LOCUS       sequence-169368-        6390 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  synthetic circular DNA
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6390)
  AUTHORS   Chow BY, Han X, Dobry AS, Qian X, Chuong AS, Li M, Henninger MA, 
            Belfort GM, Lin Y, Monahan PE, Boyden ES
  TITLE     High-performance genetically targetable optical neural silencing by 
            light-driven proton pumps.
  JOURNAL   Nature. 2010 Jan 7. 463(7277):98-102.
  PUBMED    20054397
REFERENCE   2  (bases 1 to 6390)
  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: "Nature. 
            2010 Jan 7. 463(7277):98-102."
COMMENT     Sequence Label: pAAV-CAG-Arch-GFP
FEATURES             Location/Qualifiers
     source          1..6390
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        1..278
                     /label=chicken beta-actin promoter
     primer_bind     557..579
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     641..660
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     regulatory      693..702
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             699..1472
                     /codon_start=1
                     /product="light-driven proton pump archaerhodopsin-3 from 
                     Halorubrum sodomense (Chow et al., 2010)"
                     /label=Arch
                     /translation="MDPIALQAGYDLLGDGRPETLWLGIGTLLMLIGTFYFLVRGWGVT
                     DKDAREYYAVTILVPGIASAAYLSMFFGIGLTEVTVGGEMLDIYYARYADWLFTTPLLL
                     LDLALLAKVDRVTIGTLVGVDALMIVTGLIGALSHTAIARYSWWLFSTICMIVVLYFLA
                     TSLRSAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGVVGLGIETLLFMVLD
                     VTAKVGFGFILLRSRAILGDTEAPEPSAGADVSAAD"
     CDS             join(1488..1490,1491..2204)
                     /codon_start=1
                     /product="the original enhanced GFP (Yang et al., 1996)"
                     /label=EGFP
                     /note="mammalian codon-optimized"
                     /translation="VSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLK
                     FICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDG
                     NYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV
                     NFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLE
                     FVTAAGITLGMDELYK"
     CDS             join(1488..1490,1491..2201)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="VSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLK
                     FICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDG
                     NYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV
                     NFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLE
                     FVTAAGITLGMDELYK"
     primer_bind     complement(1530..1551)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(1791..1810)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     2138..2159
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     protein_bind    complement(2215..2248)
                     /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(2319..2352)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     misc_feature    2394..2982
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(2447..2467)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2865..2876)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    3025..3146
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3036..3055)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3090..3109
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     repeat_region   3308..3437
                     /label=AAV2 ITR
     rep_origin      complement(3674..4262)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3754..3773)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4433..5224,5225..5293))
                     /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     5056..5075
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5294..5398)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(5424..5879)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5561..5582)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     5773..5792
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     repeat_region   5951..6080
                     /label=AAV2 ITR
ORIGIN
        1 tcgaggtgag ccccacgttc tgcttcactc tccccatctc ccccccctcc ccacccccaa
       61 ttttgtattt atttattttt taattatttt gtgcagcgat gggggcgggg gggggggggg
      121 ggcgcgcgcc gggcggggcg gggcggggcg aggggcgggg cggggcgagg cggagaggtg
      181 cggcggcagc caatcagagc ggcgcgctcc gaaagtttcc ttttatggcg aggcggcggc
      241 ggcggcggcc ctataaaaag cgaagcgcgc ggcgggcggg agtcgctgcg cgctgccttc
      301 gccccgtgcc ccgctccgcc gccgcctcgc gccgcccgcc ccggctctga ctgaccgcgt
      361 tactcccaca ggtgagcggg cgggacggcc cttctcctcc gggctgtaat tagcgcttgg
      421 tttaatgacg gcttgtttct tttctgtggc tgcgtgaaag ccttgagggg ctccgggagg
      481 gccctttgtg cggggggagc ggctcggggc tgtccgcggg gggacggctg ccttcggggg
      541 ggacggggca gggcggggtt cggcttctgg cgtgtgaccg gcggctctag agcctctgct
      601 aaccatgttc atgccttctt ctttttccta cagctcctgg gcaacgtgct ggttattgtg
      661 ctgtctcatc attttggcaa agaattggat ccgccaccat ggaccccatc gctctgcagg
      721 ctggttacga cctgctgggt gacggcagac ctgaaactct gtggctgggc atcggcactc
      781 tgctgatgct gattggaacc ttctactttc tggtccgcgg atggggagtc accgataagg
      841 atgcccggga atattacgct gtgactatcc tggtgcccgg aatcgcatcc gccgcatatc
      901 tgtctatgtt ctttggtatc gggcttactg aggtgaccgt cgggggcgaa atgttggata
      961 tctattatgc caggtacgcc gactggctgt ttaccacccc acttctgctg ctggatctgg
     1021 cccttctcgc taaggtggat cgggtgacca tcggcaccct ggtgggtgtg gacgccctga
     1081 tgatcgtcac tggcctcatc ggagccttga gccacacggc catagccaga tacagttggt
     1141 ggttgttctc tacaatttgc atgatagtgg tgctctattt tctggctaca tccctgcgat
     1201 ctgctgcaaa ggagcggggc cccgaggtgg catctacctt taacaccctg acagctctgg
     1261 tcttggtgct gtggaccgct taccctatcc tgtggatcat aggcactgag ggcgctggcg
     1321 tggtgggcct gggcatcgaa actctgctgt ttatggtgtt ggacgtgact gccaaggtcg
     1381 gctttggctt tatcctgttg agatcccggg ctattctggg cgacaccgag gcaccagaac
     1441 ccagtgccgg tgccgatgtc agtgccgccg accgaccggt agtagcagtg agcaagggcg
     1501 aggagctgtt caccggggtg gtgcccatcc tggtcgagct ggacggcgac gtaaacggcc
     1561 acaagttcag cgtgtccggc gagggcgagg gcgatgccac ctacggcaag ctgaccctga
     1621 agttcatctg caccaccggc aagctgcccg tgccctggcc caccctcgtg accaccctga
     1681 cctacggcgt gcagtgcttc agccgctacc ccgaccacat gaagcagcac gacttcttca
     1741 agtccgccat gcccgaaggc tacgtccagg agcgcaccat cttcttcaag gacgacggca
     1801 actacaagac ccgcgccgag gtgaagttcg agggcgacac cctggtgaac cgcatcgagc
     1861 tgaagggcat cgacttcaag gaggacggca acatcctggg gcacaagctg gagtacaact
     1921 acaacagcca caacgtctat atcatggccg acaagcagaa gaacggcatc aaggtgaact
     1981 tcaagatccg ccacaacatc gaggacggca gcgtgcagct cgccgaccac taccagcaga
     2041 acacccccat cggcgacggc cccgtgctgc tgcccgacaa ccactacctg agcacccagt
     2101 ccgccctgag caaagacccc aacgagaagc gcgatcacat ggtcctgctg gagttcgtga
     2161 ccgccgccgg gatcactctc ggcatggacg agctgtacaa gtaagaattc tagtataact
     2221 tcgtatagga tactttatac gaagttatca ttgggattct tcctattttg atccaagcat
     2281 caccatcgac cctctagtcc agatctcacc atcgacccat aacttcgtat agcatacatt
     2341 atacgaagtt atgtccctcg aagaggttcg aattcgatat caagcttatc gataatcaac
     2401 ctctggatta caaaatttgt gaaagattga ctggtattct taactatgtt gctcctttta
     2461 cgctatgtgg atacgctgct ttaatgcctt tgtatcatgc tattgcttcc cgtatggctt
     2521 tcattttctc ctccttgtat aaatcctggt tgctgtctct ttatgaggag ttgtggcccg
     2581 ttgtcaggca acgtggcgtg gtgtgcactg tgtttgctga cgcaaccccc actggttggg
     2641 gcattgccac cacctgtcag ctcctttccg ggactttcgc tttccccctc cctattgcca
     2701 cggcggaact catcgccgcc tgccttgccc gctgctggac aggggctcgg ctgttgggca
     2761 ctgacaattc cgtggtgttg tcggggaaat catcgtcctt tccttggctg ctcgcctgtg
     2821 ttgccacctg gattctgcgc gggacgtcct tctgctacgt cccttcggcc ctcaatccag
     2881 cggaccttcc ttcccgcggc ctgctgccgg ctctgcggcc tcttccgcgt cttcgccttc
     2941 gccctcagac gagtcggatc tccctttggg ccgcctcccc gcatcgatac cgtcgacccg
     3001 ggcggccgct tcgagcagac atgataagat acattgatga gtttggacaa accacaacta
     3061 gaatgcagtg aaaaaaatgc tttatttgtg aaatttgtga tgctattgct ttatttgtaa
     3121 ccattataag ctgcaataaa caagttaaca acaacaattg cattcatttt atgtttcagg
     3181 ttcaggggga gatgtgggag gttttttaaa gcaagtaaaa cctctacaaa tgtggtaaaa
     3241 tcgataagga tcttcctaga gcatggctac gtagataagt agcatggcgg gttaatcatt
     3301 aactacaagg aacccctagt gatggagttg gccactccct ctctgcgcgc tcgctcgctc
     3361 actgaggccg ggcgaccaaa ggtcgcccga cgcccgggct ttgcccgggc ggcctcagtg
     3421 agcgagcgag cgcgcagctg cattaatgaa tcggccaacg cgcggggaga ggcggtttgc
     3481 gtattgggcg ctcttccgct tcctcgctca ctgactcgct gcgctcggtc gttcggctgc
     3541 ggcgagcggt atcagctcac tcaaaggcgg taatacggtt atccacagaa tcaggggata
     3601 acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc caggaaccgt aaaaaggccg
     3661 cgttgctggc gtttttccat aggctccgcc cccctgacga gcatcacaaa aatcgacgct
     3721 caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggaa
     3781 gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc
     3841 tcccttcggg aagcgtggcg ctttctcata gctcacgctg taggtatctc agttcggtgt
     3901 aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg
     3961 ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta tcgccactgg
     4021 cagcagccac tggtaacagg attagcagag cgaggtatgt aggcggtgct acagagttct
     4081 tgaagtggtg gcctaactac ggctacacta gaagaacagt atttggtatc tgcgctctgc
     4141 tgaagccagt taccttcgga aaaagagttg gtagctcttg atccggcaaa caaaccaccg
     4201 ctggtagcgg tggttttttt gtttgcaagc agcagattac gcgcagaaaa aaaggatctc
     4261 aagaagatcc tttgatcttt tctacggggt ctgacgctca gtggaacgaa aactcacgtt
     4321 aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac ctagatcctt ttaaattaaa
     4381 aatgaagttt taaatcaatc taaagtatat atgagtaaac ttggtctgac agttaccaat
     4441 gcttaatcag tgaggcacct atctcagcga tctgtctatt tcgttcatcc atagttgcct
     4501 gactccccgt cgtgtagata actacgatac gggagggctt accatctggc cccagtgctg
     4561 caatgatacc gcgagaccca cgctcaccgg ctccagattt atcagcaata aaccagccag
     4621 ccggaagggc cgagcgcaga agtggtcctg caactttatc cgcctccatc cagtctatta
     4681 attgttgccg ggaagctaga gtaagtagtt cgccagttaa tagtttgcgc aacgttgttg
     4741 ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg tatggcttca ttcagctccg
     4801 gttcccaacg atcaaggcga gttacatgat cccccatgtt gtgcaaaaaa gcggttagct
     4861 ccttcggtcc tccgatcgtt gtcagaagta agttggccgc agtgttatca ctcatggtta
     4921 tggcagcact gcataattct cttactgtca tgccatccgt aagatgcttt tctgtgactg
     4981 gtgagtactc aaccaagtca ttctgagaat agtgtatgcg gcgaccgagt tgctcttgcc
     5041 cggcgtcaat acgggataat accgcgccac atagcagaac tttaaaagtg ctcatcattg
     5101 gaaaacgttc ttcggggcga aaactctcaa ggatcttacc gctgttgaga tccagttcga
     5161 tgtaacccac tcgtgcaccc aactgatctt cagcatcttt tactttcacc agcgtttctg
     5221 ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg aataagggcg acacggaaat
     5281 gttgaatact catactcttc ctttttcaat attattgaag catttatcag ggttattgtc
     5341 tcatgagcgg atacatattt gaatgtattt agaaaaataa acaaataggg gttccgcgca
     5401 catttccccg aaaagtgcca cctaaattgt aagcgttaat attttgttaa aattcgcgtt
     5461 aaatttttgt taaatcagct cattttttaa ccaataggcc gaaatcggca aaatccctta
     5521 taaatcaaaa gaatagaccg agatagggtt gagtgttgtt ccagtttgga acaagagtcc
     5581 actattaaag aacgtggact ccaacgtcaa agggcgaaaa accgtctatc agggcgatgg
     5641 cccactacgt gaaccatcac cctaatcaag ttttttgggg tcgaggtgcc gtaaagcact
     5701 aaatcggaac cctaaaggga gcccccgatt tagagcttga cggggaaagc cggcgaacgt
     5761 ggcgagaaag gaagggaaga aagcgaaagg agcgggcgct agggcgctgg caagtgtagc
     5821 ggtcacgctg cgcgtaacca ccacacccgc cgcgcttaat gcgccgctac agggcgcgtc
     5881 ccattcgcca ttcaggctgc gcaactgttg ggaagggcga tcggtgcggg cctcttcgct
     5941 attacgccag ctgcgcgctc gctcgctcac tgaggccgcc cgggcaaagc ccgggcgtcg
     6001 ggcgaccttt ggtcgcccgg cctcagtgag cgagcgagcg cgcagagagg gagtggccaa
     6061 ctccatcact aggggttcct tgtagttaat gattaacccg ccatgctact tatctacgta
     6121 gccatgctct aggaagagta ccattgacgt caataatgac gtatgttccc atagtaacgc
     6181 caatagggac tttccattga cgtcaatggg tggagtattt acggtaaact gcccacttgg
     6241 cagtacatca agtgtatcat atgccaagta cgccccctat tgacgtcaat gacggtaaat
     6301 ggcccgcctg gcattatgcc cagtacatga ccttatggga ctttcctact tggcagtaca
     6361 tctacgtatt agtcatcgct attaccatgg
//
