LOCUS       sequence-269245-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  UPF1 shRNA (Targeting CDS) inserted into the PLKO.1 plasmid 
            (AAGACACCTATTACACGAAGG).
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-UPF1-CDS
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             155..199
                     /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        497..745
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     497..517
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     668..687
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    842..959
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        1008..1518
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1437..1455
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1540..2139
                     /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(1540..1559)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     2036..2056
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             2267..2500
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2572..2693
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2609..2628)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2663..2682
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2733..2868
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2888..2907)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(2889..2907)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2917..2934)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2917..2933)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2926..2948)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3075..3530
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3162..3181)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3372..3393
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3556..3660
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3661..3729,3730..4521)
                     /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(3879..3898)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4692..5280
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5181..5200
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5434..5451
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5568..5589
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5604..5609,5610..5627,5628..5634)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5642..5658
                     /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     5647..5669
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5666..5682
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5666..5682
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5701..5721
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5703..5721
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5749..5975
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             5976..6156
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6203..6328
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6821..7054
                     /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 ttgcaccact gctgtgcctt ggaatgctag ttggagtaat aaatctctgg aacagatttg
       61 gaatcacacg acctggatgg agtgggacag agaaattaac aattacacaa gcttaataca
      121 ctccttaatt gaagaatcgc aaaaccagca agaaaagaat gaacaagaat tattggaatt
      181 agataaatgg gcaagtttgt ggaattggtt taacataaca aattggctgt ggtatataaa
      241 attattcata atgatagtag gaggcttggt aggtttaaga atagtttttg ctgtactttc
      301 tatagtgaat agagttaggc agggatattc accattatcg tttcagaccc acctcccaac
      361 cccgagggga cccgacaggc ccgaaggaat agaagaagaa ggtggagaga gagacagaga
      421 cagatccatt cgattagtga acggatctcg acggtatcga tcacgagact agcctcgagc
      481 ggccgccccc ttcaccgagg gcctatttcc catgattcct tcatatttgc atatacgata
      541 caaggctgtt agagagataa ttggaattaa tttgactgta aacacaaaga tattagtaca
      601 aaatacgtga cgtagaaagt aataatttct tgggtagttt gcagttttaa aattatgttt
      661 taaaatggac tatcatatgc ttaccgtaac ttgaaagtat ttcgatttct tggctttata
      721 tatcttgtgg aaaggacgaa acaccggaag acacctatta cacgaaggct cgagccttcg
      781 tgtaataggt gtcttttttt gaattctcga cctcgagaca aatggcagta ttcatccaca
      841 attttaaaag aaaagggggg attggggggt acagtgcagg ggaaagaata gtagacataa
      901 tagcaacaga catacaaact aaagaattac aaaaacaaat tacaaaaatt caaaattttc
      961 gggtttatta cagggacagc agagatccac tttggccgcg gctcgagggg gttggggttg
     1021 cgccttttcc aaggcagccc tgggtttgcg cagggacgcg gctgctctgg gcgtggttcc
     1081 gggaaacgca gcggcgccga ccctgggtct cgcacattct tcacgtccgt tcgcagcgtc
     1141 acccggatct tcgccgctac ccttgtgggc cccccggcga cgcttcctgc tccgccccta
     1201 agtcgggaag gttccttgcg gttcgcggcg tgccggacgt gacaaacgga agccgcacgt
     1261 ctcactagta ccctcgcaga cggacagcgc cagggagcaa tggcagcgcg ccgaccgcga
     1321 tgggctgtgg ccaatagcgg ctgctcagca gggcgcgccg agagcagcgg ccgggaaggg
     1381 gcggtgcggg aggcggggtg tggggcggta gtgtgggccc tgttcctgcc cgcgcggtgt
     1441 tccgcattct gcaagcctcc ggagcgcacg tcggcagtcg gctccctcgt tgaccgaatc
     1501 accgacctct ctccccaggg ggatccaccg gagcttacca tgaccgagta caagcccacg
     1561 gtgcgcctcg ccacccgcga cgacgtcccc agggccgtac gcaccctcgc cgccgcgttc
     1621 gccgactacc ccgccacgcg ccacaccgtc gatccggacc gccacatcga gcgggtcacc
     1681 gagctgcaag aactcttcct cacgcgcgtc gggctcgaca tcggcaaggt gtgggtcgcg
     1741 gacgacggcg ccgcggtggc ggtctggacc acgccggaga gcgtcgaagc gggggcggtg
     1801 ttcgccgaga tcggcccgcg catggccgag ttgagcggtt cccggctggc cgcgcagcaa
     1861 cagatggaag gcctcctggc gccgcaccgg cccaaggagc ccgcgtggtt cctggccacc
     1921 gtcggcgtct cgcccgacca ccagggcaag ggtctgggca gcgccgtcgt gctccccgga
     1981 gtggaggcgg ccgagcgcgc cggggtgccc gccttcctgg agacctccgc gccccgcaac
     2041 ctccccttct acgagcggct cggcttcacc gtcaccgccg acgtcgaggt gcccgaagga
     2101 ccgcgcacct ggtgcatgac ccgcaagccc ggtgcctgac gcccgcccca cgacccgcag
     2161 cgcccgaccg aaaggagcgc acgaccccat gcatcggtac ctttaagacc aatgacttac
     2221 aaggcagctg tagatcttag ccacttttta aaagaaaagg ggggactgga agggctaatt
     2281 cactcccaac gaagacaaga tctgcttttt gcttgtactg ggtctctctg gttagaccag
     2341 atctgagcct gggagctctc tggctaacta gggaacccac tgcttaagcc tcaataaagc
     2401 ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt gtgactctgg taactagaga
     2461 tccctcagac ccttttagtc agtgtggaaa atctctagca gtagtagttc atgtcatctt
     2521 attattcagt atttataact tgcaaagaaa tgaatatcag agagtgagag gaacttgttt
     2581 attgcagctt ataatggtta caaataaagc aatagcatca caaatttcac aaataaagca
     2641 tttttttcac tgcattctag ttgtggtttg tccaaactca tcaatgtatc ttatcatgtc
     2701 tggctctagc tatcccgccc ctaactccgc ccatcccgcc cctaactccg cccagttccg
     2761 cccattctcc gccccatggc tgactaattt tttttattta tgcagaggcc gaggccgcct
     2821 cggcctctga gctattccag aagtagtgag gaggcttttt tggaggccta gggacgtacc
     2881 caattcgccc tatagtgagt cgtattacgc gcgctcactg gccgtcgttt tacaacgtcg
     2941 tgactgggaa aaccctggcg ttacccaact taatcgcctt gcagcacatc cccctttcgc
     3001 cagctggcgt aatagcgaag aggcccgcac cgatcgccct tcccaacagt tgcgcagcct
     3061 gaatggcgaa tgggacgcgc cctgtagcgg cgcattaagc gcggcgggtg tggtggttac
     3121 gcgcagcgtg accgctacac ttgccagcgc cctagcgccc gctcctttcg ctttcttccc
     3181 ttcctttctc gccacgttcg ccggctttcc ccgtcaagct ctaaatcggg ggctcccttt
     3241 agggttccga tttagtgctt tacggcacct cgaccccaaa aaacttgatt agggtgatgg
     3301 ttcacgtagt gggccatcgc cctgatagac ggtttttcgc cctttgacgt tggagtccac
     3361 gttctttaat agtggactct tgttccaaac tggaacaaca ctcaacccta tctcggtcta
     3421 ttcttttgat ttataaggga ttttgccgat ttcggcctat tggttaaaaa atgagctgat
     3481 ttaacaaaaa tttaacgcga attttaacaa aatattaacg cttacaattt aggtggcact
     3541 tttcggggaa atgtgcgcgg aacccctatt tgtttatttt tctaaataca ttcaaatatg
     3601 tatccgctca tgagacaata accctgataa atgcttcaat aatattgaaa aaggaagagt
     3661 atgagtattc aacatttccg tgtcgccctt attccctttt ttgcggcatt ttgccttcct
     3721 gtttttgctc acccagaaac gctggtgaaa gtaaaagatg ctgaagatca gttgggtgca
     3781 cgagtgggtt acatcgaact ggatctcaac agcggtaaga tccttgagag ttttcgcccc
     3841 gaagaacgtt ttccaatgat gagcactttt aaagttctgc tatgtggcgc ggtattatcc
     3901 cgtattgacg ccgggcaaga gcaactcggt cgccgcatac actattctca gaatgacttg
     3961 gttgagtact caccagtcac agaaaagcat cttacggatg gcatgacagt aagagaatta
     4021 tgcagtgctg ccataaccat gagtgataac actgcggcca acttacttct gacaacgatc
     4081 ggaggaccga aggagctaac cgcttttttg cacaacatgg gggatcatgt aactcgcctt
     4141 gatcgttggg aaccggagct gaatgaagcc ataccaaacg acgagcgtga caccacgatg
     4201 cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg gcgaactact tactctagct
     4261 tcccggcaac aattaataga ctggatggag gcggataaag ttgcaggacc acttctgcgc
     4321 tcggcccttc cggctggctg gtttattgct gataaatctg gagccggtga gcgtgggtct
     4381 cgcggtatca ttgcagcact ggggccagat ggtaagccct cccgtatcgt agttatctac
     4441 acgacgggga gtcaggcaac tatggatgaa cgaaatagac agatcgctga gataggtgcc
     4501 tcactgatta agcattggta actgtcagac caagtttact catatatact ttagattgat
     4561 ttaaaacttc atttttaatt taaaaggatc taggtgaaga tcctttttga taatctcatg
     4621 accaaaatcc cttaacgtga gttttcgttc cactgagcgt cagaccccgt agaaaagatc
     4681 aaaggatctt cttgagatcc tttttttctg cgcgtaatct gctgcttgca aacaaaaaaa
     4741 ccaccgctac cagcggtggt ttgtttgccg gatcaagagc taccaactct ttttccgaag
     4801 gtaactggct tcagcagagc gcagatacca aatactgttc ttctagtgta gccgtagtta
     4861 ggccaccact tcaagaactc tgtagcaccg cctacatacc tcgctctgct aatcctgtta
     4921 ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg ggttggactc aagacgatag
     4981 ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca gcccagcttg
     5041 gagcgaacga cctacaccga actgagatac ctacagcgtg agctatgaga aagcgccacg
     5101 cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg aacaggagag
     5161 cgcacgaggg agcttccagg gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc
     5221 cacctctgac ttgagcgtcg atttttgtga tgctcgtcag gggggcggag cctatggaaa
     5281 aacgccagca acgcggcctt tttacggttc ctggcctttt gctggccttt tgctcacatg
     5341 ttctttcctg cgttatcccc tgattctgtg gataaccgta ttaccgcctt tgagtgagct
     5401 gataccgctc gccgcagccg aacgaccgag cgcagcgagt cagtgagcga ggaagcggaa
     5461 gagcgcccaa tacgcaaacc gcctctcccc gcgcgttggc cgattcatta atgcagctgg
     5521 cacgacaggt ttcccgactg gaaagcgggc agtgagcgca acgcaattaa tgtgagttag
     5581 ctcactcatt aggcacccca ggctttacac tttatgcttc cggctcgtat gttgtgtgga
     5641 attgtgagcg gataacaatt tcacacagga aacagctatg accatgatta cgccaagcgc
     5701 gcaattaacc ctcactaaag ggaacaaaag ctggagctgc aagcttaatg tagtcttatg
     5761 caatactctt gtagtcttgc aacatggtaa cgatgagtta gcaacatgcc ttacaaggag
     5821 agaaaaagca ccgtgcatgc cgattggtgg aagtaaggtg gtacgatcgt gccttattag
     5881 gaaggcaaca gacgggtctg acatggattg gacgaaccac tgaattgccg cattgcagag
     5941 atattgtatt taagtgccta gctcgataca taaacgggtc tctctggtta gaccagatct
     6001 gagcctggga gctctctggc taactaggga acccactgct taagcctcaa taaagcttgc
     6061 cttgagtgct tcaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc
     6121 tcagaccctt ttagtcagtg tggaaaatct ctagcagtgg cgcccgaaca gggacttgaa
     6181 agcgaaaggg aaaccagagg agctctctcg acgcaggact cggcttgctg aagcgcgcac
     6241 ggcaagaggc gaggggcggc gactggtgag tacgccaaaa attttgacta gcggaggcta
     6301 gaaggagaga gatgggtgcg agagcgtcag tattaagcgg gggagaatta gatcgcgatg
     6361 ggaaaaaatt cggttaaggc cagggggaaa gaaaaaatat aaattaaaac atatagtatg
     6421 ggcaagcagg gagctagaac gattcgcagt taatcctggc ctgttagaaa catcagaagg
     6481 ctgtagacaa atactgggac agctacaacc atcccttcag acaggatcag aagaacttag
     6541 atcattatat aatacagtag caaccctcta ttgtgtgcat caaaggatag agataaaaga
     6601 caccaaggaa gctttagaca agatagagga agagcaaaac aaaagtaaga ccaccgcaca
     6661 gcaagcggcc gctgatcttc agacctggag gaggagatat gagggacaat tggagaagtg
     6721 aattatataa atataaagta gtaaaaattg aaccattagg agtagcaccc accaaggcaa
     6781 agagaagagt ggtgcagaga gaaaaaagag cagtgggaat aggagctttg ttccttgggt
     6841 tcttgggagc agcaggaagc actatgggcg cagcgtcaat gacgctgacg gtacaggcca
     6901 gacaattatt gtctggtata gtgcagcagc agaacaattt gctgagggct attgaggcgc
     6961 aacagcatct gttgcaactc acagtctggg gcatcaagca gctccaggca agaatcctgg
     7021 ctgtggaaag atacctaaag gatcaacagc tcctggggat ttggggttgc tctggaaaac
     7081 tcat
//
