LOCUS       sequence-162239-        6445 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Cre-dependent AAV-mediated expression of tdTomato under the CAG 
            promoter.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6445)
  TITLE     Accessory plasmids for optogenetics
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6445)
  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: 
            "Unpublished"
COMMENT     Sequence Label: pAAV-FLEX-tdTomato
FEATURES             Location/Qualifiers
     source          1..6445
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     repeat_region   4..133
                     /label=AAV2 ITR
     polyA_signal    295..416
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(332..351)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     386..405
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     misc_feature    459..1047
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     CDS             565..576
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     primer_bind     974..994
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     protein_bind    1089..1122
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     protein_bind    1193..1226
                     /label=lox2272
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (AAGTATCC) (Shaw et al., 2021). lox2272 sites are 
                     compatible with each other, but incompatible with loxP or 
                     loxN sites (Lee and Saito, 1988)."
     regulatory      1243..1252
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             1249..2679
                     /codon_start=1
                     /product="tandem dimeric (pseudo-monomeric) derivative of 
                     DsRed (Shaner et al., 2004)"
                     /label=tdTomato
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEEVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYEGTQTA
                     KLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMNFEDGG
                     LVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVLKGEIH
                     QALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYERSEGRH
                     HLFLGHGTGSTGSGSSGTASSGDNNMAVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPY
                     EGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVM
                     NFEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGV
                     LKGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYE
                     RSEGRHHLFLYGMDELYK"
     protein_bind    complement(2693..2726)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     protein_bind    complement(2789..2822)
                     /label=lox2272
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (AAGTATCC) (Shaw et al., 2021). lox2272 sites are 
                     compatible with each other, but incompatible with loxP or 
                     loxN sites (Lee and Saito, 1988)."
     primer_bind     complement(2857..2876)
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     primer_bind     complement(2938..2960)
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     promoter        complement(3239..3495)
                     /label=chicken beta-actin promoter
                     /note="contains a 21-bp deletion relative to the standard 
                     chicken beta-actin promoter"
     repeat_region   3806..3935
                     /label=AAV2 ITR
     rep_origin      4007..4462
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(4094..4113)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4304..4325
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        4488..4592
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(4593..4661,4662..5453)
                     /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(4811..4830)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      5624..6212
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6113..6132
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 cagctgcgcg ctcgctcgct cactgaggcc gcccgggcaa agcccgggcg tcgggcgacc
       61 tttggtcgcc cggcctcagt gagcgagcga gcgcgcagag agggagtggc caactccatc
      121 actaggggtt ccttgtagtt aatgattaac ccgccatgct acttatctac gtagccatgc
      181 tctaggaaga tccttatcga ttttaccaca tttgtagagg ttttacttgc tttaaaaaac
      241 ctcccacatc tccccctgaa cctgaaacat aaaatgaatg caattgttgt tgttaacttg
      301 tttattgcag cttataatgg ttacaaataa agcaatagca tcacaaattt cacaaataaa
      361 gcattttttt cactgcattc tagttgtggt ttgtccaaac tcatcaatgt atcttatcat
      421 gtctgctcga agcggccgcc cgggtcgacg gtatcgatgc ggggaggcgg cccaaaggga
      481 gatccgactc gtctgagggc gaaggcgaag acgcggaaga ggccgcagag ccggcagcag
      541 gccgcgggaa ggaaggtccg ctggattgag ggccgaaggg acgtagcaga aggacgtccc
      601 gcgcagaatc caggtggcaa cacaggcgag cagccaagga aaggacgatg atttccccga
      661 caacaccacg gaattgtcag tgcccaacag ccgagcccct gtccagcagc gggcaaggca
      721 ggcggcgatg agttccgccg tggcaatagg gagggggaaa gcgaaagtcc cggaaaggag
      781 ctgacaggtg gtggcaatgc cccaaccagt gggggttgcg tcagcaaaca cagtgcacac
      841 cacgccacgt tgcctgacaa cgggccacaa ctcctcataa agagacagca accaggattt
      901 atacaaggag gagaaaatga aagccatacg ggaagcaata gcatgataca aaggcattaa
      961 agcagcgtat ccacatagcg taaaaggagc aacatagtta agaataccag tcaatctttc
     1021 acaaattttg taatccagag gttgattatc gataagcttg atatcgaatt cgaacctctt
     1081 cgagggacat aacttcgtat aatgtatgct atacgaagtt atgggtcgat ggtgagatct
     1141 ggactagagg gtcgatggtg atgcttggat caaaatagga agaatcccaa tgataacttc
     1201 gtataaagta tcctatacga agttatacta gaattcggta ccgccaccat ggtgagcaag
     1261 ggcgaggagg tcatcaaaga gttcatgcgc ttcaaggtgc gcatggaggg ctccatgaac
     1321 ggccacgagt tcgagatcga gggcgagggc gagggccgcc cctacgaggg cacccagacc
     1381 gccaagctga aggtgaccaa gggcggcccc ctgcccttcg cctgggacat cctgtccccc
     1441 cagttcatgt acggctccaa ggcgtacgtg aagcaccccg ccgacatccc cgattacaag
     1501 aagctgtcct tccccgaggg cttcaagtgg gagcgcgtga tgaacttcga ggacggcggt
     1561 ctggtgaccg tgacccagga ctcctccctg caggacggca cgctgatcta caaggtgaag
     1621 atgcgcggca ccaacttccc ccccgacggc cccgtaatgc agaagaagac catgggctgg
     1681 gaggcctcca ccgagcgcct gtacccccgc gacggcgtgc tgaagggcga gatccaccag
     1741 gccctgaagc tgaaggacgg cggccactac ctggtggagt tcaagaccat ctacatggcc
     1801 aagaagcccg tgcaactgcc cggctactac tacgtggaca ccaagctgga catcacctcc
     1861 cacaacgagg actacaccat cgtggaacag tacgagcgct ccgagggccg ccaccacctg
     1921 ttcctggggc atggcaccgg cagcaccggc agcggcagct ccggcaccgc ctcctccggg
     1981 gacaacaaca tggccgtcat caaagagttc atgcgcttca aggtgcgcat ggagggctcc
     2041 atgaacggcc acgagttcga gatcgagggc gagggcgagg gccgccccta cgagggcacc
     2101 cagaccgcca agctgaaggt gaccaagggc ggccccctgc ccttcgcctg ggacatcctg
     2161 tccccccagt tcatgtacgg ctccaaggcg tacgtgaagc accccgccga catccccgat
     2221 tacaagaagc tgtccttccc cgagggcttc aagtgggagc gcgtgatgaa cttcgaggac
     2281 ggcggtctgg tgaccgtgac ccaggactcc tccctgcagg acggcacgct gatctacaag
     2341 gtgaagatgc gcggcaccaa cttccccccc gacggccccg taatgcagaa gaagaccatg
     2401 ggctgggagg cctccaccga gcgcctgtac ccccgcgacg gcgtgctgaa gggcgagatc
     2461 caccaggccc tgaagctgaa ggacggcggc cactacctgg tggagttcaa gaccatctac
     2521 atggccaaga agcccgtgca actgcccggc tactactacg tggacaccaa gctggacatc
     2581 acctcccaca acgaggacta caccatcgtg gaacagtacg agcgctccga gggccgccac
     2641 cacctgttcc tgtacggcat ggacgagctg tacaagtaag gggatcccta gtataacttc
     2701 gtatagcata cattatacga agttatgggt cgatggtgat gcttggcaat tcgggtcgat
     2761 ggtgaagcat tggtcttcct attttgatat aacttcgtat aggatacttt atacgaagtt
     2821 atggggatcc aattctttgc caaaatgatg agacagcaca ataaccagca cgttgcccag
     2881 gagctgtagg aaaaagaaga aggcatgaac atggttagca gaggctctag agccgccggt
     2941 cacacgccag aagccgaacc ccgccctgcc ccgtcccccc cgaaggcagc cgtccccccg
     3001 cggacagccc cgagccgctc cccccgcaca aagggccctc ccggagcccc tcaaggcttt
     3061 cacgcagcca cagaaaagaa acaagccgtc attaaaccaa gcgctaatta cagcccggag
     3121 gagaagggcc gtcccgcccg ctcacctgtg ggagtaacgc ggtcagtcag agccggggcg
     3181 ggcggcgcga ggcggcggcg gagcggggca cggggcgaag gcagcgcgca gcgactcccg
     3241 cccgccgcgc gcttcgcttt ttatagggcc gccgccgccg ccgcctcgcc ataaaaggaa
     3301 actttcggag cgcgccgctc tgattggctg ccgccgcacc tctccgcctc gccccgcccc
     3361 gcccctcgcc ccgccccccc cccccccccg cccccatcgc tgcacaaaat aattaaaaaa
     3421 taaataaata caaaattggg ggtggggagg ggggggagat ggggagagtg aagcagaacg
     3481 tggggctcac ctcgaccatg gtaatagcga tgactaatac gtagatgtac tgccaagtag
     3541 gaaagtccca taaggtcatg tactgggcat aatgccaggc gggccattta ccgtcattga
     3601 cgtcaatagg gggcgtactt ggcatatgat acacttgatg tactgccaag tgggcagttt
     3661 accgtaaata ctccacccat tgacgtcaat ggaaagtccc tattggcgtt actatgggaa
     3721 catacgtcat tattgacgtc aatggtactc ttcctagagc atggctacgt agataagtag
     3781 catggcgggt taatcattaa ctacaaggaa cccctagtga tggagttggc cactccctct
     3841 ctgcgcgctc gctcgctcac tgaggccggg cgaccaaagg tcgcccgacg cccgggcttt
     3901 gcccgggcgg cctcagtgag cgagcgagcg cgcagctggc gtaatagcga agaggcccgc
     3961 accgatcgcc cttcccaaca gttgcgcagc ctgaatggcg aatgggacgc gccctgtagc
     4021 ggcgcattaa gcgcggcggg tgtggtggtt acgcgcagcg tgaccgctac acttgccagc
     4081 gccctagcgc ccgctccttt cgctttcttc ccttcctttc tcgccacgtt cgccggcttt
     4141 ccccgtcaag ctctaaatcg ggggctccct ttagggttcc gatttagtgc tttacggcac
     4201 ctcgacccca aaaaacttga ttagggtgat ggttcacgta gtgggccatc gccctgatag
     4261 acggtttttc gccctttgac gttggagtcc acgttcttta atagtggact cttgttccaa
     4321 actggaacaa cactcaaccc tatctcggtc tattcttttg atttataagg gattttgccg
     4381 atttcggcct attggttaaa aaatgagctg atttaacaaa aatttaacgc gaattttaac
     4441 aaaatattaa cgcttacaat ttaggtggca cttttcgggg aaatgtgcgc ggaaccccta
     4501 tttgtttatt tttctaaata cattcaaata tgtatccgct catgagacaa taaccctgat
     4561 aaatgcttca ataatattga aaaaggaaga gtatgagtat tcaacatttc cgtgtcgccc
     4621 ttattccctt ttttgcggca ttttgccttc ctgtttttgc tcacccagaa acgctggtga
     4681 aagtaaaaga tgctgaagat cagttgggtg cacgagtggg ttacatcgaa ctggatctca
     4741 acagcggtaa gatccttgag agttttcgcc ccgaagaacg ttttccaatg atgagcactt
     4801 ttaaagttct gctatgtggc gcggtattat cccgtattga cgccgggcaa gagcaactcg
     4861 gtcgccgcat acactattct cagaatgact tggttgagta ctcaccagtc acagaaaagc
     4921 atcttacgga tggcatgaca gtaagagaat tatgcagtgc tgccataacc atgagtgata
     4981 acactgcggc caacttactt ctgacaacga tcggaggacc gaaggagcta accgcttttt
     5041 tgcacaacat gggggatcat gtaactcgcc ttgatcgttg ggaaccggag ctgaatgaag
     5101 ccataccaaa cgacgagcgt gacaccacga tgcctgtagc aatggcaaca acgttgcgca
     5161 aactattaac tggcgaacta cttactctag cttcccggca acaattaata gactggatgg
     5221 aggcggataa agttgcagga ccacttctgc gctcggccct tccggctggc tggtttattg
     5281 ctgataaatc tggagccggt gagcgtgggt ctcgcggtat cattgcagca ctggggccag
     5341 atggtaagcc ctcccgtatc gtagttatct acacgacggg gagtcaggca actatggatg
     5401 aacgaaatag acagatcgct gagataggtg cctcactgat taagcattgg taactgtcag
     5461 accaagttta ctcatatata ctttagattg atttaaaact tcatttttaa tttaaaagga
     5521 tctaggtgaa gatccttttt gataatctca tgaccaaaat cccttaacgt gagttttcgt
     5581 tccactgagc gtcagacccc gtagaaaaga tcaaaggatc ttcttgagat cctttttttc
     5641 tgcgcgtaat ctgctgcttg caaacaaaaa aaccaccgct accagcggtg gtttgtttgc
     5701 cggatcaaga gctaccaact ctttttccga aggtaactgg cttcagcaga gcgcagatac
     5761 caaatactgt tcttctagtg tagccgtagt taggccacca cttcaagaac tctgtagcac
     5821 cgcctacata cctcgctctg ctaatcctgt taccagtggc tgctgccagt ggcgataagt
     5881 cgtgtcttac cgggttggac tcaagacgat agttaccgga taaggcgcag cggtcgggct
     5941 gaacgggggg ttcgtgcaca cagcccagct tggagcgaac gacctacacc gaactgagat
     6001 acctacagcg tgagctatga gaaagcgcca cgcttcccga agggagaaag gcggacaggt
     6061 atccggtaag cggcagggtc ggaacaggag agcgcacgag ggagcttcca gggggaaacg
     6121 cctggtatct ttatagtcct gtcgggtttc gccacctctg acttgagcgt cgatttttgt
     6181 gatgctcgtc aggggggcgg agcctatgga aaaacgccag caacgcggcc tttttacggt
     6241 tcctggcctt ttgctggcct tttgctcaca tgttctttcc tgcgttatcc cctgattctg
     6301 tggataaccg tattaccgcc tttgagtgag ctgataccgc tcgccgcagc cgaacgaccg
     6361 agcgcagcga gtcagtgagc gaggaagcgg aagagcgccc aatacgcaaa ccgcctctcc
     6421 ccgcgcgttg gccgattcat taatg
//
