LOCUS       sequence-246205-        7546 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Cre-regulated lentiviral shRNA vector. Cre addition causes both 
            mCherry and shRNA to be recombined out of the construct, turning OFF
            shRNA expression..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7546)
  AUTHORS   Gaspar-Maia A, Alajem A, Polesso F, Sridharan R, Mason MJ, 
            Heidersbach A, Ramalho-Santos J, McManus MT, Plath K, Meshorer E, 
            Ramalho-Santos M
  TITLE     Chd1 regulates open chromatin and pluripotency of embryonic stem 
            cells.
  JOURNAL   Nature. 2009 Aug 13;460(7257):863-8. doi: 10.1038/nature08212. Epub 
            2009 Jul 8.
  PUBMED    19587682
REFERENCE   2  (bases 1 to 7546)
  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/nature08212"; journalName: "Nature"; date: "2009-08-13- 
            13"; volume: "460"; issue: "7257"; pages: "863-8"
COMMENT     Sequence Label: pSicoR-mCh-empty
FEATURES             Location/Qualifiers
     source          1..7546
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        1..380
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        382..580
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     LTR             598..778
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    825..950
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1447..1680
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1865..1909
                     /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"
     misc_feature    2207..2324
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     protein_bind    complement(2577..2610)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     enhancer        2827..3130
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        3131..3334
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     regulatory      3373..3382
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             3379..4089
                     /codon_start=1
                     /product="monomeric derivative of DsRed fluorescent protein
                     (Shaner et al., 2004)"
                     /label=mCherry
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEG
                     TQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNF
                     EDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALK
                     GEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERA
                     EGRHSTGGMDELYK"
     primer_bind     complement(3524..3542)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     3792..3811
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     protein_bind    complement(4109..4142)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     misc_feature    4198..4786
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(4251..4271)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4669..4680)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     primer_bind     complement(4789..4805)
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4790..4806)
                     /label=pBluescriptKS
                     /note="For pBluescript vector"
     LTR             5315..5495
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     rep_origin      complement(5557..6145)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5637..5656)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(6316..7107,7108..7176))
                     /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     6939..6958
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(7177..7281)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(7356..7375)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
ORIGIN
        1 gacattgatt attgactagt tattaatagt aatcaattac ggggtcatta gttcatagcc
       61 catatatgga gttccgcgtt acataactta cggtaaatgg cccgcctggc tgaccgccca
      121 acgacccccg cccattgacg tcaataatga cgtatgttcc catagtaacg ccaataggga
      181 ctttccattg acgtcaatgg gtggagtatt tacggtaaac tgcccacttg gcagtacatc
      241 aagtgtatca tatgccaagt acgcccccta ttgacgtcaa tgacggtaaa tggcccgcct
      301 ggcattatgc ccagtacatg accttatggg actttcctac ttggcagtac atctacgtat
      361 tagtcatcgc tattaccatg gtgatgcggt tttggcagta catcaatggg cgtggatagc
      421 ggtttgactc acggggattt ccaagtctcc accccattga cgtcaatggg agtttgtttt
      481 ggcaccaaaa tcaacgggac tttccaaaat gtcgtaacaa ctccgcccca ttgacgcaaa
      541 tgggcggtag gcgtgtacgg tgggaggtct atataagcag cgcgttttgc ctgtactggg
      601 tctctctggt tagaccagat ctgagcctgg gagctctctg gctaactagg gaacccactg
      661 cttaagcctc aataaagctt gccttgagtg cttcaagtag tgtgtgcccg tctgttgtgt
      721 gactctggta actagagatc cctcagaccc ttttagtcag tgtggaaaat ctctagcagt
      781 ggcgcccgaa cagggacttg aaagcgaaag ggaaaccaga ggagctctct cgacgcagga
      841 ctcggcttgc tgaagcgcgc acggcaagag gcgaggggcg gcgactggtg agtacgccaa
      901 aaattttgac tagcggaggc tagaaggaga gagatgggtg cgagagcgtc agtattaagc
      961 gggggagaat tagatcgcga tgggaaaaaa ttcggttaag gccaggggga aagaaaaaat
     1021 ataaattaaa acatatagta tgggcaagca gggagctaga acgattcgca gttaatcctg
     1081 gcctgttaga aacatcagaa ggctgtagac aaatactggg acagctacaa ccatcccttc
     1141 agacaggatc agaagaactt agatcattat ataatacagt agcaaccctc tattgtgtgc
     1201 atcaaaggat agagataaaa gacaccaagg aagctttaga caagatagag gaagagcaaa
     1261 acaaaagtaa gaccaccgca cagcaagcgg ccggccgctg atcttcagac ctggaggagg
     1321 agatatgagg gacaattgga gaagtgaatt atataaatat aaagtagtaa aaattgaacc
     1381 attaggagta gcacccacca aggcaaagag aagagtggtg cagagagaaa aaagagcagt
     1441 gggaatagga gctttgttcc ttgggttctt gggagcagca ggaagcacta tgggcgcagc
     1501 gtcaatgacg ctgacggtac aggccagaca attattgtct ggtatagtgc agcagcagaa
     1561 caatttgctg agggctattg aggcgcaaca gcatctgttg caactcacag tctggggcat
     1621 caagcagctc caggcaagaa tcctggctgt ggaaagatac ctaaaggatc aacagctcct
     1681 ggggatttgg ggttgctctg gaaaactcat ttgcaccact gctgtgcctt ggaatgctag
     1741 ttggagtaat aaatctctgg aacagatttg gaatcacacg acctggatgg agtgggacag
     1801 agaaattaac aattacacaa gcttaataca ctccttaatt gaagaatcgc aaaaccagca
     1861 agaaaagaat gaacaagaat tattggaatt agataaatgg gcaagtttgt ggaattggtt
     1921 taacataaca aattggctgt ggtatataaa attattcata atgatagtag gaggcttggt
     1981 aggtttaaga atagtttttg ctgtactttc tatagtgaat agagttaggc agggatattc
     2041 accattatcg tttcagaccc acctcccaac cccgagggga cccgacaggc ccgaaggaat
     2101 agaagaagaa ggtggagaga gagacagaga cagatccatt cgattagtga acggatcggc
     2161 actgcgtgcg ccaattctgc agacaaatgg cagtattcat ccacaatttt aaaagaaaag
     2221 gggggattgg ggggtacagt gcaggggaaa gaatagtaga cataatagca acagacatac
     2281 aaactaaaga attacaaaaa caaattacaa aaattcaaaa ttttcgggtt tattacaggg
     2341 acagcagaga tccagtttgg ttagtaccgg gcccgctcta gagatccgac gcgccatctc
     2401 taggcccgcg ccggccccct cgcacagact tgtgggagaa gctcggctac tcccctgccc
     2461 cggttaattt gcatataata tttcctagta actatagagg cttaatgtgc gataaaagac
     2521 agataatctg ttctttttaa tactagctac attttacatg ataggcttgg atttctataa
     2581 cttcgtatag catacattat acgaagttat acatgtcaca aaaggaaact caccctaact
     2641 gtaaagtaat tgtgtgtttt gagactataa atatcccttg gagaaaagcc ttgttaacgc
     2701 gcggtgaccc tcgagtacta ggatccatta ggcggccgcg tggataaccg tattaccgcc
     2761 atgcattagt tattaatagt aatcaattac ggggtcatta gttcatagcc catatatgga
     2821 gttccgcgtt acataactta cggtaaatgg cccgcctggc tgaccgccca acgacccccg
     2881 cccattgacg tcaataatga cgtatgttcc catagtaacg ccaataggga ctttccattg
     2941 acgtcaatgg gtggagtatt tacggtaaac tgcccacttg gcagtacatc aagtgtatca
     3001 tatgccaagt acgcccccta ttgacgtcaa tgacggtaaa tggcccgcct ggcattatgc
     3061 ccagtacatg accttatggg actttcctac ttggcagtac atctacgtat tagtcatcgc
     3121 tattaccatg gtgatgcggt tttggcagta catcaatggg cgtggatagc ggtttgactc
     3181 acggggattt ccaagtctcc accccattga cgtcaatggg agtttgtttt ggcaccaaaa
     3241 tcaacgggac tttccaaaat gtcgtaacaa ctccgcccca ttgacgcaaa tgggcggtag
     3301 gcgtgtacgg tgggaggtct atataagcag agctggttta gtgaaccgtc agatccgcta
     3361 gcgctaccgg tcgccaccat ggtgagcaag ggcgaggagg ataacatggc catcatcaag
     3421 gagttcatgc gcttcaaggt gcacatggag ggctccgtga acggccacga gttcgagatc
     3481 gagggcgagg gcgagggccg cccctacgag ggcacccaga ccgccaagct gaaggtgacc
     3541 aagggtggcc ccctgccctt cgcctgggac atcctgtccc ctcagttcat gtacggctcc
     3601 aaggcctacg tgaagcaccc cgccgacatc cccgactact tgaagctgtc cttccccgag
     3661 ggcttcaagt gggagcgcgt gatgaacttc gaggacggcg gcgtggtgac cgtgacccag
     3721 gactcctccc tgcaggacgg cgagttcatc tacaaggtga agctgcgcgg caccaacttc
     3781 ccctccgacg gccccgtaat gcagaagaag accatgggct gggaggcctc ctccgagcgg
     3841 atgtaccccg aggacggcgc cctgaagggc gagatcaagc agaggctgaa gctgaaggac
     3901 ggcggccact acgacgctga ggtcaagacc acctacaagg ccaagaagcc cgtgcagctg
     3961 cccggcgcct acaacgtcaa catcaagttg gacatcacct cccacaacga ggactacacc
     4021 atcgtggaac agtacgaacg cgccgagggc cgccactcca ccggcggcat ggacgagctg
     4081 tacaagtaag aattcgtcga gggacctaat aacttcgtat agcatacatt atacgaagtt
     4141 atacatgttt aagggttccg gttccactag gtacaattcg atatcaagct tatcgataat
     4201 caacctctgg attacaaaat ttgtgaaaga ttgactggta ttcttaacta tgttgctcct
     4261 tttacgctat gtggatacgc tgctttaatg cctttgtatc atgctattgc ttcccgtatg
     4321 gctttcattt tctcctcctt gtataaatcc tggttgctgt ctctttatga ggagttgtgg
     4381 cccgttgtca ggcaacgtgg cgtggtgtgc actgtgtttg ctgacgcaac ccccactggt
     4441 tggggcattg ccaccacctg tcagctcctt tccgggactt tcgctttccc cctccctatt
     4501 gccacggcgg aactcatcgc cgcctgcctt gcccgctgct ggacaggggc tcggctgttg
     4561 ggcactgaca attccgtggt gttgtcgggg aaatcatcgt cctttccttg gctgctcgcc
     4621 tgtgttgcca cctggattct gcgcgggacg tccttctgct acgtcccttc ggccctcaat
     4681 ccagcggacc ttccttcccg cggcctgctg ccggctctgc ggcctcttcc gcgtcttcgc
     4741 cttcgccctc agacgagtcg gatctccctt tgggccgcct ccccgcatcg ataccgtcga
     4801 cctcgatcga gacctagaaa aacatggagc aatcacaagt agcaatacag cagctaccaa
     4861 tgctgattgt gcctggctag aagcacaaga ggaggaggag gtgggttttc cagtcacacc
     4921 tcaggtacct ttaagaccaa tgacttacaa ggcagctgta gatcttagcc actttttaaa
     4981 agaaaagggg ggactggaag ggctaattca ctcccaacga agacaagata tccttgatct
     5041 gtggatctac cacacacaag gctacttccc tgattggcag aactacacac cagggccagg
     5101 gatcagatat ccactgacct ttggatggtg ctacaagcta gtaccagttg agcaagagaa
     5161 ggtagaagaa gccaatgaag gagagaacac ccgcttgtta caccctgtga gcctgcatgg
     5221 gatggatgac ccggagagag aagtattaga gtggaggttt gacagccgcc tagcatttca
     5281 tcacatggcc cgagagctgc atccggactg tactgggtct ctctggttag accagatctg
     5341 agcctgggag ctctctggct aactagggaa cccactgctt aagcctcaat aaagcttgcc
     5401 ttgagtgctt caagtagtgt gtgcccgtct gttgtgtgac tctggtaact agagatccct
     5461 cagacccttt tagtcagtgt ggaaaatctc tagcagcatg tgagcaaaag gccagcaaaa
     5521 ggccaggaac cgtaaaaagg ccgcgttgct ggcgtttttc cataggctcc gcccccctga
     5581 cgagcatcac aaaaatcgac gctcaagtca gaggtggcga aacccgacag gactataaag
     5641 ataccaggcg tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct
     5701 taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg
     5761 ctgtaggtat ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc
     5821 ccccgttcag cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt
     5881 aagacacgac ttatcgccac tggcagcagc cactggtaac aggattagca gagcgaggta
     5941 tgtaggcggt gctacagagt tcttgaagtg gtggcctaac tacggctaca ctagaagaac
     6001 agtatttggt atctgcgctc tgctgaagcc agttaccttc ggaaaaagag ttggtagctc
     6061 ttgatccggc aaacaaacca ccgctggtag cggtggtttt tttgtttgca agcagcagat
     6121 tacgcgcaga aaaaaaggat ctcaagaaga tcctttgatc ttttctacgg ggtctgacgc
     6181 tcagtggaac gaaaactcac gttaagggat tttggtcatg agattatcaa aaaggatctt
     6241 cacctagatc cttttaaatt aaaaatgaag ttttaaatca atctaaagta tatatgagta
     6301 aacttggtct gacagttacc aatgcttaat cagtgaggca cctatctcag cgatctgtct
     6361 atttcgttca tccatagttg cctgactccc cgtcgtgtag ataactacga tacgggaggg
     6421 cttaccatct ggccccagtg ctgcaatgat accgcgagac ccacgctcac cggctccaga
     6481 tttatcagca ataaaccagc cagccggaag ggccgagcgc agaagtggtc ctgcaacttt
     6541 atccgcctcc atccagtcta ttaattgttg ccgggaagct agagtaagta gttcgccagt
     6601 taatagtttg cgcaacgttg ttgccattgc tacaggcatc gtggtgtcac gctcgtcgtt
     6661 tggtatggct tcattcagct ccggttccca acgatcaagg cgagttacat gatcccccat
     6721 gttgtgcaaa aaagcggtta gctccttcgg tcctccgatc gttgtcagaa gtaagttggc
     6781 cgcagtgtta tcactcatgg ttatggcagc actgcataat tctcttactg tcatgccatc
     6841 cgtaagatgc ttttctgtga ctggtgagta ctcaaccaag tcattctgag aatagtgtat
     6901 gcggcgaccg agttgctctt gcccggcgtc aatacgggat aataccgcgc cacatagcag
     6961 aactttaaaa gtgctcatca ttggaaaacg ttcttcgggg cgaaaactct caaggatctt
     7021 accgctgttg agatccagtt cgatgtaacc cactcgtgca cccaactgat cttcagcatc
     7081 ttttactttc accagcgttt ctgggtgagc aaaaacagga aggcaaaatg ccgcaaaaaa
     7141 gggaataagg gcgacacgga aatgttgaat actcatactc ttcctttttc aatattattg
     7201 aagcatttat cagggttatt gtctcatgag cggatacata tttgaatgta tttagaaaaa
     7261 taaacaaata ggggttccgc gcacatttcc ccgaaaagtg ccacctgacg tcgacggatc
     7321 gggagatctc ccgatcccct atggtgcact ctcagtacaa tctgctctga tgccgcatag
     7381 ttaagccagt atctgctccc tgcttgtgtg ttggaggtcg ctgagtagtg cgcgagcaaa
     7441 atttaagcta caacaaggca aggcttgacc gacaattgca tgaagaatct gcttagggtt
     7501 aggcgttttg cgctgcttcg cgatgtacgg gccagatata cgcgtt
//
