LOCUS       sequence-419385-        6323 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  flexed-ReaChR-citrine in AAV2 vector under human synapsin promoter.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6323)
  AUTHORS   Lin JY, Knutsen PM, Muller A, Kleinfeld D, Tsien RY
  TITLE     ReaChR: a red-shifted variant of channelrhodopsin enables deep 
            transcranial optogenetic excitation.
  JOURNAL   Nat Neurosci. 2013 Oct;16(10):1499-508. doi: 10.1038/nn.3502. Epub 
            2013 Sep 1.
  PUBMED    23995068
REFERENCE   2  (bases 1 to 6323)
  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/nn.3502"; 
            journalName: "Nat Neurosci"; date: "2013-10"; volume: "16"; issue: 
            "10"; pages: "1499-508"
COMMENT     Sequence Label: AAV-flex-ReaChR-citrine
FEATURES             Location/Qualifiers
     source          1..6323
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      complement(28..456)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(138..159)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     350..369
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     repeat_region   528..657
                     /label=AAV2 ITR
     promoter        739..1186
                     /label=hSyn promoter
                     /note="human synapsin I promoter; confers neuron-specific 
                     expression (Kugler et al., 2003)"
     protein_bind    complement(1232..1265)
                     /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(1316..1349)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     CDS             complement(join(1364..2074,2075..2077,2078..2080))
                     /codon_start=1
                     /product="enhanced variant of YFP (Heikal et al., 2001)"
                     /label=Citrine
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTFGYGLMCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(1406..1427)
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     primer_bind     1755..1774
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     2014..2035
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     protein_bind    3146..3179
                     /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    3230..3263
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     misc_feature    3288..3876
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3341..3361)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(3759..3770)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     primer_bind     complement(3879..3895)
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3880..3896)
                     /label=pBluescriptKS
                     /note="For pBluescript vector"
     polyA_signal    3925..4046
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3936..3955)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3990..4009
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     repeat_region   4208..4337
                     /label=AAV2 ITR
     rep_origin      complement(4574..5162)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4654..4673)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5333..6124,6125..6193))
                     /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     5956..5975
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6194..6298)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 aaattgtaag cgttaatatt ttgttaaaat tcgcgttaaa tttttgttaa atcagctcat
       61 tttttaacca ataggccgaa atcggcaaaa tcccttataa atcaaaagaa tagaccgaga
      121 tagggttgag tgttgttcca gtttggaaca agagtccact attaaagaac gtggactcca
      181 acgtcaaagg gcgaaaaacc gtctatcagg gcgatggccc actacgtgaa ccatcaccct
      241 aatcaagttt tttggggtcg aggtgccgta aagcactaaa tcggaaccct aaagggagcc
      301 cccgatttag agcttgacgg ggaaagccgg cgaacgtggc gagaaaggaa gggaagaaag
      361 cgaaaggagc gggcgctagg gcgctggcaa gtgtagcggt cacgctgcgc gtaaccacca
      421 cacccgccgc gcttaatgcg ccgctacagg gcgcgtccca ttcgccattc aggctgcgca
      481 actgttggga agggcgatcg gtgcgggcct cttcgctatt acgccagctg cgcgctcgct
      541 cgctcactga ggccgcccgg gcaaagcccg ggcgtcgggc gacctttggt cgcccggcct
      601 cagtgagcga gcgagcgcgc agagagggag tggccaactc catcactagg ggttccttgt
      661 agttaatgat taacccgcca tgctacttat ctacgtagcc atgctctagg aagatctctg
      721 cagagggccc tgcgtatgag tgcaagtggg ttttaggacc aggatgaggc ggggtggggg
      781 tgcctacctg acgaccgacc ccgacccact ggacaagcac ccaaccccca ttccccaaat
      841 tgcgcatccc ctatcagaga gggggagggg aaacaggatg cggcgaggcg cgtgcgcact
      901 gccagcttca gcaccgcgga cagtgccttc gcccccgcct ggcggcgcgc gccaccgccg
      961 cctcagcact gaaggcgcgc tgacgtcact cgccggtccc ccgcaaactc cccttcccgg
     1021 ccaccttggt cgcgtccgcg ccgccgccgg cccagccgga ccgcaccacg cgaggcgcga
     1081 gatagggggg cacgggcgcg accatctgcg ctgcggcgcc ggcgactcag cgctgcctca
     1141 gtctgcggtg ggcagcggag gagtcgtgtc gtgcctgaga gcgcagtcga attcaagctg
     1201 atagcaagga tcctctagag tcgactccgg aataacttcg tataggatac tttatacgaa
     1261 gttatgcaga atggtagctg gattgtagct gctattagca atatgaaacc tcttaataac
     1321 ttcgtatagc atacattata cgaagttatg gcgcgcccta ctacttgtac agctcgtcca
     1381 tgccgagagt gatcccggcg gcggtcacga actccagcag gaccatgtga tcgcgcttct
     1441 cgttggggtc tttgctcagg gcggactggt agctcaggta gtggttgtcg ggcagcagca
     1501 cggggccgtc gccgatgggg gtgttctgct ggtagtggtc ggcgagctgc acgctgccgt
     1561 cctcgatgtt gtggcggatc ttgaagttca ccttgatgcc gttcttctgc ttgtcggcca
     1621 tgatatagac gttgtggctg ttgtagttgt actccagctt gtgccccagg atgttgccgt
     1681 cctccttgaa gtcgatgccc ttcagctcga tgcggttcac cagggtgtcg ccctcgaact
     1741 tcacctcggc gcgggtcttg tagttgccgt cgtccttgaa gaagatggtg cgctcctgga
     1801 cgtagccttc gggcatggcg gacttgaaga agtcgtgctg cttcatgtgg tcggggtagc
     1861 gggcgaagca catcaggccg tagccgaagg tggtcacgag ggtgggccag ggcacgggca
     1921 gcttgccggt ggtgcagatg aacttcaggg tcagcttgcc gtaggtggca tcgccctcgc
     1981 cctcgccgga cacgctgaac ttgtggccgt ttacgtcgcc gtccagctcg accaggatgg
     2041 gcaccacccc ggtgaacagc tcctcgccct tgctcaccat ctcgaggctg ctctcgtact
     2101 tatcttcttc ttccgccacc agggtttcca cttccatttc ctggcccgca atggtaattt
     2161 tctgtttttt gcgaatatcg ccatacagca gaatatgttc atgaattttc acgcgcagat
     2221 agttgcccag cacgccccac atgttcttcg caatcagatc cagaatgcta tggccaatcg
     2281 cgctgccata cgggctaata tggccgaagc cctcggggcc cagcaggaac agcacgggga
     2341 acatgcccca gctcacgaag aacagccagg ccatggctct caccagctgt ctgcacaggc
     2401 ctttcggcac ggtatgaaac gcttcaatat acactttggc cgcatgaaaa taggtataca
     2461 tgccatagct caggctaatc agaaaaaaca gaattttggt ccagccggtg cacatcgcgc
     2521 tggtcgcgcc ccacacaatg cagcccacgt cgctcaccag caggcccatg gtgcgtttgc
     2581 tataatcatc tttcaggccg gtcaggttgc tcagatgaat cagaatcacg gggcaggtca
     2641 gcagccattc gccatagcgc atccacacca cgccgttgcc gctgctcagc cacagggtcg
     2701 ccgggctatc aaattcatga aacgcttcaa taatgctttt catcatttca atcagcgcca
     2761 catacacttc ttcccagccg caggtcgcgc gccacgcctg atacgcatac cagcccaggc
     2821 acgccacgct cagcgcaaac accacccact gcaggatgtt ggcggccagc ttctcggcgt
     2881 tggtgccgtt actcttcagc caggccaggc agaagcactg gccgttgttg gggatgcaga
     2941 tcacgctgcc gttgttctcc agggtgtagc tggtctggaa cagcattctc tcgtgggctc
     3001 tgtggaacac gtagtcgggg ccgtcctggg tggccacggg cacggtggcg tcgctgccgg
     3061 tgctggcgcc ggcgctgccg gcggccaggg ccacggccag ggccagggcc agcagccagg
     3121 gtcttctgct caccatggtg ctagcataac ttcgtataaa gtatcctata cgaagttatt
     3181 tgccttaacc cagaaattat cactgttatt ctttagaatg gtgcaaagaa taacttcgta
     3241 taatgtatgc tatacgaagt tatgaattcg atatcaagct tatcgataat caacctctgg
     3301 attacaaaat ttgtgaaaga ttgactggta ttcttaacta tgttgctcct tttacgctat
     3361 gtggatacgc tgctttaatg cctttgtatc atgctattgc ttcccgtatg gctttcattt
     3421 tctcctcctt gtataaatcc tggttgctgt ctctttatga ggagttgtgg cccgttgtca
     3481 ggcaacgtgg cgtggtgtgc actgtgtttg ctgacgcaac ccccactggt tggggcattg
     3541 ccaccacctg tcagctcctt tccgggactt tcgctttccc cctccctatt gccacggcgg
     3601 aactcatcgc cgcctgcctt gcccgctgct ggacaggggc tcggctgttg ggcactgaca
     3661 attccgtggt gttgtcgggg aaatcatcgt cctttccttg gctgctcgcc tgtgttgcca
     3721 cctggattct gcgcgggacg tccttctgct acgtcccttc ggccctcaat ccagcggacc
     3781 ttccttcccg cggcctgctg ccggctctgc ggcctcttcc gcgtcttcgc cttcgccctc
     3841 agacgagtcg gatctccctt tgggccgcct ccccgcatcg ataccgtcga cctcgacccg
     3901 ggcggccgct tcgagcagac atgataagat acattgatga gtttggacaa accacaacta
     3961 gaatgcagtg aaaaaaatgc tttatttgtg aaatttgtga tgctattgct ttatttgtaa
     4021 ccattataag ctgcaataaa caagttaaca acaacaattg cattcatttt atgtttcagg
     4081 ttcaggggga gatgtgggag gttttttaaa gcaagtaaaa cctctacaaa tgtggtaaaa
     4141 tcgataagga tcttcctaga gcatggctac gtagataagt agcatggcgg gttaatcatt
     4201 aactacaagg aacccctagt gatggagttg gccactccct ctctgcgcgc tcgctcgctc
     4261 actgaggccg ggcgaccaaa ggtcgcccga cgcccgggct ttgcccgggc ggcctcagtg
     4321 agcgagcgag cgcgcagctg cattaatgaa tcggccaacg cgcggggaga ggcggtttgc
     4381 gtattgggcg ctcttccgct tcctcgctca ctgactcgct gcgctcggtc gttcggctgc
     4441 ggcgagcggt atcagctcac tcaaaggcgg taatacggtt atccacagaa tcaggggata
     4501 acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc caggaaccgt aaaaaggccg
     4561 cgttgctggc gtttttccat aggctccgcc cccctgacga gcatcacaaa aatcgacgct
     4621 caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggaa
     4681 gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc
     4741 tcccttcggg aagcgtggcg ctttctcata gctcacgctg taggtatctc agttcggtgt
     4801 aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg
     4861 ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta tcgccactgg
     4921 cagcagccac tggtaacagg attagcagag cgaggtatgt aggcggtgct acagagttct
     4981 tgaagtggtg gcctaactac ggctacacta gaagaacagt atttggtatc tgcgctctgc
     5041 tgaagccagt taccttcgga aaaagagttg gtagctcttg atccggcaaa caaaccaccg
     5101 ctggtagcgg tggttttttt gtttgcaagc agcagattac gcgcagaaaa aaaggatctc
     5161 aagaagatcc tttgatcttt tctacggggt ctgacgctca gtggaacgaa aactcacgtt
     5221 aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac ctagatcctt ttaaattaaa
     5281 aatgaagttt taaatcaatc taaagtatat atgagtaaac ttggtctgac agttaccaat
     5341 gcttaatcag tgaggcacct atctcagcga tctgtctatt tcgttcatcc atagttgcct
     5401 gactccccgt cgtgtagata actacgatac gggagggctt accatctggc cccagtgctg
     5461 caatgatacc gcgagaccca cgctcaccgg ctccagattt atcagcaata aaccagccag
     5521 ccggaagggc cgagcgcaga agtggtcctg caactttatc cgcctccatc cagtctatta
     5581 attgttgccg ggaagctaga gtaagtagtt cgccagttaa tagtttgcgc aacgttgttg
     5641 ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg tatggcttca ttcagctccg
     5701 gttcccaacg atcaaggcga gttacatgat cccccatgtt gtgcaaaaaa gcggttagct
     5761 ccttcggtcc tccgatcgtt gtcagaagta agttggccgc agtgttatca ctcatggtta
     5821 tggcagcact gcataattct cttactgtca tgccatccgt aagatgcttt tctgtgactg
     5881 gtgagtactc aaccaagtca ttctgagaat agtgtatgcg gcgaccgagt tgctcttgcc
     5941 cggcgtcaat acgggataat accgcgccac atagcagaac tttaaaagtg ctcatcattg
     6001 gaaaacgttc ttcggggcga aaactctcaa ggatcttacc gctgttgaga tccagttcga
     6061 tgtaacccac tcgtgcaccc aactgatctt cagcatcttt tactttcacc agcgtttctg
     6121 ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg aataagggcg acacggaaat
     6181 gttgaatact catactcttc ctttttcaat attattgaag catttatcag ggttattgtc
     6241 tcatgagcgg atacatattt gaatgtattt agaaaaataa acaaataggg gttccgcgca
     6301 catttccccg aaaagtgcca cct
//
