LOCUS       sequence-166279-        7180 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  AAV-mediated expression of ChrimsonR-tdTomato under the Syn 
            promoter, in floxed/reversed (Cre-dependent) manner. 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 7180)
  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 7180)
  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-rc[ChrimsonR-tdTomato]
FEATURES             Location/Qualifiers
     source          1..7180
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        complement(32..479)
                     /label=hSyn promoter
                     /note="human synapsin I promoter; confers neuron-specific 
                     expression (Kugler et al., 2003)"
     repeat_region   582..711
                     /label=AAV2 ITR
     rep_origin      783..1238
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(870..889)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1080..1101
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        1264..1368
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(1369..1437,1438..2229)
                     /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(1587..1606)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      2400..2988
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     2889..2908
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     repeat_region   3225..3354
                     /label=AAV2 ITR
     polyA_signal    3524..3731
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     misc_feature    3772..4360
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     CDS             3878..3889
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     primer_bind     4287..4307
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     protein_bind    4393..4426
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     protein_bind    4497..4530
                     /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)."
     regulatory      4552..4561
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             4558..5607
                     /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(7067..7100)
                     /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(join(7163..7180,1..16))
                     /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)."
ORIGIN
        1 ctttatacga agttatggga attcttctcg actgcgctct caggcacgac acgactcctc
       61 cgctgcccac cgcagactga ggcagcgctg agtcgccggc gccgcagcgc agatggtcgc
      121 gcccgtgccc ccctatctcg cgcctcgcgt ggtgcggtcc ggctgggccg gcggcggcgc
      181 ggacgcgacc aaggtggccg ggaaggggag tttgcggggg accggcgagt gacgtcagcg
      241 cgccttcagt gctgaggcgg cggtggcgcg cgccgccagg cgggggcgaa ggcactgtcc
      301 gcggtgctga agctggcagt gcgcacgcgc ctcgccgcat cctgtttccc ctccccctct
      361 ctgatagggg atgcgcaatt tggggaatgg gggttgggtg cttgtccagt gggtcggggt
      421 cggtcgtcag gtaggcaccc ccaccccgcc tcatcctggt cctaaaaccc acttgcactc
      481 atacgcaggg ccctctgcag tctagacact taattaacct acgatcttcc tagagcatgg
      541 ctacgtagat aagtagcatg gcgggttaat cattaactac aaggaacccc tagtgatgga
      601 gttggccact ccctctctgc gcgctcgctc gctcactgag gccgggcgac caaaggtcgc
      661 ccgacgcccg ggctttgccc gggcggcctc agtgagcgag cgagcgcgca gctggcgtaa
      721 tagcgaagag gcccgcaccg atcgcccttc ccaacagttg cgcagcctga atggcgaatg
      781 ggacgcgccc tgtagcggcg cattaagcgc ggcgggtgtg gtggttacgc gcagcgtgac
      841 cgctacactt gccagcgccc tagcgcccgc tcctttcgct ttcttccctt cctttctcgc
      901 cacgttcgcc ggctttcccc gtcaagctct aaatcggggg ctccctttag ggttccgatt
      961 tagtgcttta cggcacctcg accccaaaaa acttgattag ggtgatggtt cacgtagtgg
     1021 gccatcgccc tgatagacgg tttttcgccc tttgacgttg gagtccacgt tctttaatag
     1081 tggactcttg ttccaaactg gaacaacact caaccctatc tcggtctatt cttttgattt
     1141 ataagggatt ttgccgattt cggcctattg gttaaaaaat gagctgattt aacaaaaatt
     1201 taacgcgaat tttaacaaaa tattaacgct tacaatttag gtggcacttt tcggggaaat
     1261 gtgcgcggaa cccctatttg tttatttttc taaatacatt caaatatgta tccgctcatg
     1321 agacaataac cctgataaat gcttcaataa tattgaaaaa ggaagagtat gagtattcaa
     1381 catttccgtg tcgcccttat tccctttttt gcggcatttt gccttcctgt ttttgctcac
     1441 ccagaaacgc tggtgaaagt aaaagatgct gaagatcagt tgggtgcacg agtgggttac
     1501 atcgaactgg atctcaacag cggtaagatc cttgagagtt ttcgccccga agaacgtttt
     1561 ccaatgatga gcacttttaa agttctgcta tgtggcgcgg tattatcccg tattgacgcc
     1621 gggcaagagc aactcggtcg ccgcatacac tattctcaga atgacttggt tgagtactca
     1681 ccagtcacag aaaagcatct tacggatggc atgacagtaa gagaattatg cagtgctgcc
     1741 ataaccatga gtgataacac tgcggccaac ttacttctga caacgatcgg aggaccgaag
     1801 gagctaaccg cttttttgca caacatgggg gatcatgtaa ctcgccttga tcgttgggaa
     1861 ccggagctga atgaagccat accaaacgac gagcgtgaca ccacgatgcc tgtagcaatg
     1921 gcaacaacgt tgcgcaaact attaactggc gaactactta ctctagcttc ccggcaacaa
     1981 ttaatagact ggatggaggc ggataaagtt gcaggaccac ttctgcgctc ggcccttccg
     2041 gctggctggt ttattgctga taaatctgga gccggtgagc gtgggtctcg cggtatcatt
     2101 gcagcactgg ggccagatgg taagccctcc cgtatcgtag ttatctacac gacggggagt
     2161 caggcaacta tggatgaacg aaatagacag atcgctgaga taggtgcctc actgattaag
     2221 cattggtaac tgtcagacca agtttactca tatatacttt agattgattt aaaacttcat
     2281 ttttaattta aaaggatcta ggtgaagatc ctttttgata atctcatgac caaaatccct
     2341 taacgtgagt tttcgttcca ctgagcgtca gaccccgtag aaaagatcaa aggatcttct
     2401 tgagatcctt tttttctgcg cgtaatctgc tgcttgcaaa caaaaaaacc accgctacca
     2461 gcggtggttt gtttgccgga tcaagagcta ccaactcttt ttccgaaggt aactggcttc
     2521 agcagagcgc agataccaaa tactgttctt ctagtgtagc cgtagttagg ccaccacttc
     2581 aagaactctg tagcaccgcc tacatacctc gctctgctaa tcctgttacc agtggctgct
     2641 gccagtggcg ataagtcgtg tcttaccggg ttggactcaa gacgatagtt accggataag
     2701 gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc
     2761 tacaccgaac tgagatacct acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg
     2821 agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag
     2881 cttccagggg gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca cctctgactt
     2941 gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa cgccagcaac
     3001 gcggcctttt tacggttcct ggccttttgc tggccttttg ctcacatgtt ctttcctgcg
     3061 ttatcccctg attctgtgga taaccgtatt accgcctttg agtgagctga taccgctcgc
     3121 cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg aagcggaaga gcgcccaata
     3181 cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctgcgc gctcgctcgc
     3241 tcactgaggc cgcccgggca aagcccgggc gtcgggcgac ctttggtcgc ccggcctcag
     3301 tgagcgagcg agcgcgcaga gagggagtgg ccaactccat cactaggggt tccttgtagt
     3361 taatgattaa cccgccatgc tacttatcta cgtagccatg ctctaggaag atccttatcg
     3421 attttaccac atttgtagag gttttacttg ctttaaaaaa cctcccacat ctccccctga
     3481 acctgaaaca taaaatgaat gcaattgtac agtccggacc gcatccccag catgcctgct
     3541 attgtcttcc caatcctccc ccttgctgtc ctgccccacc ccacccccca gaatagaatg
     3601 acacctactc agacaatgcg atgcaatttc ctcattttat taggaaagga cagtgggagt
     3661 ggcaccttcc agggtcaagg aaggcacggg ggaggggcaa acaacagatg gctggcaact
     3721 agaaggcaca gtcgagcttt atgagcggcc gcccgggtcg acggtatcga tgcggggagg
     3781 cggcccaaag ggagatccga ctcgtctgag ggcgaaggcg aagacgcgga agaggccgca
     3841 gagccggcag caggccgcgg gaaggaaggt ccgctggatt gagggccgaa gggacgtagc
     3901 agaaggacgt cccgcgcaga atccaggtgg caacacaggc gagcagccaa ggaaaggacg
     3961 atgatttccc cgacaacacc acggaattgt cagtgcccaa cagccgagcc cctgtccagc
     4021 agcgggcaag gcaggcggcg atgagttccg ccgtggcaat agggaggggg aaagcgaaag
     4081 tcccggaaag gagctgacag gtggtggcaa tgccccaacc agtgggggtt gcgtcagcaa
     4141 acacagtgca caccacgcca cgttgcctga caacgggcca caactcctca taaagagaca
     4201 gcaaccagga tttatacaag gaggagaaaa tgaaagccat acgggaagca atagcatgat
     4261 acaaaggcat taaagcagcg tatccacata gcgtaaaagg agcaacatag ttaagaatac
     4321 cagtcaatct ttcacaaatt ttgtaatcca gaggttgatt atcgataagc ttcgcgaacc
     4381 tcttcgaggg acataacttc gtataatgta tgctatacga agttatgggt cgatggtgag
     4441 atctggacta gagggtcgat ggtgatgctt ggatcaaaat aggaagaatc ccaatgataa
     4501 cttcgtataa agtatcctat acgaagttat actaggtacc taggccgcgc cgccaccatg
     4561 gctgagctga tcagcagcgc caccagatct ctgtttgccg ccggaggcat caacccttgg
     4621 cctaacccct accaccacga ggacatgggc tgtggaggaa tgacacctac aggcgagtgc
     4681 ttcagcaccg agtggtggtg tgacccttct tacggactga gcgacgccgg atacggatat
     4741 tgcttcgtgg aggccacagg cggctacctg gtcgtgggag tggagaagaa gcaggcttgg
     4801 ctgcacagca gaggcacacc aggagaaaag atcggcgccc aggtctgcca gtggattgct
     4861 ttcagcatcg ccatcgccct gctgacattc tacggcttca gcgcctggaa ggccacttgc
     4921 ggttgggagg aggtctacgt ctgttgcgtc gaggtgctgt tcgtgaccct ggagatcttc
     4981 aaggagttca gcagccccgc cacagtgtac ctgtctaccg gcaaccacgc ctattgcctg
     5041 cgctacttcg agtggctgct gtcttgcccc gtgatcctga tcagactgag caacctgagc
     5101 ggcctgaaga acgactacag caagcggacc atgggcctga tcgtgtcttg cgtgggaatg
     5161 atcgtgttcg gcatggccgc aggactggct accgattggc tcaagtggct gctgtatatc
     5221 gtgtcttgca tctacggcgg ctacatgtac ttccaggccg ccaagtgcta cgtggaagcc
     5281 aaccacagcg tgcctaaagg ccattgccgc atggtcgtga agctgatggc ctacgcttac
     5341 ttcgcctctt ggggcagcta cccaatcctc tgggcagtgg gaccagaagg actgctgaag
     5401 ctgagccctt acgccaacag catcggccac agcatctgcg acatcatcgc caaggagttt
     5461 tggaccttcc tggcccacca cctgaggatc aagatccacg agcacatcct gatccacggc
     5521 gacatccgga agaccaccaa gatggagatc ggaggcgagg aggtggaagt ggaagagttc
     5581 gtggaggagg aggacgagga cacagtggcg gcaccggtag tagcagtgag taagggcgag
     5641 gaagtgatca aagagttcat gcggtttaag gtgagaatgg aaggaagcat gaacggccac
     5701 gagttcgaaa ttgagggaga aggagaggga cggccctacg agggcaccca gacagccaag
     5761 ctgaaagtga caaagggcgg gcctctgcca ttcgcttggg acatcctgag cccacagttt
     5821 atgtacggct ccaaggccta tgtgaaacat ccagctgaca ttcccgatta taagaaactg
     5881 agcttccccg aggggtttaa gtgggaaaga gtgatgaact tcgaggacgg aggcctggtg
     5941 actgtgaccc aggacagctc cctgcaggat gggaccctga tctacaaggt gaaaatgaga
     6001 gggacaaatt ttccccctga tggacctgtg atgcagaaga aaactatggg atgggaggcc
     6061 tccaccgaaa ggctgtatcc acgcgacggg gtgctgaaag gagaaatcca ccaggctctg
     6121 aagctgaaag atgggggaca ttacctggtg gagttcaaga caatctacat ggccaagaaa
     6181 cctgtgcagc tgccaggcta ctattacgtg gacacaaaac tggatatcac ttcacacaac
     6241 gaggactaca ctattgtgga gcagtatgaa cggagcgagg ggagacacca tctgttcctg
     6301 ggccatggga ctggaagtac cggctcaggg tctagtggaa ccgcctcaag cgaggataac
     6361 aatatggctg tgatcaaaga gttcatgagg tttaaggtgc gcatggaggg cagcatgaat
     6421 gggcacgaat ttgagattga aggagagggc gaagggaggc cttacgaggg cacacagact
     6481 gccaagctga aagtgaccaa gggaggacca ctgcctttcg cttgggatat cctgtctcct
     6541 cagtttatgt acggaagtaa ggcctatgtc aagcatcccg ctgacattcc tgattacaag
     6601 aaactgtctt tcccagaggg ctttaagtgg gagagagtga tgaattttga agatggaggc
     6661 ctggtgaccg tgacacagga ctcctctctg caggatggca ctctgatcta caaagtcaaa
     6721 atgcgcggca ccaattttcc acccgatggg cccgtgatgc agaagaaaac aatggggtgg
     6781 gaggccagca ctgaacggct gtatcctaga gacggagtgc tgaagggcga aatccaccag
     6841 gccctgaagc tgaaagacgg cggccactac ctggtggagt tcaaaaccat ctacatggcc
     6901 aagaaaccag tgcagctgcc cggctattac tatgtggaca ccaagctgga tatcacatcc
     6961 cacaatgaag actacaccat tgtggaacag tatgagaggt ctgaaggacg ccaccatctg
     7021 tttctgtacg gcatggatga gctgtataag taatgagcta gctagtataa cttcgtatag
     7081 catacattat acgaagttat gggtcgatgg tgatgcttgg caattcgggt cgatggtgaa
     7141 gcattggtct tcctattttg atataacttc gtataggata
//
