LOCUS       sequence-459710-        5188 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Single stranded AAV genome with concatemerization-dependent 
            barcodes, for tracking AAV concatemers via SpECTr. Also expresses 
            TagBFP from SCP1 promoter and CMV enhancer..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5188)
  AUTHORS   Coughlin GM, Borsos M, Barcelona BH, Appling N, Mayfield AMH, Mackey
            ED, Eser RA, Jackson CR, Chen X, Kumar SR, Gradinaru V
  TITLE     Spatial genomics of AAV vectors reveals mechanism of transcriptional
            crosstalk that enables targeted delivery of large genetic cargo.
  JOURNAL   Nat Biotechnol. 2025 Mar 20. doi: 10.1038/s41587-025-02565-4.
  PUBMED    40113953
REFERENCE   2  (bases 1 to 5188)
  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 
            Biotechnol. 2025 Mar 20. doi: 10.1038/s41587-025-02565-4."
COMMENT     Sequence Label: pAAV.BC(p1-10)-CMVe-SCP1-TagBFP2-W3SL-BC(p1-10)
FEATURES             Location/Qualifiers
     source          1..5188
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(5..27)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     127..146
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     rep_origin      complement(163..618)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(300..321)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     512..531
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     repeat_region   693..833
                     /label=AAV2 ITR
                     /note="inverted terminal repeat of adeno-associated virus 
                     serotype 2"
     repeat_region   704..833
                     /label=AAV2 ITR
     enhancer        1118..1497
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     intron          1583..1715
                     /label=chimeric intron
                     /note="chimera between introns from human beta-globin and 
                     immunoglobulin heavy chain genes"
     CDS             1728..2429
                     /codon_start=1
                     /product="monomeric blue fluorescent protein"
                     /label=TagBFP
                     /note="mammalian codon-optimized"
                     /translation="MSELIKENMHMKLYMEGTVDNHHFKCTSEGEGKPYEGTQTMRIKV
                     VEGGPLPFAFDILATSFLYGSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTA
                     TQDTSLQDGCLIYNVKIRGVNFTSNGPVMQKKTLGWEAFTETLYPADGGLEGRNDMALK
                     LVGGSHLIANAKTTYRSKKPAKNLKMPGVYYVDYRLERIKEANNETYVEQHEVAVARYC
                     DLPSKLGHKLN"
     primer_bind     complement(2491..2511)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     repeat_region   3143..3283
                     /label=AAV2 ITR
                     /note="inverted terminal repeat of adeno-associated virus 
                     serotype 2"
     repeat_region   3143..3272
                     /label=AAV2 ITR
     rep_origin      complement(3345..3933)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3425..3444)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4104..4895,4896..4964))
                     /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     4727..4746
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(4965..5069)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     5137..5155
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
ORIGIN
        1 aaaacctctg acacatgcag ctcccggaga cggtcacagc ttgtctgtaa gcggatgccg
       61 ggagcagaca agcccgtcag ggcgcgtcag cgggtgttgg cgggtgtcgg ggctggctta
      121 actatgcggc atcagagcag attgtactga gagtgcacca taaaattgta aacgttaata
      181 ttttgttaaa attcgcgtta aatttttgtt aaatcagctc attttttaac caatagaccg
      241 aaatcggcaa aatcccttat aaatcaaaag aatagcccga gatagagttg agtgttgttc
      301 cagtttggaa caagagtcca ctattaaaga acgtggactc caacgtcaaa gggcgaaaaa
      361 ccgtctatca gggcgatggc ccactacgtg aaccatcacc caaatcaagt tttttggggt
      421 cgaggtgccg taaagcacta aatcggaacc ctaaagggag cccccgattt agagcttgac
      481 ggggaaagcc ggcgaacgtg gcgagaaagg aagggaagaa agcgaaagga gcgggcgcta
      541 aggcgctggc aagtgtagcg gtcacgctgc gcgtaaccac cacacccgcc gcgcttaatg
      601 cgccgctaca gggcgcgtac tatggttgct ttgacgtatg cggtgtgaaa taccgcacag
      661 atgcgtaagg agaaaatacc gcatcaggcg cccctgcagg cagctgcgcg ctcgctcgct
      721 cactgaggcc gcccgggcaa agcccgggcg tcgggcgacc tttggtcgcc cggcctcagt
      781 gagcgagcga gcgcgcagag agggagtggc caactccatc actaggggtt cctgctgaca
      841 ggaggattct ctcatcactg aaacaaaaga agctgttcca atccacgaac ccgaacctga
      901 atcactttct ttgaattttt tgcgactggt gttcaagctg aatttaagtt cccggtatta
      961 gacaaattcc tggccatgcc ttttatttta gaatgacgac atttccgcct tgtaccttat
     1021 tctgggttgt ttcacaagtg gggttattac accatgtgat atgccaacgt caattcttgc
     1081 tgtgtacctg catggtaatg tgatgggccg cctcgaggac attgattatt gactagttat
     1141 taatagtaat caattacggg gtcattagtt catagcccat atatggagtt ccgcgttaca
     1201 taacttacgg taaatggccc gcctggctga ccgcccaacg acccccgccc attgacgtca
     1261 ataatgacgt atgttcccat agtaacgcca atagggactt tccattgacg tcaatgggtg
     1321 gagtatttac ggtaaactgc ccacttggca gtacatcaag tgtatcatat gccaagtacg
     1381 ccccctattg acgtcaatga cggtaaatgg cccgcctggc attatgccca gtacatgacc
     1441 ttatgggact ttcctacttg gcagtacatc tacgtattag tcatcgctat taccatggta
     1501 cttatataag ggggtggggg cgcgttcgtc ctcagtcgcg atcgaacact cgagccgagc
     1561 agacgtgcct acggaccgac aggtaagtat caaggttaca agacaggttt aaggagacca
     1621 atagaaactg ggcttgtcga gacagagaag actcttgcgt ttctgatagg cacctattgg
     1681 tcttactgac atccactttg cctttctctc cacagaccgg tgccaccatg agcgagctga
     1741 ttaaggagaa catgcacatg aagctgtaca tggagggcac cgtggacaac catcacttca
     1801 agtgcacatc cgagggcgaa ggcaagccct acgagggcac ccagaccatg agaatcaagg
     1861 tggtcgaggg cggccctctc cccttcgcct tcgacatcct ggctactagc ttcctctacg
     1921 gcagcaagac cttcatcaac cacacccagg gcatccccga cttcttcaag cagtccttcc
     1981 ctgagggctt cacatgggag agagtcacca catacgaaga cgggggcgtg ctgaccgcta
     2041 cccaggacac cagcctccag gacggctgcc tcatctacaa cgtcaagatc agaggggtga
     2101 acttcacatc caacggccct gtgatgcaga agaaaacact cggctgggag gccttcaccg
     2161 agacgctgta ccccgctgac ggcggcctgg aaggcagaaa cgacatggcc ctgaagctcg
     2221 tgggcgggag ccatctgatc gcaaacgcca agaccacata tagatccaag aaacccgcta
     2281 agaacctcaa gatgcctggc gtctactatg tggactacag actggaaaga atcaaggagg
     2341 ccaacaacga gacctacgtc gagcagcacg aggtggcagt ggccagatac tgcgacctcc
     2401 ctagcaaact ggggcacaag cttaattagg aattcataat caacctctgg attacaaaat
     2461 ttgtgaaaga ttgactggta ttcttaacta tgttgctcct tttacgctat gtggatacgc
     2521 tgctttaatg cctttgtatc atgctattgc ttcccgtatg gctttcattt tctcctcctt
     2581 gtataaatcc tggttagttc ttgccacggc ggaactcatc gccgcctgcc ttgcccgctg
     2641 ctggacaggg gctcggctgt tgggcactga caattccgtg gtgtttattt gtgaaatttg
     2701 tgatgctatt gctttatttg taaccatcta gctttatttg tgaaatttgt gatgctattg
     2761 ctttatttgt aaccattata agctgcaata aacaagttaa caacaacaat tgcattcatt
     2821 ttatgtttca ggttcagggg gagatgtggg aggtttttta aacaaggtac catcacatta
     2881 ccatgcaggt acacagcaag aattgacgtt ggcatatcac atggtgtaat aaccccactt
     2941 gtgaaacaac ccagaataag gtacaaggcg gaaatgtcgt cattctaaaa taaaaggcat
     3001 ggccaggaat ttgtctaata ccgggaactt aaattcagct tgaacaccag tcgcaaaaaa
     3061 ttcaaagaaa gtgattcagg ttcgggttcg tggattggaa cagcttcttt tgtttcagtg
     3121 atgagagaat cctcctgtca gcaggaaccc ctagtgatgg agttggccac tccctctctg
     3181 cgcgctcgct cgctcactga ggccgggcga ccaaaggtcg cccgacgccc gggctttgcc
     3241 cgagcggcct cagtgagcga gcgagcgcgc agctgcctgc aggacatgtg agcaaaaggc
     3301 cagcaaaagg ccaggaaccg taaaaaggcc gcgttgctgg cgtttttcca taggctccgc
     3361 ccccctgacg agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga
     3421 ctataaagat accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc
     3481 ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat
     3541 agctcacgct gtaggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg
     3601 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
     3661 aacccggtaa gacacgactt atcgccactg gcagcagcca ctggtaacag gattagcaga
     3721 gcgaggtatg taggcggtgc tacagagttc ttgaagtggt ggcctaacta cggctacact
     3781 agaagaacag tatttggtat ctgcgctctg ctgaagccag ttaccttcgg aaaaagagtt
     3841 ggtagctctt gatccggcaa acaaaccacc gctggtagcg gtggtttttt tgtttgcaag
     3901 cagcagatta cgcgcagaaa aaaaggatct caagaagatc ctttgatctt ttctacgggg
     3961 tctgacgctc agtggaacga aaactcacgt taagggattt tggtcatgag attatcaaaa
     4021 aggatcttca cctagatcct tttaaattaa aaatgaagtt ttaaatcaat ctaaagtata
     4081 tatgagtaaa cttggtctga cagttaccaa tgcttaatca gtgaggcacc tatctcagcg
     4141 atctgtctat ttcgttcatc catagttgcc tgactccccg tcgtgtagat aactacgata
     4201 cgggagggct taccatctgg ccccagtgct gcaatgatac cgcggcttcc acgctcaccg
     4261 gctccagatt tatcagcaat aaaccagcca gccggaaggg ccgagcgcag aagtggtcct
     4321 gcaactttat ccgcctccat ccagtctatt aattgttgcc gggaagctag agtaagtagt
     4381 tcgccagtta atagtttgcg caacgttgtt gccattgcta caggcatcgt ggtgtcacgc
     4441 tcgtcgtttg gtatggcttc attcagctcc ggttcccaac gatcaaggcg agttacatga
     4501 tcccccatgt tgtgcaaaaa agcggttagc tccttcggtc ctccgatcgt tgtcagaagt
     4561 aagttggccg cagtgttatc actcatggtt atggcagcac tgcataattc tcttactgtc
     4621 atgccatccg taagatgctt ttctgtgact ggtgagtact caaccaagtc attctgagaa
     4681 tagtgtatgc ggcgaccgag ttgctcttgc ccggcgtcaa tacgggataa taccgcgcca
     4741 catagcagaa ctttaaaagt gctcatcatt ggaaaacgtt cttcggggcg aaaactctca
     4801 aggatcttac cgctgttgag atccagttcg atgtaaccca ctcgtgcacc caactgatct
     4861 tcagcatctt ttactttcac cagcgtttct gggtgagcaa aaacaggaag gcaaaatgcc
     4921 gcaaaaaagg gaataagggc gacacggaaa tgttgaatac tcatactctt cctttttcaa
     4981 tattattgaa gcatttatca gggttattgt ctcatgagcg gatacatatt tgaatgtatt
     5041 tagaaaaata aacaaatagg ggttccgcgc acatttcccc gaaaagtgcc acctgacgtc
     5101 taagaaacca ttattatcat gacattaacc tataaaaata ggcgtatcac gaggcccttt
     5161 cgtctcgcgc gtttcggtga tgacggtg
//
