LOCUS       sequence-269248-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  UPF3A shRNA (Targeting CDS) inserted into the PLKO.1 plasmid 
            (GCAGAAACCATTCTAAAGAAA).
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-UPF3A-CDS
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             92..136
                     /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        434..682
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     434..454
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     605..624
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    779..896
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        945..1455
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1374..1392
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1477..2076
                     /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(1477..1496)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     1973..1993
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             2204..2437
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2509..2630
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2546..2565)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2600..2619
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2670..2805
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2825..2844)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(2826..2844)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2854..2871)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2854..2870)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2863..2885)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3012..3467
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3099..3118)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3309..3330
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3493..3597
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3598..3666,3667..4458)
                     /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(3816..3835)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4629..5217
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5118..5137
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5371..5388
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5505..5526
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5541..5546,5547..5564,5565..5571)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5579..5595
                     /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     5584..5606
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5603..5619
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5603..5619
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5638..5658
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5640..5658
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5686..5912
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             5913..6093
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6140..6265
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6758..6991
                     /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 tcacacgacc tggatggagt gggacagaga aattaacaat tacacaagct taatacactc
       61 cttaattgaa gaatcgcaaa accagcaaga aaagaatgaa caagaattat tggaattaga
      121 taaatgggca agtttgtgga attggtttaa cataacaaat tggctgtggt atataaaatt
      181 attcataatg atagtaggag gcttggtagg tttaagaata gtttttgctg tactttctat
      241 agtgaataga gttaggcagg gatattcacc attatcgttt cagacccacc tcccaacccc
      301 gaggggaccc gacaggcccg aaggaataga agaagaaggt ggagagagag acagagacag
      361 atccattcga ttagtgaacg gatctcgacg gtatcgatca cgagactagc ctcgagcggc
      421 cgcccccttc accgagggcc tatttcccat gattccttca tatttgcata tacgatacaa
      481 ggctgttaga gagataattg gaattaattt gactgtaaac acaaagatat tagtacaaaa
      541 tacgtgacgt agaaagtaat aatttcttgg gtagtttgca gttttaaaat tatgttttaa
      601 aatggactat catatgctta ccgtaacttg aaagtatttc gatttcttgg ctttatatat
      661 cttgtggaaa ggacgaaaca ccgggcagaa accattctaa agaaactcga gtttctttag
      721 aatggtttct gctttttgaa ttctcgacct cgagacaaat ggcagtattc atccacaatt
      781 ttaaaagaaa aggggggatt ggggggtaca gtgcagggga aagaatagta gacataatag
      841 caacagacat acaaactaaa gaattacaaa aacaaattac aaaaattcaa aattttcggg
      901 tttattacag ggacagcaga gatccacttt ggccgcggct cgagggggtt ggggttgcgc
      961 cttttccaag gcagccctgg gtttgcgcag ggacgcggct gctctgggcg tggttccggg
     1021 aaacgcagcg gcgccgaccc tgggtctcgc acattcttca cgtccgttcg cagcgtcacc
     1081 cggatcttcg ccgctaccct tgtgggcccc ccggcgacgc ttcctgctcc gcccctaagt
     1141 cgggaaggtt ccttgcggtt cgcggcgtgc cggacgtgac aaacggaagc cgcacgtctc
     1201 actagtaccc tcgcagacgg acagcgccag ggagcaatgg cagcgcgccg accgcgatgg
     1261 gctgtggcca atagcggctg ctcagcaggg cgcgccgaga gcagcggccg ggaaggggcg
     1321 gtgcgggagg cggggtgtgg ggcggtagtg tgggccctgt tcctgcccgc gcggtgttcc
     1381 gcattctgca agcctccgga gcgcacgtcg gcagtcggct ccctcgttga ccgaatcacc
     1441 gacctctctc cccaggggga tccaccggag cttaccatga ccgagtacaa gcccacggtg
     1501 cgcctcgcca cccgcgacga cgtccccagg gccgtacgca ccctcgccgc cgcgttcgcc
     1561 gactaccccg ccacgcgcca caccgtcgat ccggaccgcc acatcgagcg ggtcaccgag
     1621 ctgcaagaac tcttcctcac gcgcgtcggg ctcgacatcg gcaaggtgtg ggtcgcggac
     1681 gacggcgccg cggtggcggt ctggaccacg ccggagagcg tcgaagcggg ggcggtgttc
     1741 gccgagatcg gcccgcgcat ggccgagttg agcggttccc ggctggccgc gcagcaacag
     1801 atggaaggcc tcctggcgcc gcaccggccc aaggagcccg cgtggttcct ggccaccgtc
     1861 ggcgtctcgc ccgaccacca gggcaagggt ctgggcagcg ccgtcgtgct ccccggagtg
     1921 gaggcggccg agcgcgccgg ggtgcccgcc ttcctggaga cctccgcgcc ccgcaacctc
     1981 cccttctacg agcggctcgg cttcaccgtc accgccgacg tcgaggtgcc cgaaggaccg
     2041 cgcacctggt gcatgacccg caagcccggt gcctgacgcc cgccccacga cccgcagcgc
     2101 ccgaccgaaa ggagcgcacg accccatgca tcggtacctt taagaccaat gacttacaag
     2161 gcagctgtag atcttagcca ctttttaaaa gaaaaggggg gactggaagg gctaattcac
     2221 tcccaacgaa gacaagatct gctttttgct tgtactgggt ctctctggtt agaccagatc
     2281 tgagcctggg agctctctgg ctaactaggg aacccactgc ttaagcctca ataaagcttg
     2341 ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc
     2401 ctcagaccct tttagtcagt gtggaaaatc tctagcagta gtagttcatg tcatcttatt
     2461 attcagtatt tataacttgc aaagaaatga atatcagaga gtgagaggaa cttgtttatt
     2521 gcagcttata atggttacaa ataaagcaat agcatcacaa atttcacaaa taaagcattt
     2581 ttttcactgc attctagttg tggtttgtcc aaactcatca atgtatctta tcatgtctgg
     2641 ctctagctat cccgccccta actccgccca tcccgcccct aactccgccc agttccgccc
     2701 attctccgcc ccatggctga ctaatttttt ttatttatgc agaggccgag gccgcctcgg
     2761 cctctgagct attccagaag tagtgaggag gcttttttgg aggcctaggg acgtacccaa
     2821 ttcgccctat agtgagtcgt attacgcgcg ctcactggcc gtcgttttac aacgtcgtga
     2881 ctgggaaaac cctggcgtta cccaacttaa tcgccttgca gcacatcccc ctttcgccag
     2941 ctggcgtaat agcgaagagg cccgcaccga tcgcccttcc caacagttgc gcagcctgaa
     3001 tggcgaatgg gacgcgccct gtagcggcgc attaagcgcg gcgggtgtgg tggttacgcg
     3061 cagcgtgacc gctacacttg ccagcgccct agcgcccgct cctttcgctt tcttcccttc
     3121 ctttctcgcc acgttcgccg gctttccccg tcaagctcta aatcgggggc tccctttagg
     3181 gttccgattt agtgctttac ggcacctcga ccccaaaaaa cttgattagg gtgatggttc
     3241 acgtagtggg ccatcgccct gatagacggt ttttcgccct ttgacgttgg agtccacgtt
     3301 ctttaatagt ggactcttgt tccaaactgg aacaacactc aaccctatct cggtctattc
     3361 ttttgattta taagggattt tgccgatttc ggcctattgg ttaaaaaatg agctgattta
     3421 acaaaaattt aacgcgaatt ttaacaaaat attaacgctt acaatttagg tggcactttt
     3481 cggggaaatg tgcgcggaac ccctatttgt ttatttttct aaatacattc aaatatgtat
     3541 ccgctcatga gacaataacc ctgataaatg cttcaataat attgaaaaag gaagagtatg
     3601 agtattcaac atttccgtgt cgcccttatt cccttttttg cggcattttg ccttcctgtt
     3661 tttgctcacc cagaaacgct ggtgaaagta aaagatgctg aagatcagtt gggtgcacga
     3721 gtgggttaca tcgaactgga tctcaacagc ggtaagatcc ttgagagttt tcgccccgaa
     3781 gaacgttttc caatgatgag cacttttaaa gttctgctat gtggcgcggt attatcccgt
     3841 attgacgccg ggcaagagca actcggtcgc cgcatacact attctcagaa tgacttggtt
     3901 gagtactcac cagtcacaga aaagcatctt acggatggca tgacagtaag agaattatgc
     3961 agtgctgcca taaccatgag tgataacact gcggccaact tacttctgac aacgatcgga
     4021 ggaccgaagg agctaaccgc ttttttgcac aacatggggg atcatgtaac tcgccttgat
     4081 cgttgggaac cggagctgaa tgaagccata ccaaacgacg agcgtgacac cacgatgcct
     4141 gtagcaatgg caacaacgtt gcgcaaacta ttaactggcg aactacttac tctagcttcc
     4201 cggcaacaat taatagactg gatggaggcg gataaagttg caggaccact tctgcgctcg
     4261 gcccttccgg ctggctggtt tattgctgat aaatctggag ccggtgagcg tgggtctcgc
     4321 ggtatcattg cagcactggg gccagatggt aagccctccc gtatcgtagt tatctacacg
     4381 acggggagtc aggcaactat ggatgaacga aatagacaga tcgctgagat aggtgcctca
     4441 ctgattaagc attggtaact gtcagaccaa gtttactcat atatacttta gattgattta
     4501 aaacttcatt tttaatttaa aaggatctag gtgaagatcc tttttgataa tctcatgacc
     4561 aaaatccctt aacgtgagtt ttcgttccac tgagcgtcag accccgtaga aaagatcaaa
     4621 ggatcttctt gagatccttt ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca
     4681 ccgctaccag cggtggtttg tttgccggat caagagctac caactctttt tccgaaggta
     4741 actggcttca gcagagcgca gataccaaat actgttcttc tagtgtagcc gtagttaggc
     4801 caccacttca agaactctgt agcaccgcct acatacctcg ctctgctaat cctgttacca
     4861 gtggctgctg ccagtggcga taagtcgtgt cttaccgggt tggactcaag acgatagtta
     4921 ccggataagg cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag
     4981 cgaacgacct acaccgaact gagataccta cagcgtgagc tatgagaaag cgccacgctt
     5041 cccgaaggga gaaaggcgga caggtatccg gtaagcggca gggtcggaac aggagagcgc
     5101 acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac
     5161 ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac
     5221 gccagcaacg cggccttttt acggttcctg gccttttgct ggccttttgc tcacatgttc
     5281 tttcctgcgt tatcccctga ttctgtggat aaccgtatta ccgcctttga gtgagctgat
     5341 accgctcgcc gcagccgaac gaccgagcgc agcgagtcag tgagcgagga agcggaagag
     5401 cgcccaatac gcaaaccgcc tctccccgcg cgttggccga ttcattaatg cagctggcac
     5461 gacaggtttc ccgactggaa agcgggcagt gagcgcaacg caattaatgt gagttagctc
     5521 actcattagg caccccaggc tttacacttt atgcttccgg ctcgtatgtt gtgtggaatt
     5581 gtgagcggat aacaatttca cacaggaaac agctatgacc atgattacgc caagcgcgca
     5641 attaaccctc actaaaggga acaaaagctg gagctgcaag cttaatgtag tcttatgcaa
     5701 tactcttgta gtcttgcaac atggtaacga tgagttagca acatgcctta caaggagaga
     5761 aaaagcaccg tgcatgccga ttggtggaag taaggtggta cgatcgtgcc ttattaggaa
     5821 ggcaacagac gggtctgaca tggattggac gaaccactga attgccgcat tgcagagata
     5881 ttgtatttaa gtgcctagct cgatacataa acgggtctct ctggttagac cagatctgag
     5941 cctgggagct ctctggctaa ctagggaacc cactgcttaa gcctcaataa agcttgcctt
     6001 gagtgcttca agtagtgtgt gcccgtctgt tgtgtgactc tggtaactag agatccctca
     6061 gaccctttta gtcagtgtgg aaaatctcta gcagtggcgc ccgaacaggg acttgaaagc
     6121 gaaagggaaa ccagaggagc tctctcgacg caggactcgg cttgctgaag cgcgcacggc
     6181 aagaggcgag gggcggcgac tggtgagtac gccaaaaatt ttgactagcg gaggctagaa
     6241 ggagagagat gggtgcgaga gcgtcagtat taagcggggg agaattagat cgcgatggga
     6301 aaaaattcgg ttaaggccag ggggaaagaa aaaatataaa ttaaaacata tagtatgggc
     6361 aagcagggag ctagaacgat tcgcagttaa tcctggcctg ttagaaacat cagaaggctg
     6421 tagacaaata ctgggacagc tacaaccatc ccttcagaca ggatcagaag aacttagatc
     6481 attatataat acagtagcaa ccctctattg tgtgcatcaa aggatagaga taaaagacac
     6541 caaggaagct ttagacaaga tagaggaaga gcaaaacaaa agtaagacca ccgcacagca
     6601 agcggccgct gatcttcaga cctggaggag gagatatgag ggacaattgg agaagtgaat
     6661 tatataaata taaagtagta aaaattgaac cattaggagt agcacccacc aaggcaaaga
     6721 gaagagtggt gcagagagaa aaaagagcag tgggaatagg agctttgttc cttgggttct
     6781 tgggagcagc aggaagcact atgggcgcag cgtcaatgac gctgacggta caggccagac
     6841 aattattgtc tggtatagtg cagcagcaga acaatttgct gagggctatt gaggcgcaac
     6901 agcatctgtt gcaactcaca gtctggggca tcaagcagct ccaggcaaga atcctggctg
     6961 tggaaagata cctaaaggat caacagctcc tggggatttg gggttgctct ggaaaactca
     7021 tttgcaccac tgctgtgcct tggaatgcta gttggagtaa taaatctctg gaacagattt
     7081 ggaa
//
