LOCUS       sequence-161489-        7166 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  AAV-mediated expression of ChrimsonR-tdTomato under the Syn 
            promoter, in floxed/forward (Cre-dependent) manner. Cre turns gene 
            off. Using bGHpA signal. tdTomato is a codon diversified version. .
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7166)
  AUTHORS   Klapoetke NC, Murata Y, Kim SS, Pulver SR, Birdsey-Benson A, Cho YK,
            Morimoto TK, Chuong AS, Carpenter EJ, Tian Z, Wang J, Xie Y, Yan Z, 
            Zhang Y, Chow BY, Surek B, Melkonian M, Jayaraman V, 
            Constantine-Paton M, Wong GK, Boyden ES
  TITLE     Independent optical excitation of distinct neural populations.
  JOURNAL   Nat Methods. 2014 Mar;11(3):338-46. doi: 10.1038/nmeth.2836. Epub 
            2014 Feb 9.
  PUBMED    24509633
REFERENCE   2  (bases 1 to 7166)
  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"; doi: 
            "10.1038/nmeth.2836"; journalName: "Nat Methods"; date: "2014-03"; 
            volume: "11"; issue: "3"; pages: "338-46"
COMMENT     Sequence Label: pAAV-Syn-FLEX-fd [ChrimsonR-tdTomato]
FEATURES             Location/Qualifiers
     source          1..7166
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      complement(182..770)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(262..281)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(941..1732,1733..1801))
                     /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     1564..1583
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(1802..1906)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(1932..2387)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2069..2090)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     2281..2300
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     repeat_region   2459..2588
                     /label=AAV2 ITR
     promoter        2691..3138
                     /label=hSyn promoter
                     /note="human synapsin I promoter; confers neuron-specific 
                     expression (Kugler et al., 2003)"
     protein_bind    3154..3187
                     /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    3250..3283
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     regulatory      3294..3303
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             3300..4349
                     /codon_start=1
                     /product="red light-drivable channelrhodopsin from 
                     Chlamydomonas noctigama (Klapoetke et al., 2014)"
                     /label=ChrimsonR
                     /note="K176R mutant with accelerated closing kinetics"
                     /translation="MAELISSATRSLFAAGGINPWPNPYHHEDMGCGGMTPTGECFSTE
                     WWCDPSYGLSDAGYGYCFVEATGGYLVVGVEKKQAWLHSRGTPGEKIGAQVCQWIAFSI
                     AIALLTFYGFSAWKATCGWEEVYVCCVEVLFVTLEIFKEFSSPATVYLSTGNHAYCLRY
                     FEWLLSCPVILIRLSNLSGLKNDYSKRTMGLIVSCVGMIVFGMAAGLATDWLKWLLYIV
                     SCIYGGYMYFQAAKCYVEANHSVPKGHCRMVVKLMAYAYFASWGSYPILWAVGPEGLLK
                     LSPYANSIGHSICDIIAKEFWTFLAHHLRIKIHEHILIHGDIRKTTKMEIGGEEVEVEE
                     FVEEEDEDTV"
     protein_bind    complement(5806..5839)
                     /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(5910..5943)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     misc_feature    5976..6564
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(6029..6049)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(6447..6458)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    6605..6812
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     repeat_region   6982..7111
                     /label=AAV2 ITR
ORIGIN
        1 cttccgcttc ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg cgagcggtat
       61 cagctcactc aaaggcggta atacggttat ccacagaatc aggggataac gcaggaaaga
      121 acatgtgagc aaaaggccag caaaaggcca ggaaccgtaa aaaggccgcg ttgctggcgt
      181 ttttccatag gctccgcccc cctgacgagc atcacaaaaa tcgacgctca agtcagaggt
      241 ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggaagc tccctcgtgc
      301 gctctcctgt tccgaccctg ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa
      361 gcgtggcgct ttctcatagc tcacgctgta ggtatctcag ttcggtgtag gtcgttcgct
      421 ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc ttatccggta
      481 actatcgtct tgagtccaac ccggtaagac acgacttatc gccactggca gcagccactg
      541 gtaacaggat tagcagagcg aggtatgtag gcggtgctac agagttcttg aagtggtggc
      601 ctaactacgg ctacactaga agaacagtat ttggtatctg cgctctgctg aagccagtta
      661 ccttcggaaa aagagttggt agctcttgat ccggcaaaca aaccaccgct ggtagcggtg
      721 gtttttttgt ttgcaagcag cagattacgc gcagaaaaaa aggatctcaa gaagatcctt
      781 tgatcttttc tacggggtct gacgctcagt ggaacgaaaa ctcacgttaa gggattttgg
      841 tcatgagatt atcaaaaagg atcttcacct agatcctttt aaattaaaaa tgaagtttta
      901 aatcaatcta aagtatatat gagtaaactt ggtctgacag ttaccaatgc ttaatcagtg
      961 aggcacctat ctcagcgatc tgtctatttc gttcatccat agttgcctga ctccccgtcg
     1021 tgtagataac tacgatacgg gagggcttac catctggccc cagtgctgca atgataccgc
     1081 gagacccacg ctcaccggct ccagatttat cagcaataaa ccagccagcc ggaagggccg
     1141 agcgcagaag tggtcctgca actttatccg cctccatcca gtctattaat tgttgccggg
     1201 aagctagagt aagtagttcg ccagttaata gtttgcgcaa cgttgttgcc attgctacag
     1261 gcatcgtggt gtcacgctcg tcgtttggta tggcttcatt cagctccggt tcccaacgat
     1321 caaggcgagt tacatgatcc cccatgttgt gcaaaaaagc ggttagctcc ttcggtcctc
     1381 cgatcgttgt cagaagtaag ttggccgcag tgttatcact catggttatg gcagcactgc
     1441 ataattctct tactgtcatg ccatccgtaa gatgcttttc tgtgactggt gagtactcaa
     1501 ccaagtcatt ctgagaatag tgtatgcggc gaccgagttg ctcttgcccg gcgtcaatac
     1561 gggataatac cgcgccacat agcagaactt taaaagtgct catcattgga aaacgttctt
     1621 cggggcgaaa actctcaagg atcttaccgc tgttgagatc cagttcgatg taacccactc
     1681 gtgcacccaa ctgatcttca gcatctttta ctttcaccag cgtttctggg tgagcaaaaa
     1741 caggaaggca aaatgccgca aaaaagggaa taagggcgac acggaaatgt tgaatactca
     1801 tactcttcct ttttcaatat tattgaagca tttatcaggg ttattgtctc atgagcggat
     1861 acatatttga atgtatttag aaaaataaac aaataggggt tccgcgcaca tttccccgaa
     1921 aagtgccacc taaattgtaa gcgttaatat tttgttaaaa ttcgcgttaa atttttgtta
     1981 aatcagctca ttttttaacc aataggccga aatcggcaaa atcccttata aatcaaaaga
     2041 atagaccgag atagggttga gtgttgttcc agtttggaac aagagtccac tattaaagaa
     2101 cgtggactcc aacgtcaaag ggcgaaaaac cgtctatcag ggcgatggcc cactacgtga
     2161 accatcaccc taatcaagtt ttttggggtc gaggtgccgt aaagcactaa atcggaaccc
     2221 taaagggagc ccccgattta gagcttgacg gggaaagccg gcgaacgtgg cgagaaagga
     2281 agggaagaaa gcgaaaggag cgggcgctag ggcgctggca agtgtagcgg tcacgctgcg
     2341 cgtaaccacc acacccgccg cgcttaatgc gccgctacag ggcgcgtccc attcgccatt
     2401 caggctgcgc aactgttggg aagggcgatc ggtgcgggcc tcttcgctat tacgccagct
     2461 gcgcgctcgc tcgctcactg aggccgcccg ggcaaagccc gggcgtcggg cgacctttgg
     2521 tcgcccggcc tcagtgagcg agcgagcgcg cagagaggga gtggccaact ccatcactag
     2581 gggttccttg tagttaatga ttaacccgcc atgctactta tctacgtagc catgctctag
     2641 gaagatcgta ggttaattaa gtgtctagac tgcagagggc cctgcgtatg agtgcaagtg
     2701 ggttttagga ccaggatgag gcggggtggg ggtgcctacc tgacgaccga ccccgaccca
     2761 ctggacaagc acccaacccc cattccccaa attgcgcatc ccctatcaga gagggggagg
     2821 ggaaacagga tgcggcgagg cgcgtgcgca ctgccagctt cagcaccgcg gacagtgcct
     2881 tcgcccccgc ctggcggcgc gcgccaccgc cgcctcagca ctgaaggcgc gctgacgtca
     2941 ctcgccggtc ccccgcaaac tccccttccc ggccaccttg gtcgcgtccg cgccgccgcc
     3001 ggcccagccg gaccgcacca cgcgaggcgc gagatagggg ggcacgggcg cgaccatctg
     3061 cgctgcggcg ccggcgactc agcgctgcct cagtctgcgg tgggcagcgg aggagtcgtg
     3121 tcgtgcctga gagcgcagtc gagaagaatt cccataactt cgtataaagt atcctatacg
     3181 aagttatatc aaaataggaa gaccaatgct tcaccatcga cccgaattgc caagcatcac
     3241 catcgaccca taacttcgta taatgtatgc tatacgaagt tatactagct agcgccacca
     3301 tggctgagct gatcagcagc gccaccagat ctctgtttgc cgccggaggc atcaaccctt
     3361 ggcctaaccc ctaccaccac gaggacatgg gctgtggagg aatgacacct acaggcgagt
     3421 gcttcagcac cgagtggtgg tgtgaccctt cttacggact gagcgacgcc ggatacggat
     3481 attgcttcgt ggaggccaca ggcggctacc tggtcgtggg agtggagaag aagcaggctt
     3541 ggctgcacag cagaggcaca ccaggagaaa agatcggcgc ccaggtctgc cagtggattg
     3601 ctttcagcat cgccatcgcc ctgctgacat tctacggctt cagcgcctgg aaggccactt
     3661 gcggttggga ggaggtctac gtctgttgcg tcgaggtgct gttcgtgacc ctggagatct
     3721 tcaaggagtt cagcagcccc gccacagtgt acctgtctac cggcaaccac gcctattgcc
     3781 tgcgctactt cgagtggctg ctgtcttgcc ccgtgatcct gatcagactg agcaacctga
     3841 gcggcctgaa gaacgactac agcaagcgga ccatgggcct gatcgtgtct tgcgtgggaa
     3901 tgatcgtgtt cggcatggcc gcaggactgg ctaccgattg gctcaagtgg ctgctgtata
     3961 tcgtgtcttg catctacggc ggctacatgt acttccaggc cgccaagtgc tacgtggaag
     4021 ccaaccacag cgtgcctaaa ggccattgcc gcatggtcgt gaagctgatg gcctacgctt
     4081 acttcgcctc ttggggcagc tacccaatcc tctgggcagt gggaccagaa ggactgctga
     4141 agctgagccc ttacgccaac agcatcggcc acagcatctg cgacatcatc gccaaggagt
     4201 tttggacctt cctggcccac cacctgagga tcaagatcca cgagcacatc ctgatccacg
     4261 gcgacatccg gaagaccacc aagatggaga tcggaggcga ggaggtggaa gtggaagagt
     4321 tcgtggagga ggaggacgag gacacagtgg cggcaccggt agtagcagtg agtaagggcg
     4381 aggaagtgat caaagagttc atgcggttta aggtgagaat ggaaggaagc atgaacggcc
     4441 acgagttcga aattgaggga gaaggagagg gacggcccta cgagggcacc cagacagcca
     4501 agctgaaagt gacaaagggc gggcctctgc cattcgcttg ggacatcctg agcccacagt
     4561 ttatgtacgg ctccaaggcc tatgtgaaac atccagctga cattcccgat tataagaaac
     4621 tgagcttccc cgaggggttt aagtgggaaa gagtgatgaa cttcgaggac ggaggcctgg
     4681 tgactgtgac ccaggacagc tccctgcagg atgggaccct gatctacaag gtgaaaatga
     4741 gagggacaaa ttttccccct gatggacctg tgatgcagaa gaaaactatg ggatgggagg
     4801 cctccaccga aaggctgtat ccacgcgacg gggtgctgaa aggagaaatc caccaggctc
     4861 tgaagctgaa agatggggga cattacctgg tggagttcaa gacaatctac atggccaaga
     4921 aacctgtgca gctgccaggc tactattacg tggacacaaa actggatatc acttcacaca
     4981 acgaggacta cactattgtg gagcagtatg aacggagcga ggggagacac catctgttcc
     5041 tgggccatgg gactggaagt accggctcag ggtctagtgg aaccgcctca agcgaggata
     5101 acaatatggc tgtgatcaaa gagttcatga ggtttaaggt gcgcatggag ggcagcatga
     5161 atgggcacga atttgagatt gaaggagagg gcgaagggag gccttacgag ggcacacaga
     5221 ctgccaagct gaaagtgacc aagggaggac cactgccttt cgcttgggat atcctgtctc
     5281 ctcagtttat gtacggaagt aaggcctatg tcaagcatcc cgctgacatt cctgattaca
     5341 agaaactgtc tttcccagag ggctttaagt gggagagagt gatgaatttt gaagatggag
     5401 gcctggtgac cgtgacacag gactcctctc tgcaggatgg cactctgatc tacaaagtca
     5461 aaatgcgcgg caccaatttt ccacccgatg ggcccgtgat gcagaagaaa acaatggggt
     5521 gggaggccag cactgaacgg ctgtatccta gagacggagt gctgaagggc gaaatccacc
     5581 aggccctgaa gctgaaagac ggcggccact acctggtgga gttcaaaacc atctacatgg
     5641 ccaagaaacc agtgcagctg cccggctatt actatgtgga caccaagctg gatatcacat
     5701 cccacaatga agactacacc attgtggaac agtatgagag gtctgaagga cgccaccatc
     5761 tgtttctgta cggcatggat gagctgtata agtaaggtac ctagtataac ttcgtatagg
     5821 atactttata cgaagttatc attgggattc ttcctatttt gatccaagca tcaccatcga
     5881 ccctctagtc cagatctcac catcgaccca taacttcgta tagcatacat tatacgaagt
     5941 tatgtccctc gaagaggttc gcgaagctta tcgataatca acctctggat tacaaaattt
     6001 gtgaaagatt gactggtatt cttaactatg ttgctccttt tacgctatgt ggatacgctg
     6061 ctttaatgcc tttgtatcat gctattgctt cccgtatggc tttcattttc tcctccttgt
     6121 ataaatcctg gttgctgtct ctttatgagg agttgtggcc cgttgtcagg caacgtggcg
     6181 tggtgtgcac tgtgtttgct gacgcaaccc ccactggttg gggcattgcc accacctgtc
     6241 agctcctttc cgggactttc gctttccccc tccctattgc cacggcggaa ctcatcgccg
     6301 cctgccttgc ccgctgctgg acaggggctc ggctgttggg cactgacaat tccgtggtgt
     6361 tgtcggggaa atcatcgtcc tttccttggc tgctcgcctg tgttgccacc tggattctgc
     6421 gcgggacgtc cttctgctac gtcccttcgg ccctcaatcc agcggacctt ccttcccgcg
     6481 gcctgctgcc ggctctgcgg cctcttccgc gtcttcgcct tcgccctcag acgagtcgga
     6541 tctccctttg ggccgcctcc ccgcatcgat accgtcgacc cgggcggccg ctcataaagc
     6601 tcgactgtgc cttctagttg ccagccatct gttgtttgcc cctcccccgt gccttccttg
     6661 accctggaag gtgccactcc cactgtcctt tcctaataaa atgaggaaat tgcatcgcat
     6721 tgtctgagta ggtgtcattc tattctgggg ggtggggtgg ggcaggacag caagggggag
     6781 gattgggaag acaatagcag gcatgctggg gatgcggtcc ggactgtaca attgcattca
     6841 ttttatgttt caggttcagg gggagatgtg ggaggttttt taaagcaagt aaaacctcta
     6901 caaatgtggt aaaatcgata aggatcttcc tagagcatgg ctacgtagat aagtagcatg
     6961 gcgggttaat cattaactac aaggaacccc tagtgatgga gttggccact ccctctctgc
     7021 gcgctcgctc gctcactgag gccgggcgac caaaggtcgc ccgacgcccg ggctttgccc
     7081 gggcggcctc agtgagcgag cgagcgcgca gctgcattaa tgaatcggcc aacgcgcggg
     7141 gagaggcggt ttgcgtattg ggcgct
//
