LOCUS       sequence-242270-        7470 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  AAV-mediated expression of ChrimsonR-tdTomato under the EF1-alpha 
            promoter (1.1kb short version).tdTomato has codons varied to reduce 
            recombination. Using SV40 pA signal..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7470)
  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 7470)
  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-EF1-alpha-1.1-ChrimsonR-tdTomato
FEATURES             Location/Qualifiers
     source          1..7470
                     /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        2661..3839
                     /label=EF-1-alpha promoter
                     /note="strong constitutive promoter for human elongation 
                     factor EF-1-alpha"
     intron          2892..3830
                     /label=EF-1-alpha intron A
                     /note="intron upstream of the start codon of human 
                     EF-1-alpha"
     primer_bind     3787..3807
                     /label=EF1a-F
                     /note="Human elongation factor-1a promoter, forward primer"
     regulatory      3846..3855
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             3852..4901
                     /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"
     misc_feature    6372..6960
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(6425..6445)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(6843..6854)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    7003..7124
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(7014..7033)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     7068..7087
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     repeat_region   7286..7415
                     /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 ggctccggtg cccgtcagtg ggcagagcgc acatcgccca
     2701 cagtccccga gaagttgggg ggaggggtcg gcaattgaac cggtgcctag agaaggtggc
     2761 gcggggtaaa ctgggaaagt gatgtcgtgt actggctccg cctttttccc gagggtgggg
     2821 gagaaccgta tataagtgca gtagtcgccg tgaacgttct ttttcgcaac gggtttgccg
     2881 ccagaacaca ggtaagtgcc gtgtgtggtt cccgcgggcc tggcctcttt acgggttatg
     2941 gcccttgcgt gccttgaatt acttccacct ggctgcagta cgtgattctt gatcccgagc
     3001 ttcgggttgg aagtgggtgg gagagttcga ggccttgcgc ttaaggagcc ccttcgcctc
     3061 gtgcttgagt tgaggcctgg cctgggcgct ggggccgccg cgtgcgaatc tggtggcacc
     3121 ttcgcgcctg tctcgctgct ttcgataagt ctctagccat ttaaaatttt tgatgacctg
     3181 ctgcgacgct ttttttctgg caagatagtc ttgtaaatgc gggccaagat ctgcacactg
     3241 gtatttcggt ttttggggcc gcgggcggcg acggggcccg tgcgtcccag cgcacatgtt
     3301 cgacgaggcg gggcctgcga gcgcggccac cgagaatcgg acgggggtag tctcaagctg
     3361 gccggcctgc tctggtgcct ggcctcgcgc cgccgtgtat cgccccgccc tgggcggcaa
     3421 ggctggcccg gtcggcacca gttgcgtgag cggaaagatg gccgcttccc ggccctgctg
     3481 cagggagctc aaaatggagg acgcggcgct cgggagagcg ggcgggtgag tcacccacac
     3541 aaaggaaaag ggcctttccg tcctcagccg tcgcttcatg tgactccacg gagtaccggg
     3601 cgccgtccag gcacctcgat tagttctcga gcttttggag tacgtcgtct ttaggttggg
     3661 gggaggggtt ttatgcgatg gagtttcccc acactgagtg ggtggagact gaagttaggc
     3721 cagcttggca cttgatgtaa ttctccttgg aatttgccct ttttgagttt ggatcttggt
     3781 tcattctcaa gcctcagaca gtggttcaaa gtttttttct tccatttcag gtgtcgtgag
     3841 gatccgccac catggctgag ctgatcagca gcgccaccag atctctgttt gccgccggag
     3901 gcatcaaccc ttggcctaac ccctaccacc acgaggacat gggctgtgga ggaatgacac
     3961 ctacaggcga gtgcttcagc accgagtggt ggtgtgaccc ttcttacgga ctgagcgacg
     4021 ccggatacgg atattgcttc gtggaggcca caggcggcta cctggtcgtg ggagtggaga
     4081 agaagcaggc ttggctgcac agcagaggca caccaggaga aaagatcggc gcccaggtct
     4141 gccagtggat tgctttcagc atcgccatcg ccctgctgac attctacggc ttcagcgcct
     4201 ggaaggccac ttgcggttgg gaggaggtct acgtctgttg cgtcgaggtg ctgttcgtga
     4261 ccctggagat cttcaaggag ttcagcagcc ccgccacagt gtacctgtct accggcaacc
     4321 acgcctattg cctgcgctac ttcgagtggc tgctgtcttg ccccgtgatc ctgatcagac
     4381 tgagcaacct gagcggcctg aagaacgact acagcaagcg gaccatgggc ctgatcgtgt
     4441 cttgcgtggg aatgatcgtg ttcggcatgg ccgcaggact ggctaccgat tggctcaagt
     4501 ggctgctgta tatcgtgtct tgcatctacg gcggctacat gtacttccag gccgccaagt
     4561 gctacgtgga agccaaccac agcgtgccta aaggccattg ccgcatggtc gtgaagctga
     4621 tggcctacgc ttacttcgcc tcttggggca gctacccaat cctctgggca gtgggaccag
     4681 aaggactgct gaagctgagc ccttacgcca acagcatcgg ccacagcatc tgcgacatca
     4741 tcgccaagga gttttggacc ttcctggccc accacctgag gatcaagatc cacgagcaca
     4801 tcctgatcca cggcgacatc cggaagacca ccaagatgga gatcggaggc gaggaggtgg
     4861 aagtggaaga gttcgtggag gaggaggacg aggacacagt ggcggcaccg gtagtagcag
     4921 tgagtaaggg cgaggaagtg atcaaagagt tcatgcggtt taaggtgaga atggaaggaa
     4981 gcatgaacgg ccacgagttc gaaattgagg gagaaggaga gggacggccc tacgagggca
     5041 cccagacagc caagctgaaa gtgacaaagg gcgggcctct gccattcgct tgggacatcc
     5101 tgagcccaca gtttatgtac ggctccaagg cctatgtgaa acatccagct gacattcccg
     5161 attataagaa actgagcttc cccgaggggt ttaagtggga aagagtgatg aacttcgagg
     5221 acggaggcct ggtgactgtg acccaggaca gctccctgca ggatgggacc ctgatctaca
     5281 aggtgaaaat gagagggaca aattttcccc ctgatggacc tgtgatgcag aagaaaacta
     5341 tgggatggga ggcctccacc gaaaggctgt atccacgcga cggggtgctg aaaggagaaa
     5401 tccaccaggc tctgaagctg aaagatgggg gacattacct ggtggagttc aagacaatct
     5461 acatggccaa gaaacctgtg cagctgccag gctactatta cgtggacaca aaactggata
     5521 tcacttcaca caacgaggac tacactattg tggagcagta tgaacggagc gaggggagac
     5581 accatctgtt cctgggccat gggactggaa gtaccggctc agggtctagt ggaaccgcct
     5641 caagcgagga taacaatatg gctgtgatca aagagttcat gaggtttaag gtgcgcatgg
     5701 agggcagcat gaatgggcac gaatttgaga ttgaaggaga gggcgaaggg aggccttacg
     5761 agggcacaca gactgccaag ctgaaagtga ccaagggagg accactgcct ttcgcttggg
     5821 atatcctgtc tcctcagttt atgtacggaa gtaaggccta tgtcaagcat cccgctgaca
     5881 ttcctgatta caagaaactg tctttcccag agggctttaa gtgggagaga gtgatgaatt
     5941 ttgaagatgg aggcctggtg accgtgacac aggactcctc tctgcaggat ggcactctga
     6001 tctacaaagt caaaatgcgc ggcaccaatt ttccacccga tgggcccgtg atgcagaaga
     6061 aaacaatggg gtgggaggcc agcactgaac ggctgtatcc tagagacgga gtgctgaagg
     6121 gcgaaatcca ccaggccctg aagctgaaag acggcggcca ctacctggtg gagttcaaaa
     6181 ccatctacat ggccaagaaa ccagtgcagc tgcccggcta ttactatgtg gacaccaagc
     6241 tggatatcac atcccacaat gaagactaca ccattgtgga acagtatgag aggtctgaag
     6301 gacgccacca tctgtttctg tacggcatgg atgagctgta taagtaagaa ttcgatatca
     6361 agcttatcga taatcaacct ctggattaca aaatttgtga aagattgact ggtattctta
     6421 actatgttgc tccttttacg ctatgtggat acgctgcttt aatgcctttg tatcatgcta
     6481 ttgcttcccg tatggctttc attttctcct ccttgtataa atcctggttg ctgtctcttt
     6541 atgaggagtt gtggcccgtt gtcaggcaac gtggcgtggt gtgcactgtg tttgctgacg
     6601 caacccccac tggttggggc attgccacca cctgtcagct cctttccggg actttcgctt
     6661 tccccctccc tattgccacg gcggaactca tcgccgcctg ccttgcccgc tgctggacag
     6721 gggctcggct gttgggcact gacaattccg tggtgttgtc ggggaaatca tcgtcctttc
     6781 cttggctgct cgcctgtgtt gccacctgga ttctgcgcgg gacgtccttc tgctacgtcc
     6841 cttcggccct caatccagcg gaccttcctt cccgcggcct gctgccggct ctgcggcctc
     6901 ttccgcgtct tcgccttcgc cctcagacga gtcggatctc cctttgggcc gcctccccgc
     6961 atcgataccg tcgacccggg cggccgcttc gagcagacat gataagatac attgatgagt
     7021 ttggacaaac cacaactaga atgcagtgaa aaaaatgctt tatttgtgaa atttgtgatg
     7081 ctattgcttt atttgtaacc attataagct gcaataaaca agttaacaac aacaattgca
     7141 ttcattttat gtttcaggtt cagggggaga tgtgggaggt tttttaaagc aagtaaaacc
     7201 tctacaaatg tggtaaaatc gataaggatc ttcctagagc atggctacgt agataagtag
     7261 catggcgggt taatcattaa ctacaaggaa cccctagtga tggagttggc cactccctct
     7321 ctgcgcgctc gctcgctcac tgaggccggg cgaccaaagg tcgcccgacg cccgggcttt
     7381 gcccgggcgg cctcagtgag cgagcgagcg cgcagctgca ttaatgaatc ggccaacgcg
     7441 cggggagagg cggtttgcgt attgggcgct
//
