LOCUS       sequence-292304-        7083 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  USP10 shRNA (Targeting 3'UTR) inserted into the PLKO.1 plasmid 
            (GCCTCTCTTTAGTGGCTCTTT).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7083)
  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 7083)
  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-USP10-3'UTR
FEATURES             Location/Qualifiers
     source          1..7083
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             98..142
                     /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        440..688
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     440..460
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     611..630
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    784..901
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        950..1460
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1379..1397
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1482..2081
                     /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(1482..1501)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     1978..1998
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             2209..2442
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2514..2635
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2551..2570)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2605..2624
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      2675..2810
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2830..2849)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(2831..2849)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2859..2876)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2859..2875)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2868..2890)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3017..3472
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3104..3123)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3314..3335
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3498..3602
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3603..3671,3672..4463)
                     /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(3821..3840)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4634..5222
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5123..5142
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5376..5393
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5510..5531
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5546..5551,5552..5569,5570..5576)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5584..5600
                     /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     5589..5611
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5608..5624
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5608..5624
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5643..5663
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5645..5663
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        5691..5917
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             5918..6098
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6145..6270
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    6763..6996
                     /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 ttggaatcac acgacctgga tggagtggga cagagaaatt aacaattaca caagcttaat
       61 acactcctta attgaagaat cgcaaaacca gcaagaaaag aatgaacaag aattattgga
      121 attagataaa tgggcaagtt tgtggaattg gtttaacata acaaattggc tgtggtatat
      181 aaaattattc ataatgatag taggaggctt ggtaggttta agaatagttt ttgctgtact
      241 ttctatagtg aatagagtta ggcagggata ttcaccatta tcgtttcaga cccacctccc
      301 aaccccgagg ggacccgaca ggcccgaagg aatagaagaa gaaggtggag agagagacag
      361 agacagatcc attcgattag tgaacggatc tcgacggtat cgatcacgag actagcctcg
      421 agcggccgcc cccttcaccg agggcctatt tcccatgatt ccttcatatt tgcatatacg
      481 atacaaggct gttagagaga taattggaat taatttgact gtaaacacaa agatattagt
      541 acaaaatacg tgacgtagaa agtaataatt tcttgggtag tttgcagttt taaaattatg
      601 ttttaaaatg gactatcata tgcttaccgt aacttgaaag tatttcgatt tcttggcttt
      661 atatatcttg tggaaaggac gaaacaccgg gcctctcttt atggctcttt ctcgagaaag
      721 agccactaaa gagaggcttt ttgaattctc gacctcgaga caaatggcag tattcatcca
      781 caattttaaa agaaaagggg ggattggggg gtacagtgca ggggaaagaa tagtagacat
      841 aatagcaaca gacatacaaa ctaaagaatt acaaaaacaa attacaaaaa ttcaaaattt
      901 tcgggtttat tacagggaca gcagagatcc actttggccg cggctcgagg gggttggggt
      961 tgcgcctttt ccaaggcagc cctgggtttg cgcagggacg cggctgctct gggcgtggtt
     1021 ccgggaaacg cagcggcgcc gaccctgggt ctcgcacatt cttcacgtcc gttcgcagcg
     1081 tcacccggat cttcgccgct acccttgtgg gccccccggc gacgcttcct gctccgcccc
     1141 taagtcggga aggttccttg cggttcgcgg cgtgccggac gtgacaaacg gaagccgcac
     1201 gtctcactag taccctcgca gacggacagc gccagggagc aatggcagcg cgccgaccgc
     1261 gatgggctgt ggccaatagc ggctgctcag cagggcgcgc cgagagcagc ggccgggaag
     1321 gggcggtgcg ggaggcgggg tgtggggcgg tagtgtgggc cctgttcctg cccgcgcggt
     1381 gttccgcatt ctgcaagcct ccggagcgca cgtcggcagt cggctccctc gttgaccgaa
     1441 tcaccgacct ctctccccag ggggatccac cggagcttac catgaccgag tacaagccca
     1501 cggtgcgcct cgccacccgc gacgacgtcc ccagggccgt acgcaccctc gccgccgcgt
     1561 tcgccgacta ccccgccacg cgccacaccg tcgatccgga ccgccacatc gagcgggtca
     1621 ccgagctgca agaactcttc ctcacgcgcg tcgggctcga catcggcaag gtgtgggtcg
     1681 cggacgacgg cgccgcggtg gcggtctgga ccacgccgga gagcgtcgaa gcgggggcgg
     1741 tgttcgccga gatcggcccg cgcatggccg agttgagcgg ttcccggctg gccgcgcagc
     1801 aacagatgga aggcctcctg gcgccgcacc ggcccaagga gcccgcgtgg ttcctggcca
     1861 ccgtcggcgt ctcgcccgac caccagggca agggtctggg cagcgccgtc gtgctccccg
     1921 gagtggaggc ggccgagcgc gccggggtgc ccgccttcct ggagacctcc gcgccccgca
     1981 acctcccctt ctacgagcgg ctcggcttca ccgtcaccgc cgacgtcgag gtgcccgaag
     2041 gaccgcgcac ctggtgcatg acccgcaagc ccggtgcctg acgcccgccc cacgacccgc
     2101 agcgcccgac cgaaaggagc gcacgacccc atgcatcggt acctttaaga ccaatgactt
     2161 acaaggcagc tgtagatctt agccactttt taaaagaaaa ggggggactg gaagggctaa
     2221 ttcactccca acgaagacaa gatctgcttt ttgcttgtac tgggtctctc tggttagacc
     2281 agatctgagc ctgggagctc tctggctaac tagggaaccc actgcttaag cctcaataaa
     2341 gcttgccttg agtgcttcaa gtagtgtgtg cccgtctgtt gtgtgactct ggtaactaga
     2401 gatccctcag acccttttag tcagtgtgga aaatctctag cagtagtagt tcatgtcatc
     2461 ttattattca gtatttataa cttgcaaaga aatgaatatc agagagtgag aggaacttgt
     2521 ttattgcagc ttataatggt tacaaataaa gcaatagcat cacaaatttc acaaataaag
     2581 catttttttc actgcattct agttgtggtt tgtccaaact catcaatgta tcttatcatg
     2641 tctggctcta gctatcccgc ccctaactcc gcccatcccg cccctaactc cgcccagttc
     2701 cgcccattct ccgccccatg gctgactaat tttttttatt tatgcagagg ccgaggccgc
     2761 ctcggcctct gagctattcc agaagtagtg aggaggcttt tttggaggcc tagggacgta
     2821 cccaattcgc cctatagtga gtcgtattac gcgcgctcac tggccgtcgt tttacaacgt
     2881 cgtgactggg aaaaccctgg cgttacccaa cttaatcgcc ttgcagcaca tccccctttc
     2941 gccagctggc gtaatagcga agaggcccgc accgatcgcc cttcccaaca gttgcgcagc
     3001 ctgaatggcg aatgggacgc gccctgtagc ggcgcattaa gcgcggcggg tgtggtggtt
     3061 acgcgcagcg tgaccgctac acttgccagc gccctagcgc ccgctccttt cgctttcttc
     3121 ccttcctttc tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg ggggctccct
     3181 ttagggttcc gatttagtgc tttacggcac ctcgacccca aaaaacttga ttagggtgat
     3241 ggttcacgta gtgggccatc gccctgatag acggtttttc gccctttgac gttggagtcc
     3301 acgttcttta atagtggact cttgttccaa actggaacaa cactcaaccc tatctcggtc
     3361 tattcttttg atttataagg gattttgccg atttcggcct attggttaaa aaatgagctg
     3421 atttaacaaa aatttaacgc gaattttaac aaaatattaa cgcttacaat ttaggtggca
     3481 cttttcgggg aaatgtgcgc ggaaccccta tttgtttatt tttctaaata cattcaaata
     3541 tgtatccgct catgagacaa taaccctgat aaatgcttca ataatattga aaaaggaaga
     3601 gtatgagtat tcaacatttc cgtgtcgccc ttattccctt ttttgcggca ttttgccttc
     3661 ctgtttttgc tcacccagaa acgctggtga aagtaaaaga tgctgaagat cagttgggtg
     3721 cacgagtggg ttacatcgaa ctggatctca acagcggtaa gatccttgag agttttcgcc
     3781 ccgaagaacg ttttccaatg atgagcactt ttaaagttct gctatgtggc gcggtattat
     3841 cccgtattga cgccgggcaa gagcaactcg gtcgccgcat acactattct cagaatgact
     3901 tggttgagta ctcaccagtc acagaaaagc atcttacgga tggcatgaca gtaagagaat
     3961 tatgcagtgc tgccataacc atgagtgata acactgcggc caacttactt ctgacaacga
     4021 tcggaggacc gaaggagcta accgcttttt tgcacaacat gggggatcat gtaactcgcc
     4081 ttgatcgttg ggaaccggag ctgaatgaag ccataccaaa cgacgagcgt gacaccacga
     4141 tgcctgtagc aatggcaaca acgttgcgca aactattaac tggcgaacta cttactctag
     4201 cttcccggca acaattaata gactggatgg aggcggataa agttgcagga ccacttctgc
     4261 gctcggccct tccggctggc tggtttattg ctgataaatc tggagccggt gagcgtgggt
     4321 ctcgcggtat cattgcagca ctggggccag atggtaagcc ctcccgtatc gtagttatct
     4381 acacgacggg gagtcaggca actatggatg aacgaaatag acagatcgct gagataggtg
     4441 cctcactgat taagcattgg taactgtcag accaagttta ctcatatata ctttagattg
     4501 atttaaaact tcatttttaa tttaaaagga tctaggtgaa gatccttttt gataatctca
     4561 tgaccaaaat cccttaacgt gagttttcgt tccactgagc gtcagacccc gtagaaaaga
     4621 tcaaaggatc ttcttgagat cctttttttc tgcgcgtaat ctgctgcttg caaacaaaaa
     4681 aaccaccgct accagcggtg gtttgtttgc cggatcaaga gctaccaact ctttttccga
     4741 aggtaactgg cttcagcaga gcgcagatac caaatactgt tcttctagtg tagccgtagt
     4801 taggccacca cttcaagaac tctgtagcac cgcctacata cctcgctctg ctaatcctgt
     4861 taccagtggc tgctgccagt ggcgataagt cgtgtcttac cgggttggac tcaagacgat
     4921 agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca cagcccagct
     4981 tggagcgaac gacctacacc gaactgagat acctacagcg tgagctatga gaaagcgcca
     5041 cgcttcccga agggagaaag gcggacaggt atccggtaag cggcagggtc ggaacaggag
     5101 agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct gtcgggtttc
     5161 gccacctctg acttgagcgt cgatttttgt gatgctcgtc aggggggcgg agcctatgga
     5221 aaaacgccag caacgcggcc tttttacggt tcctggcctt ttgctggcct tttgctcaca
     5281 tgttctttcc tgcgttatcc cctgattctg tggataaccg tattaccgcc tttgagtgag
     5341 ctgataccgc tcgccgcagc cgaacgaccg agcgcagcga gtcagtgagc gaggaagcgg
     5401 aagagcgccc aatacgcaaa ccgcctctcc ccgcgcgttg gccgattcat taatgcagct
     5461 ggcacgacag gtttcccgac tggaaagcgg gcagtgagcg caacgcaatt aatgtgagtt
     5521 agctcactca ttaggcaccc caggctttac actttatgct tccggctcgt atgttgtgtg
     5581 gaattgtgag cggataacaa tttcacacag gaaacagcta tgaccatgat tacgccaagc
     5641 gcgcaattaa ccctcactaa agggaacaaa agctggagct gcaagcttaa tgtagtctta
     5701 tgcaatactc ttgtagtctt gcaacatggt aacgatgagt tagcaacatg ccttacaagg
     5761 agagaaaaag caccgtgcat gccgattggt ggaagtaagg tggtacgatc gtgccttatt
     5821 aggaaggcaa cagacgggtc tgacatggat tggacgaacc actgaattgc cgcattgcag
     5881 agatattgta tttaagtgcc tagctcgata cataaacggg tctctctggt tagaccagat
     5941 ctgagcctgg gagctctctg gctaactagg gaacccactg cttaagcctc aataaagctt
     6001 gccttgagtg cttcaagtag tgtgtgcccg tctgttgtgt gactctggta actagagatc
     6061 cctcagaccc ttttagtcag tgtggaaaat ctctagcagt ggcgcccgaa cagggacttg
     6121 aaagcgaaag ggaaaccaga ggagctctct cgacgcagga ctcggcttgc tgaagcgcgc
     6181 acggcaagag gcgaggggcg gcgactggtg agtacgccaa aaattttgac tagcggaggc
     6241 tagaaggaga gagatgggtg cgagagcgtc agtattaagc gggggagaat tagatcgcga
     6301 tgggaaaaaa ttcggttaag gccaggggga aagaaaaaat ataaattaaa acatatagta
     6361 tgggcaagca gggagctaga acgattcgca gttaatcctg gcctgttaga aacatcagaa
     6421 ggctgtagac aaatactggg acagctacaa ccatcccttc agacaggatc agaagaactt
     6481 agatcattat ataatacagt agcaaccctc tattgtgtgc atcaaaggat agagataaaa
     6541 gacaccaagg aagctttaga caagatagag gaagagcaaa acaaaagtaa gaccaccgca
     6601 cagcaagcgg ccgctgatct tcagacctgg aggaggagat atgagggaca attggagaag
     6661 tgaattatat aaatataaag tagtaaaaat tgaaccatta ggagtagcac ccaccaaggc
     6721 aaagagaaga gtggtgcaga gagaaaaaag agcagtggga ataggagctt tgttccttgg
     6781 gttcttggga gcagcaggaa gcactatggg cgcagcgtca atgacgctga cggtacaggc
     6841 cagacaatta ttgtctggta tagtgcagca gcagaacaat ttgctgaggg ctattgaggc
     6901 gcaacagcat ctgttgcaac tcacagtctg gggcatcaag cagctccagg caagaatcct
     6961 ggctgtggaa agatacctaa aggatcaaca gctcctgggg atttggggtt gctctggaaa
     7021 actcatttgc accactgctg tgccttggaa tgctagttgg agtaataaat ctctggaaca
     7081 gat
//
