LOCUS       sequence-269423-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  STAU2 shRNA (Targeting 3'UTR) inserted into the PLKO.1 plasmid 
            (GCCAGGTAGTTGTTAGTGTTT).
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-STAU2-3'UTR
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(18..35)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(189..777)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(269..288)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(948..1739,1740..1808))
                     /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     1571..1590
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(1809..1913)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(1939..2394)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2076..2097)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     2288..2307
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2521..2543
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     2535..2552
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     2536..2552
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     2562..2581
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        2562..2580
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     rep_origin      2601..2736
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    2776..2897
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2787..2806)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     2841..2860
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     LTR             2969..3202
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     CDS             complement(3330..3929)
                     /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(3413..3433)
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     primer_bind     3910..3929
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     promoter        complement(3951..4461)
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     complement(4014..4032)
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     misc_feature    4510..4627
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        complement(4724..4972)
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     complement(4782..4801)
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     primer_bind     complement(4952..4972)
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     CDS             complement(5270..5314)
                     /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    5499..5732
                     /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    6225..6350
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     LTR             6397..6577
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     promoter        complement(6578..6804)
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     primer_bind     complement(6832..6852)
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        complement(6832..6850)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(6871..6887)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(6871..6887)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(6884..6906)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    6895..6911
                     /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(6919..6925,6926..6943,6944..6949))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6964..6985
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
ORIGIN
        1 gggcgctctt ccgcttcctc gctcactgac tcgctgcgct cggtcgttcg gctgcggcga
       61 gcggtatcag ctcactcaaa ggcggtaata cggttatcca cagaatcagg ggataacgca
      121 ggaaagaaca tgtgagcaaa aggccagcaa aaggccagga accgtaaaaa ggccgcgttg
      181 ctggcgtttt tccataggct ccgcccccct gacgagcatc acaaaaatcg acgctcaagt
      241 cagaggtggc gaaacccgac aggactataa agataccagg cgtttccccc tggaagctcc
      301 ctcgtgcgct ctcctgttcc gaccctgccg cttaccggat acctgtccgc ctttctccct
      361 tcgggaagcg tggcgctttc tcatagctca cgctgtaggt atctcagttc ggtgtaggtc
      421 gttcgctcca agctgggctg tgtgcacgaa ccccccgttc agcccgaccg ctgcgcctta
      481 tccggtaact atcgtcttga gtccaacccg gtaagacacg acttatcgcc actggcagca
      541 gccactggta acaggattag cagagcgagg tatgtaggcg gtgctacaga gttcttgaag
      601 tggtggccta actacggcta cactagaaga acagtatttg gtatctgcgc tctgctgaag
      661 ccagttacct tcggaaaaag agttggtagc tcttgatccg gcaaacaaac caccgctggt
      721 agcggtggtt tttttgtttg caagcagcag attacgcgca gaaaaaaagg atctcaagaa
      781 gatcctttga tcttttctac ggggtctgac gctcagtgga acgaaaactc acgttaaggg
      841 attttggtca tgagattatc aaaaaggatc ttcacctaga tccttttaaa ttaaaaatga
      901 agttttaaat caatctaaag tatatatgag taaacttggt ctgacagtta ccaatgctta
      961 atcagtgagg cacctatctc agcgatctgt ctatttcgtt catccatagt tgcctgactc
     1021 cccgtcgtgt agataactac gatacgggag ggcttaccat ctggccccag tgctgcaatg
     1081 ataccgcgag acccacgctc accggctcca gatttatcag caataaacca gccagccgga
     1141 agggccgagc gcagaagtgg tcctgcaact ttatccgcct ccatccagtc tattaattgt
     1201 tgccgggaag ctagagtaag tagttcgcca gttaatagtt tgcgcaacgt tgttgccatt
     1261 gctacaggca tcgtggtgtc acgctcgtcg tttggtatgg cttcattcag ctccggttcc
     1321 caacgatcaa ggcgagttac atgatccccc atgttgtgca aaaaagcggt tagctccttc
     1381 ggtcctccga tcgttgtcag aagtaagttg gccgcagtgt tatcactcat ggttatggca
     1441 gcactgcata attctcttac tgtcatgcca tccgtaagat gcttttctgt gactggtgag
     1501 tactcaacca agtcattctg agaatagtgt atgcggcgac cgagttgctc ttgcccggcg
     1561 tcaatacggg ataataccgc gccacatagc agaactttaa aagtgctcat cattggaaaa
     1621 cgttcttcgg ggcgaaaact ctcaaggatc ttaccgctgt tgagatccag ttcgatgtaa
     1681 cccactcgtg cacccaactg atcttcagca tcttttactt tcaccagcgt ttctgggtga
     1741 gcaaaaacag gaaggcaaaa tgccgcaaaa aagggaataa gggcgacacg gaaatgttga
     1801 atactcatac tcttcctttt tcaatattat tgaagcattt atcagggtta ttgtctcatg
     1861 agcggataca tatttgaatg tatttagaaa aataaacaaa taggggttcc gcgcacattt
     1921 ccccgaaaag tgccacctaa attgtaagcg ttaatatttt gttaaaattc gcgttaaatt
     1981 tttgttaaat cagctcattt tttaaccaat aggccgaaat cggcaaaatc ccttataaat
     2041 caaaagaata gaccgagata gggttgagtg ttgttccagt ttggaacaag agtccactat
     2101 taaagaacgt ggactccaac gtcaaagggc gaaaaaccgt ctatcagggc gatggcccac
     2161 tacgtgaacc atcaccctaa tcaagttttt tggggtcgag gtgccgtaaa gcactaaatc
     2221 ggaaccctaa agggagcccc cgatttagag cttgacgggg aaagccggcg aacgtggcga
     2281 gaaaggaagg gaagaaagcg aaaggagcgg gcgctagggc gctggcaagt gtagcggtca
     2341 cgctgcgcgt aaccaccaca cccgccgcgc ttaatgcgcc gctacagggc gcgtcccatt
     2401 cgccattcag gctgcgcaac tgttgggaag ggcgatcggt gcgggcctct tcgctattac
     2461 gccagctggc gaaaggggga tgtgctgcaa ggcgattaag ttgggtaacg ccagggtttt
     2521 cccagtcacg acgttgtaaa acgacggcca gtgagcgcgc gtaatacgac tcactatagg
     2581 gcgaattggg tacgtcccta ggcctccaaa aaagcctcct cactacttct ggaatagctc
     2641 agaggccgag gcggcctcgg cctctgcata aataaaaaaa attagtcagc catggggcgg
     2701 agaatgggcg gaactgggcg gagttagggg cgggatgggc ggagttaggg gcgggatagc
     2761 tagagccaga catgataaga tacattgatg agtttggaca aaccacaact agaatgcagt
     2821 gaaaaaaatg ctttatttgt gaaatttgtg atgctattgc tttatttgta accattataa
     2881 gctgcaataa acaagttcct ctcactctct gatattcatt tctttgcaag ttataaatac
     2941 tgaataataa gatgacatga actactactg ctagagattt tccacactga ctaaaagggt
     3001 ctgagggatc tctagttacc agagtcacac aacagacggg cacacactac ttgaagcact
     3061 caaggcaagc tttattgagg cttaagcagt gggttcccta gttagccaga gagctcccag
     3121 gctcagatct ggtctaacca gagagaccca gtacaagcaa aaagcagatc ttgtcttcgt
     3181 tgggagtgaa ttagcccttc cagtcccccc ttttctttta aaaagtggct aagatctaca
     3241 gctgccttgt aagtcattgg tcttaaaggt accgatgcat ggggtcgtgc gctcctttcg
     3301 gtcgggcgct gcgggtcgtg gggcgggcgt caggcaccgg gcttgcgggt catgcaccag
     3361 gtgcgcggtc cttcgggcac ctcgacgtcg gcggtgacgg tgaagccgag ccgctcgtag
     3421 aaggggaggt tgcggggcgc ggaggtctcc aggaaggcgg gcaccccggc gcgctcggcc
     3481 gcctccactc cggggagcac gacggcgctg cccagaccct tgccctggtg gtcgggcgag
     3541 acgccgacgg tggccaggaa ccacgcgggc tccttgggcc ggtgcggcgc caggaggcct
     3601 tccatctgtt gctgcgcggc cagccgggaa ccgctcaact cggccatgcg cgggccgatc
     3661 tcggcgaaca ccgcccccgc ttcgacgctc tccggcgtgg tccagaccgc caccgcggcg
     3721 ccgtcgtccg cgacccacac cttgccgatg tcgagcccga cgcgcgtgag gaagagttct
     3781 tgcagctcgg tgacccgctc gatgtggcgg tccggatcga cggtgtggcg cgtggcgggg
     3841 tagtcggcga acgcggcggc gagggtgcgt acggccctgg ggacgtcgtc gcgggtggcg
     3901 aggcgcaccg tgggcttgta ctcggtcatg gtaagctccg gtggatcccc ctggggagag
     3961 aggtcggtga ttcggtcaac gagggagccg actgccgacg tgcgctccgg aggcttgcag
     4021 aatgcggaac accgcgcggg caggaacagg gcccacacta ccgccccaca ccccgcctcc
     4081 cgcaccgccc cttcccggcc gctgctctcg gcgcgccctg ctgagcagcc gctattggcc
     4141 acagcccatc gcggtcggcg cgctgccatt gctccctggc gctgtccgtc tgcgagggta
     4201 ctagtgagac gtgcggcttc cgtttgtcac gtccggcacg ccgcgaaccg caaggaacct
     4261 tcccgactta ggggcggagc aggaagcgtc gccggggggc ccacaagggt agcggcgaag
     4321 atccgggtga cgctgcgaac ggacgtgaag aatgtgcgag acccagggtc ggcgccgctg
     4381 cgtttcccgg aaccacgccc agagcagccg cgtccctgcg caaacccagg gctgccttgg
     4441 aaaaggcgca accccaaccc cctcgagccg cggccaaagt ggatctctgc tgtccctgta
     4501 ataaacccga aaattttgaa tttttgtaat ttgtttttgt aattctttag tttgtatgtc
     4561 tgttgctatt atgtctacta ttctttcccc tgcactgtac cccccaatcc ccccttttct
     4621 tttaaaattg tggatgaata ctgccatttg tctcgaggtc gagaattcaa aaagccaggt
     4681 agttgttagt gtttctcgag aaacactaac aactacctgg cccggtgttt cgtcctttcc
     4741 acaagatata taaagccaag aaatcgaaat actttcaagt tacggtaagc atatgatagt
     4801 ccattttaaa acataatttt aaaactgcaa actacccaag aaattattac tttctacgtc
     4861 acgtattttg tactaatatc tttgtgttta cagtcaaatt aattccaatt atctctctaa
     4921 cagccttgta tcgtatatgc aaatatgaag gaatcatggg aaataggccc tcggtgaagg
     4981 gggcggccgc tcgaggctag tctcgtgatc gataccgtcg agatccgttc actaatcgaa
     5041 tggatctgtc tctgtctctc tctccacctt cttcttctat tccttcgggc ctgtcgggtc
     5101 ccctcggggt tgggaggtgg gtctgaaacg ataatggtga atatccctgc ctaactctat
     5161 tcactataga aagtacagca aaaactattc ttaaacctac caagcctcct actatcatta
     5221 tgaataattt tatataccac agccaatttg ttatgttaaa ccaattccac aaacttgccc
     5281 atttatctaa ttccaataat tcttgttcat tcttttcttg ctggttttgc gattcttcaa
     5341 ttaaggagtg tattaagctt gtgtaattgt taatttctct gtcccactcc atccaggtcg
     5401 tgtgattcca aatctgttcc agagatttat tactccaact agcattccaa ggcacagcag
     5461 tggtgcaaat gagttttcca gagcaacccc aaatccccag gagctgttga tcctttaggt
     5521 atctttccac agccaggatt cttgcctgga gctgcttgat gccccagact gtgagttgca
     5581 acagatgctg ttgcgcctca atagccctca gcaaattgtt ctgctgctgc actataccag
     5641 acaataattg tctggcctgt accgtcagcg tcattgacgc tgcgcccata gtgcttcctg
     5701 ctgctcccaa gaacccaagg aacaaagctc ctattcccac tgctcttttt tctctctgca
     5761 ccactcttct ctttgccttg gtgggtgcta ctcctaatgg ttcaattttt actactttat
     5821 atttatataa ttcacttctc caattgtccc tcatatctcc tcctccaggt ctgaagatca
     5881 gcggccgctt gctgtgcggt ggtcttactt ttgttttgct cttcctctat cttgtctaaa
     5941 gcttccttgg tgtcttttat ctctatcctt tgatgcacac aatagagggt tgctactgta
     6001 ttatataatg atctaagttc ttctgatcct gtctgaaggg atggttgtag ctgtcccagt
     6061 atttgtctac agccttctga tgtttctaac aggccaggat taactgcgaa tcgttctagc
     6121 tccctgcttg cccatactat atgttttaat ttatattttt tctttccccc tggccttaac
     6181 cgaatttttt cccatcgcga tctaattctc ccccgcttaa tactgacgct ctcgcaccca
     6241 tctctctcct tctagcctcc gctagtcaaa atttttggcg tactcaccag tcgccgcccc
     6301 tcgcctcttg ccgtgcgcgc ttcagcaagc cgagtcctgc gtcgagagag ctcctctggt
     6361 ttccctttcg ctttcaagtc cctgttcggg cgccactgct agagattttc cacactgact
     6421 aaaagggtct gagggatctc tagttaccag agtcacacaa cagacgggca cacactactt
     6481 gaagcactca aggcaagctt tattgaggct taagcagtgg gttccctagt tagccagaga
     6541 gctcccaggc tcagatctgg tctaaccaga gagacccgtt tatgtatcga gctaggcact
     6601 taaatacaat atctctgcaa tgcggcaatt cagtggttcg tccaatccat gtcagacccg
     6661 tctgttgcct tcctaataag gcacgatcgt accaccttac ttccaccaat cggcatgcac
     6721 ggtgcttttt ctctccttgt aaggcatgtt gctaactcat cgttaccatg ttgcaagact
     6781 acaagagtat tgcataagac tacattaagc ttgcagctcc agcttttgtt ccctttagtg
     6841 agggttaatt gcgcgcttgg cgtaatcatg gtcatagctg tttcctgtgt gaaattgtta
     6901 tccgctcaca attccacaca acatacgagc cggaagcata aagtgtaaag cctggggtgc
     6961 ctaatgagtg agctaactca cattaattgc gttgcgctca ctgcccgctt tccagtcggg
     7021 aaacctgtcg tgccagctgc attaatgaat cggccaacgc gcggggagag gcggtttgcg
     7081 tatt
//
