttatttatgc agaggccgag gccgcctcgg cctctgagct attccagaag
     3001 tagtgaggag gcttttttgg aggcctaggg acgtacccaa ttcgccctat agtgagtcgt
     3061 attacgcgcg ctcactggcc gtcgttttac aacgtcgtga ctgggaaaac cctggcgtta
     3121 cccaacttaa tcgccttgca gcacatcccc ctttcgccag ctggcgtaat agcgaagagg
     3181 cccgcaccga tcgcccttcc caacagttgc gcagcctgaa tggcgaatgg gacgcgccct
     3241 gtagcggcgc attaagcgcg gcgggtgtgg tggttacgcg cagcgtgacc gctacacttg
     3301 ccagcgccct agcgcccgct cctttcgctt tcttcccttc ctttctcgcc acgttcgccg
     3361 gctttccccg tcaagctcta aatcgggggc tccctttagg gttccgattt agtgctttac
     3421 ggcacctcga ccccaaaaaa cttgattagg gtgatggttc acgtagtggg ccatcgccct
     3481 gatagacggt ttttcgccct ttgacgttgg agtccacgtt ctttaatagt ggactcttgt
     3541 tccaaactgg aacaacactc aaccctatct cggtctattc ttttgattta taagggattt
     3601 tgccgatttc ggcctattgg ttaaaaaatg agctgattta acaaaaattt aacgcgaatt
     3661 ttaacaaaat attaacgctt acaatttagg tggcactttt cggggaaatg tgcgcggaac
     3721 ccctatttgt ttatttttct aaatacattc aaatatgtat ccgctcatga gacaataacc
     3781 ctgataaatg cttcaataat attgaaaaag gaagagtatg agtattcaac atttccgtgt
     3841 cgcccttatt cccttttttg cggcattttg ccttcctgtt tttgctcacc cagaaacgct
     3901 ggtgaaagta aaagatgctg aagatcagtt gggtgcacga gtgggttaca tcgaactgga
     3961 tctcaacagc ggtaagatcc ttgagagttt tcgccccgaa gaacgttttc caatgatgag
     4021 cacttttaaa gttctgctat gtggcgcggt attatcccgt attgacgccg ggcaagagca
     4081 actcggtcgc cgcatacact attctcagaa tgacttggtt gagtactcac cagtcacaga
     4141 aaagcatctt acggatggca tgacagtaag agaattatgc agtgctgcca taaccatgag
     4201 tgataacact gcggccaact tacttctgac aacgatcgga ggaccgaagg agctaaccgc
     4261 ttttttgcac aacatggggg atcatgtaac tcgccttgat cgttgggaac cggagctgaa
     4321 tgaagccata ccaaacgacg agcgtgacac cacgatgcct gtagcaatgg caacaacgtt
     4381 gcgcaaacta ttaactggcg aactacttac tctagcttcc cggcaacaat taatagactg
     4441 gatggaggcg gataaagttg caggaccact tctgcgctcg gcccttccgg ctggctggtt
     4501 tattgctgat aaatctggag ccggtgagcg tgggtctcgc ggtatcattg cagcactggg
     4561 gccagatggt aagccctccc gtatcgtagt tatctacacg acggggagtc aggcaactat
     4621 ggatgaacga aatagacaga tcgctgagat aggtgcctca ctgattaagc attggtaact
     4681 gtcagaccaa gtttactcat atatacttta gattgattta aaacttcatt tttaatttaa
     4741 aaggatctag gtgaagatcc tttttgataa tctcatgacc aaaatccctt aacgtgagtt
     4801 ttcgttccac tgagcgtcag accccgtaga aaagatcaaa ggatcttctt gagatccttt
     4861 ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca ccgctaccag cggtggtttg
     4921 tttgccggat caagagctac caactctttt tccgaaggta actggcttca gcagagcgca
     4981 gataccaaat actgttcttc tagtgtagcc gtagttaggc caccacttca agaactctgt
     5041 agcaccgcct acatacctcg ctctgctaat cctgttacca gtggctgctg ccagtggcga
     5101 taagtcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg cgcagcggtc
     5161 gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct acaccgaact
     5221 gagataccta cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga
     5281 caggtatccg gtaagcggca gggtcggaac aggagagcgc acgagggagc ttccaggggg
     5341 aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt
     5401 tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gccagcaacg cggccttttt
     5461 acggttcctg gccttttgct ggccttttgc tcacatgttc tttcctgcgt tatcccctga
     5521 ttctgtggat aaccgtatta ccgcctttga gtgagctgat accgctcgcc gcagccgaac
     5581 gaccgagcgc agcgagtcag tgagcgagga agcggaagag cgcccaatac gcaaaccgcc
     5641 tctccccgcg cgttggccga ttcattaatg cagctggcac gacaggtttc ccgactggaa
     5701 agcgggcagt gagcgcaacg caattaatgt gagttagctc actcattagg caccccaggc
     5761 tttacacttt atgcttccgg ctcgtatgtt gtgtggaatt gtgagcggat aacaatttca
     5821 cacaggaaac agctatgacc atgattacgc caagcgcgca attaaccctc actaaaggga
     5881 acaaaagctg gagctgcaag cttaatgtag tcttatgcaa tactcttgta gtcttgcaac
     5941 atggtaacga tgagttagca acatgcctta caaggagaga aaaagcaccg tgcatgccga
     6001 ttggtggaag taaggtggta cgatcgtgcc ttattaggaa ggcaacagac gggtctgaca
     6061 tggattggac gaaccactga attgccgcat tgcagagata ttgtatttaa gtgcctagct
     6121 cgatacataa acgggtctct ctggttagac cagatctgag cctgggagct ctctggctaa
     6181 ctagggaacc cactgcttaa gcctcaataa agcttgcctt gagtgcttca agtagtgtgt
     6241 gcccgtctgt tgtgtgactc tggtaactag agatccctca gaccctttta gtcagtgtgg
     6301 aaaatctcta gcagtggcgc ccgaacaggg acttgaaagc gaaagggaaa ccagaggagc
     6361 tctctcgacg caggactcgg cttgctgaag cgcgcacggc aagaggcgag gggcggcgac
     6421 tggtgagtac gccaaaaatt ttgactagcg gaggctagaa ggagagagat gggtgcgaga
     6481 gcgtcagtat taagcggggg agaattagat cgcgatggga aaaaattcgg ttaaggccag
     6541 ggggaaagaa aaaatataaa ttaaaacata tagtatgggc aagcagggag ctagaacgat
     6601 tcgcagttaa tcctggcctg ttagaaacat cagaaggctg tagacaaata ctgggacagc
     6661 tacaaccatc ccttcagaca ggatcagaag aacttagatc attatataat acagtagcaa
     6721 ccctctattg tgtgcatcaa aggatagaga taaaagacac caaggaagct ttagacaaga
     6781 tagaggaaga gcaaaacaaa agtaagacca ccgcacagca agcggccgct gatcttcaga
     6841 cctggaggag gagatatgag ggacaattgg agaagtgaat tatataaata taaagtagta
     6901 aaaattgaac cattaggagt agcacccacc aaggcaaaga gaagagtggt gcagagagaa
     6961 aaaagagcag tgggaatagg agctttgttc cttgggttct tgggagcagc aggaagcact
     7021 atgggcgcag cgtcaatgac gctgacggta caggccagac aattattgtc tggtatagtg
     7081 cagcagcaga acaatttgct gagggctatt gaggcgcaac agcatctgtt gcaactcaca
     7141 gtctggggca tcaagcagct ccaggcaaga atcctggctg tggaaagata cctaaaggat
     7201 caacagctcc tggggatttg gggttgctct ggaaaactca tttgcaccac tgctgtgcct
     7261 tggaatgcta gttggagtaa taaatctctg gaacagattt ggaatcacac gacctggatg
     7321 gagtgggaca gagaaattaa caattacaca agcttaatac actccttaat tgaagaatcg
     7381 caaaaccagc aagaaaagaa tgaacaagaa ttattggaat tagataaatg ggcaagtttg
     7441 tggaattggt ttaacataac aaattggctg tggtatataa aattattcat aatgatagta
     7501 ggaggcttgg taggtttaag aatagttttt gctgtacttt ctatagtgaa tagagttagg
     7561 cagggatatt caccattatc gtttcagacc cacctcccaa ccccgagggg acccgacagg
     7621 ccc
//