LOCUS       sequence-269274-        7080 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  CAPRIN1 shRNA (Targeting 3'UTR) inserted into the PLKO.1 plasmid 
            (GCCACGTTAGTGTCACAAATT).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7080)
  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 7080)
  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-CAPRIN1-3'UTR
FEATURES             Location/Qualifiers
     source          1..7080
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     133..152
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     386..403
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    520..541
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(556..561,562..579,580..586)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    594..610
                     /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     599..621
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     618..634
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     618..634
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     653..673
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        655..673
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        701..927
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             928..1108
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    1155..1280
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1773..2006
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             2191..2235
                     /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        2533..2781
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     2533..2553
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     2704..2723
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_feature    2874..2991
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        3040..3550
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     3469..3487
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             3572..4171
                     /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(3572..3591)
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     primer_bind     4068..4088
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     LTR             4299..4532
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    4604..4725
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4641..4660)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4695..4714
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      4765..4900
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(4920..4939)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(4921..4939)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(4949..4966)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(4949..4965)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4958..4980)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      5107..5562
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5194..5213)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5404..5425
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        5588..5692
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5693..5761,5762..6553)
                     /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(5911..5930)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      join(6724..7080,1..232)
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
ORIGIN
        1 gacctacacc gaactgagat acctacagcg tgagctatga gaaagcgcca cgcttcccga
       61 agggagaaag gcggacaggt atccggtaag cggcagggtc ggaacaggag agcgcacgag
      121 ggagcttcca gggggaaacg cctggtatct ttatagtcct gtcgggtttc gccacctctg
      181 acttgagcgt cgatttttgt gatgctcgtc aggggggcgg agcctatgga aaaacgccag
      241 caacgcggcc tttttacggt tcctggcctt ttgctggcct tttgctcaca tgttctttcc
      301 tgcgttatcc cctgattctg tggataaccg tattaccgcc tttgagtgag ctgataccgc
      361 tcgccgcagc cgaacgaccg agcgcagcga gtcagtgagc gaggaagcgg aagagcgccc
      421 aatacgcaaa ccgcctctcc ccgcgcgttg gccgattcat taatgcagct ggcacgacag
      481 gtttcccgac tggaaagcgg gcagtgagcg caacgcaatt aatgtgagtt agctcactca
      541 ttaggcaccc caggctttac actttatgct tccggctcgt atgttgtgtg gaattgtgag
      601 cggataacaa tttcacacag gaaacagcta tgaccatgat tacgccaagc gcgcaattaa
      661 ccctcactaa agggaacaaa agctggagct gcaagcttaa tgtagtctta tgcaatactc
      721 ttgtagtctt gcaacatggt aacgatgagt tagcaacatg ccttacaagg agagaaaaag
      781 caccgtgcat gccgattggt ggaagtaagg tggtacgatc gtgccttatt aggaaggcaa
      841 cagacgggtc tgacatggat tggacgaacc actgaattgc cgcattgcag agatattgta
      901 tttaagtgcc tagctcgata cataaacggg tctctctggt tagaccagat ctgagcctgg
      961 gagctctctg gctaactagg gaacccactg cttaagcctc aataaagctt gccttgagtg
     1021 cttcaagtag tgtgtgcccg tctgttgtgt gactctggta actagagatc cctcagaccc
     1081 ttttagtcag tgtggaaaat ctctagcagt ggcgcccgaa cagggacttg aaagcgaaag
     1141 ggaaaccaga ggagctctct cgacgcagga ctcggcttgc tgaagcgcgc acggcaagag
     1201 gcgaggggcg gcgactggtg agtacgccaa aaattttgac tagcggaggc tagaaggaga
     1261 gagatgggtg cgagagcgtc agtattaagc gggggagaat tagatcgcga tgggaaaaaa
     1321 ttcggttaag gccaggggga aagaaaaaat ataaattaaa acatatagta tgggcaagca
     1381 gggagctaga acgattcgca gttaatcctg gcctgttaga aacatcagaa ggctgtagac
     1441 aaatactggg acagctacaa ccatcccttc agacaggatc agaagaactt agatcattat
     1501 ataatacagt agcaaccctc tattgtgtgc atcaaaggat agagataaaa gacaccaagg
     1561 aagctttaga caagatagag gaagagcaaa acaaaagtaa gaccaccgca cagcaagcgg
     1621 ccgctgatct tcagacctgg aggaggagat atgagggaca attggagaag tgaattatat
     1681 aaatataaag tagtaaaaat tgaaccatta ggagtagcac ccaccaaggc aaagagaaga
     1741 gtggtgcaga gagaaaaaag agcagtggga ataggagctt tgttccttgg gttcttggga
     1801 gcagcaggaa gcactatggg cgcagcgtca atgacgctga cggtacaggc cagacaatta
     1861 ttgtctggta tagtgcagca gcagaacaat ttgctgaggg ctattgaggc gcaacagcat
     1921 ctgttgcaac tcacagtctg gggcatcaag cagctccagg caagaatcct ggctgtggaa
     1981 agatacctaa aggatcaaca gctcctgggg atttggggtt gctctggaaa actcatttgc
     2041 accactgctg tgccttggaa tgctagttgg agtaataaat ctctggaaca gatttggaat
     2101 cacacgacct ggatggagtg ggacagagaa attaacaatt acacaagctt aatacactcc
     2161 ttaattgaag aatcgcaaaa ccagcaagaa aagaatgaac aagaattatt ggaattagat
     2221 aaatgggcaa gtttgtggaa ttggtttaac ataacaaatt ggctgtggta tataaaatta
     2281 ttcataatga tagtaggagg cttggtaggt ttaagaatag tttttgctgt actttctata
     2341 gtgaatagag ttaggcaggg atattcacca ttatcgtttc agacccacct cccaaccccg
     2401 aggggacccg acaggcccga aggaatagaa gaagaaggtg gagagagaga cagagacaga
     2461 tccattcgat tagtgaacgg atctcgacgg tatcgatcac gagactagcc tcgagcggcc
     2521 gcccccttca ccgagggcct atttcccatg attccttcat atttgcatat acgatacaag
     2581 gctgttagag agataattgg aattaatttg actgtaaaca caaagatatt agtacaaaat
     2641 acgtgacgta gaaagtaata atttcttggg tagtttgcag ttttaaaatt atgttttaaa
     2701 atggactatc atatgcttac cgtaacttga aagtatttcg atttcttggc tttatatatc
     2761 ttgtggaaag gacgaaacac cgggccacgt tagtgtcaca attctcgaga atttgtgaca
     2821 ctaaggcttt ttgaattctc gacctcgaga caaatggcag tattcatcca caattttaaa
     2881 agaaaagggg ggattggggg gtacagtgca ggggaaagaa tagtagacat aatagcaaca
     2941 gacatacaaa ctaaagaatt acaaaaacaa attacaaaaa ttcaaaattt tcgggtttat
     3001 tacagggaca gcagagatcc actttggccg cggctcgagg gggttggggt tgcgcctttt
     3061 ccaaggcagc cctgggtttg cgcagggacg cggctgctct gggcgtggtt ccgggaaacg
     3121 cagcggcgcc gaccctgggt ctcgcacatt cttcacgtcc gttcgcagcg tcacccggat
     3181 cttcgccgct acccttgtgg gccccccggc gacgcttcct gctccgcccc taagtcggga
     3241 aggttccttg cggttcgcgg cgtgccggac gtgacaaacg gaagccgcac gtctcactag
     3301 taccctcgca gacggacagc gccagggagc aatggcagcg cgccgaccgc gatgggctgt
     3361 ggccaatagc ggctgctcag cagggcgcgc cgagagcagc ggccgggaag gggcggtgcg
     3421 ggaggcgggg tgtggggcgg tagtgtgggc cctgttcctg cccgcgcggt gttccgcatt
     3481 ctgcaagcct ccggagcgca cgtcggcagt cggctccctc gttgaccgaa tcaccgacct
     3541 ctctccccag ggggatccac cggagcttac catgaccgag tacaagccca cggtgcgcct
     3601 cgccacccgc gacgacgtcc ccagggccgt acgcaccctc gccgccgcgt tcgccgacta
     3661 ccccgccacg cgccacaccg tcgatccgga ccgccacatc gagcgggtca ccgagctgca
     3721 agaactcttc ctcacgcgcg tcgggctcga catcggcaag gtgtgggtcg cggacgacgg
     3781 cgccgcggtg gcggtctgga ccacgccgga gagcgtcgaa gcgggggcgg tgttcgccga
     3841 gatcggcccg cgcatggccg agttgagcgg ttcccggctg gccgcgcagc aacagatgga
     3901 aggcctcctg gcgccgcacc ggcccaagga gcccgcgtgg ttcctggcca ccgtcggcgt
     3961 ctcgcccgac caccagggca agggtctggg cagcgccgtc gtgctccccg gagtggaggc
     4021 ggccgagcgc gccggggtgc ccgccttcct ggagacctcc gcgccccgca acctcccctt
     4081 ctacgagcgg ctcggcttca ccgtcaccgc cgacgtcgag gtgcccgaag gaccgcgcac
     4141 ctggtgcatg acccgcaagc ccggtgcctg acgcccgccc cacgacccgc agcgcccgac
     4201 cgaaaggagc gcacgacccc atgcatcggt acctttaaga ccaatgactt acaaggcagc
     4261 tgtagatctt agccactttt taaaagaaaa ggggggactg gaagggctaa ttcactccca
     4321 acgaagacaa gatctgcttt ttgcttgtac tgggtctctc tggttagacc agatctgagc
     4381 ctgggagctc tctggctaac tagggaaccc actgcttaag cctcaataaa gcttgccttg
     4441 agtgcttcaa gtagtgtgtg cccgtctgtt gtgtgactct ggtaactaga gatccctcag
     4501 acccttttag tcagtgtgga aaatctctag cagtagtagt tcatgtcatc ttattattca
     4561 gtatttataa cttgcaaaga aatgaatatc agagagtgag aggaacttgt ttattgcagc
     4621 ttataatggt tacaaataaa gcaatagcat cacaaatttc acaaataaag catttttttc
     4681 actgcattct agttgtggtt tgtccaaact catcaatgta tcttatcatg tctggctcta
     4741 gctatcccgc ccctaactcc gcccatcccg cccctaactc cgcccagttc cgcccattct
     4801 ccgccccatg gctgactaat tttttttatt tatgcagagg ccgaggccgc ctcggcctct
     4861 gagctattcc agaagtagtg aggaggcttt tttggaggcc tagggacgta cccaattcgc
     4921 cctatagtga gtcgtattac gcgcgctcac tggccgtcgt tttacaacgt cgtgactggg
     4981 aaaaccctgg cgttacccaa cttaatcgcc ttgcagcaca tccccctttc gccagctggc
     5041 gtaatagcga agaggcccgc accgatcgcc cttcccaaca gttgcgcagc ctgaatggcg
     5101 aatgggacgc gccctgtagc ggcgcattaa gcgcggcggg tgtggtggtt acgcgcagcg
     5161 tgaccgctac acttgccagc gccctagcgc ccgctccttt cgctttcttc ccttcctttc
     5221 tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg ggggctccct ttagggttcc
     5281 gatttagtgc tttacggcac ctcgacccca aaaaacttga ttagggtgat ggttcacgta
     5341 gtgggccatc gccctgatag acggtttttc gccctttgac gttggagtcc acgttcttta
     5401 atagtggact cttgttccaa actggaacaa cactcaaccc tatctcggtc tattcttttg
     5461 atttataagg gattttgccg atttcggcct attggttaaa aaatgagctg atttaacaaa
     5521 aatttaacgc gaattttaac aaaatattaa cgcttacaat ttaggtggca cttttcgggg
     5581 aaatgtgcgc ggaaccccta tttgtttatt tttctaaata cattcaaata tgtatccgct
     5641 catgagacaa taaccctgat aaatgcttca ataatattga aaaaggaaga gtatgagtat
     5701 tcaacatttc cgtgtcgccc ttattccctt ttttgcggca ttttgccttc ctgtttttgc
     5761 tcacccagaa acgctggtga aagtaaaaga tgctgaagat cagttgggtg cacgagtggg
     5821 ttacatcgaa ctggatctca acagcggtaa gatccttgag agttttcgcc ccgaagaacg
     5881 ttttccaatg atgagcactt ttaaagttct gctatgtggc gcggtattat cccgtattga
     5941 cgccgggcaa gagcaactcg gtcgccgcat acactattct cagaatgact tggttgagta
     6001 ctcaccagtc acagaaaagc atcttacgga tggcatgaca gtaagagaat tatgcagtgc
     6061 tgccataacc atgagtgata acactgcggc caacttactt ctgacaacga tcggaggacc
     6121 gaaggagcta accgcttttt tgcacaacat gggggatcat gtaactcgcc ttgatcgttg
     6181 ggaaccggag ctgaatgaag ccataccaaa cgacgagcgt gacaccacga tgcctgtagc
     6241 aatggcaaca acgttgcgca aactattaac tggcgaacta cttactctag cttcccggca
     6301 acaattaata gactggatgg aggcggataa agttgcagga ccacttctgc gctcggccct
     6361 tccggctggc tggtttattg ctgataaatc tggagccggt gagcgtgggt ctcgcggtat
     6421 cattgcagca ctggggccag atggtaagcc ctcccgtatc gtagttatct acacgacggg
     6481 gagtcaggca actatggatg aacgaaatag acagatcgct gagataggtg cctcactgat
     6541 taagcattgg taactgtcag accaagttta ctcatatata ctttagattg atttaaaact
     6601 tcatttttaa tttaaaagga tctaggtgaa gatccttttt gataatctca tgaccaaaat
     6661 cccttaacgt gagttttcgt tccactgagc gtcagacccc gtagaaaaga tcaaaggatc
     6721 ttcttgagat cctttttttc tgcgcgtaat ctgctgcttg caaacaaaaa aaccaccgct
     6781 accagcggtg gtttgtttgc cggatcaaga gctaccaact ctttttccga aggtaactgg
     6841 cttcagcaga gcgcagatac caaatactgt tcttctagtg tagccgtagt taggccacca
     6901 cttcaagaac tctgtagcac cgcctacata cctcgctctg ctaatcctgt taccagtggc
     6961 tgctgccagt ggcgataagt cgtgtcttac cgggttggac tcaagacgat agttaccgga
     7021 taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca cagcccagct tggagcgaac
//
