LOCUS       sequence-269250-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  SMG6 shRNA (Targeting CDS #1) inserted into the PLKO.1 plasmid 
            (AACTTGTAAGTAACCTGCAGC).
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-SMG6-CDS-1
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             63..107
                     /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        405..653
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     405..425
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     576..595
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    750..867
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        916..1426
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1345..1363
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1448..2047
                     /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(1448..1467)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     1944..1964
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             2175..2408
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2480..2601
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2517..2536)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2571..2590
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2641..2776
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2796..2815)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(2797..2815)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2825..2842)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2825..2841)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2834..2856)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      2983..3438
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3070..3089)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3280..3301
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3464..3568
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3569..3637,3638..4429)
                     /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(3787..3806)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4600..5188
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5089..5108
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5342..5359
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5476..5497
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5512..5517,5518..5535,5536..5542)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5550..5566
                     /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     5555..5577
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5574..5590
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5574..5590
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5609..5629
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5611..5629
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5657..5883
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             5884..6064
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6111..6236
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6729..6962
                     /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 aaattaacaa ttacacaagc ttaatacact ccttaattga agaatcgcaa aaccagcaag
       61 aaaagaatga acaagaatta ttggaattag ataaatgggc aagtttgtgg aattggttta
      121 acataacaaa ttggctgtgg tatataaaat tattcataat gatagtagga ggcttggtag
      181 gtttaagaat agtttttgct gtactttcta tagtgaatag agttaggcag ggatattcac
      241 cattatcgtt tcagacccac ctcccaaccc cgaggggacc cgacaggccc gaaggaatag
      301 aagaagaagg tggagagaga gacagagaca gatccattcg attagtgaac ggatctcgac
      361 ggtatcgatc acgagactag cctcgagcgg ccgccccctt caccgagggc ctatttccca
      421 tgattccttc atatttgcat atacgataca aggctgttag agagataatt ggaattaatt
      481 tgactgtaaa cacaaagata ttagtacaaa atacgtgacg tagaaagtaa taatttcttg
      541 ggtagtttgc agttttaaaa ttatgtttta aaatggacta tcatatgctt accgtaactt
      601 gaaagtattt cgatttcttg gctttatata tcttgtggaa aggacgaaac accggaactt
      661 gtaagtaacc tgcagcctcg aggctgcagg ttacttacaa gtttttttga attctcgacc
      721 tcgagacaaa tggcagtatt catccacaat tttaaaagaa aaggggggat tggggggtac
      781 agtgcagggg aaagaatagt agacataata gcaacagaca tacaaactaa agaattacaa
      841 aaacaaatta caaaaattca aaattttcgg gtttattaca gggacagcag agatccactt
      901 tggccgcggc tcgagggggt tggggttgcg ccttttccaa ggcagccctg ggtttgcgca
      961 gggacgcggc tgctctgggc gtggttccgg gaaacgcagc ggcgccgacc ctgggtctcg
     1021 cacattcttc acgtccgttc gcagcgtcac ccggatcttc gccgctaccc ttgtgggccc
     1081 cccggcgacg cttcctgctc cgcccctaag tcgggaaggt tccttgcggt tcgcggcgtg
     1141 ccggacgtga caaacggaag ccgcacgtct cactagtacc ctcgcagacg gacagcgcca
     1201 gggagcaatg gcagcgcgcc gaccgcgatg ggctgtggcc aatagcggct gctcagcagg
     1261 gcgcgccgag agcagcggcc gggaaggggc ggtgcgggag gcggggtgtg gggcggtagt
     1321 gtgggccctg ttcctgcccg cgcggtgttc cgcattctgc aagcctccgg agcgcacgtc
     1381 ggcagtcggc tccctcgttg accgaatcac cgacctctct ccccaggggg atccaccgga
     1441 gcttaccatg accgagtaca agcccacggt gcgcctcgcc acccgcgacg acgtccccag
     1501 ggccgtacgc accctcgccg ccgcgttcgc cgactacccc gccacgcgcc acaccgtcga
     1561 tccggaccgc cacatcgagc gggtcaccga gctgcaagaa ctcttcctca cgcgcgtcgg
     1621 gctcgacatc ggcaaggtgt gggtcgcgga cgacggcgcc gcggtggcgg tctggaccac
     1681 gccggagagc gtcgaagcgg gggcggtgtt cgccgagatc ggcccgcgca tggccgagtt
     1741 gagcggttcc cggctggccg cgcagcaaca gatggaaggc ctcctggcgc cgcaccggcc
     1801 caaggagccc gcgtggttcc tggccaccgt cggcgtctcg cccgaccacc agggcaaggg
     1861 tctgggcagc gccgtcgtgc tccccggagt ggaggcggcc gagcgcgccg gggtgcccgc
     1921 cttcctggag acctccgcgc cccgcaacct ccccttctac gagcggctcg gcttcaccgt
     1981 caccgccgac gtcgaggtgc ccgaaggacc gcgcacctgg tgcatgaccc gcaagcccgg
     2041 tgcctgacgc ccgccccacg acccgcagcg cccgaccgaa aggagcgcac gaccccatgc
     2101 atcggtacct ttaagaccaa tgacttacaa ggcagctgta gatcttagcc actttttaaa
     2161 agaaaagggg ggactggaag ggctaattca ctcccaacga agacaagatc tgctttttgc
     2221 ttgtactggg tctctctggt tagaccagat ctgagcctgg gagctctctg gctaactagg
     2281 gaacccactg cttaagcctc aataaagctt gccttgagtg cttcaagtag tgtgtgcccg
     2341 tctgttgtgt gactctggta actagagatc cctcagaccc ttttagtcag tgtggaaaat
     2401 ctctagcagt agtagttcat gtcatcttat tattcagtat ttataacttg caaagaaatg
     2461 aatatcagag agtgagagga acttgtttat tgcagcttat aatggttaca aataaagcaa
     2521 tagcatcaca aatttcacaa ataaagcatt tttttcactg cattctagtt gtggtttgtc
     2581 caaactcatc aatgtatctt atcatgtctg gctctagcta tcccgcccct aactccgccc
     2641 atcccgcccc taactccgcc cagttccgcc cattctccgc cccatggctg actaattttt
     2701 tttatttatg cagaggccga ggccgcctcg gcctctgagc tattccagaa gtagtgagga
     2761 ggcttttttg gaggcctagg gacgtaccca attcgcccta tagtgagtcg tattacgcgc
     2821 gctcactggc cgtcgtttta caacgtcgtg actgggaaaa ccctggcgtt acccaactta
     2881 atcgccttgc agcacatccc cctttcgcca gctggcgtaa tagcgaagag gcccgcaccg
     2941 atcgcccttc ccaacagttg cgcagcctga atggcgaatg ggacgcgccc tgtagcggcg
     3001 cattaagcgc ggcgggtgtg gtggttacgc gcagcgtgac cgctacactt gccagcgccc
     3061 tagcgcccgc tcctttcgct ttcttccctt cctttctcgc cacgttcgcc ggctttcccc
     3121 gtcaagctct aaatcggggg ctccctttag ggttccgatt tagtgcttta cggcacctcg
     3181 accccaaaaa acttgattag ggtgatggtt cacgtagtgg gccatcgccc tgatagacgg
     3241 tttttcgccc tttgacgttg gagtccacgt tctttaatag tggactcttg ttccaaactg
     3301 gaacaacact caaccctatc tcggtctatt cttttgattt ataagggatt ttgccgattt
     3361 cggcctattg gttaaaaaat gagctgattt aacaaaaatt taacgcgaat tttaacaaaa
     3421 tattaacgct tacaatttag gtggcacttt tcggggaaat gtgcgcggaa cccctatttg
     3481 tttatttttc taaatacatt caaatatgta tccgctcatg agacaataac cctgataaat
     3541 gcttcaataa tattgaaaaa ggaagagtat gagtattcaa catttccgtg tcgcccttat
     3601 tccctttttt gcggcatttt gccttcctgt ttttgctcac ccagaaacgc tggtgaaagt
     3661 aaaagatgct gaagatcagt tgggtgcacg agtgggttac atcgaactgg atctcaacag
     3721 cggtaagatc cttgagagtt ttcgccccga agaacgtttt ccaatgatga gcacttttaa
     3781 agttctgcta tgtggcgcgg tattatcccg tattgacgcc gggcaagagc aactcggtcg
     3841 ccgcatacac tattctcaga atgacttggt tgagtactca ccagtcacag aaaagcatct
     3901 tacggatggc atgacagtaa gagaattatg cagtgctgcc ataaccatga gtgataacac
     3961 tgcggccaac ttacttctga caacgatcgg aggaccgaag gagctaaccg cttttttgca
     4021 caacatgggg gatcatgtaa ctcgccttga tcgttgggaa ccggagctga atgaagccat
     4081 accaaacgac gagcgtgaca ccacgatgcc tgtagcaatg gcaacaacgt tgcgcaaact
     4141 attaactggc gaactactta ctctagcttc ccggcaacaa ttaatagact ggatggaggc
     4201 ggataaagtt gcaggaccac ttctgcgctc ggcccttccg gctggctggt ttattgctga
     4261 taaatctgga gccggtgagc gtgggtctcg cggtatcatt gcagcactgg ggccagatgg
     4321 taagccctcc cgtatcgtag ttatctacac gacggggagt caggcaacta tggatgaacg
     4381 aaatagacag atcgctgaga taggtgcctc actgattaag cattggtaac tgtcagacca
     4441 agtttactca tatatacttt agattgattt aaaacttcat ttttaattta aaaggatcta
     4501 ggtgaagatc ctttttgata atctcatgac caaaatccct taacgtgagt tttcgttcca
     4561 ctgagcgtca gaccccgtag aaaagatcaa aggatcttct tgagatcctt tttttctgcg
     4621 cgtaatctgc tgcttgcaaa caaaaaaacc accgctacca gcggtggttt gtttgccgga
     4681 tcaagagcta ccaactcttt ttccgaaggt aactggcttc agcagagcgc agataccaaa
     4741 tactgttctt ctagtgtagc cgtagttagg ccaccacttc aagaactctg tagcaccgcc
     4801 tacatacctc gctctgctaa tcctgttacc agtggctgct gccagtggcg ataagtcgtg
     4861 tcttaccggg ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac
     4921 ggggggttcg tgcacacagc ccagcttgga gcgaacgacc tacaccgaac tgagatacct
     4981 acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc
     5041 ggtaagcggc agggtcggaa caggagagcg cacgagggag cttccagggg gaaacgcctg
     5101 gtatctttat agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg
     5161 ctcgtcaggg gggcggagcc tatggaaaaa cgccagcaac gcggcctttt tacggttcct
     5221 ggccttttgc tggccttttg ctcacatgtt ctttcctgcg ttatcccctg attctgtgga
     5281 taaccgtatt accgcctttg agtgagctga taccgctcgc cgcagccgaa cgaccgagcg
     5341 cagcgagtca gtgagcgagg aagcggaaga gcgcccaata cgcaaaccgc ctctccccgc
     5401 gcgttggccg attcattaat gcagctggca cgacaggttt cccgactgga aagcgggcag
     5461 tgagcgcaac gcaattaatg tgagttagct cactcattag gcaccccagg ctttacactt
     5521 tatgcttccg gctcgtatgt tgtgtggaat tgtgagcgga taacaatttc acacaggaaa
     5581 cagctatgac catgattacg ccaagcgcgc aattaaccct cactaaaggg aacaaaagct
     5641 ggagctgcaa gcttaatgta gtcttatgca atactcttgt agtcttgcaa catggtaacg
     5701 atgagttagc aacatgcctt acaaggagag aaaaagcacc gtgcatgccg attggtggaa
     5761 gtaaggtggt acgatcgtgc cttattagga aggcaacaga cgggtctgac atggattgga
     5821 cgaaccactg aattgccgca ttgcagagat attgtattta agtgcctagc tcgatacata
     5881 aacgggtctc tctggttaga ccagatctga gcctgggagc tctctggcta actagggaac
     5941 ccactgctta agcctcaata aagcttgcct tgagtgcttc aagtagtgtg tgcccgtctg
     6001 ttgtgtgact ctggtaacta gagatccctc agaccctttt agtcagtgtg gaaaatctct
     6061 agcagtggcg cccgaacagg gacttgaaag cgaaagggaa accagaggag ctctctcgac
     6121 gcaggactcg gcttgctgaa gcgcgcacgg caagaggcga ggggcggcga ctggtgagta
     6181 cgccaaaaat tttgactagc ggaggctaga aggagagaga tgggtgcgag agcgtcagta
     6241 ttaagcgggg gagaattaga tcgcgatggg aaaaaattcg gttaaggcca gggggaaaga
     6301 aaaaatataa attaaaacat atagtatggg caagcaggga gctagaacga ttcgcagtta
     6361 atcctggcct gttagaaaca tcagaaggct gtagacaaat actgggacag ctacaaccat
     6421 cccttcagac aggatcagaa gaacttagat cattatataa tacagtagca accctctatt
     6481 gtgtgcatca aaggatagag ataaaagaca ccaaggaagc tttagacaag atagaggaag
     6541 agcaaaacaa aagtaagacc accgcacagc aagcggccgc tgatcttcag acctggagga
     6601 ggagatatga gggacaattg gagaagtgaa ttatataaat ataaagtagt aaaaattgaa
     6661 ccattaggag tagcacccac caaggcaaag agaagagtgg tgcagagaga aaaaagagca
     6721 gtgggaatag gagctttgtt ccttgggttc ttgggagcag caggaagcac tatgggcgca
     6781 gcgtcaatga cgctgacggt acaggccaga caattattgt ctggtatagt gcagcagcag
     6841 aacaatttgc tgagggctat tgaggcgcaa cagcatctgt tgcaactcac agtctggggc
     6901 atcaagcagc tccaggcaag aatcctggct gtggaaagat acctaaagga tcaacagctc
     6961 ctggggattt ggggttgctc tggaaaactc atttgcacca ctgctgtgcc ttggaatgct
     7021 agttggagta ataaatctct ggaacagatt tggaatcaca cgacctggat ggagtgggac
     7081 agag
//
