LOCUS       sequence-292305-        7084 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  USP10 shRNA (Targeting CDS) inserted into the PLKO.1 plasmid 
            (CCTATGTGGAAACTAAGTATT).
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-USP10-CDS
FEATURES             Location/Qualifiers
     source          1..7084
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             88..132
                     /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        430..678
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     430..450
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     601..620
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    775..892
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        941..1451
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1370..1388
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1473..2072
                     /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(1473..1492)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     1969..1989
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             2200..2433
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2505..2626
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2542..2561)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2596..2615
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2666..2801
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2821..2840)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(2822..2840)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2850..2867)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2850..2866)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2859..2881)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3008..3463
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3095..3114)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3305..3326
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3489..3593
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3594..3662,3663..4454)
                     /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(3812..3831)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4625..5213
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5114..5133
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5367..5384
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5501..5522
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5537..5542,5543..5560,5561..5567)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5575..5591
                     /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     5580..5602
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5599..5615
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5599..5615
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5634..5654
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5636..5654
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5682..5908
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             5909..6089
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6136..6261
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6754..6987
                     /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 acgacctgga tggagtggga cagagaaatt aacaattaca caagcttaat acactcctta
       61 attgaagaat cgcaaaacca gcaagaaaag aatgaacaag aattattgga attagataaa
      121 tgggcaagtt tgtggaattg gtttaacata acaaattggc tgtggtatat aaaattattc
      181 ataatgatag taggaggctt ggtaggttta agaatagttt ttgctgtact ttctatagtg
      241 aatagagtta ggcagggata ttcaccatta tcgtttcaga cccacctccc aaccccgagg
      301 ggacccgaca ggcccgaagg aatagaagaa gaaggtggag agagagacag agacagatcc
      361 attcgattag tgaacggatc tcgacggtat cgatcacgag actagcctcg agcggccgcc
      421 cccttcaccg agggcctatt tcccatgatt ccttcatatt tgcatatacg atacaaggct
      481 gttagagaga taattggaat taatttgact gtaaacacaa agatattagt acaaaatacg
      541 tgacgtagaa agtaataatt tcttgggtag tttgcagttt taaaattatg ttttaaaatg
      601 gactatcata tgcttaccgt aacttgaaag tatttcgatt tcttggcttt atatatcttg
      661 tggaaaggac gaaacaccgg cctatgtgga aactaagtat tctcgagaat acttagtttc
      721 cacataggtt tttgaattct cgacctcgag acaaatggca gtattcatcc acaattttaa
      781 aagaaaaggg gggattgggg ggtacagtgc aggggaaaga atagtagaca taatagcaac
      841 agacatacaa actaaagaat tacaaaaaca aattacaaaa attcaaaatt ttcgggttta
      901 ttacagggac agcagagatc cactttggcc gcggctcgag ggggttgggg ttgcgccttt
      961 tccaaggcag ccctgggttt gcgcagggac gcggctgctc tgggcgtggt tccgggaaac
     1021 gcagcggcgc cgaccctggg tctcgcacat tcttcacgtc cgttcgcagc gtcacccgga
     1081 tcttcgccgc tacccttgtg ggccccccgg cgacgcttcc tgctccgccc ctaagtcggg
     1141 aaggttcctt gcggttcgcg gcgtgccgga cgtgacaaac ggaagccgca cgtctcacta
     1201 gtaccctcgc agacggacag cgccagggag caatggcagc gcgccgaccg cgatgggctg
     1261 tggccaatag cggctgctca gcagggcgcg ccgagagcag cggccgggaa ggggcggtgc
     1321 gggaggcggg gtgtggggcg gtagtgtggg ccctgttcct gcccgcgcgg tgttccgcat
     1381 tctgcaagcc tccggagcgc acgtcggcag tcggctccct cgttgaccga atcaccgacc
     1441 tctctcccca gggggatcca ccggagctta ccatgaccga gtacaagccc acggtgcgcc
     1501 tcgccacccg cgacgacgtc cccagggccg tacgcaccct cgccgccgcg ttcgccgact
     1561 accccgccac gcgccacacc gtcgatccgg accgccacat cgagcgggtc accgagctgc
     1621 aagaactctt cctcacgcgc gtcgggctcg acatcggcaa ggtgtgggtc gcggacgacg
     1681 gcgccgcggt ggcggtctgg accacgccgg agagcgtcga agcgggggcg gtgttcgccg
     1741 agatcggccc gcgcatggcc gagttgagcg gttcccggct ggccgcgcag caacagatgg
     1801 aaggcctcct ggcgccgcac cggcccaagg agcccgcgtg gttcctggcc accgtcggcg
     1861 tctcgcccga ccaccagggc aagggtctgg gcagcgccgt cgtgctcccc ggagtggagg
     1921 cggccgagcg cgccggggtg cccgccttcc tggagacctc cgcgccccgc aacctcccct
     1981 tctacgagcg gctcggcttc accgtcaccg ccgacgtcga ggtgcccgaa ggaccgcgca
     2041 cctggtgcat gacccgcaag cccggtgcct gacgcccgcc ccacgacccg cagcgcccga
     2101 ccgaaaggag cgcacgaccc catgcatcgg tacctttaag accaatgact tacaaggcag
     2161 ctgtagatct tagccacttt ttaaaagaaa aggggggact ggaagggcta attcactccc
     2221 aacgaagaca agatctgctt tttgcttgta ctgggtctct ctggttagac cagatctgag
     2281 cctgggagct ctctggctaa ctagggaacc cactgcttaa gcctcaataa agcttgcctt
     2341 gagtgcttca agtagtgtgt gcccgtctgt tgtgtgactc tggtaactag agatccctca
     2401 gaccctttta gtcagtgtgg aaaatctcta gcagtagtag ttcatgtcat cttattattc
     2461 agtatttata acttgcaaag aaatgaatat cagagagtga gaggaacttg tttattgcag
     2521 cttataatgg ttacaaataa agcaatagca tcacaaattt cacaaataaa gcattttttt
     2581 cactgcattc tagttgtggt ttgtccaaac tcatcaatgt atcttatcat gtctggctct
     2641 agctatcccg cccctaactc cgcccatccc gcccctaact ccgcccagtt ccgcccattc
     2701 tccgccccat ggctgactaa ttttttttat ttatgcagag gccgaggccg cctcggcctc
     2761 tgagctattc cagaagtagt gaggaggctt ttttggaggc ctagggacgt acccaattcg
     2821 ccctatagtg agtcgtatta cgcgcgctca ctggccgtcg ttttacaacg tcgtgactgg
     2881 gaaaaccctg gcgttaccca acttaatcgc cttgcagcac atcccccttt cgccagctgg
     2941 cgtaatagcg aagaggcccg caccgatcgc ccttcccaac agttgcgcag cctgaatggc
     3001 gaatgggacg cgccctgtag cggcgcatta agcgcggcgg gtgtggtggt tacgcgcagc
     3061 gtgaccgcta cacttgccag cgccctagcg cccgctcctt tcgctttctt cccttccttt
     3121 ctcgccacgt tcgccggctt tccccgtcaa gctctaaatc gggggctccc tttagggttc
     3181 cgatttagtg ctttacggca cctcgacccc aaaaaacttg attagggtga tggttcacgt
     3241 agtgggccat cgccctgata gacggttttt cgccctttga cgttggagtc cacgttcttt
     3301 aatagtggac tcttgttcca aactggaaca acactcaacc ctatctcggt ctattctttt
     3361 gatttataag ggattttgcc gatttcggcc tattggttaa aaaatgagct gatttaacaa
     3421 aaatttaacg cgaattttaa caaaatatta acgcttacaa tttaggtggc acttttcggg
     3481 gaaatgtgcg cggaacccct atttgtttat ttttctaaat acattcaaat atgtatccgc
     3541 tcatgagaca ataaccctga taaatgcttc aataatattg aaaaaggaag agtatgagta
     3601 ttcaacattt ccgtgtcgcc cttattccct tttttgcggc attttgcctt cctgtttttg
     3661 ctcacccaga aacgctggtg aaagtaaaag atgctgaaga tcagttgggt gcacgagtgg
     3721 gttacatcga actggatctc aacagcggta agatccttga gagttttcgc cccgaagaac
     3781 gttttccaat gatgagcact tttaaagttc tgctatgtgg cgcggtatta tcccgtattg
     3841 acgccgggca agagcaactc ggtcgccgca tacactattc tcagaatgac ttggttgagt
     3901 actcaccagt cacagaaaag catcttacgg atggcatgac agtaagagaa ttatgcagtg
     3961 ctgccataac catgagtgat aacactgcgg ccaacttact tctgacaacg atcggaggac
     4021 cgaaggagct aaccgctttt ttgcacaaca tgggggatca tgtaactcgc cttgatcgtt
     4081 gggaaccgga gctgaatgaa gccataccaa acgacgagcg tgacaccacg atgcctgtag
     4141 caatggcaac aacgttgcgc aaactattaa ctggcgaact acttactcta gcttcccggc
     4201 aacaattaat agactggatg gaggcggata aagttgcagg accacttctg cgctcggccc
     4261 ttccggctgg ctggtttatt gctgataaat ctggagccgg tgagcgtggg tctcgcggta
     4321 tcattgcagc actggggcca gatggtaagc cctcccgtat cgtagttatc tacacgacgg
     4381 ggagtcaggc aactatggat gaacgaaata gacagatcgc tgagataggt gcctcactga
     4441 ttaagcattg gtaactgtca gaccaagttt actcatatat actttagatt gatttaaaac
     4501 ttcattttta atttaaaagg atctaggtga agatcctttt tgataatctc atgaccaaaa
     4561 tcccttaacg tgagttttcg ttccactgag cgtcagaccc cgtagaaaag atcaaaggat
     4621 cttcttgaga tccttttttt ctgcgcgtaa tctgctgctt gcaaacaaaa aaaccaccgc
     4681 taccagcggt ggtttgtttg ccggatcaag agctaccaac tctttttccg aaggtaactg
     4741 gcttcagcag agcgcagata ccaaatactg ttcttctagt gtagccgtag ttaggccacc
     4801 acttcaagaa ctctgtagca ccgcctacat acctcgctct gctaatcctg ttaccagtgg
     4861 ctgctgccag tggcgataag tcgtgtctta ccgggttgga ctcaagacga tagttaccgg
     4921 ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac acagcccagc ttggagcgaa
     4981 cgacctacac cgaactgaga tacctacagc gtgagctatg agaaagcgcc acgcttcccg
     5041 aagggagaaa ggcggacagg tatccggtaa gcggcagggt cggaacagga gagcgcacga
     5101 gggagcttcc agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccacctct
     5161 gacttgagcg tcgatttttg tgatgctcgt caggggggcg gagcctatgg aaaaacgcca
     5221 gcaacgcggc ctttttacgg ttcctggcct tttgctggcc ttttgctcac atgttctttc
     5281 ctgcgttatc ccctgattct gtggataacc gtattaccgc ctttgagtga gctgataccg
     5341 ctcgccgcag ccgaacgacc gagcgcagcg agtcagtgag cgaggaagcg gaagagcgcc
     5401 caatacgcaa accgcctctc cccgcgcgtt ggccgattca ttaatgcagc tggcacgaca
     5461 ggtttcccga ctggaaagcg ggcagtgagc gcaacgcaat taatgtgagt tagctcactc
     5521 attaggcacc ccaggcttta cactttatgc ttccggctcg tatgttgtgt ggaattgtga
     5581 gcggataaca atttcacaca ggaaacagct atgaccatga ttacgccaag cgcgcaatta
     5641 accctcacta aagggaacaa aagctggagc tgcaagctta atgtagtctt atgcaatact
     5701 cttgtagtct tgcaacatgg taacgatgag ttagcaacat gccttacaag gagagaaaaa
     5761 gcaccgtgca tgccgattgg tggaagtaag gtggtacgat cgtgccttat taggaaggca
     5821 acagacgggt ctgacatgga ttggacgaac cactgaattg ccgcattgca gagatattgt
     5881 atttaagtgc ctagctcgat acataaacgg gtctctctgg ttagaccaga tctgagcctg
     5941 ggagctctct ggctaactag ggaacccact gcttaagcct caataaagct tgccttgagt
     6001 gcttcaagta gtgtgtgccc gtctgttgtg tgactctggt aactagagat ccctcagacc
     6061 cttttagtca gtgtggaaaa tctctagcag tggcgcccga acagggactt gaaagcgaaa
     6121 gggaaaccag aggagctctc tcgacgcagg actcggcttg ctgaagcgcg cacggcaaga
     6181 ggcgaggggc ggcgactggt gagtacgcca aaaattttga ctagcggagg ctagaaggag
     6241 agagatgggt gcgagagcgt cagtattaag cgggggagaa ttagatcgcg atgggaaaaa
     6301 attcggttaa ggccaggggg aaagaaaaaa tataaattaa aacatatagt atgggcaagc
     6361 agggagctag aacgattcgc agttaatcct ggcctgttag aaacatcaga aggctgtaga
     6421 caaatactgg gacagctaca accatccctt cagacaggat cagaagaact tagatcatta
     6481 tataatacag tagcaaccct ctattgtgtg catcaaagga tagagataaa agacaccaag
     6541 gaagctttag acaagataga ggaagagcaa aacaaaagta agaccaccgc acagcaagcg
     6601 gccgctgatc ttcagacctg gaggaggaga tatgagggac aattggagaa gtgaattata
     6661 taaatataaa gtagtaaaaa ttgaaccatt aggagtagca cccaccaagg caaagagaag
     6721 agtggtgcag agagaaaaaa gagcagtggg aataggagct ttgttccttg ggttcttggg
     6781 agcagcagga agcactatgg gcgcagcgtc aatgacgctg acggtacagg ccagacaatt
     6841 attgtctggt atagtgcagc agcagaacaa tttgctgagg gctattgagg cgcaacagca
     6901 tctgttgcaa ctcacagtct ggggcatcaa gcagctccag gcaagaatcc tggctgtgga
     6961 aagataccta aaggatcaac agctcctggg gatttggggt tgctctggaa aactcatttg
     7021 caccactgct gtgccttgga atgctagttg gagtaataaa tctctggaac agatttggaa
     7081 tcac
//
