LOCUS       sequence-311040-        8093 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  This plasmid is a RAR pathway reporter. It has a Retinoic Acid 
            Receptor Response Element promoter driving the expression of 
            mStrawberry-pGK-BSD.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8093)
  AUTHORS   Kaufman T, Nitzan E, Firestein N, Ginzberg MB, Iyengar S, Patel N, 
            Ben-Hamo R, Porat Z, Hunter J, Hilfinger A, Rotter V, Kafri R, 
            Straussman R
  TITLE     Visual barcodes for clonal-multiplexing of live microscopy-based 
            assays.
  JOURNAL   Nat Commun. 2022 May 18;13(1):2725. doi: 10.1038/s41467-022-30008-0.
  PUBMED    35585055
REFERENCE   2  (bases 1 to 8093)
  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"; journalName: "Nat 
            Commun."; date: "2022-05-18"; volume: "13(1):2725. doi"; pages: " 
            10.1038/s41467-022-30008-0"
COMMENT     Sequence Label: RAR-TRE-mStrawberry reporter
FEATURES             Location/Qualifiers
     source          1..8093
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        1..197
                     /label=SV40 promoter
                     /note="SV40 early promoter"
     rep_origin      48..183
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     CDS             237..947
                     /codon_start=1
                     /product="monomeric derivative of DsRed fluorescent 
                     protein"
                     /label=mStrawberry
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEENNMAIIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEG
                     TQTAKLKVTKGGPLPFAWDILTPNFTYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNF
                     EDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALK
                     GEIKMRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYIVGIKLDITSHNEDYTIVELYERA
                     EGRHSTGGMDELYK"
     primer_bind     complement(382..400)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     650..669
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     misc_feature    989..1106
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        1155..1665
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1584..1602
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1677..2072
                     /codon_start=1
                     /gene="Aspergillus terreus BSD"
                     /product="blasticidin S deaminase"
                     /label=BSD
                     /note="confers resistance to blasticidin"
                     /translation="MAKPLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTG
                     VNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGI
                     KAIVKDSDGQPTAVGIRELLPSGYVWEG"
     misc_feature    2108..2696
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(2161..2181)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2579..2590)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             2768..3001
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    3079..3200
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3116..3135)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     3170..3189
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      3240..3375
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(3395..3414)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(3396..3414)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(3424..3441)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(3424..3440)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3433..3455)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3582..4037
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3669..3688)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3879..3900
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        4063..4167
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(4168..4236,4237..5028)
                     /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(4386..4405)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      5199..5787
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5688..5707
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5941..5958
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    6075..6096
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(6111..6116,6117..6134,6135..6141)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6149..6165
                     /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     6154..6176
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     6173..6189
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     6173..6189
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     6208..6228
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        6210..6228
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        6256..6482
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             6483..6663
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6710..6835
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    7328..7561
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             7746..7790
                     /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"
ORIGIN
        1 tgcatctcaa ttagtcagca accatagtcc cgcccctaac tccgcccatc ccgcccctaa
       61 ctccgcccag ttccgcccat tctccgcccc atcgctgact aatttttttt atttatgcag
      121 aggccgaggc cgcctcggcc tctgagctat tccagaagta gtgaggaggc ttttttggag
      181 gcctaggctt ttgcaaaaag cttggcattc cggtactgtt ggtaaagcca cgacccatgg
      241 tgagcaaggg cgaggagaat aacatggcca tcatcaagga gttcatgcgc ttcaaggtgc
      301 gcatggaggg ctccgtgaac ggccacgagt tcgagatcga gggcgagggc gagggccgcc
      361 cctacgaggg cacccagacc gccaagctga aggtgaccaa gggtggcccc ctgcccttcg
      421 cctgggacat cctaaccccc aacttcacct acggctccaa ggcctacgtg aagcaccccg
      481 ccgacatccc cgactacttg aagctgtcct tccccgaggg cttcaagtgg gagcgcgtga
      541 tgaacttcga ggacggcggc gtggtgaccg tgacccagga ctcctccctg caggacggcg
      601 agttcatcta caaggtgaag ctgcgcggca ccaacttccc ctccgacggc cccgtaatgc
      661 agaagaagac catgggctgg gaggcctcct ccgagcggat gtaccccgag gacggcgccc
      721 tgaagggcga gatcaagatg aggctgaagc tgaaggacgg cggccactac gacgctgagg
      781 tcaagaccac ctacaaggcc aagaagcccg tgcagctgcc cggcgcctac atcgtcggca
      841 tcaagttgga catcacctcc cacaacgagg actacaccat cgtggaactg tacgaacgcg
      901 ccgagggccg ccactccacc ggcggcatgg acgagctgta caagtaagaa ttctagatct
      961 tgagacaaat ggcagtattc atccacaatt ttaaaagaaa aggggggatt ggggggtaca
     1021 gtgcagggga aagaatagta gacataatag caacagacat acaaactaaa gaattacaaa
     1081 aacaaattac aaaaattcaa aattttcggg tttattacag ggacagcaga gatccacttt
     1141 ggcgccggct cgagggggcc cgggttgcgc cttttccaag gcagccctgg gtttgcgcag
     1201 ggacgcggct gctctgggcg tggttccggg aaacgcagcg gcgccgaccc tgggtctcgc
     1261 acattcttca cgtccgttcg cagcgtcacc cggatcttcg ccgctaccct tgtgggcccc
     1321 ccggcgacgc ttcctgctcc gcccctaagt cgggaaggtt ccttgcggtt cgcggcgtgc
     1381 cggacgtgac aaacggaagc cgcacgtctc actagtaccc tcgcagacgg acagcgccag
     1441 ggagcaatgg cagcgcgccg accgcgatgg gctgtggcca atagcggctg ctcagcaggg
     1501 cgcgccgaga gcagcggccg ggaaggggcg gtgcgggagg cggggtgtgg ggcggtagtg
     1561 tgggccctgt tcctgcccgc gcggtgttcc gcattctgca agcctccgga gcgcacgtcg
     1621 gcagtcggct ccctcgttga ccgaatcacc gacctctctc cccagggggt accaccatgg
     1681 ccaagccttt gtctcaagaa gaatccaccc tcattgaaag agcaacggct acaatcaaca
     1741 gcatccccat ctctgaagac tacagcgtcg ccagcgcagc tctctctagc gacggccgca
     1801 tcttcactgg tgtcaatgta tatcatttta ctgggggacc ttgtgcagaa ctcgtggtgc
     1861 tgggcactgc tgctgctgcg gcagctggca acctgacttg tatcgtcgcg atcggaaatg
     1921 agaacagggg catcttgagc ccctgcggac ggtgccgaca ggtgcttctc gatctgcatc
     1981 ctgggatcaa agccatagtg aaggacagtg atggacagcc gacggcagtt gggattcgtg
     2041 aattgctgcc ctctggttat gtgtgggagg gcctgcagct gcagtagtaa agacgcgtta
     2101 agtcgacaat caacctctgg attacaaaat ttgtgaaaga ttgactggta ttcttaacta
     2161 tgttgctcct tttacgctat gtggatacgc tgctttaatg cctttgtatc atgctattgc
     2221 ttcccgtatg gctttcattt tctcctcctt gtataaatcc tggttgctgt ctctttatga
     2281 ggagttgtgg cccgttgtca ggcaacgtgg cgtggtgtgc actgtgtttg ctgacgcaac
     2341 ccccactggt tggggcattg ccaccacctg tcagctcctt tccgggactt tcgctttccc
     2401 cctccctatt gccacggcgg aactcatcgc cgcctgcctt gcccgctgct ggacaggggc
     2461 tcggctgttg ggcactgaca attccgtggt gttgtcgggg aaatcatcgt cctttccttg
     2521 gctgctcgcc tgtgttgcca cctggattct gcgcgggacg tccttctgct acgtcccttc
     2581 ggccctcaat ccagcggacc ttccttcccg cggcctgctg ccggctctgc ggcctcttcc
     2641 gcgtcttcgc cttcgccctc agacgagtcg gatctccctt tgggccgcct ccccgcgtcg
     2701 actttaagac caatgactta caaggcagct gtagatctta gccacttttt aaaagaaaag
     2761 gggggactgg aagggctaat tcactcccaa cgaagacaag atctgctttt tgcttgtact
     2821 gggtctctct ggttagacca gatctgagcc tgggagctct ctggctaact agggaaccca
     2881 ctgcttaagc ctcaataaag cttgccttga gtgcttcaag tagtgtgtgc ccgtctgttg
     2941 tgtgactctg gtaactagag atccctcaga cccttttagt cagtgtggaa aatctctagc
     3001 agtacgtata gtagttcatg tcatcttatt attcagtatt tataacttgc aaagaaatga
     3061 atatcagaga gtgagaggaa cttgtttatt gcagcttata atggttacaa ataaagcaat
     3121 agcatcacaa atttcacaaa taaagcattt ttttcactgc attctagttg tggtttgtcc
     3181 aaactcatca atgtatctta tcatgtctgg ctctagctat cccgccccta actccgccca
     3241 tcccgcccct aactccgccc agttccgccc attctccgcc ccatggctga ctaatttttt
     3301 ttatttatgc agaggccgag gccgcctcgg cctctgagct attccagaag tagtgaggag
     3361 gcttttttgg aggcctaggg acgtacccaa ttcgccctat agtgagtcgt attacgcgcg
     3421 ctcactggcc gtcgttttac aacgtcgtga ctgggaaaac cctggcgtta cccaacttaa
     3481 tcgccttgca gcacatcccc ctttcgccag ctggcgtaat agcgaagagg cccgcaccga
     3541 tcgcccttcc caacagttgc gcagcctgaa tggcgaatgg gacgcgccct gtagcggcgc
     3601 attaagcgcg gcgggtgtgg tggttacgcg cagcgtgacc gctacacttg ccagcgccct
     3661 agcgcccgct cctttcgctt tcttcccttc ctttctcgcc acgttcgccg gctttccccg
     3721 tcaagctcta aatcgggggc tccctttagg gttccgattt agtgctttac ggcacctcga
     3781 ccccaaaaaa cttgattagg gtgatggttc acgtagtggg ccatcgccct gatagacggt
     3841 ttttcgccct ttgacgttgg agtccacgtt ctttaatagt ggactcttgt tccaaactgg
     3901 aacaacactc aaccctatct cggtctattc ttttgattta taagggattt tgccgatttc
     3961 ggcctattgg ttaaaaaatg agctgattta acaaaaattt aacgcgaatt ttaacaaaat
     4021 attaacgctt acaatttagg tggcactttt cggggaaatg tgcgcggaac ccctatttgt
     4081 ttatttttct aaatacattc aaatatgtat ccgctcatga gacaataacc ctgataaatg
     4141 cttcaataat attgaaaaag gaagagtatg agtattcaac atttccgtgt cgcccttatt
     4201 cccttttttg cggcattttg ccttcctgtt tttgctcacc cagaaacgct ggtgaaagta
     4261 aaagatgctg aagatcagtt gggtgcacga gtgggttaca tcgaactgga tctcaacagc
     4321 ggtaagatcc ttgagagttt tcgccccgaa gaacgttttc caatgatgag cacttttaaa
     4381 gttctgctat gtggcgcggt attatcccgt attgacgccg ggcaagagca actcggtcgc
     4441 cgcatacact attctcagaa tgacttggtt gagtactcac cagtcacaga aaagcatctt
     4501 acggatggca tgacagtaag agaattatgc agtgctgcca taaccatgag tgataacact
     4561 gcggccaact tacttctgac aacgatcgga ggaccgaagg agctaaccgc ttttttgcac
     4621 aacatggggg atcatgtaac tcgccttgat cgttgggaac cggagctgaa tgaagccata
     4681 ccaaacgacg agcgtgacac cacgatgcct gtagcaatgg caacaacgtt gcgcaaacta
     4741 ttaactggcg aactacttac tctagcttcc cggcaacaat taatagactg gatggaggcg
     4801 gataaagttg caggaccact tctgcgctcg gcccttccgg ctggctggtt tattgctgat
     4861 aaatctggag ccggtgagcg tgggtctcgc ggtatcattg cagcactggg gccagatggt
     4921 aagccctccc gtatcgtagt tatctacacg acggggagtc aggcaactat ggatgaacga
     4981 aatagacaga tcgctgagat aggtgcctca ctgattaagc attggtaact gtcagaccaa
     5041 gtttactcat atatacttta gattgattta aaacttcatt tttaatttaa aaggatctag
     5101 gtgaagatcc tttttgataa tctcatgacc aaaatccctt aacgtgagtt ttcgttccac
     5161 tgagcgtcag accccgtaga aaagatcaaa ggatcttctt gagatccttt ttttctgcgc
     5221 gtaatctgct gcttgcaaac aaaaaaacca ccgctaccag cggtggtttg tttgccggat
     5281 caagagctac caactctttt tccgaaggta actggcttca gcagagcgca gataccaaat
     5341 actgttcttc tagtgtagcc gtagttaggc caccacttca agaactctgt agcaccgcct
     5401 acatacctcg ctctgctaat cctgttacca gtggctgctg ccagtggcga taagtcgtgt
     5461 cttaccgggt tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg
     5521 gggggttcgt gcacacagcc cagcttggag cgaacgacct acaccgaact gagataccta
     5581 cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg
     5641 gtaagcggca gggtcggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg
     5701 tatctttata gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc
     5761 tcgtcagggg ggcggagcct atggaaaaac gccagcaacg cggccttttt acggttcctg
     5821 gccttttgct ggccttttgc tcacatgttc tttcctgcgt tatcccctga ttctgtggat
     5881 aaccgtatta ccgcctttga gtgagctgat accgctcgcc gcagccgaac gaccgagcgc
     5941 agcgagtcag tgagcgagga agcggaagag cgcccaatac gcaaaccgcc tctccccgcg
     6001 cgttggccga ttcattaatg cagctggcac gacaggtttc ccgactggaa agcgggcagt
     6061 gagcgcaacg caattaatgt gagttagctc actcattagg caccccaggc tttacacttt
     6121 atgcttccgg ctcgtatgtt gtgtggaatt gtgagcggat aacaatttca cacaggaaac
     6181 agctatgacc atgattacgc caagcgcgca attaaccctc actaaaggga acaaaagctg
     6241 gagctgcaag cttaatgtag tcttatgcaa tactcttgta gtcttgcaac atggtaacga
     6301 tgagttagca acatgcctta caaggagaga aaaagcaccg tgcatgccga ttggtggaag
     6361 taaggtggta cgatcgtgcc ttattaggaa ggcaacagac gggtctgaca tggattggac
     6421 gaaccactga attgccgcat tgcagagata ttgtatttaa gtgcctagct cgatacataa
     6481 acgggtctct ctggttagac cagatctgag cctgggagct ctctggctaa ctagggaacc
     6541 cactgcttaa gcctcaataa agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt
     6601 tgtgtgactc tggtaactag agatccctca gaccctttta gtcagtgtgg aaaatctcta
     6661 gcagtggcgc ccgaacaggg acttgaaagc gaaagggaaa ccagaggagc tctctcgacg
     6721 caggactcgg cttgctgaag cgcgcacggc aagaggcgag gggcggcgac tggtgagtac
     6781 gccaaaaatt ttgactagcg gaggctagaa ggagagagat gggtgcgaga gcgtcagtat
     6841 taagcggggg agaattagat cgcgatggga aaaaattcgg ttaaggccag ggggaaagaa
     6901 aaaatataaa ttaaaacata tagtatgggc aagcagggag ctagaacgat tcgcagttaa
     6961 tcctggcctg ttagaaacat cagaaggctg tagacaaata ctgggacagc tacaaccatc
     7021 ccttcagaca ggatcagaag aacttagatc attatataat acagtagcaa ccctctattg
     7081 tgtgcatcaa aggatagaga taaaagacac caaggaagct ttagacaaga tagaggaaga
     7141 gcaaaacaaa agtaagacca ccgcacagca agcggccgct gatcttcaga cctggaggag
     7201 gagatatgag ggacaattgg agaagtgaat tatataaata taaagtagta aaaattgaac
     7261 cattaggagt agcacccacc aaggcaaaga gaagagtggt gcagagagaa aaaagagcag
     7321 tgggaatagg agctttgttc cttgggttct tgggagcagc aggaagcact atgggcgcag
     7381 cgtcaatgac gctgacggta caggccagac aattattgtc tggtatagtg cagcagcaga
     7441 acaatttgct gagggctatt gaggcgcaac agcatctgtt gcaactcaca gtctggggca
     7501 tcaagcagct ccaggcaaga atcctggctg tggaaagata cctaaaggat caacagctcc
     7561 tggggatttg gggttgctct ggaaaactca tttgcaccac tgctgtgcct tggaatgcta
     7621 gttggagtaa taaatctctg gaacagattt ggaatcacac gacctggatg gagtgggaca
     7681 gagaaattaa caattacaca agcttaatac actccttaat tgaagaatcg caaaaccagc
     7741 aagaaaagaa tgaacaagaa ttattggaat tagataaatg ggcaagtttg tggaattggt
     7801 ttaacataac aaattggctg tggtatataa aattattcat aatgatagta ggaggcttgg
     7861 taggtttaag aatagttttt gctgtacttt ctatagtgaa tagagttagg cagggatatt
     7921 caccattatc gtttcagacc cacctcccaa ccccgagggg gtaccgagct cggtgaactt
     7981 tcggtgaacc ctaccctcga gtgaactttc ggtgaaccct accctcgagg gtagggttca
     8041 ccgaaagttc actcgacgaa ttccagtcta gcccgggctc gagatctgcg atc
//
