LOCUS       sequence-269247-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  UPF2 shRNA (Targeting CDS) inserted into the PLKO.1 plasmid 
            (GCGTTATGTTTGGTGGAAGAA).
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-UPF2-CDS
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      complement(126..714)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(206..225)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(885..1676,1677..1745))
                     /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     1508..1527
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(1746..1850)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(1876..2331)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2013..2034)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     2225..2244
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2458..2480
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     2472..2489
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     2473..2489
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     2499..2518
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        2499..2517
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     rep_origin      2538..2673
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    2713..2834
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2724..2743)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     2778..2797
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     LTR             2906..3139
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     CDS             complement(3267..3866)
                     /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(3350..3370)
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     primer_bind     3847..3866
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     promoter        complement(3888..4398)
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     complement(3951..3969)
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     misc_feature    4447..4564
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        complement(4661..4909)
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     complement(4719..4738)
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     primer_bind     complement(4889..4909)
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     CDS             complement(5207..5251)
                     /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"
     misc_feature    5436..5669
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     misc_feature    6162..6287
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     LTR             6334..6514
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     promoter        complement(6515..6741)
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     primer_bind     complement(6769..6789)
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        complement(6769..6787)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(6808..6824)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(6808..6824)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(6821..6843)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    6832..6848
                     /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)."
     promoter        complement(join(6856..6862,6863..6880,6881..6886))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6901..6922
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(7039..7056)
                     /label=L4440
                     /note="L4440 vector, forward primer"
ORIGIN
        1 gtatcagctc actcaaaggc ggtaatacgg ttatccacag aatcagggga taacgcagga
       61 aagaacatgt gagcaaaagg ccagcaaaag gccaggaacc gtaaaaaggc cgcgttgctg
      121 gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaatcgacg ctcaagtcag
      181 aggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg aagctccctc
      241 gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt tctcccttcg
      301 ggaagcgtgg cgctttctca tagctcacgc tgtaggtatc tcagttcggt gtaggtcgtt
      361 cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg cgccttatcc
      421 ggtaactatc gtcttgagtc caacccggta agacacgact tatcgccact ggcagcagcc
      481 actggtaaca ggattagcag agcgaggtat gtaggcggtg ctacagagtt cttgaagtgg
      541 tggcctaact acggctacac tagaagaaca gtatttggta tctgcgctct gctgaagcca
      601 gttaccttcg gaaaaagagt tggtagctct tgatccggca aacaaaccac cgctggtagc
      661 ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa aaaaaggatc tcaagaagat
      721 cctttgatct tttctacggg gtctgacgct cagtggaacg aaaactcacg ttaagggatt
      781 ttggtcatga gattatcaaa aaggatcttc acctagatcc ttttaaatta aaaatgaagt
      841 tttaaatcaa tctaaagtat atatgagtaa acttggtctg acagttacca atgcttaatc
      901 agtgaggcac ctatctcagc gatctgtcta tttcgttcat ccatagttgc ctgactcccc
      961 gtcgtgtaga taactacgat acgggagggc ttaccatctg gccccagtgc tgcaatgata
     1021 ccgcgagacc cacgctcacc ggctccagat ttatcagcaa taaaccagcc agccggaagg
     1081 gccgagcgca gaagtggtcc tgcaacttta tccgcctcca tccagtctat taattgttgc
     1141 cgggaagcta gagtaagtag ttcgccagtt aatagtttgc gcaacgttgt tgccattgct
     1201 acaggcatcg tggtgtcacg ctcgtcgttt ggtatggctt cattcagctc cggttcccaa
     1261 cgatcaaggc gagttacatg atcccccatg ttgtgcaaaa aagcggttag ctccttcggt
     1321 cctccgatcg ttgtcagaag taagttggcc gcagtgttat cactcatggt tatggcagca
     1381 ctgcataatt ctcttactgt catgccatcc gtaagatgct tttctgtgac tggtgagtac
     1441 tcaaccaagt cattctgaga atagtgtatg cggcgaccga gttgctcttg cccggcgtca
     1501 atacgggata ataccgcgcc acatagcaga actttaaaag tgctcatcat tggaaaacgt
     1561 tcttcggggc gaaaactctc aaggatctta ccgctgttga gatccagttc gatgtaaccc
     1621 actcgtgcac ccaactgatc ttcagcatct tttactttca ccagcgtttc tgggtgagca
     1681 aaaacaggaa ggcaaaatgc cgcaaaaaag ggaataaggg cgacacggaa atgttgaata
     1741 ctcatactct tcctttttca atattattga agcatttatc agggttattg tctcatgagc
     1801 ggatacatat ttgaatgtat ttagaaaaat aaacaaatag gggttccgcg cacatttccc
     1861 cgaaaagtgc cacctaaatt gtaagcgtta atattttgtt aaaattcgcg ttaaattttt
     1921 gttaaatcag ctcatttttt aaccaatagg ccgaaatcgg caaaatccct tataaatcaa
     1981 aagaatagac cgagataggg ttgagtgttg ttccagtttg gaacaagagt ccactattaa
     2041 agaacgtgga ctccaacgtc aaagggcgaa aaaccgtcta tcagggcgat ggcccactac
     2101 gtgaaccatc accctaatca agttttttgg ggtcgaggtg ccgtaaagca ctaaatcgga
     2161 accctaaagg gagcccccga tttagagctt gacggggaaa gccggcgaac gtggcgagaa
     2221 aggaagggaa gaaagcgaaa ggagcgggcg ctagggcgct ggcaagtgta gcggtcacgc
     2281 tgcgcgtaac caccacaccc gccgcgctta atgcgccgct acagggcgcg tcccattcgc
     2341 cattcaggct gcgcaactgt tgggaagggc gatcggtgcg ggcctcttcg ctattacgcc
     2401 agctggcgaa agggggatgt gctgcaaggc gattaagttg ggtaacgcca gggttttccc
     2461 agtcacgacg ttgtaaaacg acggccagtg agcgcgcgta atacgactca ctatagggcg
     2521 aattgggtac gtccctaggc ctccaaaaaa gcctcctcac tacttctgga atagctcaga
     2581 ggccgaggcg gcctcggcct ctgcataaat aaaaaaaatt agtcagccat ggggcggaga
     2641 atgggcggaa ctgggcggag ttaggggcgg gatgggcgga gttaggggcg ggatagctag
     2701 agccagacat gataagatac attgatgagt ttggacaaac cacaactaga atgcagtgaa
     2761 aaaaatgctt tatttgtgaa atttgtgatg ctattgcttt atttgtaacc attataagct
     2821 gcaataaaca agttcctctc actctctgat attcatttct ttgcaagtta taaatactga
     2881 ataataagat gacatgaact actactgcta gagattttcc acactgacta aaagggtctg
     2941 agggatctct agttaccaga gtcacacaac agacgggcac acactacttg aagcactcaa
     3001 ggcaagcttt attgaggctt aagcagtggg ttccctagtt agccagagag ctcccaggct
     3061 cagatctggt ctaaccagag agacccagta caagcaaaaa gcagatcttg tcttcgttgg
     3121 gagtgaatta gcccttccag tccccccttt tcttttaaaa agtggctaag atctacagct
     3181 gccttgtaag tcattggtct taaaggtacc gatgcatggg gtcgtgcgct cctttcggtc
     3241 gggcgctgcg ggtcgtgggg cgggcgtcag gcaccgggct tgcgggtcat gcaccaggtg
     3301 cgcggtcctt cgggcacctc gacgtcggcg gtgacggtga agccgagccg ctcgtagaag
     3361 gggaggttgc ggggcgcgga ggtctccagg aaggcgggca ccccggcgcg ctcggccgcc
     3421 tccactccgg ggagcacgac ggcgctgccc agacccttgc cctggtggtc gggcgagacg
     3481 ccgacggtgg ccaggaacca cgcgggctcc ttgggccggt gcggcgccag gaggccttcc
     3541 atctgttgct gcgcggccag ccgggaaccg ctcaactcgg ccatgcgcgg gccgatctcg
     3601 gcgaacaccg cccccgcttc gacgctctcc ggcgtggtcc agaccgccac cgcggcgccg
     3661 tcgtccgcga cccacacctt gccgatgtcg agcccgacgc gcgtgaggaa gagttcttgc
     3721 agctcggtga cccgctcgat gtggcggtcc ggatcgacgg tgtggcgcgt ggcggggtag
     3781 tcggcgaacg cggcggcgag ggtgcgtacg gccctgggga cgtcgtcgcg ggtggcgagg
     3841 cgcaccgtgg gcttgtactc ggtcatggta agctccggtg gatccccctg gggagagagg
     3901 tcggtgattc ggtcaacgag ggagccgact gccgacgtgc gctccggagg cttgcagaat
     3961 gcggaacacc gcgcgggcag gaacagggcc cacactaccg ccccacaccc cgcctcccgc
     4021 accgcccctt cccggccgct gctctcggcg cgccctgctg agcagccgct attggccaca
     4081 gcccatcgcg gtcggcgcgc tgccattgct ccctggcgct gtccgtctgc gagggtacta
     4141 gtgagacgtg cggcttccgt ttgtcacgtc cggcacgccg cgaaccgcaa ggaaccttcc
     4201 cgacttaggg gcggagcagg aagcgtcgcc ggggggccca caagggtagc ggcgaagatc
     4261 cgggtgacgc tgcgaacgga cgtgaagaat gtgcgagacc cagggtcggc gccgctgcgt
     4321 ttcccggaac cacgcccaga gcagccgcgt ccctgcgcaa acccagggct gccttggaaa
     4381 aggcgcaacc ccaaccccct cgagccgcgg ccaaagtgga tctctgctgt ccctgtaata
     4441 aacccgaaaa ttttgaattt ttgtaatttg tttttgtaat tctttagttt gtatgtctgt
     4501 tgctattatg tctactattc tttcccctgc actgtacccc ccaatccccc cttttctttt
     4561 aaaattgtgg atgaatactg ccatttgtct cgaggtcgag aattcaaaaa gcgttatgtt
     4621 tggtggaaga actcgagttc ttccaccaaa cataacgccc ggtgtttcgt cctttccaca
     4681 agatatataa agccaagaaa tcgaaatact ttcaagttac ggtaagcata tgatagtcca
     4741 ttttaaaaca taattttaaa actgcaaact acccaagaaa ttattacttt ctacgtcacg
     4801 tattttgtac taatatcttt gtgtttacag tcaaattaat tccaattatc tctctaacag
     4861 ccttgtatcg tatatgcaaa tatgaaggaa tcatgggaaa taggccctcg gtgaaggggg
     4921 cggccgctcg aggctagtct cgtgatcgat accgtcgaga tccgttcact aatcgaatgg
     4981 atctgtctct gtctctctct ccaccttctt cttctattcc ttcgggcctg tcgggtcccc
     5041 tcggggttgg gaggtgggtc tgaaacgata atggtgaata tccctgccta actctattca
     5101 ctatagaaag tacagcaaaa actattctta aacctaccaa gcctcctact atcattatga
     5161 ataattttat ataccacagc caatttgtta tgttaaacca attccacaaa cttgcccatt
     5221 tatctaattc caataattct tgttcattct tttcttgctg gttttgcgat tcttcaatta
     5281 aggagtgtat taagcttgtg taattgttaa tttctctgtc ccactccatc caggtcgtgt
     5341 gattccaaat ctgttccaga gatttattac tccaactagc attccaaggc acagcagtgg
     5401 tgcaaatgag ttttccagag caaccccaaa tccccaggag ctgttgatcc tttaggtatc
     5461 tttccacagc caggattctt gcctggagct gcttgatgcc ccagactgtg agttgcaaca
     5521 gatgctgttg cgcctcaata gccctcagca aattgttctg ctgctgcact ataccagaca
     5581 ataattgtct ggcctgtacc gtcagcgtca ttgacgctgc gcccatagtg cttcctgctg
     5641 ctcccaagaa cccaaggaac aaagctccta ttcccactgc tcttttttct ctctgcacca
     5701 ctcttctctt tgccttggtg ggtgctactc ctaatggttc aatttttact actttatatt
     5761 tatataattc acttctccaa ttgtccctca tatctcctcc tccaggtctg aagatcagcg
     5821 gccgcttgct gtgcggtggt cttacttttg ttttgctctt cctctatctt gtctaaagct
     5881 tccttggtgt cttttatctc tatcctttga tgcacacaat agagggttgc tactgtatta
     5941 tataatgatc taagttcttc tgatcctgtc tgaagggatg gttgtagctg tcccagtatt
     6001 tgtctacagc cttctgatgt ttctaacagg ccaggattaa ctgcgaatcg ttctagctcc
     6061 ctgcttgccc atactatatg ttttaattta tattttttct ttccccctgg ccttaaccga
     6121 attttttccc atcgcgatct aattctcccc cgcttaatac tgacgctctc gcacccatct
     6181 ctctccttct agcctccgct agtcaaaatt tttggcgtac tcaccagtcg ccgcccctcg
     6241 cctcttgccg tgcgcgcttc agcaagccga gtcctgcgtc gagagagctc ctctggtttc
     6301 cctttcgctt tcaagtccct gttcgggcgc cactgctaga gattttccac actgactaaa
     6361 agggtctgag ggatctctag ttaccagagt cacacaacag acgggcacac actacttgaa
     6421 gcactcaagg caagctttat tgaggcttaa gcagtgggtt ccctagttag ccagagagct
     6481 cccaggctca gatctggtct aaccagagag acccgtttat gtatcgagct aggcacttaa
     6541 atacaatatc tctgcaatgc ggcaattcag tggttcgtcc aatccatgtc agacccgtct
     6601 gttgccttcc taataaggca cgatcgtacc accttacttc caccaatcgg catgcacggt
     6661 gctttttctc tccttgtaag gcatgttgct aactcatcgt taccatgttg caagactaca
     6721 agagtattgc ataagactac attaagcttg cagctccagc ttttgttccc tttagtgagg
     6781 gttaattgcg cgcttggcgt aatcatggtc atagctgttt cctgtgtgaa attgttatcc
     6841 gctcacaatt ccacacaaca tacgagccgg aagcataaag tgtaaagcct ggggtgccta
     6901 atgagtgagc taactcacat taattgcgtt gcgctcactg cccgctttcc agtcgggaaa
     6961 cctgtcgtgc cagctgcatt aatgaatcgg ccaacgcgcg gggagaggcg gtttgcgtat
     7021 tgggcgctct tccgcttcct cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg
     7081 agcg
//
