LOCUS       sequence-269422-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  STAU1 shRNA (Targeting 3'UTR) inserted into the PLKO.1 plasmid 
            (CCATCACCACTGCTTTCTCTT).
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-STAU1-3'UTR
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(29..46)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(200..788)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(280..299)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(959..1750,1751..1819))
                     /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     1582..1601
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(1820..1924)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(1950..2405)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2087..2108)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     2299..2318
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2532..2554
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     2546..2563
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     2547..2563
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     2573..2592
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        2573..2591
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     rep_origin      2612..2747
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    2787..2908
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2798..2817)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     2852..2871
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     LTR             2980..3213
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     CDS             complement(3341..3940)
                     /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(3424..3444)
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     primer_bind     3921..3940
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     promoter        complement(3962..4472)
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     complement(4025..4043)
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     misc_feature    4521..4638
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        complement(4735..4983)
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     complement(4793..4812)
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     primer_bind     complement(4963..4983)
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     CDS             complement(5281..5325)
                     /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    5510..5743
                     /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    6236..6361
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     LTR             6408..6588
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     promoter        complement(6589..6815)
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     primer_bind     complement(6843..6863)
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        complement(6843..6861)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(6882..6898)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(6882..6898)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(6895..6917)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    6906..6922
                     /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(6930..6936,6937..6954,6955..6960))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6975..6996
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
ORIGIN
        1 gtttgcgtat tgggcgctct tccgcttcct cgctcactga ctcgctgcgc tcggtcgttc
       61 ggctgcggcg agcggtatca gctcactcaa aggcggtaat acggttatcc acagaatcag
      121 gggataacgc aggaaagaac atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa
      181 aggccgcgtt gctggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc
      241 gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc
      301 ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg
      361 cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgtagg tatctcagtt
      421 cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc
      481 gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac gacttatcgc
      541 cactggcagc agccactggt aacaggatta gcagagcgag gtatgtaggc ggtgctacag
      601 agttcttgaa gtggtggcct aactacggct acactagaag aacagtattt ggtatctgcg
      661 ctctgctgaa gccagttacc ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa
      721 ccaccgctgg tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag
      781 gatctcaaga agatcctttg atcttttcta cggggtctga cgctcagtgg aacgaaaact
      841 cacgttaagg gattttggtc atgagattat caaaaaggat cttcacctag atccttttaa
      901 attaaaaatg aagttttaaa tcaatctaaa gtatatatga gtaaacttgg tctgacagtt
      961 accaatgctt aatcagtgag gcacctatct cagcgatctg tctatttcgt tcatccatag
     1021 ttgcctgact ccccgtcgtg tagataacta cgatacggga gggcttacca tctggcccca
     1081 gtgctgcaat gataccgcga gacccacgct caccggctcc agatttatca gcaataaacc
     1141 agccagccgg aagggccgag cgcagaagtg gtcctgcaac tttatccgcc tccatccagt
     1201 ctattaattg ttgccgggaa gctagagtaa gtagttcgcc agttaatagt ttgcgcaacg
     1261 ttgttgccat tgctacaggc atcgtggtgt cacgctcgtc gtttggtatg gcttcattca
     1321 gctccggttc ccaacgatca aggcgagtta catgatcccc catgttgtgc aaaaaagcgg
     1381 ttagctcctt cggtcctccg atcgttgtca gaagtaagtt ggccgcagtg ttatcactca
     1441 tggttatggc agcactgcat aattctctta ctgtcatgcc atccgtaaga tgcttttctg
     1501 tgactggtga gtactcaacc aagtcattct gagaatagtg tatgcggcga ccgagttgct
     1561 cttgcccggc gtcaatacgg gataataccg cgccacatag cagaacttta aaagtgctca
     1621 tcattggaaa acgttcttcg gggcgaaaac tctcaaggat cttaccgctg ttgagatcca
     1681 gttcgatgta acccactcgt gcacccaact gatcttcagc atcttttact ttcaccagcg
     1741 tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata agggcgacac
     1801 ggaaatgttg aatactcata ctcttccttt ttcaatatta ttgaagcatt tatcagggtt
     1861 attgtctcat gagcggatac atatttgaat gtatttagaa aaataaacaa ataggggttc
     1921 cgcgcacatt tccccgaaaa gtgccaccta aattgtaagc gttaatattt tgttaaaatt
     1981 cgcgttaaat ttttgttaaa tcagctcatt ttttaaccaa taggccgaaa tcggcaaaat
     2041 cccttataaa tcaaaagaat agaccgagat agggttgagt gttgttccag tttggaacaa
     2101 gagtccacta ttaaagaacg tggactccaa cgtcaaaggg cgaaaaaccg tctatcaggg
     2161 cgatggccca ctacgtgaac catcacccta atcaagtttt ttggggtcga ggtgccgtaa
     2221 agcactaaat cggaacccta aagggagccc ccgatttaga gcttgacggg gaaagccggc
     2281 gaacgtggcg agaaaggaag ggaagaaagc gaaaggagcg ggcgctaggg cgctggcaag
     2341 tgtagcggtc acgctgcgcg taaccaccac acccgccgcg cttaatgcgc cgctacaggg
     2401 cgcgtcccat tcgccattca ggctgcgcaa ctgttgggaa gggcgatcgg tgcgggcctc
     2461 ttcgctatta cgccagctgg cgaaaggggg atgtgctgca aggcgattaa gttgggtaac
     2521 gccagggttt tcccagtcac gacgttgtaa aacgacggcc agtgagcgcg cgtaatacga
     2581 ctcactatag ggcgaattgg gtacgtccct aggcctccaa aaaagcctcc tcactacttc
     2641 tggaatagct cagaggccga ggcggcctcg gcctctgcat aaataaaaaa aattagtcag
     2701 ccatggggcg gagaatgggc ggaactgggc ggagttaggg gcgggatggg cggagttagg
     2761 ggcgggatag ctagagccag acatgataag atacattgat gagtttggac aaaccacaac
     2821 tagaatgcag tgaaaaaaat gctttatttg tgaaatttgt gatgctattg ctttatttgt
     2881 aaccattata agctgcaata aacaagttcc tctcactctc tgatattcat ttctttgcaa
     2941 gttataaata ctgaataata agatgacatg aactactact gctagagatt ttccacactg
     3001 actaaaaggg tctgagggat ctctagttac cagagtcaca caacagacgg gcacacacta
     3061 cttgaagcac tcaaggcaag ctttattgag gcttaagcag tgggttccct agttagccag
     3121 agagctccca ggctcagatc tggtctaacc agagagaccc agtacaagca aaaagcagat
     3181 cttgtcttcg ttgggagtga attagccctt ccagtccccc cttttctttt aaaaagtggc
     3241 taagatctac agctgccttg taagtcattg gtcttaaagg taccgatgca tggggtcgtg
     3301 cgctcctttc ggtcgggcgc tgcgggtcgt ggggcgggcg tcaggcaccg ggcttgcggg
     3361 tcatgcacca ggtgcgcggt ccttcgggca cctcgacgtc ggcggtgacg gtgaagccga
     3421 gccgctcgta gaaggggagg ttgcggggcg cggaggtctc caggaaggcg ggcaccccgg
     3481 cgcgctcggc cgcctccact ccggggagca cgacggcgct gcccagaccc ttgccctggt
     3541 ggtcgggcga gacgccgacg gtggccagga accacgcggg ctccttgggc cggtgcggcg
     3601 ccaggaggcc ttccatctgt tgctgcgcgg ccagccggga accgctcaac tcggccatgc
     3661 gcgggccgat ctcggcgaac accgcccccg cttcgacgct ctccggcgtg gtccagaccg
     3721 ccaccgcggc gccgtcgtcc gcgacccaca ccttgccgat gtcgagcccg acgcgcgtga
     3781 ggaagagttc ttgcagctcg gtgacccgct cgatgtggcg gtccggatcg acggtgtggc
     3841 gcgtggcggg gtagtcggcg aacgcggcgg cgagggtgcg tacggccctg gggacgtcgt
     3901 cgcgggtggc gaggcgcacc gtgggcttgt actcggtcat ggtaagctcc ggtggatccc
     3961 cctggggaga gaggtcggtg attcggtcaa cgagggagcc gactgccgac gtgcgctccg
     4021 gaggcttgca gaatgcggaa caccgcgcgg gcaggaacag ggcccacact accgccccac
     4081 accccgcctc ccgcaccgcc ccttcccggc cgctgctctc ggcgcgccct gctgagcagc
     4141 cgctattggc cacagcccat cgcggtcggc gcgctgccat tgctccctgg cgctgtccgt
     4201 ctgcgagggt actagtgaga cgtgcggctt ccgtttgtca cgtccggcac gccgcgaacc
     4261 gcaaggaacc ttcccgactt aggggcggag caggaagcgt cgccgggggg cccacaaggg
     4321 tagcggcgaa gatccgggtg acgctgcgaa cggacgtgaa gaatgtgcga gacccagggt
     4381 cggcgccgct gcgtttcccg gaaccacgcc cagagcagcc gcgtccctgc gcaaacccag
     4441 ggctgccttg gaaaaggcgc aaccccaacc ccctcgagcc gcggccaaag tggatctctg
     4501 ctgtccctgt aataaacccg aaaattttga atttttgtaa tttgtttttg taattcttta
     4561 gtttgtatgt ctgttgctat tatgtctact attctttccc ctgcactgta ccccccaatc
     4621 cccccttttc ttttaaaatt gtggatgaat actgccattt gtctcgaggt cgagaattca
     4681 aaaaccatca ccactgcttt ctcttctcga gaagagaaag cagtggtgat ggccggtgtt
     4741 tcgtcctttc cacaagatat ataaagccaa gaaatcgaaa tactttcaag ttacggtaag
     4801 catatgatag tccattttaa aacataattt taaaactgca aactacccaa gaaattatta
     4861 ctttctacgt cacgtatttt gtactaatat ctttgtgttt acagtcaaat taattccaat
     4921 tatctctcta acagccttgt atcgtatatg caaatatgaa ggaatcatgg gaaataggcc
     4981 ctcggtgaag ggggcggccg ctcgaggcta gtctcgtgat cgataccgtc gagatccgtt
     5041 cactaatcga atggatctgt ctctgtctct ctctccacct tcttcttcta ttccttcggg
     5101 cctgtcgggt cccctcgggg ttgggaggtg ggtctgaaac gataatggtg aatatccctg
     5161 cctaactcta ttcactatag aaagtacagc aaaaactatt cttaaaccta ccaagcctcc
     5221 tactatcatt atgaataatt ttatatacca cagccaattt gttatgttaa accaattcca
     5281 caaacttgcc catttatcta attccaataa ttcttgttca ttcttttctt gctggttttg
     5341 cgattcttca attaaggagt gtattaagct tgtgtaattg ttaatttctc tgtcccactc
     5401 catccaggtc gtgtgattcc aaatctgttc cagagattta ttactccaac tagcattcca
     5461 aggcacagca gtggtgcaaa tgagttttcc agagcaaccc caaatcccca ggagctgttg
     5521 atcctttagg tatctttcca cagccaggat tcttgcctgg agctgcttga tgccccagac
     5581 tgtgagttgc aacagatgct gttgcgcctc aatagccctc agcaaattgt tctgctgctg
     5641 cactatacca gacaataatt gtctggcctg taccgtcagc gtcattgacg ctgcgcccat
     5701 agtgcttcct gctgctccca agaacccaag gaacaaagct cctattccca ctgctctttt
     5761 ttctctctgc accactcttc tctttgcctt ggtgggtgct actcctaatg gttcaatttt
     5821 tactacttta tatttatata attcacttct ccaattgtcc ctcatatctc ctcctccagg
     5881 tctgaagatc agcggccgct tgctgtgcgg tggtcttact tttgttttgc tcttcctcta
     5941 tcttgtctaa agcttccttg gtgtctttta tctctatcct ttgatgcaca caatagaggg
     6001 ttgctactgt attatataat gatctaagtt cttctgatcc tgtctgaagg gatggttgta
     6061 gctgtcccag tatttgtcta cagccttctg atgtttctaa caggccagga ttaactgcga
     6121 atcgttctag ctccctgctt gcccatacta tatgttttaa tttatatttt ttctttcccc
     6181 ctggccttaa ccgaattttt tcccatcgcg atctaattct cccccgctta atactgacgc
     6241 tctcgcaccc atctctctcc ttctagcctc cgctagtcaa aatttttggc gtactcacca
     6301 gtcgccgccc ctcgcctctt gccgtgcgcg cttcagcaag ccgagtcctg cgtcgagaga
     6361 gctcctctgg tttccctttc gctttcaagt ccctgttcgg gcgccactgc tagagatttt
     6421 ccacactgac taaaagggtc tgagggatct ctagttacca gagtcacaca acagacgggc
     6481 acacactact tgaagcactc aaggcaagct ttattgaggc ttaagcagtg ggttccctag
     6541 ttagccagag agctcccagg ctcagatctg gtctaaccag agagacccgt ttatgtatcg
     6601 agctaggcac ttaaatacaa tatctctgca atgcggcaat tcagtggttc gtccaatcca
     6661 tgtcagaccc gtctgttgcc ttcctaataa ggcacgatcg taccacctta cttccaccaa
     6721 tcggcatgca cggtgctttt tctctccttg taaggcatgt tgctaactca tcgttaccat
     6781 gttgcaagac tacaagagta ttgcataaga ctacattaag cttgcagctc cagcttttgt
     6841 tccctttagt gagggttaat tgcgcgcttg gcgtaatcat ggtcatagct gtttcctgtg
     6901 tgaaattgtt atccgctcac aattccacac aacatacgag ccggaagcat aaagtgtaaa
     6961 gcctggggtg cctaatgagt gagctaactc acattaattg cgttgcgctc actgcccgct
     7021 ttccagtcgg gaaacctgtc gtgccagctg cattaatgaa tcggccaacg cgcggggaga
     7081 ggcg
//
