LOCUS       sequence-486029-        5652 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  AAV transfer plasmid expressing eGFP-TY1 under a CAG promoter..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5652)
  AUTHORS   Park SY, Sheridan A, An B, Jarvis E, Lyudchik J, Patton W, Axup JY, 
            Chan SW, Damstra HGJ, Leible D, Leung KS, Magno CA, Meeran A, 
            Michalska JM, Rieger F, Wang C, Wu M, Church GM, Funke J, Huffman T,
            Leeper KGC, Truckenbrodt S, Winnubst J, Kornfeld JMR, Boyden ES, 
            Rodriques SG, Payne AC
  TITLE     Combinatorial protein barcodes enable self-correcting neuron tracing
            with nanoscale molecular context
  JOURNAL   bioRxiv 2025.09.26.678648
REFERENCE   2  (bases 1 to 5652)
  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: "bioRxiv 
            2025.09.26.678648"
COMMENT     Sequence Label: pAAV-CAG-eGFP-TY1
FEATURES             Location/Qualifiers
     source          1..5652
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             complement(join(27..818,819..887))
                     /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     650..669
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(888..992)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(1018..1473)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1155..1176)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     1367..1386
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     repeat_region   1545..1674
                     /label=AAV2 ITR
     promoter        1985..2261
                     /label=chicken beta-actin promoter
     primer_bind     2540..2562
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     2624..2643
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     regulatory      2676..2685
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             join(2682..2684,2685..2687,2688..3398)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     CDS             join(2682..2684,2685..2687,2688..3398)
                     /codon_start=1
                     /product="the original enhanced GFP (Yang et al., 1996)"
                     /label=EGFP
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(2727..2748)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(2988..3007)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     3335..3356
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     misc_feature    3640..4228
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3693..3713)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4111..4122)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    4271..4392
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4282..4301)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     4336..4355
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     repeat_region   4554..4683
                     /label=AAV2 ITR
     rep_origin      complement(4920..5508)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5000..5019)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 atatatgagt aaacttggtc tgacagttac caatgcttaa tcagtgaggc acctatctca
       61 gcgatctgtc tatttcgttc atccatagtt gcctgactcc ccgtcgtgta gataactacg
      121 atacgggagg gcttaccatc tggccccagt gctgcaatga taccgcgaga cccacgctca
      181 ccggctccag atttatcagc aataaaccag ccagccggaa gggccgagcg cagaagtggt
      241 cctgcaactt tatccgcctc catccagtct attaattgtt gccgggaagc tagagtaagt
      301 agttcgccag ttaatagttt gcgcaacgtt gttgccattg ctacaggcat cgtggtgtca
      361 cgctcgtcgt ttggtatggc ttcattcagc tccggttccc aacgatcaag gcgagttaca
      421 tgatccccca tgttgtgcaa aaaagcggtt agctccttcg gtcctccgat cgttgtcaga
      481 agtaagttgg ccgcagtgtt atcactcatg gttatggcag cactgcataa ttctcttact
      541 gtcatgccat ccgtaagatg cttttctgtg actggtgagt actcaaccaa gtcattctga
      601 gaatagtgta tgcggcgacc gagttgctct tgcccggcgt caatacggga taataccgcg
      661 ccacatagca gaactttaaa agtgctcatc attggaaaac gttcttcggg gcgaaaactc
      721 tcaaggatct taccgctgtt gagatccagt tcgatgtaac ccactcgtgc acccaactga
      781 tcttcagcat cttttacttt caccagcgtt tctgggtgag caaaaacagg aaggcaaaat
      841 gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa tactcatact cttccttttt
      901 caatattatt gaagcattta tcagggttat tgtctcatga gcggatacat atttgaatgt
      961 atttagaaaa ataaacaaat aggggttccg cgcacatttc cccgaaaagt gccacctaaa
     1021 ttgtaagcgt taatattttg ttaaaattcg cgttaaattt ttgttaaatc agctcatttt
     1081 ttaaccaata ggccgaaatc ggcaaaatcc cttataaatc aaaagaatag accgagatag
     1141 ggttgagtgt tgttccagtt tggaacaaga gtccactatt aaagaacgtg gactccaacg
     1201 tcaaagggcg aaaaaccgtc tatcagggcg atggcccact acgtgaacca tcaccctaat
     1261 caagtttttt ggggtcgagg tgccgtaaag cactaaatcg gaaccctaaa gggagccccc
     1321 gatttagagc ttgacgggga aagccggcga acgtggcgag aaaggaaggg aagaaagcga
     1381 aaggagcggg cgctagggcg ctggcaagtg tagcggtcac gctgcgcgta accaccacac
     1441 ccgccgcgct taatgcgccg ctacagggcg cgtcccattc gccattcagg ctgcgcaact
     1501 gttgggaagg gcgatcggtg cgggcctctt cgctattacg ccagctgcgc gctcgctcgc
     1561 tcactgaggc cgcccgggca aagcccgggc gtcgggcgac ctttggtcgc ccggcctcag
     1621 tgagcgagcg agcgcgcaga gagggagtgg ccaactccat cactaggggt tccttgtagt
     1681 taatgattaa cccgccatgc tacttatcta cgtagccatg ctctaggaag agtaccattg
     1741 acgtcaataa tgacgtatgt tcccatagta acgccaatag ggactttcca ttgacgtcaa
     1801 tgggtggagt atttacggta aactgcccac ttggcagtac atcaagtgta tcatatgcca
     1861 agtacgcccc ctattgacgt caatgacggt aaatggcccg cctggcatta tgcccagtac
     1921 atgaccttat gggactttcc tacttggcag tacatctacg tattagtcat cgctattacc
     1981 atggtcgagg tgagccccac gttctgcttc actctcccca tctccccccc ctccccaccc
     2041 ccaattttgt atttatttat tttttaatta ttttgtgcag cgatgggggc gggggggggg
     2101 gggggcgcgc gccaggcggg gcggggcggg gcgaggggcg gggcggggcg aggcggagag
     2161 gtgcggcggc agccaatcag agcggcgcgc tccgaaagtt tccttttatg gcgaggcggc
     2221 ggcggcggcg gccctataaa aagcgaagcg cgcggcgggc gggagtcgct gcgcgctgcc
     2281 ttcgccccgt gccccgctcc gccgccgcct cgcgccgccc gccccggctc tgactgaccg
     2341 cgttactccc acaggtgagc gggcgggacg gcccttctcc tccgggctgt aattagcgct
     2401 tggtttaatg acggcttgtt tcttttctgt ggctgcgtga aagccttgag gggctccggg
     2461 agggcccttt gtgcgggggg agcggctcgg ggctgtccgc ggggggacgg ctgccttcgg
     2521 gggggacggg gcagggcggg gttcggcttc tggcgtgtga ccggcggctc tagagcctct
     2581 gctaaccatg ttcatgcctt cttctttttc ctacagctcc tgggcaacgt gctggttatt
     2641 gtgctgtctc atcattttgg caaagaattg gatccgccac catggtgagc aagggcgagg
     2701 agctgttcac cggggtggtg cccatcctgg tcgagctgga cggcgacgta aacggccaca
     2761 agttcagcgt gtccggcgag ggcgagggcg atgccaccta cggcaagctg accctgaagt
     2821 tcatttgcac caccggcaag ctgcccgtgc cctggcccac cctcgtgacc accctgacct
     2881 acggcgtgca gtgcttcagc cgctaccccg accacatgaa gcagcacgac ttcttcaagt
     2941 ccgccatgcc cgaaggctac gtccaggagc gcaccatctt cttcaaggac gacggcaact
     3001 acaagacccg cgccgaggtg aagttcgagg gcgacaccct ggtgaaccgc atcgagctga
     3061 agggcatcga cttcaaggag gacggcaaca tcctggggca caagctggag tacaactaca
     3121 acagccacaa cgtctatatc atggccgaca agcagaagaa cggcatcaag gtgaacttca
     3181 agatccgcca caacatcgag gacggcagcg tgcagctcgc cgaccactac cagcagaaca
     3241 cccccatcgg cgacggcccc gtgctgctgc ccgacaacca ctacctgagc acccagtccg
     3301 ccctgagcaa agaccccaac gagaagcgcg atcacatggt cctgctggag ttcgtgaccg
     3361 ccgccgggat cactctcggc atggacgagc tgtacaaggg tggtagcgga ggatcagagg
     3421 ttcatactaa ccaagaccca ttggacgggg ggtccggtgg atctgaagtg catacaaacc
     3481 aggaccctct cgatggtggc agcggcggct cagaagtaca tactaatcag gatccccttg
     3541 attaagaatt cttcagtagg actggtccga tgttgacgga ctaatcctga cccaggtcaa
     3601 gcttatcgat aatcagaatt cgatatcaag cttatcgata atcaacctct ggattacaaa
     3661 atttgtgaaa gattgactgg tattcttaac tatgttgctc cttttacgct atgtggatac
     3721 gctgctttaa tgcctttgta tcatgctatt gcttcccgta tggctttcat tttctcctcc
     3781 ttgtataaat cctggttgct gtctctttat gaggagttgt ggcccgttgt caggcaacgt
     3841 ggcgtggtgt gcactgtgtt tgctgacgca acccccactg gttggggcat tgccaccacc
     3901 tgtcagctcc tttccgggac tttcgctttc cccctcccta ttgccacggc ggaactcatc
     3961 gccgcctgcc ttgcccgctg ctggacaggg gctcggctgt tgggcactga caattccgtg
     4021 gtgttgtcgg ggaaatcatc gtcctttcct tggctgctcg cctgtgttgc cacctggatt
     4081 ctgcgcggga cgtccttctg ctacgtccct tcggccctca atccagcgga ccttccttcc
     4141 cgcggcctgc tgccggctct gcggcctctt ccgcgtcttc gccttcgccc tcagacgagt
     4201 cggatctccc tttgggccgc ctccccgcat cgataccgtc gacccgggcg gccgcttcga
     4261 gcagacatga taagatacat tgatgagttt ggacaaacca caactagaat gcagtgaaaa
     4321 aaatgcttta tttgtgaaat ttgtgatgct attgctttat ttgtaaccat tataagctgc
     4381 aataaacaag ttaacaacaa caattgcatt cattttatgt ttcaggttca gggggagatg
     4441 tgggaggttt tttaaagcaa gtaaaacctc tacaaatgtg gtaaaatcga taaggatctt
     4501 cctagagcat ggctacgtag ataagtagca tggcgggtta atcattaact acaaggaacc
     4561 cctagtgatg gagttggcca ctccctctct gcgcgctcgc tcgctcactg aggccgggcg
     4621 accaaaggtc gcccgacgcc cgggctttgc ccgggcggcc tcagtgagcg agcgagcgcg
     4681 cagctgcatt aatgaatcgg ccaacgcgcg gggagaggcg gtttgcgtat tgggcgctct
     4741 tccgcttcct cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg agcggtatca
     4801 gctcactcaa aggcggtaat acggttatcc acagaatcag gggataacgc aggaaagaac
     4861 atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa aggccgcgtt gctggcgttt
     4921 ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg
     4981 cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc
     5041 tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc
     5101 gtggcgcttt ctcatagctc acgctgtagg tatctcagtt cggtgtaggt cgttcgctcc
     5161 aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac
     5221 tatcgtcttg agtccaaccc ggtaagacac gacttatcgc cactggcagc agccactggt
     5281 aacaggatta gcagagcgag gtatgtaggc ggtgctacag agttcttgaa gtggtggcct
     5341 aactacggct acactagaag aacagtattt ggtatctgcg ctctgctgaa gccagttacc
     5401 ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg tagcggtggt
     5461 ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga agatcctttg
     5521 atcttttcta cggggtctga cgctcagtgg aacgaaaact cacgttaagg gattttggtc
     5581 atgagattat caaaaaggat cttcacctag atccttttaa attaaaaatg aagttttaaa
     5641 tcaatctaaa gt
//
