LOCUS       sequence-269277-        7080 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  STAU2 shRNA (Targeting CDS) inserted into the PLKO.1 plasmid 
            (GATATGAACCAACCTTCAA).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7080)
  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 7080)
  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-STAU2-CDS
FEATURES             Location/Qualifiers
     source          1..7080
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      complement(170..758)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(250..269)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(929..1720,1721..1789))
                     /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     1552..1571
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(1790..1894)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(1920..2375)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2057..2078)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     2269..2288
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2502..2524
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     2516..2533
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     2517..2533
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     2543..2562
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        2543..2561
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     rep_origin      2582..2717
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    2757..2878
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2768..2787)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     2822..2841
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     LTR             2950..3183
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     CDS             complement(3311..3910)
                     /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(3394..3414)
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     primer_bind     3891..3910
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     promoter        complement(3932..4442)
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     complement(3995..4013)
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     misc_feature    4491..4608
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        complement(4701..4949)
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     complement(4759..4778)
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     primer_bind     complement(4929..4949)
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     CDS             complement(5247..5291)
                     /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    5476..5709
                     /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    6202..6327
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     LTR             6374..6554
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     promoter        complement(6555..6781)
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     primer_bind     complement(6809..6829)
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        complement(6809..6827)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(6848..6864)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(6848..6864)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(6861..6883)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    6872..6888
                     /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(6896..6902,6903..6920,6921..6926))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6941..6962
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(join(7079..7080,1..16))
                     /label=L4440
                     /note="L4440 vector, forward primer"
ORIGIN
        1 cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg agcggtatca gctcactcaa
       61 aggcggtaat acggttatcc acagaatcag gggataacgc aggaaagaac atgtgagcaa
      121 aaggccagca aaaggccagg aaccgtaaaa aggccgcgtt gctggcgttt ttccataggc
      181 tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga
      241 caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc
      301 cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt
      361 ctcatagctc acgctgtagg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct
      421 gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg
      481 agtccaaccc ggtaagacac gacttatcgc cactggcagc agccactggt aacaggatta
      541 gcagagcgag gtatgtaggc ggtgctacag agttcttgaa gtggtggcct aactacggct
      601 acactagaag aacagtattt ggtatctgcg ctctgctgaa gccagttacc ttcggaaaaa
      661 gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg tagcggtggt ttttttgttt
      721 gcaagcagca gattacgcgc agaaaaaaag gatctcaaga agatcctttg atcttttcta
      781 cggggtctga cgctcagtgg aacgaaaact cacgttaagg gattttggtc atgagattat
      841 caaaaaggat cttcacctag atccttttaa attaaaaatg aagttttaaa tcaatctaaa
      901 gtatatatga gtaaacttgg tctgacagtt accaatgctt aatcagtgag gcacctatct
      961 cagcgatctg tctatttcgt tcatccatag ttgcctgact ccccgtcgtg tagataacta
     1021 cgatacggga gggcttacca tctggcccca gtgctgcaat gataccgcga gacccacgct
     1081 caccggctcc agatttatca gcaataaacc agccagccgg aagggccgag cgcagaagtg
     1141 gtcctgcaac tttatccgcc tccatccagt ctattaattg ttgccgggaa gctagagtaa
     1201 gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat tgctacaggc atcgtggtgt
     1261 cacgctcgtc gtttggtatg gcttcattca gctccggttc ccaacgatca aggcgagtta
     1321 catgatcccc catgttgtgc aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca
     1381 gaagtaagtt ggccgcagtg ttatcactca tggttatggc agcactgcat aattctctta
     1441 ctgtcatgcc atccgtaaga tgcttttctg tgactggtga gtactcaacc aagtcattct
     1501 gagaatagtg tatgcggcga ccgagttgct cttgcccggc gtcaatacgg gataataccg
     1561 cgccacatag cagaacttta aaagtgctca tcattggaaa acgttcttcg gggcgaaaac
     1621 tctcaaggat cttaccgctg ttgagatcca gttcgatgta acccactcgt gcacccaact
     1681 gatcttcagc atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa
     1741 atgccgcaaa aaagggaata agggcgacac ggaaatgttg aatactcata ctcttccttt
     1801 ttcaatatta ttgaagcatt tatcagggtt attgtctcat gagcggatac atatttgaat
     1861 gtatttagaa aaataaacaa ataggggttc cgcgcacatt tccccgaaaa gtgccaccta
     1921 aattgtaagc gttaatattt tgttaaaatt cgcgttaaat ttttgttaaa tcagctcatt
     1981 ttttaaccaa taggccgaaa tcggcaaaat cccttataaa tcaaaagaat agaccgagat
     2041 agggttgagt gttgttccag tttggaacaa gagtccacta ttaaagaacg tggactccaa
     2101 cgtcaaaggg cgaaaaaccg tctatcaggg cgatggccca ctacgtgaac catcacccta
     2161 atcaagtttt ttggggtcga ggtgccgtaa agcactaaat cggaacccta aagggagccc
     2221 ccgatttaga gcttgacggg gaaagccggc gaacgtggcg agaaaggaag ggaagaaagc
     2281 gaaaggagcg ggcgctaggg cgctggcaag tgtagcggtc acgctgcgcg taaccaccac
     2341 acccgccgcg cttaatgcgc cgctacaggg cgcgtcccat tcgccattca ggctgcgcaa
     2401 ctgttgggaa gggcgatcgg tgcgggcctc ttcgctatta cgccagctgg cgaaaggggg
     2461 atgtgctgca aggcgattaa gttgggtaac gccagggttt tcccagtcac gacgttgtaa
     2521 aacgacggcc agtgagcgcg cgtaatacga ctcactatag ggcgaattgg gtacgtccct
     2581 aggcctccaa aaaagcctcc tcactacttc tggaatagct cagaggccga ggcggcctcg
     2641 gcctctgcat aaataaaaaa aattagtcag ccatggggcg gagaatgggc ggaactgggc
     2701 ggagttaggg gcgggatggg cggagttagg ggcgggatag ctagagccag acatgataag
     2761 atacattgat gagtttggac aaaccacaac tagaatgcag tgaaaaaaat gctttatttg
     2821 tgaaatttgt gatgctattg ctttatttgt aaccattata agctgcaata aacaagttcc
     2881 tctcactctc tgatattcat ttctttgcaa gttataaata ctgaataata agatgacatg
     2941 aactactact gctagagatt ttccacactg actaaaaggg tctgagggat ctctagttac
     3001 cagagtcaca caacagacgg gcacacacta cttgaagcac tcaaggcaag ctttattgag
     3061 gcttaagcag tgggttccct agttagccag agagctccca ggctcagatc tggtctaacc
     3121 agagagaccc agtacaagca aaaagcagat cttgtcttcg ttgggagtga attagccctt
     3181 ccagtccccc cttttctttt aaaaagtggc taagatctac agctgccttg taagtcattg
     3241 gtcttaaagg taccgatgca tggggtcgtg cgctcctttc ggtcgggcgc tgcgggtcgt
     3301 ggggcgggcg tcaggcaccg ggcttgcggg tcatgcacca ggtgcgcggt ccttcgggca
     3361 cctcgacgtc ggcggtgacg gtgaagccga gccgctcgta gaaggggagg ttgcggggcg
     3421 cggaggtctc caggaaggcg ggcaccccgg cgcgctcggc cgcctccact ccggggagca
     3481 cgacggcgct gcccagaccc ttgccctggt ggtcgggcga gacgccgacg gtggccagga
     3541 accacgcggg ctccttgggc cggtgcggcg ccaggaggcc ttccatctgt tgctgcgcgg
     3601 ccagccggga accgctcaac tcggccatgc gcgggccgat ctcggcgaac accgcccccg
     3661 cttcgacgct ctccggcgtg gtccagaccg ccaccgcggc gccgtcgtcc gcgacccaca
     3721 ccttgccgat gtcgagcccg acgcgcgtga ggaagagttc ttgcagctcg gtgacccgct
     3781 cgatgtggcg gtccggatcg acggtgtggc gcgtggcggg gtagtcggcg aacgcggcgg
     3841 cgagggtgcg tacggccctg gggacgtcgt cgcgggtggc gaggcgcacc gtgggcttgt
     3901 actcggtcat ggtaagctcc ggtggatccc cctggggaga gaggtcggtg attcggtcaa
     3961 cgagggagcc gactgccgac gtgcgctccg gaggcttgca gaatgcggaa caccgcgcgg
     4021 gcaggaacag ggcccacact accgccccac accccgcctc ccgcaccgcc ccttcccggc
     4081 cgctgctctc ggcgcgccct gctgagcagc cgctattggc cacagcccat cgcggtcggc
     4141 gcgctgccat tgctccctgg cgctgtccgt ctgcgagggt actagtgaga cgtgcggctt
     4201 ccgtttgtca cgtccggcac gccgcgaacc gcaaggaacc ttcccgactt aggggcggag
     4261 caggaagcgt cgccgggggg cccacaaggg tagcggcgaa gatccgggtg acgctgcgaa
     4321 cggacgtgaa gaatgtgcga gacccagggt cggcgccgct gcgtttcccg gaaccacgcc
     4381 cagagcagcc gcgtccctgc gcaaacccag ggctgccttg gaaaaggcgc aaccccaacc
     4441 ccctcgagcc gcggccaaag tggatctctg ctgtccctgt aataaacccg aaaattttga
     4501 atttttgtaa tttgtttttg taattcttta gtttgtatgt ctgttgctat tatgtctact
     4561 attctttccc ctgcactgta ccccccaatc cccccttttc ttttaaaatt gtggatgaat
     4621 actgccattt gtctcgaggt cgagaattca aaaagatatg aaccaacctt caactcgagt
     4681 tgaaggttgg ttcatatccc ggtgtttcgt cctttccaca agatatataa agccaagaaa
     4741 tcgaaatact ttcaagttac ggtaagcata tgatagtcca ttttaaaaca taattttaaa
     4801 actgcaaact acccaagaaa ttattacttt ctacgtcacg tattttgtac taatatcttt
     4861 gtgtttacag tcaaattaat tccaattatc tctctaacag ccttgtatcg tatatgcaaa
     4921 tatgaaggaa tcatgggaaa taggccctcg gtgaaggggg cggccgctcg aggctagtct
     4981 cgtgatcgat accgtcgaga tccgttcact aatcgaatgg atctgtctct gtctctctct
     5041 ccaccttctt cttctattcc ttcgggcctg tcgggtcccc tcggggttgg gaggtgggtc
     5101 tgaaacgata atggtgaata tccctgccta actctattca ctatagaaag tacagcaaaa
     5161 actattctta aacctaccaa gcctcctact atcattatga ataattttat ataccacagc
     5221 caatttgtta tgttaaacca attccacaaa cttgcccatt tatctaattc caataattct
     5281 tgttcattct tttcttgctg gttttgcgat tcttcaatta aggagtgtat taagcttgtg
     5341 taattgttaa tttctctgtc ccactccatc caggtcgtgt gattccaaat ctgttccaga
     5401 gatttattac tccaactagc attccaaggc acagcagtgg tgcaaatgag ttttccagag
     5461 caaccccaaa tccccaggag ctgttgatcc tttaggtatc tttccacagc caggattctt
     5521 gcctggagct gcttgatgcc ccagactgtg agttgcaaca gatgctgttg cgcctcaata
     5581 gccctcagca aattgttctg ctgctgcact ataccagaca ataattgtct ggcctgtacc
     5641 gtcagcgtca ttgacgctgc gcccatagtg cttcctgctg ctcccaagaa cccaaggaac
     5701 aaagctccta ttcccactgc tcttttttct ctctgcacca ctcttctctt tgccttggtg
     5761 ggtgctactc ctaatggttc aatttttact actttatatt tatataattc acttctccaa
     5821 ttgtccctca tatctcctcc tccaggtctg aagatcagcg gccgcttgct gtgcggtggt
     5881 cttacttttg ttttgctctt cctctatctt gtctaaagct tccttggtgt cttttatctc
     5941 tatcctttga tgcacacaat agagggttgc tactgtatta tataatgatc taagttcttc
     6001 tgatcctgtc tgaagggatg gttgtagctg tcccagtatt tgtctacagc cttctgatgt
     6061 ttctaacagg ccaggattaa ctgcgaatcg ttctagctcc ctgcttgccc atactatatg
     6121 ttttaattta tattttttct ttccccctgg ccttaaccga attttttccc atcgcgatct
     6181 aattctcccc cgcttaatac tgacgctctc gcacccatct ctctccttct agcctccgct
     6241 agtcaaaatt tttggcgtac tcaccagtcg ccgcccctcg cctcttgccg tgcgcgcttc
     6301 agcaagccga gtcctgcgtc gagagagctc ctctggtttc cctttcgctt tcaagtccct
     6361 gttcgggcgc cactgctaga gattttccac actgactaaa agggtctgag ggatctctag
     6421 ttaccagagt cacacaacag acgggcacac actacttgaa gcactcaagg caagctttat
     6481 tgaggcttaa gcagtgggtt ccctagttag ccagagagct cccaggctca gatctggtct
     6541 aaccagagag acccgtttat gtatcgagct aggcacttaa atacaatatc tctgcaatgc
     6601 ggcaattcag tggttcgtcc aatccatgtc agacccgtct gttgccttcc taataaggca
     6661 cgatcgtacc accttacttc caccaatcgg catgcacggt gctttttctc tccttgtaag
     6721 gcatgttgct aactcatcgt taccatgttg caagactaca agagtattgc ataagactac
     6781 attaagcttg cagctccagc ttttgttccc tttagtgagg gttaattgcg cgcttggcgt
     6841 aatcatggtc atagctgttt cctgtgtgaa attgttatcc gctcacaatt ccacacaaca
     6901 tacgagccgg aagcataaag tgtaaagcct ggggtgccta atgagtgagc taactcacat
     6961 taattgcgtt gcgctcactg cccgctttcc agtcgggaaa cctgtcgtgc cagctgcatt
     7021 aatgaatcgg ccaacgcgcg gggagaggcg gtttgcgtat tgggcgctct tccgcttcct
//
