LOCUS       sequence-269276-        7084 bp    DNA     circular SYN 15-APR-2025
DEFINITION  REG1 shRNA (Targeting CDS) inserted into the PLKO.1 plasmid 
            (TATGGGATCAAGTGCCGATTC).
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 Apr 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-REG1-CDS
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             169..213
                     /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        511..759
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     511..531
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     682..701
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    856..973
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        1022..1532
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1451..1469
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1554..2153
                     /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(1554..1573)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     2050..2070
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             2281..2514
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2586..2707
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2623..2642)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2677..2696
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2747..2882
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2902..2921)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(2903..2921)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2931..2948)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2931..2947)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2940..2962)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3089..3544
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3176..3195)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3386..3407
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3570..3674
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3675..3743,3744..4535)
                     /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(3893..3912)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4706..5294
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5195..5214
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5448..5465
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5582..5603
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5618..5623,5624..5641,5642..5648)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5656..5672
                     /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     5661..5683
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5680..5696
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5680..5696
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5715..5735
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5717..5735
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5763..5989
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             5990..6170
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6217..6342
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6835..7068
                     /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 tctggaaaac tcatttgcac cactgctgtg ccttggaatg ctagttggag taataaatct
       61 ctggaacaga tttggaatca cacgacctgg atggagtggg acagagaaat taacaattac
      121 acaagcttaa tacactcctt aattgaagaa tcgcaaaacc agcaagaaaa gaatgaacaa
      181 gaattattgg aattagataa atgggcaagt ttgtggaatt ggtttaacat aacaaattgg
      241 ctgtggtata taaaattatt cataatgata gtaggaggct tggtaggttt aagaatagtt
      301 tttgctgtac tttctatagt gaatagagtt aggcagggat attcaccatt atcgtttcag
      361 acccacctcc caaccccgag gggacccgac aggcccgaag gaatagaaga agaaggtgga
      421 gagagagaca gagacagatc cattcgatta gtgaacggat ctcgacggta tcgatcacga
      481 gactagcctc gagcggccgc ccccttcacc gagggcctat ttcccatgat tccttcatat
      541 ttgcatatac gatacaaggc tgttagagag ataattggaa ttaatttgac tgtaaacaca
      601 aagatattag tacaaaatac gtgacgtaga aagtaataat ttcttgggta gtttgcagtt
      661 ttaaaattat gttttaaaat ggactatcat atgcttaccg taacttgaaa gtatttcgat
      721 ttcttggctt tatatatctt gtggaaagga cgaaacaccg gtatgggatc aagtgccgat
      781 tcctcgagga atcggcactt gatcccatat ttttgaattc tcgacctcga gacaaatggc
      841 agtattcatc cacaatttta aaagaaaagg ggggattggg gggtacagtg caggggaaag
      901 aatagtagac ataatagcaa cagacataca aactaaagaa ttacaaaaac aaattacaaa
      961 aattcaaaat tttcgggttt attacaggga cagcagagat ccactttggc cgcggctcga
     1021 gggggttggg gttgcgcctt ttccaaggca gccctgggtt tgcgcaggga cgcggctgct
     1081 ctgggcgtgg ttccgggaaa cgcagcggcg ccgaccctgg gtctcgcaca ttcttcacgt
     1141 ccgttcgcag cgtcacccgg atcttcgccg ctacccttgt gggccccccg gcgacgcttc
     1201 ctgctccgcc cctaagtcgg gaaggttcct tgcggttcgc ggcgtgccgg acgtgacaaa
     1261 cggaagccgc acgtctcact agtaccctcg cagacggaca gcgccaggga gcaatggcag
     1321 cgcgccgacc gcgatgggct gtggccaata gcggctgctc agcagggcgc gccgagagca
     1381 gcggccggga aggggcggtg cgggaggcgg ggtgtggggc ggtagtgtgg gccctgttcc
     1441 tgcccgcgcg gtgttccgca ttctgcaagc ctccggagcg cacgtcggca gtcggctccc
     1501 tcgttgaccg aatcaccgac ctctctcccc agggggatcc accggagctt accatgaccg
     1561 agtacaagcc cacggtgcgc ctcgccaccc gcgacgacgt ccccagggcc gtacgcaccc
     1621 tcgccgccgc gttcgccgac taccccgcca cgcgccacac cgtcgatccg gaccgccaca
     1681 tcgagcgggt caccgagctg caagaactct tcctcacgcg cgtcgggctc gacatcggca
     1741 aggtgtgggt cgcggacgac ggcgccgcgg tggcggtctg gaccacgccg gagagcgtcg
     1801 aagcgggggc ggtgttcgcc gagatcggcc cgcgcatggc cgagttgagc ggttcccggc
     1861 tggccgcgca gcaacagatg gaaggcctcc tggcgccgca ccggcccaag gagcccgcgt
     1921 ggttcctggc caccgtcggc gtctcgcccg accaccaggg caagggtctg ggcagcgccg
     1981 tcgtgctccc cggagtggag gcggccgagc gcgccggggt gcccgccttc ctggagacct
     2041 ccgcgccccg caacctcccc ttctacgagc ggctcggctt caccgtcacc gccgacgtcg
     2101 aggtgcccga aggaccgcgc acctggtgca tgacccgcaa gcccggtgcc tgacgcccgc
     2161 cccacgaccc gcagcgcccg accgaaagga gcgcacgacc ccatgcatcg gtacctttaa
     2221 gaccaatgac ttacaaggca gctgtagatc ttagccactt tttaaaagaa aaggggggac
     2281 tggaagggct aattcactcc caacgaagac aagatctgct ttttgcttgt actgggtctc
     2341 tctggttaga ccagatctga gcctgggagc tctctggcta actagggaac ccactgctta
     2401 agcctcaata aagcttgcct tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact
     2461 ctggtaacta gagatccctc agaccctttt agtcagtgtg gaaaatctct agcagtagta
     2521 gttcatgtca tcttattatt cagtatttat aacttgcaaa gaaatgaata tcagagagtg
     2581 agaggaactt gtttattgca gcttataatg gttacaaata aagcaatagc atcacaaatt
     2641 tcacaaataa agcatttttt tcactgcatt ctagttgtgg tttgtccaaa ctcatcaatg
     2701 tatcttatca tgtctggctc tagctatccc gcccctaact ccgcccatcc cgcccctaac
     2761 tccgcccagt tccgcccatt ctccgcccca tggctgacta atttttttta tttatgcaga
     2821 ggccgaggcc gcctcggcct ctgagctatt ccagaagtag tgaggaggct tttttggagg
     2881 cctagggacg tacccaattc gccctatagt gagtcgtatt acgcgcgctc actggccgtc
     2941 gttttacaac gtcgtgactg ggaaaaccct ggcgttaccc aacttaatcg ccttgcagca
     3001 catccccctt tcgccagctg gcgtaatagc gaagaggccc gcaccgatcg cccttcccaa
     3061 cagttgcgca gcctgaatgg cgaatgggac gcgccctgta gcggcgcatt aagcgcggcg
     3121 ggtgtggtgg ttacgcgcag cgtgaccgct acacttgcca gcgccctagc gcccgctcct
     3181 ttcgctttct tcccttcctt tctcgccacg ttcgccggct ttccccgtca agctctaaat
     3241 cgggggctcc ctttagggtt ccgatttagt gctttacggc acctcgaccc caaaaaactt
     3301 gattagggtg atggttcacg tagtgggcca tcgccctgat agacggtttt tcgccctttg
     3361 acgttggagt ccacgttctt taatagtgga ctcttgttcc aaactggaac aacactcaac
     3421 cctatctcgg tctattcttt tgatttataa gggattttgc cgatttcggc ctattggtta
     3481 aaaaatgagc tgatttaaca aaaatttaac gcgaatttta acaaaatatt aacgcttaca
     3541 atttaggtgg cacttttcgg ggaaatgtgc gcggaacccc tatttgttta tttttctaaa
     3601 tacattcaaa tatgtatccg ctcatgagac aataaccctg ataaatgctt caataatatt
     3661 gaaaaaggaa gagtatgagt attcaacatt tccgtgtcgc ccttattccc ttttttgcgg
     3721 cattttgcct tcctgttttt gctcacccag aaacgctggt gaaagtaaaa gatgctgaag
     3781 atcagttggg tgcacgagtg ggttacatcg aactggatct caacagcggt aagatccttg
     3841 agagttttcg ccccgaagaa cgttttccaa tgatgagcac ttttaaagtt ctgctatgtg
     3901 gcgcggtatt atcccgtatt gacgccgggc aagagcaact cggtcgccgc atacactatt
     3961 ctcagaatga cttggttgag tactcaccag tcacagaaaa gcatcttacg gatggcatga
     4021 cagtaagaga attatgcagt gctgccataa ccatgagtga taacactgcg gccaacttac
     4081 ttctgacaac gatcggagga ccgaaggagc taaccgcttt tttgcacaac atgggggatc
     4141 atgtaactcg ccttgatcgt tgggaaccgg agctgaatga agccatacca aacgacgagc
     4201 gtgacaccac gatgcctgta gcaatggcaa caacgttgcg caaactatta actggcgaac
     4261 tacttactct agcttcccgg caacaattaa tagactggat ggaggcggat aaagttgcag
     4321 gaccacttct gcgctcggcc cttccggctg gctggtttat tgctgataaa tctggagccg
     4381 gtgagcgtgg gtctcgcggt atcattgcag cactggggcc agatggtaag ccctcccgta
     4441 tcgtagttat ctacacgacg gggagtcagg caactatgga tgaacgaaat agacagatcg
     4501 ctgagatagg tgcctcactg attaagcatt ggtaactgtc agaccaagtt tactcatata
     4561 tactttagat tgatttaaaa cttcattttt aatttaaaag gatctaggtg aagatccttt
     4621 ttgataatct catgaccaaa atcccttaac gtgagttttc gttccactga gcgtcagacc
     4681 ccgtagaaaa gatcaaagga tcttcttgag atcctttttt tctgcgcgta atctgctgct
     4741 tgcaaacaaa aaaaccaccg ctaccagcgg tggtttgttt gccggatcaa gagctaccaa
     4801 ctctttttcc gaaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag
     4861 tgtagccgta gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc
     4921 tgctaatcct gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg
     4981 actcaagacg atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca
     5041 cacagcccag cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat
     5101 gagaaagcgc cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg
     5161 tcggaacagg agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc
     5221 ctgtcgggtt tcgccacctc tgacttgagc gtcgattttt gtgatgctcg tcaggggggc
     5281 ggagcctatg gaaaaacgcc agcaacgcgg cctttttacg gttcctggcc ttttgctggc
     5341 cttttgctca catgttcttt cctgcgttat cccctgattc tgtggataac cgtattaccg
     5401 cctttgagtg agctgatacc gctcgccgca gccgaacgac cgagcgcagc gagtcagtga
     5461 gcgaggaagc ggaagagcgc ccaatacgca aaccgcctct ccccgcgcgt tggccgattc
     5521 attaatgcag ctggcacgac aggtttcccg actggaaagc gggcagtgag cgcaacgcaa
     5581 ttaatgtgag ttagctcact cattaggcac cccaggcttt acactttatg cttccggctc
     5641 gtatgttgtg tggaattgtg agcggataac aatttcacac aggaaacagc tatgaccatg
     5701 attacgccaa gcgcgcaatt aaccctcact aaagggaaca aaagctggag ctgcaagctt
     5761 aatgtagtct tatgcaatac tcttgtagtc ttgcaacatg gtaacgatga gttagcaaca
     5821 tgccttacaa ggagagaaaa agcaccgtgc atgccgattg gtggaagtaa ggtggtacga
     5881 tcgtgcctta ttaggaaggc aacagacggg tctgacatgg attggacgaa ccactgaatt
     5941 gccgcattgc agagatattg tatttaagtg cctagctcga tacataaacg ggtctctctg
     6001 gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac tgcttaagcc
     6061 tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt gtgactctgg
     6121 taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca gtggcgcccg
     6181 aacagggact tgaaagcgaa agggaaacca gaggagctct ctcgacgcag gactcggctt
     6241 gctgaagcgc gcacggcaag aggcgagggg cggcgactgg tgagtacgcc aaaaattttg
     6301 actagcggag gctagaagga gagagatggg tgcgagagcg tcagtattaa gcgggggaga
     6361 attagatcgc gatgggaaaa aattcggtta aggccagggg gaaagaaaaa atataaatta
     6421 aaacatatag tatgggcaag cagggagcta gaacgattcg cagttaatcc tggcctgtta
     6481 gaaacatcag aaggctgtag acaaatactg ggacagctac aaccatccct tcagacagga
     6541 tcagaagaac ttagatcatt atataataca gtagcaaccc tctattgtgt gcatcaaagg
     6601 atagagataa aagacaccaa ggaagcttta gacaagatag aggaagagca aaacaaaagt
     6661 aagaccaccg cacagcaagc ggccgctgat cttcagacct ggaggaggag atatgaggga
     6721 caattggaga agtgaattat ataaatataa agtagtaaaa attgaaccat taggagtagc
     6781 acccaccaag gcaaagagaa gagtggtgca gagagaaaaa agagcagtgg gaataggagc
     6841 tttgttcctt gggttcttgg gagcagcagg aagcactatg ggcgcagcgt caatgacgct
     6901 gacggtacag gccagacaat tattgtctgg tatagtgcag cagcagaaca atttgctgag
     6961 ggctattgag gcgcaacagc atctgttgca actcacagtc tggggcatca agcagctcca
     7021 ggcaagaatc ctggctgtgg aaagatacct aaaggatcaa cagctcctgg ggatttgggg
     7081 ttgc
//
