LOCUS       sequence-371394-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  shRNA mediated knockdown.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7084)
  AUTHORS   Asimi V, Sampath Kumar A, Niskanen H, Riemenschneider C, Hetzel S, 
            Naderi J, Fasching N, Popitsch N, Du M, Kretzmer H, Smith ZD, 
            Weigert R, Walther M, Mamde S, Meierhofer D, Wittler L, Buschow R, 
            Timmermann B, Cisse II, Ameres SL, Meissner A, Hnisz D
  TITLE     Hijacking of transcriptional condensates by endogenous retroviruses.
  JOURNAL   Nat Genet. 2022 Aug;54(8):1238-1247. doi: 
            10.1038/s41588-022-01132-w. Epub 2022 Jul 21.
  PUBMED    35864192
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: 
            "10.1038/s41588-022-01132-w"; journalName: "Nat Genet"; date: 
            "2022-08"; volume: "54"; issue: "8"; pages: "1238-1247"
COMMENT     Sequence Label: pLKO.1-Tet-Puro-shMMETn_2 (inducible)
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        1..511
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     430..448
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             533..1132
                     /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(533..552)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     1029..1049
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             1260..1493
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    1565..1686
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(1602..1621)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     1656..1675
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      1726..1861
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(1881..1900)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(1882..1900)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(1910..1927)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(1910..1926)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1919..1941)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      2068..2523
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2155..2174)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2365..2386
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        2549..2653
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(2654..2722,2723..3514)
                     /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(2872..2891)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      3685..4273
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     4174..4193
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     4427..4444
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    4561..4582
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(4597..4602,4603..4620,4621..4627)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4635..4651
                     /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     4640..4662
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     4659..4675
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     4659..4675
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     4694..4714
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        4696..4714
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        4742..4968
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             4969..5149
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    5196..5321
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    5814..6047
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             6232..6276
                     /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        6574..6822
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     6574..6594
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     6745..6764
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    6919..7036
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
ORIGIN
        1 ggggttgggg ttgcgccttt tccaaggcag ccctgggttt gcgcagggac gcggctgctc
       61 tgggcgtggt tccgggaaac gcagcggcgc cgaccctggg tctcgcacat tcttcacgtc
      121 cgttcgcagc gtcacccgga tcttcgccgc tacccttgtg ggccccccgg cgacgcttcc
      181 tgctccgccc ctaagtcggg aaggttcctt gcggttcgcg gcgtgccgga cgtgacaaac
      241 ggaagccgca cgtctcacta gtaccctcgc agacggacag cgccagggag caatggcagc
      301 gcgccgaccg cgatgggctg tggccaatag cggctgctca gcagggcgcg ccgagagcag
      361 cggccgggaa ggggcggtgc gggaggcggg gtgtggggcg gtagtgtggg ccctgttcct
      421 gcccgcgcgg tgttccgcat tctgcaagcc tccggagcgc acgtcggcag tcggctccct
      481 cgttgaccga atcaccgacc tctctcccca gggggatcca ccggagctta ccatgaccga
      541 gtacaagccc acggtgcgcc tcgccacccg cgacgacgtc cccagggccg tacgcaccct
      601 cgccgccgcg ttcgccgact accccgccac gcgccacacc gtcgatccgg accgccacat
      661 cgagcgggtc accgagctgc aagaactctt cctcacgcgc gtcgggctcg acatcggcaa
      721 ggtgtgggtc gcggacgacg gcgccgcggt ggcggtctgg accacgccgg agagcgtcga
      781 agcgggggcg gtgttcgccg agatcggccc gcgcatggcc gagttgagcg gttcccggct
      841 ggccgcgcag caacagatgg aaggcctcct ggcgccgcac cggcccaagg agcccgcgtg
      901 gttcctggcc accgtcggcg tctcgcccga ccaccagggc aagggtctgg gcagcgccgt
      961 cgtgctcccc ggagtggagg cggccgagcg cgccggggtg cccgccttcc tggagacctc
     1021 cgcgccccgc aacctcccct tctacgagcg gctcggcttc accgtcaccg ccgacgtcga
     1081 ggtgcccgaa ggaccgcgca cctggtgcat gacccgcaag cccggtgcct gacgcccgcc
     1141 ccacgacccg cagcgcccga ccgaaaggag cgcacgaccc catgcatcgg tacctttaag
     1201 accaatgact tacaaggcag ctgtagatct tagccacttt ttaaaagaaa aggggggact
     1261 ggaagggcta attcactccc aacgaagaca agatctgctt tttgcttgta ctgggtctct
     1321 ctggttagac cagatctgag cctgggagct ctctggctaa ctagggaacc cactgcttaa
     1381 gcctcaataa agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt tgtgtgactc
     1441 tggtaactag agatccctca gaccctttta gtcagtgtgg aaaatctcta gcagtagtag
     1501 ttcatgtcat cttattattc agtatttata acttgcaaag aaatgaatat cagagagtga
     1561 gaggaacttg tttattgcag cttataatgg ttacaaataa agcaatagca tcacaaattt
     1621 cacaaataaa gcattttttt cactgcattc tagttgtggt ttgtccaaac tcatcaatgt
     1681 atcttatcat gtctggctct agctatcccg cccctaactc cgcccatccc gcccctaact
     1741 ccgcccagtt ccgcccattc tccgccccat ggctgactaa ttttttttat ttatgcagag
     1801 gccgaggccg cctcggcctc tgagctattc cagaagtagt gaggaggctt ttttggaggc
     1861 ctagggacgt acccaattcg ccctatagtg agtcgtatta cgcgcgctca ctggccgtcg
     1921 ttttacaacg tcgtgactgg gaaaaccctg gcgttaccca acttaatcgc cttgcagcac
     1981 atcccccttt cgccagctgg cgtaatagcg aagaggcccg caccgatcgc ccttcccaac
     2041 agttgcgcag cctgaatggc gaatgggacg cgccctgtag cggcgcatta agcgcggcgg
     2101 gtgtggtggt tacgcgcagc gtgaccgcta cacttgccag cgccctagcg cccgctcctt
     2161 tcgctttctt cccttccttt ctcgccacgt tcgccggctt tccccgtcaa gctctaaatc
     2221 gggggctccc tttagggttc cgatttagtg ctttacggca cctcgacccc aaaaaacttg
     2281 attagggtga tggttcacgt agtgggccat cgccctgata gacggttttt cgccctttga
     2341 cgttggagtc cacgttcttt aatagtggac tcttgttcca aactggaaca acactcaacc
     2401 ctatctcggt ctattctttt gatttataag ggattttgcc gatttcggcc tattggttaa
     2461 aaaatgagct gatttaacaa aaatttaacg cgaattttaa caaaatatta acgcttacaa
     2521 tttaggtggc acttttcggg gaaatgtgcg cggaacccct atttgtttat ttttctaaat
     2581 acattcaaat atgtatccgc tcatgagaca ataaccctga taaatgcttc aataatattg
     2641 aaaaaggaag agtatgagta ttcaacattt ccgtgtcgcc cttattccct tttttgcggc
     2701 attttgcctt cctgtttttg ctcacccaga aacgctggtg aaagtaaaag atgctgaaga
     2761 tcagttgggt gcacgagtgg gttacatcga actggatctc aacagcggta agatccttga
     2821 gagttttcgc cccgaagaac gttttccaat gatgagcact tttaaagttc tgctatgtgg
     2881 cgcggtatta tcccgtattg acgccgggca agagcaactc ggtcgccgca tacactattc
     2941 tcagaatgac ttggttgagt actcaccagt cacagaaaag catcttacgg atggcatgac
     3001 agtaagagaa ttatgcagtg ctgccataac catgagtgat aacactgcgg ccaacttact
     3061 tctgacaacg atcggaggac cgaaggagct aaccgctttt ttgcacaaca tgggggatca
     3121 tgtaactcgc cttgatcgtt gggaaccgga gctgaatgaa gccataccaa acgacgagcg
     3181 tgacaccacg atgcctgtag caatggcaac aacgttgcgc aaactattaa ctggcgaact
     3241 acttactcta gcttcccggc aacaattaat agactggatg gaggcggata aagttgcagg
     3301 accacttctg cgctcggccc ttccggctgg ctggtttatt gctgataaat ctggagccgg
     3361 tgagcgtggg tctcgcggta tcattgcagc actggggcca gatggtaagc cctcccgtat
     3421 cgtagttatc tacacgacgg ggagtcaggc aactatggat gaacgaaata gacagatcgc
     3481 tgagataggt gcctcactga ttaagcattg gtaactgtca gaccaagttt actcatatat
     3541 actttagatt gatttaaaac ttcattttta atttaaaagg atctaggtga agatcctttt
     3601 tgataatctc atgaccaaaa tcccttaacg tgagttttcg ttccactgag cgtcagaccc
     3661 cgtagaaaag atcaaaggat cttcttgaga tccttttttt ctgcgcgtaa tctgctgctt
     3721 gcaaacaaaa aaaccaccgc taccagcggt ggtttgtttg ccggatcaag agctaccaac
     3781 tctttttccg aaggtaactg gcttcagcag agcgcagata ccaaatactg ttcttctagt
     3841 gtagccgtag ttaggccacc acttcaagaa ctctgtagca ccgcctacat acctcgctct
     3901 gctaatcctg ttaccagtgg ctgctgccag tggcgataag tcgtgtctta ccgggttgga
     3961 ctcaagacga tagttaccgg ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac
     4021 acagcccagc ttggagcgaa cgacctacac cgaactgaga tacctacagc gtgagctatg
     4081 agaaagcgcc acgcttcccg aagggagaaa ggcggacagg tatccggtaa gcggcagggt
     4141 cggaacagga gagcgcacga gggagcttcc agggggaaac gcctggtatc tttatagtcc
     4201 tgtcgggttt cgccacctct gacttgagcg tcgatttttg tgatgctcgt caggggggcg
     4261 gagcctatgg aaaaacgcca gcaacgcggc ctttttacgg ttcctggcct tttgctggcc
     4321 ttttgctcac atgttctttc ctgcgttatc ccctgattct gtggataacc gtattaccgc
     4381 ctttgagtga gctgataccg ctcgccgcag ccgaacgacc gagcgcagcg agtcagtgag
     4441 cgaggaagcg gaagagcgcc caatacgcaa accgcctctc cccgcgcgtt ggccgattca
     4501 ttaatgcagc tggcacgaca ggtttcccga ctggaaagcg ggcagtgagc gcaacgcaat
     4561 taatgtgagt tagctcactc attaggcacc ccaggcttta cactttatgc ttccggctcg
     4621 tatgttgtgt ggaattgtga gcggataaca atttcacaca ggaaacagct atgaccatga
     4681 ttacgccaag cgcgcaatta accctcacta aagggaacaa aagctggagc tgcaagctta
     4741 atgtagtctt atgcaatact cttgtagtct tgcaacatgg taacgatgag ttagcaacat
     4801 gccttacaag gagagaaaaa gcaccgtgca tgccgattgg tggaagtaag gtggtacgat
     4861 cgtgccttat taggaaggca acagacgggt ctgacatgga ttggacgaac cactgaattg
     4921 ccgcattgca gagatattgt atttaagtgc ctagctcgat acataaacgg gtctctctgg
     4981 ttagaccaga tctgagcctg ggagctctct ggctaactag ggaacccact gcttaagcct
     5041 caataaagct tgccttgagt gcttcaagta gtgtgtgccc gtctgttgtg tgactctggt
     5101 aactagagat ccctcagacc cttttagtca gtgtggaaaa tctctagcag tggcgcccga
     5161 acagggactt gaaagcgaaa gggaaaccag aggagctctc tcgacgcagg actcggcttg
     5221 ctgaagcgcg cacggcaaga ggcgaggggc ggcgactggt gagtacgcca aaaattttga
     5281 ctagcggagg ctagaaggag agagatgggt gcgagagcgt cagtattaag cgggggagaa
     5341 ttagatcgcg atgggaaaaa attcggttaa ggccaggggg aaagaaaaaa tataaattaa
     5401 aacatatagt atgggcaagc agggagctag aacgattcgc agttaatcct ggcctgttag
     5461 aaacatcaga aggctgtaga caaatactgg gacagctaca accatccctt cagacaggat
     5521 cagaagaact tagatcatta tataatacag tagcaaccct ctattgtgtg catcaaagga
     5581 tagagataaa agacaccaag gaagctttag acaagataga ggaagagcaa aacaaaagta
     5641 agaccaccgc acagcaagcg gccgctgatc ttcagacctg gaggaggaga tatgagggac
     5701 aattggagaa gtgaattata taaatataaa gtagtaaaaa ttgaaccatt aggagtagca
     5761 cccaccaagg caaagagaag agtggtgcag agagaaaaaa gagcagtggg aataggagct
     5821 ttgttccttg ggttcttggg agcagcagga agcactatgg gcgcagcgtc aatgacgctg
     5881 acggtacagg ccagacaatt attgtctggt atagtgcagc agcagaacaa tttgctgagg
     5941 gctattgagg cgcaacagca tctgttgcaa ctcacagtct ggggcatcaa gcagctccag
     6001 gcaagaatcc tggctgtgga aagataccta aaggatcaac agctcctggg gatttggggt
     6061 tgctctggaa aactcatttg caccactgct gtgccttgga atgctagttg gagtaataaa
     6121 tctctggaac agatttggaa tcacacgacc tggatggagt gggacagaga aattaacaat
     6181 tacacaagct taatacactc cttaattgaa gaatcgcaaa accagcaaga aaagaatgaa
     6241 caagaattat tggaattaga taaatgggca agtttgtgga attggtttaa cataacaaat
     6301 tggctgtggt atataaaatt attcataatg atagtaggag gcttggtagg tttaagaata
     6361 gtttttgctg tactttctat agtgaataga gttaggcagg gatattcacc attatcgttt
     6421 cagacccacc tcccaacccc gaggggaccc gacaggcccg aaggaataga agaagaaggt
     6481 ggagagagag acagagacag atccattcga ttagtgaacg gatctcgacg gtatcgatca
     6541 cgagactagc ctcgagcggc cgcccccttc accgagggcc tatttcccat gattccttca
     6601 tatttgcata tacgatacaa ggctgttaga gagataattg gaattaattt gactgtaaac
     6661 acaaagatat tagtacaaaa tacgtgacgt agaaagtaat aatttcttgg gtagtttgca
     6721 gttttaaaat tatgttttaa aatggactat catatgctta ccgtaacttg aaagtatttc
     6781 gatttcttgg ctttatatat cttgtggaaa ggacgaaaca ccgggacatc caaacttcgt
     6841 aatatctcga gatattacga agtttggatg tctttttgaa ttctcgacct cgagacaaat
     6901 ggcagtattc atccacaatt ttaaaagaaa aggggggatt ggggggtaca gtgcagggga
     6961 aagaatagta gacataatag caacagacat acaaactaaa gaattacaaa aacaaattac
     7021 aaaaattcaa aattttcggg tttattacag ggacagcaga gatccacttt ggccgcggct
     7081 cgag
//
