LOCUS       sequence-269244-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  UPF1 shRNA (Targeting 3'UTR) inserted into the PLKO.1 plasmid 
            (TTATTACCCAGAATAAGATGC).
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-UPF1-3'UTR
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             51..95
                     /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        393..641
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     393..413
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     564..583
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    738..855
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        904..1414
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1333..1351
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1436..2035
                     /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(1436..1455)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     1932..1952
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             2163..2396
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2468..2589
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2505..2524)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2559..2578
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2629..2764
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2784..2803)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(2785..2803)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2813..2830)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2813..2829)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2822..2844)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      2971..3426
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3058..3077)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3268..3289
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3452..3556
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3557..3625,3626..4417)
                     /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(3775..3794)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4588..5176
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5077..5096
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5330..5347
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5464..5485
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5500..5505,5506..5523,5524..5530)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5538..5554
                     /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     5543..5565
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5562..5578
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5562..5578
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5597..5617
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5599..5617
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5645..5871
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             5872..6052
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6099..6224
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6717..6950
                     /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 acacaagctt aatacactcc ttaattgaag aatcgcaaaa ccagcaagaa aagaatgaac
       61 aagaattatt ggaattagat aaatgggcaa gtttgtggaa ttggtttaac ataacaaatt
      121 ggctgtggta tataaaatta ttcataatga tagtaggagg cttggtaggt ttaagaatag
      181 tttttgctgt actttctata gtgaatagag ttaggcaggg atattcacca ttatcgtttc
      241 agacccacct cccaaccccg aggggacccg acaggcccga aggaatagaa gaagaaggtg
      301 gagagagaga cagagacaga tccattcgat tagtgaacgg atctcgacgg tatcgatcac
      361 gagactagcc tcgagcggcc gcccccttca ccgagggcct atttcccatg attccttcat
      421 atttgcatat acgatacaag gctgttagag agataattgg aattaatttg actgtaaaca
      481 caaagatatt agtacaaaat acgtgacgta gaaagtaata atttcttggg tagtttgcag
      541 ttttaaaatt atgttttaaa atggactatc atatgcttac cgtaacttga aagtatttcg
      601 atttcttggc tttatatatc ttgtggaaag gacgaaacac cggttattac ccagaataag
      661 atgcctcgag gcatcttatt ctgggtaata atttttgaat tctcgacctc gagacaaatg
      721 gcagtattca tccacaattt taaaagaaaa ggggggattg gggggtacag tgcaggggaa
      781 agaatagtag acataatagc aacagacata caaactaaag aattacaaaa acaaattaca
      841 aaaattcaaa attttcgggt ttattacagg gacagcagag atccactttg gccgcggctc
      901 gagggggttg gggttgcgcc ttttccaagg cagccctggg tttgcgcagg gacgcggctg
      961 ctctgggcgt ggttccggga aacgcagcgg cgccgaccct gggtctcgca cattcttcac
     1021 gtccgttcgc agcgtcaccc ggatcttcgc cgctaccctt gtgggccccc cggcgacgct
     1081 tcctgctccg cccctaagtc gggaaggttc cttgcggttc gcggcgtgcc ggacgtgaca
     1141 aacggaagcc gcacgtctca ctagtaccct cgcagacgga cagcgccagg gagcaatggc
     1201 agcgcgccga ccgcgatggg ctgtggccaa tagcggctgc tcagcagggc gcgccgagag
     1261 cagcggccgg gaaggggcgg tgcgggaggc ggggtgtggg gcggtagtgt gggccctgtt
     1321 cctgcccgcg cggtgttccg cattctgcaa gcctccggag cgcacgtcgg cagtcggctc
     1381 cctcgttgac cgaatcaccg acctctctcc ccagggggat ccaccggagc ttaccatgac
     1441 cgagtacaag cccacggtgc gcctcgccac ccgcgacgac gtccccaggg ccgtacgcac
     1501 cctcgccgcc gcgttcgccg actaccccgc cacgcgccac accgtcgatc cggaccgcca
     1561 catcgagcgg gtcaccgagc tgcaagaact cttcctcacg cgcgtcgggc tcgacatcgg
     1621 caaggtgtgg gtcgcggacg acggcgccgc ggtggcggtc tggaccacgc cggagagcgt
     1681 cgaagcgggg gcggtgttcg ccgagatcgg cccgcgcatg gccgagttga gcggttcccg
     1741 gctggccgcg cagcaacaga tggaaggcct cctggcgccg caccggccca aggagcccgc
     1801 gtggttcctg gccaccgtcg gcgtctcgcc cgaccaccag ggcaagggtc tgggcagcgc
     1861 cgtcgtgctc cccggagtgg aggcggccga gcgcgccggg gtgcccgcct tcctggagac
     1921 ctccgcgccc cgcaacctcc ccttctacga gcggctcggc ttcaccgtca ccgccgacgt
     1981 cgaggtgccc gaaggaccgc gcacctggtg catgacccgc aagcccggtg cctgacgccc
     2041 gccccacgac ccgcagcgcc cgaccgaaag gagcgcacga ccccatgcat cggtaccttt
     2101 aagaccaatg acttacaagg cagctgtaga tcttagccac tttttaaaag aaaagggggg
     2161 actggaaggg ctaattcact cccaacgaag acaagatctg ctttttgctt gtactgggtc
     2221 tctctggtta gaccagatct gagcctggga gctctctggc taactaggga acccactgct
     2281 taagcctcaa taaagcttgc cttgagtgct tcaagtagtg tgtgcccgtc tgttgtgtga
     2341 ctctggtaac tagagatccc tcagaccctt ttagtcagtg tggaaaatct ctagcagtag
     2401 tagttcatgt catcttatta ttcagtattt ataacttgca aagaaatgaa tatcagagag
     2461 tgagaggaac ttgtttattg cagcttataa tggttacaaa taaagcaata gcatcacaaa
     2521 tttcacaaat aaagcatttt tttcactgca ttctagttgt ggtttgtcca aactcatcaa
     2581 tgtatcttat catgtctggc tctagctatc ccgcccctaa ctccgcccat cccgccccta
     2641 actccgccca gttccgccca ttctccgccc catggctgac taattttttt tatttatgca
     2701 gaggccgagg ccgcctcggc ctctgagcta ttccagaagt agtgaggagg cttttttgga
     2761 ggcctaggga cgtacccaat tcgccctata gtgagtcgta ttacgcgcgc tcactggccg
     2821 tcgttttaca acgtcgtgac tgggaaaacc ctggcgttac ccaacttaat cgccttgcag
     2881 cacatccccc tttcgccagc tggcgtaata gcgaagaggc ccgcaccgat cgcccttccc
     2941 aacagttgcg cagcctgaat ggcgaatggg acgcgccctg tagcggcgca ttaagcgcgg
     3001 cgggtgtggt ggttacgcgc agcgtgaccg ctacacttgc cagcgcccta gcgcccgctc
     3061 ctttcgcttt cttcccttcc tttctcgcca cgttcgccgg ctttccccgt caagctctaa
     3121 atcgggggct ccctttaggg ttccgattta gtgctttacg gcacctcgac cccaaaaaac
     3181 ttgattaggg tgatggttca cgtagtgggc catcgccctg atagacggtt tttcgccctt
     3241 tgacgttgga gtccacgttc tttaatagtg gactcttgtt ccaaactgga acaacactca
     3301 accctatctc ggtctattct tttgatttat aagggatttt gccgatttcg gcctattggt
     3361 taaaaaatga gctgatttaa caaaaattta acgcgaattt taacaaaata ttaacgctta
     3421 caatttaggt ggcacttttc ggggaaatgt gcgcggaacc cctatttgtt tatttttcta
     3481 aatacattca aatatgtatc cgctcatgag acaataaccc tgataaatgc ttcaataata
     3541 ttgaaaaagg aagagtatga gtattcaaca tttccgtgtc gcccttattc ccttttttgc
     3601 ggcattttgc cttcctgttt ttgctcaccc agaaacgctg gtgaaagtaa aagatgctga
     3661 agatcagttg ggtgcacgag tgggttacat cgaactggat ctcaacagcg gtaagatcct
     3721 tgagagtttt cgccccgaag aacgttttcc aatgatgagc acttttaaag ttctgctatg
     3781 tggcgcggta ttatcccgta ttgacgccgg gcaagagcaa ctcggtcgcc gcatacacta
     3841 ttctcagaat gacttggttg agtactcacc agtcacagaa aagcatctta cggatggcat
     3901 gacagtaaga gaattatgca gtgctgccat aaccatgagt gataacactg cggccaactt
     3961 acttctgaca acgatcggag gaccgaagga gctaaccgct tttttgcaca acatggggga
     4021 tcatgtaact cgccttgatc gttgggaacc ggagctgaat gaagccatac caaacgacga
     4081 gcgtgacacc acgatgcctg tagcaatggc aacaacgttg cgcaaactat taactggcga
     4141 actacttact ctagcttccc ggcaacaatt aatagactgg atggaggcgg ataaagttgc
     4201 aggaccactt ctgcgctcgg cccttccggc tggctggttt attgctgata aatctggagc
     4261 cggtgagcgt gggtctcgcg gtatcattgc agcactgggg ccagatggta agccctcccg
     4321 tatcgtagtt atctacacga cggggagtca ggcaactatg gatgaacgaa atagacagat
     4381 cgctgagata ggtgcctcac tgattaagca ttggtaactg tcagaccaag tttactcata
     4441 tatactttag attgatttaa aacttcattt ttaatttaaa aggatctagg tgaagatcct
     4501 ttttgataat ctcatgacca aaatccctta acgtgagttt tcgttccact gagcgtcaga
     4561 ccccgtagaa aagatcaaag gatcttcttg agatcctttt tttctgcgcg taatctgctg
     4621 cttgcaaaca aaaaaaccac cgctaccagc ggtggtttgt ttgccggatc aagagctacc
     4681 aactcttttt ccgaaggtaa ctggcttcag cagagcgcag ataccaaata ctgttcttct
     4741 agtgtagccg tagttaggcc accacttcaa gaactctgta gcaccgccta catacctcgc
     4801 tctgctaatc ctgttaccag tggctgctgc cagtggcgat aagtcgtgtc ttaccgggtt
     4861 ggactcaaga cgatagttac cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg
     4921 cacacagccc agcttggagc gaacgaccta caccgaactg agatacctac agcgtgagct
     4981 atgagaaagc gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag
     5041 ggtcggaaca ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag
     5101 tcctgtcggg tttcgccacc tctgacttga gcgtcgattt ttgtgatgct cgtcaggggg
     5161 gcggagccta tggaaaaacg ccagcaacgc ggccttttta cggttcctgg ccttttgctg
     5221 gccttttgct cacatgttct ttcctgcgtt atcccctgat tctgtggata accgtattac
     5281 cgcctttgag tgagctgata ccgctcgccg cagccgaacg accgagcgca gcgagtcagt
     5341 gagcgaggaa gcggaagagc gcccaatacg caaaccgcct ctccccgcgc gttggccgat
     5401 tcattaatgc agctggcacg acaggtttcc cgactggaaa gcgggcagtg agcgcaacgc
     5461 aattaatgtg agttagctca ctcattaggc accccaggct ttacacttta tgcttccggc
     5521 tcgtatgttg tgtggaattg tgagcggata acaatttcac acaggaaaca gctatgacca
     5581 tgattacgcc aagcgcgcaa ttaaccctca ctaaagggaa caaaagctgg agctgcaagc
     5641 ttaatgtagt cttatgcaat actcttgtag tcttgcaaca tggtaacgat gagttagcaa
     5701 catgccttac aaggagagaa aaagcaccgt gcatgccgat tggtggaagt aaggtggtac
     5761 gatcgtgcct tattaggaag gcaacagacg ggtctgacat ggattggacg aaccactgaa
     5821 ttgccgcatt gcagagatat tgtatttaag tgcctagctc gatacataaa cgggtctctc
     5881 tggttagacc agatctgagc ctgggagctc tctggctaac tagggaaccc actgcttaag
     5941 cctcaataaa gcttgccttg agtgcttcaa gtagtgtgtg cccgtctgtt gtgtgactct
     6001 ggtaactaga gatccctcag acccttttag tcagtgtgga aaatctctag cagtggcgcc
     6061 cgaacaggga cttgaaagcg aaagggaaac cagaggagct ctctcgacgc aggactcggc
     6121 ttgctgaagc gcgcacggca agaggcgagg ggcggcgact ggtgagtacg ccaaaaattt
     6181 tgactagcgg aggctagaag gagagagatg ggtgcgagag cgtcagtatt aagcggggga
     6241 gaattagatc gcgatgggaa aaaattcggt taaggccagg gggaaagaaa aaatataaat
     6301 taaaacatat agtatgggca agcagggagc tagaacgatt cgcagttaat cctggcctgt
     6361 tagaaacatc agaaggctgt agacaaatac tgggacagct acaaccatcc cttcagacag
     6421 gatcagaaga acttagatca ttatataata cagtagcaac cctctattgt gtgcatcaaa
     6481 ggatagagat aaaagacacc aaggaagctt tagacaagat agaggaagag caaaacaaaa
     6541 gtaagaccac cgcacagcaa gcggccgctg atcttcagac ctggaggagg agatatgagg
     6601 gacaattgga gaagtgaatt atataaatat aaagtagtaa aaattgaacc attaggagta
     6661 gcacccacca aggcaaagag aagagtggtg cagagagaaa aaagagcagt gggaatagga
     6721 gctttgttcc ttgggttctt gggagcagca ggaagcacta tgggcgcagc gtcaatgacg
     6781 ctgacggtac aggccagaca attattgtct ggtatagtgc agcagcagaa caatttgctg
     6841 agggctattg aggcgcaaca gcatctgttg caactcacag tctggggcat caagcagctc
     6901 caggcaagaa tcctggctgt ggaaagatac ctaaaggatc aacagctcct ggggatttgg
     6961 ggttgctctg gaaaactcat ttgcaccact gctgtgcctt ggaatgctag ttggagtaat
     7021 aaatctctgg aacagatttg gaatcacacg acctggatgg agtgggacag agaaattaac
     7081 aatt
//
