LOCUS       sequence-309765-        7728 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  This plasmid serves as the backbone for the TRE reporters described 
            in our paper. It's a promoterless-mStrawberry-pGK-BSD backbone to 
            which we insert a pathway specific promoter before the mStrawberry.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7728)
  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 7728)
  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: TRE reporter backbone
FEATURES             Location/Qualifiers
     source          1..7728
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             1..711
                     /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(146..164)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     414..433
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     misc_feature    753..870
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        919..1429
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     1348..1366
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             1441..1836
                     /codon_start=1
                     /gene="Aspergillus terreus BSD"
                     /product="blasticidin S deaminase"
                     /label=BSD
                     /note="confers resistance to blasticidin"
                     /translation="MAKPLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTG
                     VNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGI
                     KAIVKDSDGQPTAVGIRELLPSGYVWEG"
     misc_feature    1872..2460
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(1925..1945)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2343..2354)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             2532..2765
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    2843..2964
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2880..2899)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     2934..2953
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      3004..3139
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(3159..3178)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(3160..3178)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(3188..3205)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(3188..3204)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3197..3219)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      3346..3801
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3433..3452)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3643..3664
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        3827..3931
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(3932..4000,4001..4792)
                     /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(4150..4169)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      4963..5551
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     5452..5471
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     5705..5722
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    5839..5860
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5875..5880,5881..5898,5899..5905)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5913..5929
                     /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     5918..5940
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5937..5953
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5937..5953
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     5972..5992
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        5974..5992
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        6020..6246
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
     LTR             6247..6427
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    6474..6599
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    7092..7325
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             7510..7554
                     /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 atggtgagca agggcgagga gaataacatg gccatcatca aggagttcat gcgcttcaag
       61 gtgcgcatgg agggctccgt gaacggccac gagttcgaga tcgagggcga gggcgagggc
      121 cgcccctacg agggcaccca gaccgccaag ctgaaggtga ccaagggtgg ccccctgccc
      181 ttcgcctggg acatcctaac ccccaacttc acctacggct ccaaggccta cgtgaagcac
      241 cccgccgaca tccccgacta cttgaagctg tccttccccg agggcttcaa gtgggagcgc
      301 gtgatgaact tcgaggacgg cggcgtggtg accgtgaccc aggactcctc cctgcaggac
      361 ggcgagttca tctacaaggt gaagctgcgc ggcaccaact tcccctccga cggccccgta
      421 atgcagaaga agaccatggg ctgggaggcc tcctccgagc ggatgtaccc cgaggacggc
      481 gccctgaagg gcgagatcaa gatgaggctg aagctgaagg acggcggcca ctacgacgct
      541 gaggtcaaga ccacctacaa ggccaagaag cccgtgcagc tgcccggcgc ctacatcgtc
      601 ggcatcaagt tggacatcac ctcccacaac gaggactaca ccatcgtgga actgtacgaa
      661 cgcgccgagg gccgccactc caccggcggc atggacgagc tgtacaagta agaattctag
      721 atcttgagac aaatggcagt attcatccac aattttaaaa gaaaaggggg gattgggggg
      781 tacagtgcag gggaaagaat agtagacata atagcaacag acatacaaac taaagaatta
      841 caaaaacaaa ttacaaaaat tcaaaatttt cgggtttatt acagggacag cagagatcca
      901 ctttggcgcc ggctcgaggg ggcccgggtt gcgccttttc caaggcagcc ctgggtttgc
      961 gcagggacgc ggctgctctg ggcgtggttc cgggaaacgc agcggcgccg accctgggtc
     1021 tcgcacattc ttcacgtccg ttcgcagcgt cacccggatc ttcgccgcta cccttgtggg
     1081 ccccccggcg acgcttcctg ctccgcccct aagtcgggaa ggttccttgc ggttcgcggc
     1141 gtgccggacg tgacaaacgg aagccgcacg tctcactagt accctcgcag acggacagcg
     1201 ccagggagca atggcagcgc gccgaccgcg atgggctgtg gccaatagcg gctgctcagc
     1261 agggcgcgcc gagagcagcg gccgggaagg ggcggtgcgg gaggcggggt gtggggcggt
     1321 agtgtgggcc ctgttcctgc ccgcgcggtg ttccgcattc tgcaagcctc cggagcgcac
     1381 gtcggcagtc ggctccctcg ttgaccgaat caccgacctc tctccccagg gggtaccacc
     1441 atggccaagc ctttgtctca agaagaatcc accctcattg aaagagcaac ggctacaatc
     1501 aacagcatcc ccatctctga agactacagc gtcgccagcg cagctctctc tagcgacggc
     1561 cgcatcttca ctggtgtcaa tgtatatcat tttactgggg gaccttgtgc agaactcgtg
     1621 gtgctgggca ctgctgctgc tgcggcagct ggcaacctga cttgtatcgt cgcgatcgga
     1681 aatgagaaca ggggcatctt gagcccctgc ggacggtgcc gacaggtgct tctcgatctg
     1741 catcctggga tcaaagccat agtgaaggac agtgatggac agccgacggc agttgggatt
     1801 cgtgaattgc tgccctctgg ttatgtgtgg gagggcctgc agctgcagta gtaaagacgc
     1861 gttaagtcga caatcaacct ctggattaca aaatttgtga aagattgact ggtattctta
     1921 actatgttgc tccttttacg ctatgtggat acgctgcttt aatgcctttg tatcatgcta
     1981 ttgcttcccg tatggctttc attttctcct ccttgtataa atcctggttg ctgtctcttt
     2041 atgaggagtt gtggcccgtt gtcaggcaac gtggcgtggt gtgcactgtg tttgctgacg
     2101 caacccccac tggttggggc attgccacca cctgtcagct cctttccggg actttcgctt
     2161 tccccctccc tattgccacg gcggaactca tcgccgcctg ccttgcccgc tgctggacag
     2221 gggctcggct gttgggcact gacaattccg tggtgttgtc ggggaaatca tcgtcctttc
     2281 cttggctgct cgcctgtgtt gccacctgga ttctgcgcgg gacgtccttc tgctacgtcc
     2341 cttcggccct caatccagcg gaccttcctt cccgcggcct gctgccggct ctgcggcctc
     2401 ttccgcgtct tcgccttcgc cctcagacga gtcggatctc cctttgggcc gcctccccgc
     2461 gtcgacttta agaccaatga cttacaaggc agctgtagat cttagccact ttttaaaaga
     2521 aaagggggga ctggaagggc taattcactc ccaacgaaga caagatctgc tttttgcttg
     2581 tactgggtct ctctggttag accagatctg agcctgggag ctctctggct aactagggaa
     2641 cccactgctt aagcctcaat aaagcttgcc ttgagtgctt caagtagtgt gtgcccgtct
     2701 gttgtgtgac tctggtaact agagatccct cagacccttt tagtcagtgt ggaaaatctc
     2761 tagcagtacg tatagtagtt catgtcatct tattattcag tatttataac ttgcaaagaa
     2821 atgaatatca gagagtgaga ggaacttgtt tattgcagct tataatggtt acaaataaag
     2881 caatagcatc acaaatttca caaataaagc atttttttca ctgcattcta gttgtggttt
     2941 gtccaaactc atcaatgtat cttatcatgt ctggctctag ctatcccgcc cctaactccg
     3001 cccatcccgc ccctaactcc gcccagttcc gcccattctc cgccccatgg ctgactaatt
     3061 ttttttattt atgcagaggc cgaggccgcc tcggcctctg agctattcca gaagtagtga
     3121 ggaggctttt ttggaggcct agggacgtac ccaattcgcc ctatagtgag tcgtattacg
     3181 cgcgctcact ggccgtcgtt ttacaacgtc gtgactggga aaaccctggc gttacccaac
     3241 ttaatcgcct tgcagcacat ccccctttcg ccagctggcg taatagcgaa gaggcccgca
     3301 ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atgggacgcg ccctgtagcg
     3361 gcgcattaag cgcggcgggt gtggtggtta cgcgcagcgt gaccgctaca cttgccagcg
     3421 ccctagcgcc cgctcctttc gctttcttcc cttcctttct cgccacgttc gccggctttc
     3481 cccgtcaagc tctaaatcgg gggctccctt tagggttccg atttagtgct ttacggcacc
     3541 tcgaccccaa aaaacttgat tagggtgatg gttcacgtag tgggccatcg ccctgataga
     3601 cggtttttcg ccctttgacg ttggagtcca cgttctttaa tagtggactc ttgttccaaa
     3661 ctggaacaac actcaaccct atctcggtct attcttttga tttataaggg attttgccga
     3721 tttcggccta ttggttaaaa aatgagctga tttaacaaaa atttaacgcg aattttaaca
     3781 aaatattaac gcttacaatt taggtggcac ttttcgggga aatgtgcgcg gaacccctat
     3841 ttgtttattt ttctaaatac attcaaatat gtatccgctc atgagacaat aaccctgata
     3901 aatgcttcaa taatattgaa aaaggaagag tatgagtatt caacatttcc gtgtcgccct
     3961 tattcccttt tttgcggcat tttgccttcc tgtttttgct cacccagaaa cgctggtgaa
     4021 agtaaaagat gctgaagatc agttgggtgc acgagtgggt tacatcgaac tggatctcaa
     4081 cagcggtaag atccttgaga gttttcgccc cgaagaacgt tttccaatga tgagcacttt
     4141 taaagttctg ctatgtggcg cggtattatc ccgtattgac gccgggcaag agcaactcgg
     4201 tcgccgcata cactattctc agaatgactt ggttgagtac tcaccagtca cagaaaagca
     4261 tcttacggat ggcatgacag taagagaatt atgcagtgct gccataacca tgagtgataa
     4321 cactgcggcc aacttacttc tgacaacgat cggaggaccg aaggagctaa ccgctttttt
     4381 gcacaacatg ggggatcatg taactcgcct tgatcgttgg gaaccggagc tgaatgaagc
     4441 cataccaaac gacgagcgtg acaccacgat gcctgtagca atggcaacaa cgttgcgcaa
     4501 actattaact ggcgaactac ttactctagc ttcccggcaa caattaatag actggatgga
     4561 ggcggataaa gttgcaggac cacttctgcg ctcggccctt ccggctggct ggtttattgc
     4621 tgataaatct ggagccggtg agcgtgggtc tcgcggtatc attgcagcac tggggccaga
     4681 tggtaagccc tcccgtatcg tagttatcta cacgacgggg agtcaggcaa ctatggatga
     4741 acgaaataga cagatcgctg agataggtgc ctcactgatt aagcattggt aactgtcaga
     4801 ccaagtttac tcatatatac tttagattga tttaaaactt catttttaat ttaaaaggat
     4861 ctaggtgaag atcctttttg ataatctcat gaccaaaatc ccttaacgtg agttttcgtt
     4921 ccactgagcg tcagaccccg tagaaaagat caaaggatct tcttgagatc ctttttttct
     4981 gcgcgtaatc tgctgcttgc aaacaaaaaa accaccgcta ccagcggtgg tttgtttgcc
     5041 ggatcaagag ctaccaactc tttttccgaa ggtaactggc ttcagcagag cgcagatacc
     5101 aaatactgtt cttctagtgt agccgtagtt aggccaccac ttcaagaact ctgtagcacc
     5161 gcctacatac ctcgctctgc taatcctgtt accagtggct gctgccagtg gcgataagtc
     5221 gtgtcttacc gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg
     5281 aacggggggt tcgtgcacac agcccagctt ggagcgaacg acctacaccg aactgagata
     5341 cctacagcgt gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta
     5401 tccggtaagc ggcagggtcg gaacaggaga gcgcacgagg gagcttccag ggggaaacgc
     5461 ctggtatctt tatagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttttgtg
     5521 atgctcgtca ggggggcgga gcctatggaa aaacgccagc aacgcggcct ttttacggtt
     5581 cctggccttt tgctggcctt ttgctcacat gttctttcct gcgttatccc ctgattctgt
     5641 ggataaccgt attaccgcct ttgagtgagc tgataccgct cgccgcagcc gaacgaccga
     5701 gcgcagcgag tcagtgagcg aggaagcgga agagcgccca atacgcaaac cgcctctccc
     5761 cgcgcgttgg ccgattcatt aatgcagctg gcacgacagg tttcccgact ggaaagcggg
     5821 cagtgagcgc aacgcaatta atgtgagtta gctcactcat taggcacccc aggctttaca
     5881 ctttatgctt ccggctcgta tgttgtgtgg aattgtgagc ggataacaat ttcacacagg
     5941 aaacagctat gaccatgatt acgccaagcg cgcaattaac cctcactaaa gggaacaaaa
     6001 gctggagctg caagcttaat gtagtcttat gcaatactct tgtagtcttg caacatggta
     6061 acgatgagtt agcaacatgc cttacaagga gagaaaaagc accgtgcatg ccgattggtg
     6121 gaagtaaggt ggtacgatcg tgccttatta ggaaggcaac agacgggtct gacatggatt
     6181 ggacgaacca ctgaattgcc gcattgcaga gatattgtat ttaagtgcct agctcgatac
     6241 ataaacgggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctaactaggg
     6301 aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt
     6361 ctgttgtgtg actctggtaa ctagagatcc ctcagaccct tttagtcagt gtggaaaatc
     6421 tctagcagtg gcgcccgaac agggacttga aagcgaaagg gaaaccagag gagctctctc
     6481 gacgcaggac tcggcttgct gaagcgcgca cggcaagagg cgaggggcgg cgactggtga
     6541 gtacgccaaa aattttgact agcggaggct agaaggagag agatgggtgc gagagcgtca
     6601 gtattaagcg ggggagaatt agatcgcgat gggaaaaaat tcggttaagg ccagggggaa
     6661 agaaaaaata taaattaaaa catatagtat gggcaagcag ggagctagaa cgattcgcag
     6721 ttaatcctgg cctgttagaa acatcagaag gctgtagaca aatactggga cagctacaac
     6781 catcccttca gacaggatca gaagaactta gatcattata taatacagta gcaaccctct
     6841 attgtgtgca tcaaaggata gagataaaag acaccaagga agctttagac aagatagagg
     6901 aagagcaaaa caaaagtaag accaccgcac agcaagcggc cgctgatctt cagacctgga
     6961 ggaggagata tgagggacaa ttggagaagt gaattatata aatataaagt agtaaaaatt
     7021 gaaccattag gagtagcacc caccaaggca aagagaagag tggtgcagag agaaaaaaga
     7081 gcagtgggaa taggagcttt gttccttggg ttcttgggag cagcaggaag cactatgggc
     7141 gcagcgtcaa tgacgctgac ggtacaggcc agacaattat tgtctggtat agtgcagcag
     7201 cagaacaatt tgctgagggc tattgaggcg caacagcatc tgttgcaact cacagtctgg
     7261 ggcatcaagc agctccaggc aagaatcctg gctgtggaaa gatacctaaa ggatcaacag
     7321 ctcctgggga tttggggttg ctctggaaaa ctcatttgca ccactgctgt gccttggaat
     7381 gctagttgga gtaataaatc tctggaacag atttggaatc acacgacctg gatggagtgg
     7441 gacagagaaa ttaacaatta cacaagctta atacactcct taattgaaga atcgcaaaac
     7501 cagcaagaaa agaatgaaca agaattattg gaattagata aatgggcaag tttgtggaat
     7561 tggtttaaca taacaaattg gctgtggtat ataaaattat tcataatgat agtaggaggc
     7621 ttggtaggtt taagaatagt ttttgctgta ctttctatag tgaatagagt taggcaggga
     7681 tattcaccat tatcgtttca gacccacctc ccaaccccga ggggaccc
//
