LOCUS       sequence-485971-        5642 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  AAV transfer plasmid expressing eGFP-S1 under a CAG promoter..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5642)
  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 5642)
  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-S1
FEATURES             Location/Qualifiers
     source          1..5642
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     11..30
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(249..353)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(379..834)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(516..537)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     728..747
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     repeat_region   906..1035
                     /label=AAV2 ITR
     primer_bind     1900..1922
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     1984..2003
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     regulatory      2036..2045
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             join(2042..2044,2045..2047,2048..2758)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     CDS             join(2042..2044,2045..2047,2048..2758)
                     /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(2087..2108)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(2348..2367)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     2695..2716
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     misc_feature    2991..3579
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3044..3064)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(3462..3473)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    3622..3743
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3633..3652)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3687..3706
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     repeat_region   3905..4034
                     /label=AAV2 ITR
     rep_origin      complement(4271..4859)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4351..4370)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5030..5642,1..179,180..248))
                     /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"
ORIGIN
        1 tcaatacggg ataataccgc gccacatagc agaactttaa aagtgctcat cattggaaaa
       61 cgttcttcgg ggcgaaaact ctcaaggatc ttaccgctgt tgagatccag ttcgatgtaa
      121 cccactcgtg cacccaactg atcttcagca tcttttactt tcaccagcgt ttctgggtga
      181 gcaaaaacag gaaggcaaaa tgccgcaaaa aagggaataa gggcgacacg gaaatgttga
      241 atactcatac tcttcctttt tcaatattat tgaagcattt atcagggtta ttgtctcatg
      301 agcggataca tatttgaatg tatttagaaa aataaacaaa taggggttcc gcgcacattt
      361 ccccgaaaag tgccacctaa attgtaagcg ttaatatttt gttaaaattc gcgttaaatt
      421 tttgttaaat cagctcattt tttaaccaat aggccgaaat cggcaaaatc ccttataaat
      481 caaaagaata gaccgagata gggttgagtg ttgttccagt ttggaacaag agtccactat
      541 taaagaacgt ggactccaac gtcaaagggc gaaaaaccgt ctatcagggc gatggcccac
      601 tacgtgaacc atcaccctaa tcaagttttt tggggtcgag gtgccgtaaa gcactaaatc
      661 ggaaccctaa agggagcccc cgatttagag cttgacgggg aaagccggcg aacgtggcga
      721 gaaaggaagg gaagaaagcg aaaggagcgg gcgctagggc gctggcaagt gtagcggtca
      781 cgctgcgcgt aaccaccaca cccgccgcgc ttaatgcgcc gctacagggc gcgtcccatt
      841 cgccattcag gctgcgcaac tgttgggaag ggcgatcggt gcgggcctct tcgctattac
      901 gccagctgcg cgctcgctcg ctcactgagg ccgcccgggc aaagcccggg cgtcgggcga
      961 cctttggtcg cccggcctca gtgagcgagc gagcgcgcag agagggagtg gccaactcca
     1021 tcactagggg ttccttgtag ttaatgatta acccgccatg ctacttatct acgtagccat
     1081 gctctaggaa gagtaccatt gacgtcaata atgacgtatg ttcccatagt aacgccaata
     1141 gggactttcc attgacgtca atgggtggag tatttacggt aaactgccca cttggcagta
     1201 catcaagtgt atcatatgcc aagtacgccc cctattgacg tcaatgacgg taaatggccc
     1261 gcctggcatt atgcccagta catgacctta tgggactttc ctacttggca gtacatctac
     1321 gtattagtca tcgctattac catggtcgag gtgagcccca cgttctgctt cactctcccc
     1381 atctcccccc cctccccacc cccaattttg tatttattta ttttttaatt attttgtgca
     1441 gcgatggggg cggggggggg gggggsgcgc gccrggsggg gsggggsggg gsgggggggg
     1501 gggsggggsg rggsggrgrg gkgcggcggc agccaatcag agcggcgcgc tccgaaagtt
     1561 tccttttatg gcgaggcggc ggcggcggcg gccctataaa aagcgaagcg cgcggcgggc
     1621 gggagtcgct gcgcgctgcc ttcgccccgt gccccgctcc gccgccgcct cgcgccgccc
     1681 gccccggctc tgactgaccg cgttactccc acaggtgagc gggcgggacg gcccttctcc
     1741 tccgggctgt aattagcgct tggtttaatg acggcttgtt tcttttctgt ggctgcgtga
     1801 aagccttgag gggctccggg agggcccttt gtgcgggggg agcggctcgg ggctgtccgc
     1861 ggggggacgg ctgccttcgg gggggacggg gcagggcggg gttcggcttc tggcgtgtga
     1921 ccggcggctc tagagcctct gctaaccatg ttcatgcctt cttctttttc ctacagctcc
     1981 tgggcaacgt gctggttatt gtgctgtctc atcattttgg caaagaattg gatccgccac
     2041 catggtgagc aagggcgagg agctgttcac cggggtggtg cccatcctgg tcgagctgga
     2101 cggcgacgta aacggccaca agttcagcgt gtccggcgag ggcgagggcg atgccaccta
     2161 cggcaagctg accctgaagt tcatttgcac caccggcaag ctgcccgtgc cctggcccac
     2221 cctcgtgacc accctgacct acggcgtgca gtgcttcagc cgctaccccg accacatgaa
     2281 gcagcacgac ttcttcaagt ccgccatgcc cgaaggctac gtccaggagc gcaccatctt
     2341 cttcaaggac gacggcaact acaagacccg cgccgaggtg aagttcgagg gcgacaccct
     2401 ggtgaaccgc atcgagctga agggcatcga cttcaaggag gacggcaaca tcctggggca
     2461 caagctggag tacaactaca acagccacaa cgtctatatc atggccgaca agcagaagaa
     2521 cggcatcaag gtgaacttca agatccgcca caacatcgag gacggcagcg tgcagctcgc
     2581 cgaccactac cagcagaaca cccccatcgg cgacggcccc gtgctgctgc ccgacaacca
     2641 ctacctgagc acccagtccg ccctgagcaa agaccccaac gagaagcgcg atcacatggt
     2701 cctgctggag ttcgtgaccg ccgccgggat cactctcggc atggacgagc tgtacaaggg
     2761 tggctccggt ggctctaatg caaacaatcc tgattgggat tttggaggat caggcgggag
     2821 taacgcaaat aatcccgatt gggactttgg cggctctggg ggatcaaacg ctaacaaccc
     2881 cgactgggac ttttaagaat tcttcagtag gactggtgtt tatcgggcgt ggtgctcgca
     2941 taccaggtca agcttatcga taatcagaat tcgatatcaa gcttatcgat aatcaacctc
     3001 tggattacaa aatttgtgaa agattgactg gtattcttaa ctatgttgct ccttttacgc
     3061 tatgtggata cgctgcttta atgcctttgt atcatgctat tgcttcccgt atggctttca
     3121 ttttctcctc cttgtataaa tcctggttgc tgtctcttta tgaggagttg tggcccgttg
     3181 tcaggcaacg tggcgtggtg tgcactgtgt ttgctgacgc aacccccact ggttggggca
     3241 ttgccaccac ctgtcagctc ctttccggga ctttcgcttt ccccctccct attgccacgg
     3301 cggaactcat cgccgcctgc cttgcccgct gctggacagg ggctcggctg ttgggcactg
     3361 acaattccgt ggtgttgtcg gggaaatcat cgtcctttcc ttggctgctc gcctgtgttg
     3421 ccacctggat tctgcgcggg acgtccttct gctacgtccc ttcggccctc aatccagcgg
     3481 accttccttc ccgcggcctg ctgccggctc tgcggcctct tccgcgtctt cgccttcgcc
     3541 ctcagacgag tcggatctcc ctttgggccg cctccccgca tcgataccgt cgacccgggc
     3601 ggccgcttcg agcagacatg ataagataca ttgatgagtt tggacaaacc acaactagaa
     3661 tgcagtgaaa aaaatgcttt atttgtgaaa tttgtgatgc tattgcttta tttgtaacca
     3721 ttataagctg caataaacaa gttaacaaca acaattgcat tcattttatg tttcaggttc
     3781 agggggagat gtgggaggtt ttttaaagca agtaaaacct ctacaaatgt ggtaaaatcg
     3841 ataaggatct tcctagagca tggctacgta gataagtagc atggcgggtt aatcattaac
     3901 tacaaggaac ccctagtgat ggagttggcc actccctctc tgcgcgctcg ctcgctcact
     3961 gaggccgggc gaccaaaggt cgcccgacgc ccgggctttg cccgggcggc ctcagtgagc
     4021 gagcgagcgc gcagctgcat taatgaatcg gccaacgcgc ggggagaggc ggtttgcgta
     4081 ttgggcgctc ttccgcttcc tcgctcactg actcgctgcg ctcggtcgtt cggctgcggc
     4141 gagcggtatc agctcactca aaggcggtaa tacggttatc cacagaatca ggggataacg
     4201 caggaaagaa catgtgagca aaaggccagc aaaaggccag gaaccgtaaa aaggccgcgt
     4261 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgacgctcaa
     4321 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct
     4381 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc
     4441 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg
     4501 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct
     4561 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag
     4621 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga
     4681 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga
     4741 agccagttac cttcggaaaa agagttggta gctcttgatc cggcaaacaa accaccgctg
     4801 gtagcggtgg tttttttgtt tgcaagcagc agattacgcg cagaaaaaaa ggatctcaag
     4861 aagatccttt gatcttttct acggggtctg acgctcagtg gaacgaaaac tcacgttaag
     4921 ggattttggt catgagatta tcaaaaagga tcttcaccta gatcctttta aattaaaaat
     4981 gaagttttaa atcaatctaa agtatatatg agtaaacttg gtctgacagt taccaatgct
     5041 taatcagtga ggcacctatc tcagcgatct gtctatttcg ttcatccata gttgcctgac
     5101 tccccgtcgt gtagataact acgatacggg agggcttacc atctggcccc agtgctgcaa
     5161 tgataccgcg agacccacgc tcaccggctc cagatttatc agcaataaac cagccagccg
     5221 gaagggccga gcgcagaagt ggtcctgcaa ctttatccgc ctccatccag tctattaatt
     5281 gttgccggga agctagagta agtagttcgc cagttaatag tttgcgcaac gttgttgcca
     5341 ttgctacagg catcgtggtg tcacgctcgt cgtttggtat ggcttcattc agctccggtt
     5401 cccaacgatc aaggcgagtt acatgatccc ccatgttgtg caaaaaagcg gttagctcct
     5461 tcggtcctcc gatcgttgtc agaagtaagt tggccgcagt gttatcactc atggttatgg
     5521 cagcactgca taattctctt actgtcatgc catccgtaag atgcttttct gtgactggtg
     5581 agtactcaac caagtcattc tgagaatagt gtatgcggcg accgagttgc tcttgcccgg
     5641 cg
//
