LOCUS       sequence-494694-        4675 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Used for AAV1 tracing experiment..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 4675)
  AUTHORS   Chen D, Isakova A, Wan ZJ, Wagner MJ, Wu Y, Zhao BS
  TITLE     Connectome-seq: High-throughput Mapping of Neuronal Connectivity at 
            Single-Synapse Resolution via Barcode Sequencing.
  JOURNAL   bioRxiv [Preprint]. 2025 May 26:2025.02.13.638129. doi: 
            10.1101/2025.02.13.638129.
  PUBMED    41030982
REFERENCE   2  (bases 1 to 4675)
  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 
            [Preprint]. 2025 May 26:2025.02.13.638129. doi: 
            10.1101/2025.02.13.638129."
COMMENT     Sequence Label: sCAG-DIO-oScarlet3
FEATURES             Location/Qualifiers
     source          1..4675
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     636..658
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     720..739
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     protein_bind    complement(773..806)
                     /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)."
     protein_bind    complement(857..890)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     regulatory      1585..1594
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     protein_bind    1601..1634
                     /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)."
     protein_bind    1685..1718
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     primer_bind     1761..1780
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(2030..2047)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(2030..2046)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2039..2061)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     complement(2255..2274)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     2374..2396
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(2434..2452)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        2520..2624
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(2625..2693,2694..3485)
                     /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(2843..2862)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      3656..4244
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     4145..4164
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     protein_bind    4532..4553
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(4568..4573,4574..4591,4592..4598)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4606..4622
                     /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     4611..4633
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     4630..4646
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     4630..4646
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
ORIGIN
        1 aaagcttccc ggggggatct gggccactcc ctctctgcgc gctcgctcgc tcactgaggc
       61 cgggcgacca aaggtcgccc ggcctcagtg agcgagcgag cgcgcagaga gggagtggcc
      121 aactccatca ctaggggttc ctggaggggt ggagtcgtga cctaggccat tgacgtcaat
      181 aatgacgtat gttcccatag taacgccaat agggactttc cattgacgtc aatgggtgga
      241 gtatttacgg taaactgccc acttggcagt acatcaagtg tatcatatgc caagtacgcc
      301 ccctattgac gtcaatgacg gtaaatggcc cgcctggcat tatgcccagt acatgacctt
      361 atgggacttt cctacttggc agtacatcta cgtattagtc atcgctatta ccatggtcga
      421 ggtgagcccc acgttctgct tcactctccc catctccccc ccctccccac ccccaatttt
      481 gtatttattt attttttaat tattttgtgc agcgatgggg gcgggggggg gggggggggg
      541 ggccccgggg gggggggggg gggggggggg gggggggggg gggggggggg gggggggggg
      601 ggggggcggg gggggggggg gggggggcag ggcggggttc ggcttctggc gtgtgaccgg
      661 cggctctaga gcctctgcta accatgttca tgccttcttc tttttcctac agctcctggg
      721 caacgtgctg gttattgtgc tgtctcatca ttttggcaaa gaattgggat ccataacttc
      781 gtataggata ctttatacga agttatgcag aatggtagct ggattgtagc tgctattagc
      841 aatatgaaac ctcttaataa cttcgtatag catacattat acgaagttat ggcgcgcctc
      901 aggaaccacc agaccccccg gtgctatgcc gagcgacgct gcgctcgtac tgctccacca
      961 ctgtataatc ttcattatgt gaagttatgt ccagcttcct gtcaatgttg aaggctcctg
     1021 gcatctggac aggtttcttt gcgcggtagg tagttttaaa gtctgccagg tatcggccac
     1081 catcttttaa tcgcaacgcc attttgatat cccctttcaa aactacatcc tcgggatata
     1141 gtctttccgt ggaggcctcc cagcccatag tcttcttctg catcactggt ccatctgggg
     1201 ggaagttggt gccccgaagc ttgaccttgt agatgagcgt tccatcctcc agtgaggtgt
     1261 cctgggccac agatactgcc cctccgtctt caaagttcat gacacggtcc cacttgaatc
     1321 cttctgggaa actttgtttc cagtagtccg gaatgtcagc agggtgcttt gtaaaagctc
     1381 tagagccata catgaactgg ggactcagga tatcccagct gaaaggcaga ggacccccct
     1441 tggtaaccct gagcttggct gtttgagtgc cctcataggg cctcccttct ccctcacctt
     1501 caatctcaaa ttcgtggcca ttcatggagc cctccatgtg cactttgaat ctcataaact
     1561 ccttgatcac agcttctgtg ctgtccatgg tggcgctagc ataacttcgt ataaagtatc
     1621 ctatacgaag ttatttgcct taacccagaa attatcactg ttattcttta gaatggtgca
     1681 aagaataact tcgtataatg tatgctatac gaagttatgc ggccgctagg cctcacctgc
     1741 gatctcgatg ctttatttgt gaaatttgtg atgctattgc tttatttgta accattataa
     1801 gctgcaataa acaagttaac aacaacaatt gcattcattt tatgtttcag gttcaggggg
     1861 aggtgtggga ggttttttaa actagtccac tccctctctg cgcgctcgct cgctcactga
     1921 ggccgggcga ccaaaggtcg cccgacgccc gggctttgcc cgggcggcct cagtgagcga
     1981 gcgagcgcgc agagagggac agatccgggc ccgcatgcgt cgacaattca ctggccgtcg
     2041 ttttacaacg tcgtgactgg gaaaaccctg gcgttaccca acttaatcgc cttgcagcac
     2101 atcccccttt cgccagctgg cgtaatagcg aagaggcccg caccgatcgc ccttcccaac
     2161 agttgcgcag cctgaatggc gaatggcgcc tgatgcggta ttttctcctt acgcatctgt
     2221 gcggtatttc acaccgcata tggtgcactc tcagtacaat ctgctctgat gccgcatagt
     2281 taagccagcc ccgacacccg ccaacacccg ctgacgcgcc ctgacgggct tgtctgctcc
     2341 cggcatccgc ttacagacaa gctgtgaccg tctccgggag ctgcatgtgt cagaggtttt
     2401 caccgtcatc accgaaacgc gcgagacgaa agggcctcgt gatacgccta tttttatagg
     2461 ttaatgtcat gataataatg gtttcttaga cgtcaggtgg cacttttcgg ggaaatgtgc
     2521 gcggaacccc tatttgttta tttttctaaa tacattcaaa tatgtatccg ctcatgagac
     2581 aataaccctg ataaatgctt caataatatt gaaaaaggaa gagtatgagt attcaacatt
     2641 tccgtgtcgc ccttattccc ttttttgcgg cattttgcct tcctgttttt gctcacccag
     2701 aaacgctggt gaaagtaaaa gatgctgaag atcagttggg tgcacgagtg ggttacatcg
     2761 aactggatct caacagcggt aagatccttg agagttttcg ccccgaagaa cgttttccaa
     2821 tgatgagcac ttttaaagtt ctgctatgtg gcgcggtatt atcccgtatt gacgccgggc
     2881 aagagcaact cggtcgccgc atacactatt ctcagaatga cttggttgag tactcaccag
     2941 tcacagaaaa gcatcttacg gatggcatga cagtaagaga attatgcagt gctgccataa
     3001 ccatgagtga taacactgcg gccaacttac ttctgacaac gatcggagga ccgaaggagc
     3061 taaccgcttt tttgcacaac atgggggatc atgtaactcg ccttgatcgt tgggaaccgg
     3121 agctgaatga agccatacca aacgacgagc gtgacaccac gatgcctgta gcaatggcaa
     3181 caacgttgcg caaactatta actggcgaac tacttactct agcttcccgg caacaattaa
     3241 tagactggat ggaggcggat aaagttgcag gaccacttct gcgctcggcc cttccggctg
     3301 gctggtttat tgctgataaa tctggagccg gtgagcgtgg gtctcgcggt atcattgcag
     3361 cactggggcc agatggtaag ccctcccgta tcgtagttat ctacacgacg gggagtcagg
     3421 caactatgga tgaacgaaat agacagatcg ctgagatagg tgcctcactg attaagcatt
     3481 ggtaactgtc agaccaagtt tactcatata tactttagat tgatttaaaa cttcattttt
     3541 aatttaaaag gatctaggtg aagatccttt ttgataatct catgaccaaa atcccttaac
     3601 gtgagttttc gttccactga gcgtcagacc ccgtagaaaa gatcaaagga tcttcttgag
     3661 atcctttttt tctgcgcgta atctgctgct tgcaaacaaa aaaaccaccg ctaccagcgg
     3721 tggtttgttt gccggatcaa gagctaccaa ctctttttcc gaaggtaact ggcttcagca
     3781 gagcgcagat accaaatact gttcttctag tgtagccgta gttaggccac cacttcaaga
     3841 actctgtagc accgcctaca tacctcgctc tgctaatcct gttaccagtg gctgctgcca
     3901 gtggcgataa gtcgtgtctt accgggttgg actcaagacg atagttaccg gataaggcgc
     3961 agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca
     4021 ccgaactgag atacctacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa
     4081 aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagcttc
     4141 cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc
     4201 gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc agcaacgcgg
     4261 cctttttacg gttcctggcc ttttgctggc cttttgctca catgttcttt cctgcgttat
     4321 cccctgattc tgtggataac cgtattaccg cctttgagtg agctgatacc gctcgccgca
     4381 gccgaacgac cgagcgcagc gagtcagtga gcgaggaagc ggaagagcgc ccaatacgca
     4441 aaccgcctct ccccgcgcgt tggccgattc attaatgcag ctggcacgac aggtttcccg
     4501 actggaaagc gggcagtgag cgcaacgcaa ttaatgtgag ttagctcact cattaggcac
     4561 cccaggcttt acactttatg cttccggctc gtatgttgtg tggaattgtg agcggataac
     4621 aatttcacac aggaaacagc tatgaccatg attacgccaa gctctcgaga tctag
//
