LOCUS       sequence-269241-        7083 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  UPF2 shRNA (Targeting 3'UTR) inserted into the PLKO.1 plasmid 
            (CGCGAGGGTTAATCTTCTCTT).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7083)
  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 7083)
  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-UPF2-3'UTR
FEATURES             Location/Qualifiers
     source          1..7083
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     23..43
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             254..487
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    559..680
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(596..615)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     650..669
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      720..855
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(875..894)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(876..894)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(904..921)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(904..920)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(913..935)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      1062..1517
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1149..1168)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1359..1380
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        1543..1647
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(1648..1716,1717..2508)
                     /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(1866..1885)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      2679..3267
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     3168..3187
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     3421..3438
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    3555..3576
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(3591..3596,3597..3614,3615..3621)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    3629..3645
                     /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     3634..3656
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     3653..3669
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     3653..3669
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     3688..3708
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        3690..3708
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        3736..3962
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             3963..4143
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    4190..4315
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    4808..5041
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             5226..5270
                     /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        5568..5816
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     5568..5588
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     5739..5758
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    5912..6029
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        6078..6588
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     6507..6525
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             join(6610..7083,1..126)
                     /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(6610..6629)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
ORIGIN
        1 ttcctggaga cctccgcgcc ccgcaacctc cccttctacg agcggctcgg cttcaccgtc
       61 accgccgacg tcgaggtgcc cgaaggaccg cgcacctggt gcatgacccg caagcccggt
      121 gcctgacgcc cgccccacga cccgcagcgc ccgaccgaaa ggagcgcacg accccatgca
      181 tcggtacctt taagaccaat gacttacaag gcagctgtag atcttagcca ctttttaaaa
      241 gaaaaggggg gactggaagg gctaattcac tcccaacgaa gacaagatct gctttttgct
      301 tgtactgggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctaactaggg
      361 aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt
      421 ctgttgtgtg actctggtaa ctagagatcc ctcagaccct tttagtcagt gtggaaaatc
      481 tctagcagta gtagttcatg tcatcttatt attcagtatt tataacttgc aaagaaatga
      541 atatcagaga gtgagaggaa cttgtttatt gcagcttata atggttacaa ataaagcaat
      601 agcatcacaa atttcacaaa taaagcattt ttttcactgc attctagttg tggtttgtcc
      661 aaactcatca atgtatctta tcatgtctgg ctctagctat cccgccccta actccgccca
      721 tcccgcccct aactccgccc agttccgccc attctccgcc ccatggctga ctaatttttt
      781 ttatttatgc agaggccgag gccgcctcgg cctctgagct attccagaag tagtgaggag
      841 gcttttttgg aggcctaggg acgtacccaa ttcgccctat agtgagtcgt attacgcgcg
      901 ctcactggcc gtcgttttac aacgtcgtga ctgggaaaac cctggcgtta cccaacttaa
      961 tcgccttgca gcacatcccc ctttcgccag ctggcgtaat agcgaagagg cccgcaccga
     1021 tcgcccttcc caacagttgc gcagcctgaa tggcgaatgg gacgcgccct gtagcggcgc
     1081 attaagcgcg gcgggtgtgg tggttacgcg cagcgtgacc gctacacttg ccagcgccct
     1141 agcgcccgct cctttcgctt tcttcccttc ctttctcgcc acgttcgccg gctttccccg
     1201 tcaagctcta aatcgggggc tccctttagg gttccgattt agtgctttac ggcacctcga
     1261 ccccaaaaaa cttgattagg gtgatggttc acgtagtggg ccatcgccct gatagacggt
     1321 ttttcgccct ttgacgttgg agtccacgtt ctttaatagt ggactcttgt tccaaactgg
     1381 aacaacactc aaccctatct cggtctattc ttttgattta taagggattt tgccgatttc
     1441 ggcctattgg ttaaaaaatg agctgattta acaaaaattt aacgcgaatt ttaacaaaat
     1501 attaacgctt acaatttagg tggcactttt cggggaaatg tgcgcggaac ccctatttgt
     1561 ttatttttct aaatacattc aaatatgtat ccgctcatga gacaataacc ctgataaatg
     1621 cttcaataat attgaaaaag gaagagtatg agtattcaac atttccgtgt cgcccttatt
     1681 cccttttttg cggcattttg ccttcctgtt tttgctcacc cagaaacgct ggtgaaagta
     1741 aaagatgctg aagatcagtt gggtgcacga gtgggttaca tcgaactgga tctcaacagc
     1801 ggtaagatcc ttgagagttt tcgccccgaa gaacgttttc caatgatgag cacttttaaa
     1861 gttctgctat gtggcgcggt attatcccgt attgacgccg ggcaagagca actcggtcgc
     1921 cgcatacact attctcagaa tgacttggtt gagtactcac cagtcacaga aaagcatctt
     1981 acggatggca tgacagtaag agaattatgc agtgctgcca taaccatgag tgataacact
     2041 gcggccaact tacttctgac aacgatcgga ggaccgaagg agctaaccgc ttttttgcac
     2101 aacatggggg atcatgtaac tcgccttgat cgttgggaac cggagctgaa tgaagccata
     2161 ccaaacgacg agcgtgacac cacgatgcct gtagcaatgg caacaacgtt gcgcaaacta
     2221 ttaactggcg aactacttac tctagcttcc cggcaacaat taatagactg gatggaggcg
     2281 gataaagttg caggaccact tctgcgctcg gcccttccgg ctggctggtt tattgctgat
     2341 aaatctggag ccggtgagcg tgggtctcgc ggtatcattg cagcactggg gccagatggt
     2401 aagccctccc gtatcgtagt tatctacacg acggggagtc aggcaactat ggatgaacga
     2461 aatagacaga tcgctgagat aggtgcctca ctgattaagc attggtaact gtcagaccaa
     2521 gtttactcat atatacttta gattgattta aaacttcatt tttaatttaa aaggatctag
     2581 gtgaagatcc tttttgataa tctcatgacc aaaatccctt aacgtgagtt ttcgttccac
     2641 tgagcgtcag accccgtaga aaagatcaaa ggatcttctt gagatccttt ttttctgcgc
     2701 gtaatctgct gcttgcaaac aaaaaaacca ccgctaccag cggtggtttg tttgccggat
     2761 caagagctac caactctttt tccgaaggta actggcttca gcagagcgca gataccaaat
     2821 actgttcttc tagtgtagcc gtagttaggc caccacttca agaactctgt agcaccgcct
     2881 acatacctcg ctctgctaat cctgttacca gtggctgctg ccagtggcga taagtcgtgt
     2941 cttaccgggt tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg
     3001 gggggttcgt gcacacagcc cagcttggag cgaacgacct acaccgaact gagataccta
     3061 cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg
     3121 gtaagcggca gggtcggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg
     3181 tatctttata gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc
     3241 tcgtcagggg ggcggagcct atggaaaaac gccagcaacg cggccttttt acggttcctg
     3301 gccttttgct ggccttttgc tcacatgttc tttcctgcgt tatcccctga ttctgtggat
     3361 aaccgtatta ccgcctttga gtgagctgat accgctcgcc gcagccgaac gaccgagcgc
     3421 agcgagtcag tgagcgagga agcggaagag cgcccaatac gcaaaccgcc tctccccgcg
     3481 cgttggccga ttcattaatg cagctggcac gacaggtttc ccgactggaa agcgggcagt
     3541 gagcgcaacg caattaatgt gagttagctc actcattagg caccccaggc tttacacttt
     3601 atgcttccgg ctcgtatgtt gtgtggaatt gtgagcggat aacaatttca cacaggaaac
     3661 agctatgacc atgattacgc caagcgcgca attaaccctc actaaaggga acaaaagctg
     3721 gagctgcaag cttaatgtag tcttatgcaa tactcttgta gtcttgcaac atggtaacga
     3781 tgagttagca acatgcctta caaggagaga aaaagcaccg tgcatgccga ttggtggaag
     3841 taaggtggta cgatcgtgcc ttattaggaa ggcaacagac gggtctgaca tggattggac
     3901 gaaccactga attgccgcat tgcagagata ttgtatttaa gtgcctagct cgatacataa
     3961 acgggtctct ctggttagac cagatctgag cctgggagct ctctggctaa ctagggaacc
     4021 cactgcttaa gcctcaataa agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt
     4081 tgtgtgactc tggtaactag agatccctca gaccctttta gtcagtgtgg aaaatctcta
     4141 gcagtggcgc ccgaacaggg acttgaaagc gaaagggaaa ccagaggagc tctctcgacg
     4201 caggactcgg cttgctgaag cgcgcacggc aagaggcgag gggcggcgac tggtgagtac
     4261 gccaaaaatt ttgactagcg gaggctagaa ggagagagat gggtgcgaga gcgtcagtat
     4321 taagcggggg agaattagat cgcgatggga aaaaattcgg ttaaggccag ggggaaagaa
     4381 aaaatataaa ttaaaacata tagtatgggc aagcagggag ctagaacgat tcgcagttaa
     4441 tcctggcctg ttagaaacat cagaaggctg tagacaaata ctgggacagc tacaaccatc
     4501 ccttcagaca ggatcagaag aacttagatc attatataat acagtagcaa ccctctattg
     4561 tgtgcatcaa aggatagaga taaaagacac caaggaagct ttagacaaga tagaggaaga
     4621 gcaaaacaaa agtaagacca ccgcacagca agcggccgct gatcttcaga cctggaggag
     4681 gagatatgag ggacaattgg agaagtgaat tatataaata taaagtagta aaaattgaac
     4741 cattaggagt agcacccacc aaggcaaaga gaagagtggt gcagagagaa aaaagagcag
     4801 tgggaatagg agctttgttc cttgggttct tgggagcagc aggaagcact atgggcgcag
     4861 cgtcaatgac gctgacggta caggccagac aattattgtc tggtatagtg cagcagcaga
     4921 acaatttgct gagggctatt gaggcgcaac agcatctgtt gcaactcaca gtctggggca
     4981 tcaagcagct ccaggcaaga atcctggctg tggaaagata cctaaaggat caacagctcc
     5041 tggggatttg gggttgctct ggaaaactca tttgcaccac tgctgtgcct tggaatgcta
     5101 gttggagtaa taaatctctg gaacagattt ggaatcacac gacctggatg gagtgggaca
     5161 gagaaattaa caattacaca agcttaatac actccttaat tgaagaatcg caaaaccagc
     5221 aagaaaagaa tgaacaagaa ttattggaat tagataaatg ggcaagtttg tggaattggt
     5281 ttaacataac aaattggctg tggtatataa aattattcat aatgatagta ggaggcttgg
     5341 taggtttaag aatagttttt gctgtacttt ctatagtgaa tagagttagg cagggatatt
     5401 caccattatc gtttcagacc cacctcccaa ccccgagggg acccgacagg cccgaaggaa
     5461 tagaagaaga aggtggagag agagacagag acagatccat tcgattagtg aacggatctc
     5521 gacggtatcg atcacgagac tagcctcgag cggccgcccc cttcaccgag ggcctatttc
     5581 ccatgattcc ttcatatttg catatacgat acaaggctgt tagagagata attggaatta
     5641 atttgactgt aaacacaaag atattagtac aaaatacgtg acgtagaaag taataatttc
     5701 ttgggtagtt tgcagtttta aaattatgtt ttaaaatgga ctatcatatg cttaccgtaa
     5761 cttgaaagta tttcgatttc ttggctttat atatcttgtg gaaaggacga aacaccggcg
     5821 cgagggtaat cttctcttct cgagaagaga agattaaccc tcgcgttttt gaattctcga
     5881 cctcgagaca aatggcagta ttcatccaca attttaaaag aaaagggggg attggggggt
     5941 acagtgcagg ggaaagaata gtagacataa tagcaacaga catacaaact aaagaattac
     6001 aaaaacaaat tacaaaaatt caaaattttc gggtttatta cagggacagc agagatccac
     6061 tttggccgcg gctcgagggg gttggggttg cgccttttcc aaggcagccc tgggtttgcg
     6121 cagggacgcg gctgctctgg gcgtggttcc gggaaacgca gcggcgccga ccctgggtct
     6181 cgcacattct tcacgtccgt tcgcagcgtc acccggatct tcgccgctac ccttgtgggc
     6241 cccccggcga cgcttcctgc tccgccccta agtcgggaag gttccttgcg gttcgcggcg
     6301 tgccggacgt gacaaacgga agccgcacgt ctcactagta ccctcgcaga cggacagcgc
     6361 cagggagcaa tggcagcgcg ccgaccgcga tgggctgtgg ccaatagcgg ctgctcagca
     6421 gggcgcgccg agagcagcgg ccgggaaggg gcggtgcggg aggcggggtg tggggcggta
     6481 gtgtgggccc tgttcctgcc cgcgcggtgt tccgcattct gcaagcctcc ggagcgcacg
     6541 tcggcagtcg gctccctcgt tgaccgaatc accgacctct ctccccaggg ggatccaccg
     6601 gagcttacca tgaccgagta caagcccacg gtgcgcctcg ccacccgcga cgacgtcccc
     6661 agggccgtac gcaccctcgc cgccgcgttc gccgactacc ccgccacgcg ccacaccgtc
     6721 gatccggacc gccacatcga gcgggtcacc gagctgcaag aactcttcct cacgcgcgtc
     6781 gggctcgaca tcggcaaggt gtgggtcgcg gacgacggcg ccgcggtggc ggtctggacc
     6841 acgccggaga gcgtcgaagc gggggcggtg ttcgccgaga tcggcccgcg catggccgag
     6901 ttgagcggtt cccggctggc cgcgcagcaa cagatggaag gcctcctggc gccgcaccgg
     6961 cccaaggagc ccgcgtggtt cctggccacc gtcggcgtct cgcccgacca ccagggcaag
     7021 ggtctgggca gcgccgtcgt gctccccgga gtggaggcgg ccgagcgcgc cggggtgccc
     7081 gcc
//
