LOCUS       sequence-177044-        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"
     repeat_region   3..132
                     /label=AAV2 ITR
     polyA_signal    302..509
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     misc_feature    550..1138
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     CDS             656..667
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     primer_bind     1065..1085
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     protein_bind    1171..1204
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     protein_bind    1275..1308
                     /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)."
     CDS             complement(2765..3814)
                     /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"
     regulatory      3811..3820
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     protein_bind    complement(3831..3864)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     protein_bind    complement(3927..3960)
                     /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)."
     promoter        complement(3976..4423)
                     /label=hSyn promoter
                     /note="human synapsin I promoter; confers neuron-specific 
                     expression (Kugler et al., 2003)"
     repeat_region   4526..4655
                     /label=AAV2 ITR
     rep_origin      4727..5182
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(4814..4833)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5024..5045
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        5208..5312
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5313..5381,5382..6173)
                     /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(5531..5550)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      6344..6932
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6833..6852
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 agctgcgcgc tcgctcgctc actgaggccg cccgggcaaa gcccgggcgt cgggcgacct
       61 ttggtcgccc ggcctcagtg agcgagcgag cgcgcagaga gggagtggcc aactccatca
      121 ctaggggttc cttgtagtta atgattaacc cgccatgcta cttatctacg tagccatgct
      181 ctaggaagat ccttatcgat tttaccacat ttgtagaggt tttacttgct ttaaaaaacc
      241 tcccacatct ccccctgaac ctgaaacata aaatgaatgc aattgtacag tccggaccgc
      301 atccccagca tgcctgctat tgtcttccca atcctccccc ttgctgtcct gccccacccc
      361 accccccaga atagaatgac acctactcag acaatgcgat gcaatttcct cattttatta
      421 ggaaaggaca gtgggagtgg caccttccag ggtcaaggaa ggcacggggg aggggcaaac
      481 aacagatggc tggcaactag aaggcacagt cgagctttat gagcggccgc ccgggtcgac
      541 ggtatcgatg cggggaggcg gcccaaaggg agatccgact cgtctgaggg cgaaggcgaa
      601 gacgcggaag aggccgcaga gccggcagca ggccgcggga aggaaggtcc gctggattga
      661 gggccgaagg gacgtagcag aaggacgtcc cgcgcagaat ccaggtggca acacaggcga
      721 gcagccaagg aaaggacgat gatttccccg acaacaccac ggaattgtca gtgcccaaca
      781 gccgagcccc tgtccagcag cgggcaaggc aggcggcgat gagttccgcc gtggcaatag
      841 ggagggggaa agcgaaagtc ccggaaagga gctgacaggt ggtggcaatg ccccaaccag
      901 tgggggttgc gtcagcaaac acagtgcaca ccacgccacg ttgcctgaca acgggccaca
      961 actcctcata aagagacagc aaccaggatt tatacaagga ggagaaaatg aaagccatac
     1021 gggaagcaat agcatgatac aaaggcatta aagcagcgta tccacatagc gtaaaaggag
     1081 caacatagtt aagaatacca gtcaatcttt cacaaatttt gtaatccaga ggttgattat
     1141 cgataagctt cgcgaacctc ttcgagggac ataacttcgt ataatgtatg ctatacgaag
     1201 ttatgggtcg atggtgagat ctggactaga gggtcgatgg tgatgcttgg atcaaaatag
     1261 gaagaatccc aatgataact tcgtataaag tatcctatac gaagttatac taggtacctt
     1321 acttatacag ctcatccatg ccgtacagaa acagatggtg gcgtccttca gacctctcat
     1381 actgttccac aatggtgtag tcttcattgt gggatgtgat atccagcttg gtgtccacat
     1441 agtaatagcc gggcagctgc actggtttct tggccatgta gatggttttg aactccacca
     1501 ggtagtggcc gccgtctttc agcttcaggg cctggtggat ttcgcccttc agcactccgt
     1561 ctctaggata cagccgttca gtgctggcct cccaccccat tgttttcttc tgcatcacgg
     1621 gcccatcggg tggaaaattg gtgccgcgca ttttgacttt gtagatcaga gtgccatcct
     1681 gcagagagga gtcctgtgtc acggtcacca ggcctccatc ttcaaaattc atcactctct
     1741 cccacttaaa gccctctggg aaagacagtt tcttgtaatc aggaatgtca gcgggatgct
     1801 tgacataggc cttacttccg tacataaact gaggagacag gatatcccaa gcgaaaggca
     1861 gtggtcctcc cttggtcact ttcagcttgg cagtctgtgt gccctcgtaa ggcctccctt
     1921 cgccctctcc ttcaatctca aattcgtgcc cattcatgct gccctccatg cgcaccttaa
     1981 acctcatgaa ctctttgatc acagccatat tgttatcctc gcttgaggcg gttccactag
     2041 accctgagcc ggtacttcca gtcccatggc ccaggaacag atggtgtctc ccctcgctcc
     2101 gttcatactg ctccacaata gtgtagtcct cgttgtgtga agtgatatcc agttttgtgt
     2161 ccacgtaata gtagcctggc agctgcacag gtttcttggc catgtagatt gtcttgaact
     2221 ccaccaggta atgtccccca tctttcagct tcagagcctg gtggatttct cctttcagca
     2281 ccccgtcgcg tggatacagc ctttcggtgg aggcctccca tcccatagtt ttcttctgca
     2341 tcacaggtcc atcaggggga aaatttgtcc ctctcatttt caccttgtag atcagggtcc
     2401 catcctgcag ggagctgtcc tgggtcacag tcaccaggcc tccgtcctcg aagttcatca
     2461 ctctttccca cttaaacccc tcggggaagc tcagtttctt ataatcggga atgtcagctg
     2521 gatgtttcac ataggccttg gagccgtaca taaactgtgg gctcaggatg tcccaagcga
     2581 atggcagagg cccgcccttt gtcactttca gcttggctgt ctgggtgccc tcgtagggcc
     2641 gtccctctcc ttctccctca atttcgaact cgtggccgtt catgcttcct tccattctca
     2701 ccttaaaccg catgaactct ttgatcactt cctcgccctt actcactgct actaccggtg
     2761 ccgccactgt gtcctcgtcc tcctcctcca cgaactcttc cacttccacc tcctcgcctc
     2821 cgatctccat cttggtggtc ttccggatgt cgccgtggat caggatgtgc tcgtggatct
     2881 tgatcctcag gtggtgggcc aggaaggtcc aaaactcctt ggcgatgatg tcgcagatgc
     2941 tgtggccgat gctgttggcg taagggctca gcttcagcag tccttctggt cccactgccc
     3001 agaggattgg gtagctgccc caagaggcga agtaagcgta ggccatcagc ttcacgacca
     3061 tgcggcaatg gcctttaggc acgctgtggt tggcttccac gtagcacttg gcggcctgga
     3121 agtacatgta gccgccgtag atgcaagaca cgatatacag cagccacttg agccaatcgg
     3181 tagccagtcc tgcggccatg ccgaacacga tcattcccac gcaagacacg atcaggccca
     3241 tggtccgctt gctgtagtcg ttcttcaggc cgctcaggtt gctcagtctg atcaggatca
     3301 cggggcaaga cagcagccac tcgaagtagc gcaggcaata ggcgtggttg ccggtagaca
     3361 ggtacactgt ggcggggctg ctgaactcct tgaagatctc cagggtcacg aacagcacct
     3421 cgacgcaaca gacgtagacc tcctcccaac cgcaagtggc cttccaggcg ctgaagccgt
     3481 agaatgtcag cagggcgatg gcgatgctga aagcaatcca ctggcagacc tgggcgccga
     3541 tcttttctcc tggtgtgcct ctgctgtgca gccaagcctg cttcttctcc actcccacga
     3601 ccaggtagcc gcctgtggcc tccacgaagc aatatccgta tccggcgtcg ctcagtccgt
     3661 aagaagggtc acaccaccac tcggtgctga agcactcgcc tgtaggtgtc attcctccac
     3721 agcccatgtc ctcgtggtgg taggggttag gccaagggtt gatgcctccg gcggcaaaca
     3781 gagatctggt ggcgctgctg atcagctcag ccatggtggc gctagctagt ataacttcgt
     3841 atagcataca ttatacgaag ttatgggtcg atggtgatgc ttggcaattc gggtcgatgg
     3901 tgaagcattg gtcttcctat tttgatataa cttcgtatag gatactttat acgaagttat
     3961 gggaattctt ctcgactgcg ctctcaggca cgacacgact cctccgctgc ccaccgcaga
     4021 ctgaggcagc gctgagtcgc cggcgccgca gcgcagatgg tcgcgcccgt gcccccctat
     4081 ctcgcgcctc gcgtggtgcg gtccggctgg gccggcggcg gcgcggacgc gaccaaggtg
     4141 gccgggaagg ggagtttgcg ggggaccggc gagtgacgtc agcgcgcctt cagtgctgag
     4201 gcggcggtgg cgcgcgccgc caggcggggg cgaaggcact gtccgcggtg ctgaagctgg
     4261 cagtgcgcac gcgcctcgcc gcatcctgtt tcccctcccc ctctctgata ggggatgcgc
     4321 aatttgggga atgggggttg ggtgcttgtc cagtgggtcg gggtcggtcg tcaggtaggc
     4381 acccccaccc cgcctcatcc tggtcctaaa acccacttgc actcatacgc agggccctct
     4441 gcagtctaga cacttaatta acctacgatc ttcctagagc atggctacgt agataagtag
     4501 catggcgggt taatcattaa ctacaaggaa cccctagtga tggagttggc cactccctct
     4561 ctgcgcgctc gctcgctcac tgaggccggg cgaccaaagg tcgcccgacg cccgggcttt
     4621 gcccgggcgg cctcagtgag cgagcgagcg cgcagctggc gtaatagcga agaggcccgc
     4681 accgatcgcc cttcccaaca gttgcgcagc ctgaatggcg aatgggacgc gccctgtagc
     4741 ggcgcattaa gcgcggcggg tgtggtggtt acgcgcagcg tgaccgctac acttgccagc
     4801 gccctagcgc ccgctccttt cgctttcttc ccttcctttc tcgccacgtt cgccggcttt
     4861 ccccgtcaag ctctaaatcg ggggctccct ttagggttcc gatttagtgc tttacggcac
     4921 ctcgacccca aaaaacttga ttagggtgat ggttcacgta gtgggccatc gccctgatag
     4981 acggtttttc gccctttgac gttggagtcc acgttcttta atagtggact cttgttccaa
     5041 actggaacaa cactcaaccc tatctcggtc tattcttttg atttataagg gattttgccg
     5101 atttcggcct attggttaaa aaatgagctg atttaacaaa aatttaacgc gaattttaac
     5161 aaaatattaa cgcttacaat ttaggtggca cttttcgggg aaatgtgcgc ggaaccccta
     5221 tttgtttatt tttctaaata cattcaaata tgtatccgct catgagacaa taaccctgat
     5281 aaatgcttca ataatattga aaaaggaaga gtatgagtat tcaacatttc cgtgtcgccc
     5341 ttattccctt ttttgcggca ttttgccttc ctgtttttgc tcacccagaa acgctggtga
     5401 aagtaaaaga tgctgaagat cagttgggtg cacgagtggg ttacatcgaa ctggatctca
     5461 acagcggtaa gatccttgag agttttcgcc ccgaagaacg ttttccaatg atgagcactt
     5521 ttaaagttct gctatgtggc gcggtattat cccgtattga cgccgggcaa gagcaactcg
     5581 gtcgccgcat acactattct cagaatgact tggttgagta ctcaccagtc acagaaaagc
     5641 atcttacgga tggcatgaca gtaagagaat tatgcagtgc tgccataacc atgagtgata
     5701 acactgcggc caacttactt ctgacaacga tcggaggacc gaaggagcta accgcttttt
     5761 tgcacaacat gggggatcat gtaactcgcc ttgatcgttg ggaaccggag ctgaatgaag
     5821 ccataccaaa cgacgagcgt gacaccacga tgcctgtagc aatggcaaca acgttgcgca
     5881 aactattaac tggcgaacta cttactctag cttcccggca acaattaata gactggatgg
     5941 aggcggataa agttgcagga ccacttctgc gctcggccct tccggctggc tggtttattg
     6001 ctgataaatc tggagccggt gagcgtgggt ctcgcggtat cattgcagca ctggggccag
     6061 atggtaagcc ctcccgtatc gtagttatct acacgacggg gagtcaggca actatggatg
     6121 aacgaaatag acagatcgct gagataggtg cctcactgat taagcattgg taactgtcag
     6181 accaagttta ctcatatata ctttagattg atttaaaact tcatttttaa tttaaaagga
     6241 tctaggtgaa gatccttttt gataatctca tgaccaaaat cccttaacgt gagttttcgt
     6301 tccactgagc gtcagacccc gtagaaaaga tcaaaggatc ttcttgagat cctttttttc
     6361 tgcgcgtaat ctgctgcttg caaacaaaaa aaccaccgct accagcggtg gtttgtttgc
     6421 cggatcaaga gctaccaact ctttttccga aggtaactgg cttcagcaga gcgcagatac
     6481 caaatactgt tcttctagtg tagccgtagt taggccacca cttcaagaac tctgtagcac
     6541 cgcctacata cctcgctctg ctaatcctgt taccagtggc tgctgccagt ggcgataagt
     6601 cgtgtcttac cgggttggac tcaagacgat agttaccgga taaggcgcag cggtcgggct
     6661 gaacgggggg ttcgtgcaca cagcccagct tggagcgaac gacctacacc gaactgagat
     6721 acctacagcg tgagctatga gaaagcgcca cgcttcccga agggagaaag gcggacaggt
     6781 atccggtaag cggcagggtc ggaacaggag agcgcacgag ggagcttcca gggggaaacg
     6841 cctggtatct ttatagtcct gtcgggtttc gccacctctg acttgagcgt cgatttttgt
     6901 gatgctcgtc aggggggcgg agcctatgga aaaacgccag caacgcggcc tttttacggt
     6961 tcctggcctt ttgctggcct tttgctcaca tgttctttcc tgcgttatcc cctgattctg
     7021 tggataaccg tattaccgcc tttgagtgag ctgataccgc tcgccgcagc cgaacgaccg
     7081 agcgcagcga gtcagtgagc gaggaagcgg aagagcgccc aatacgcaaa ccgcctctcc
     7141 ccgcgcgttg gccgattcat taatgc
//
