LOCUS       sequence-91606-e        7609 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expression vector for Chrimson-tdTomato in a floxed/forward-reading,
            Cre-dependent manner (Cre turns gene off).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7609)
  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 7609)
  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: pCAG-FLEX-fwd[Chrimson-tdT]
FEATURES             Location/Qualifiers
     source          1..7609
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        4..383
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        385..660
                     /label=chicken beta-actin promoter
     intron          661..1674
                     /label=chimeric intron
                     /note="chimera between introns from chicken beta-actin and 
                     rabbit beta-globin"
     primer_bind     1598..1620
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     1682..1701
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     protein_bind    1731..1764
                     /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    1827..1860
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     regulatory      1874..1883
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             1880..2929
                     /codon_start=1
                     /product="red light-drivable channelrhodopsin from 
                     Chlamydomonas noctigama (Klapoetke et al., 2014)"
                     /label=Chrimson
                     /translation="MAELISSATRSLFAAGGINPWPNPYHHEDMGCGGMTPTGECFSTE
                     WWCDPSYGLSDAGYGYCFVEATGGYLVVGVEKKQAWLHSRGTPGEKIGAQVCQWIAFSI
                     AIALLTFYGFSAWKATCGWEEVYVCCVEVLFVTLEIFKEFSSPATVYLSTGNHAYCLRY
                     FEWLLSCPVILIKLSNLSGLKNDYSKRTMGLIVSCVGMIVFGMAAGLATDWLKWLLYIV
                     SCIYGGYMYFQAAKCYVEANHSVPKGHCRMVVKLMAYAYFASWGSYPILWAVGPEGLLK
                     LSPYANSIGHSICDIIAKEFWTFLAHHLRIKIHEHILIHGDIRKTTKMEIGGEEVEVEE
                     FVEEEDEDTV"
     protein_bind    complement(4391..4424)
                     /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(4495..4528)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     primer_bind     complement(4631..4650)
                     /label=Bglob-pA-R
                     /note="Rabbit beta-globin polyA region, reverse primer"
     polyA_signal    4696..4751
                     /label=beta-globin poly(A) signal
                     /note="rabbit beta-globin polyadenylation signal (Gil and 
                     Proudfoot, 1987)"
     primer_bind     complement(4750..4769)
                     /label=rbglobpA-R
                     /note="Rabbit beta-globin polyA, reverse primer. Also 
                     called rb-glob-pA-term-R"
     primer_bind     complement(5112..5128)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(5112..5128)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(5125..5147)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    5136..5152
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     promoter        complement(join(5160..5166,5167..5184,5185..5190))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5205..5226
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        5285..5480
                     /label=SV40 promoter
                     /note="SV40 early promoter"
     rep_origin      5331..5466
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    5486..5620
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(5523..5542)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     5577..5596
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(5688..5705)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(5859..6447)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5939..5958)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(6618..7409,7410..7478))
                     /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     7241..7260
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(7479..7583)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 gtcgacattg attattgact agttattaat agtaatcaat tacggggtca ttagttcata
       61 gcccatatat ggagttccgc gttacataac ttacggtaaa tggcccgcct ggctgaccgc
      121 ccaacgaccc ccgcccattg acgtcaataa tgacgtatgt tcccatagta acgccaatag
      181 ggactttcca ttgacgtcaa tgggtggagt atttacggta aactgcccac ttggcagtac
      241 atcaagtgta tcatatgcca agtacgcccc ctattgacgt caatgacggt aaatggcccg
      301 cctggcatta tgcccagtac atgaccttat gggactttcc tacttggcag tacatctacg
      361 tattagtcat cgctattacc atggtcgagg tgagccccac gttctgcttc actctcccca
      421 tctccccccc ctccccaccc ccaattttgt atttatttat tttttaatta ttttgtgcag
      481 cgatgggggc gggggggggg ggggcgcgcg ccaggcgggg cggggcgggg cgaggggcgg
      541 ggcggggcga ggcggagagg tgcggcggca gccaatcaga gcggcgcgct ccgaaagttt
      601 ccttttatgg cgaggcggcg gcggcggcgg ccctataaaa agcgaagcgc gcggcgggcg
      661 ggagtcgctg cgttgccttc gccccgtgcc ccgctccgcg ccgcctcgcg ccgcccgccc
      721 cggctctgac tgaccgcgtt actcccacag gtgagcgggc gggacggccc ttctcctccg
      781 ggctgtaatt agcgcttggt ttaatgacgg ctcgtttctt ttctgtggct gcgtgaaagc
      841 cttaaagggc tccgggaggg ccctttgtgc ggggggagcg gctcgggggg tgcgtgcgtg
      901 tgtgtgtgcg tggggagcgc cgcgtgcggc tccgcgctgc ccggcggctg tgagcgctgc
      961 gggcgcggcg cggggctttg tgcgctccgc agtgtgcgcg aggggagcgc ggccgggggc
     1021 ggtgccccgc ggtgcggggg gggctgcgag gggaacaaag gctgcgtgcg gggtgtgtgc
     1081 gtgggggggt gagcaggggg tgtgggcgcg tcggtcgggc tgcaaccccc cctgcacccc
     1141 cctccccgag ttgctgagca cggcccggct tcgggtgcgg ggctccgtac ggggcgtggc
     1201 gcggggctcg ccgtgccggg cggggggtgg cggcaggtgg gggtgccggg cggggcgggg
     1261 ccgcctcggg ccggggaggg ctcgggggag gggcgcggcg gcccccggag cgccggcggc
     1321 tgtcgaggcg cggcgagccg cagccattgc cttttatggt aatcgtgcga gagggcgcag
     1381 ggacttcctt tgtcccaaat ctgtgcggag ccgaaatctg ggaggcgccg ccgcaccccc
     1441 tctagcgggc gcggggcgaa gcggtgcggc gccggcagga aggaaatggg cggggagggc
     1501 cttcgtgcgt cgccgcgccg ccgtcccctt ctccctctcc agcctcgggg ctgtccgcgg
     1561 ggggacggct gccttcgggg gggacggggc agggcggggt tcggcttctg gcgtgtgacc
     1621 ggcggctcta gagcctctgc taaccatgtt catgccttct tctttttcct acagctcctg
     1681 ggcaacgtgc tggttattgt gctgtctcat cattttggca aagaattccc ataacttcgt
     1741 ataaagtatc ctatacgaag ttatatcaaa ataggaagac caatgcttca ccatcgaccc
     1801 gaattgccaa gcatcaccat cgacccataa cttcgtataa tgtatgctat acgaagttat
     1861 actagctagc gccgccacca tggctgagct gatcagcagc gccaccagat ctctgtttgc
     1921 cgccggaggc atcaaccctt ggcctaaccc ctaccaccac gaggacatgg gctgtggagg
     1981 aatgacacct acaggcgagt gcttcagcac cgagtggtgg tgtgaccctt cttacggact
     2041 gagcgacgcc ggatacggat attgcttcgt ggaggccaca ggcggctacc tggtcgtggg
     2101 agtggagaag aagcaggctt ggctgcacag cagaggcaca ccaggagaaa agatcggcgc
     2161 ccaggtctgc cagtggattg ctttcagcat cgccatcgcc ctgctgacat tctacggctt
     2221 cagcgcctgg aaggccactt gcggttggga ggaggtctac gtctgttgcg tcgaggtgct
     2281 gttcgtgacc ctggagatct tcaaggagtt cagcagcccc gccacagtgt acctgtctac
     2341 cggcaaccac gcctattgcc tgcgctactt cgagtggctg ctgtcttgcc ccgtgatcct
     2401 gatcaagctg agcaacctga gcggcctgaa gaacgactac agcaagcgga ccatgggcct
     2461 gatcgtgtct tgcgtgggaa tgatcgtgtt cggcatggcc gcaggactgg ctaccgattg
     2521 gctcaagtgg ctgctgtata tcgtgtcttg catctacggc ggctacatgt acttccaggc
     2581 cgccaagtgc tacgtggaag ccaaccacag cgtgcctaaa ggccattgcc gcatggtcgt
     2641 gaagctgatg gcctacgctt acttcgcctc ttggggcagc tacccaatcc tctgggcagt
     2701 gggaccagaa ggactgctga agctgagccc ttacgccaac agcatcggcc acagcatctg
     2761 cgacatcatc gccaaggagt tttggacctt cctggcccac cacctgagga tcaagatcca
     2821 cgagcacatc ctgatccacg gcgacatccg gaagaccacc aagatggaga tcggaggcga
     2881 ggaggtggaa gtggaagagt tcgtggagga ggaggacgag gacacagtgg cggcaccggt
     2941 agtagcagtg agtaagggcg aggaagtgat caaagagttc atgcggttta aggtgagaat
     3001 ggaaggaagc atgaacggcc acgagttcga aattgaggga gaaggagagg gacggcccta
     3061 cgagggcacc cagacagcca agctgaaagt gacaaagggc gggcctctgc cattcgcttg
     3121 ggacatcctg agcccacagt ttatgtacgg ctccaaggcc tatgtgaaac atccagctga
     3181 cattcccgat tataagaaac tgagcttccc cgaggggttt aagtgggaaa gagtgatgaa
     3241 cttcgaggac ggaggcctgg tgactgtgac ccaggacagc tccctgcagg atgggaccct
     3301 gatctacaag gtgaaaatga gagggacaaa ttttccccct gatggacctg tgatgcagaa
     3361 gaaaactatg ggatgggagg cctccaccga aaggctgtat ccacgcgacg gggtgctgaa
     3421 aggagaaatc caccaggctc tgaagctgaa agatggggga cattacctgg tggagttcaa
     3481 gacaatctac atggccaaga aacctgtgca gctgccaggc tactattacg tggacacaaa
     3541 actggatatc acttcacaca acgaggacta cactattgtg gagcagtatg aacggagcga
     3601 ggggagacac catctgttcc tgggccatgg gactggaagt accggctcag ggtctagtgg
     3661 aaccgcctca agcgaggata acaatatggc tgtgatcaaa gagttcatga ggtttaaggt
     3721 gcgcatggag ggcagcatga atgggcacga atttgagatt gaaggagagg gcgaagggag
     3781 gccttacgag ggcacacaga ctgccaagct gaaagtgacc aagggaggac cactgccttt
     3841 cgcttgggat atcctgtctc ctcagtttat gtacggaagt aaggcctatg tcaagcatcc
     3901 cgctgacatt cctgattaca agaaactgtc tttcccagag ggctttaagt gggagagagt
     3961 gatgaatttt gaagatggag gcctggtgac cgtgacacag gactcctctc tgcaggatgg
     4021 cactctgatc tacaaagtca aaatgcgcgg caccaatttt ccacccgatg ggcccgtgat
     4081 gcagaagaaa acaatggggt gggaggccag cactgaacgg ctgtatccta gagacggagt
     4141 gctgaagggc gaaatccacc aggccctgaa gctgaaagac ggcggccact acctggtgga
     4201 gttcaaaacc atctacatgg ccaagaaacc agtgcagctg cccggctatt actatgtgga
     4261 caccaagctg gatatcacat cccacaatga agactacacc attgtggaac agtatgagag
     4321 gtctgaagga cgccaccatc tgtttctgta cggcatggat gagctgtata agtaagccta
     4381 ggtacctagt ataacttcgt ataggatact ttatacgaag ttatcattgg gattcttcct
     4441 attttgatcc aagcatcacc atcgaccctc tagtccagat ctcaccatcg acccataact
     4501 tcgtatagca tacattatac gaagttatgt ccctcgaaga ggttcgcggc cgcactcctc
     4561 aggtgcaggc tgcctatcag aaggtggtgg ctggtgtggc caatgccctg gctcacaaat
     4621 accactgaga tctttttccc tctgccaaaa attatgggga catcatgaag ccccttgagc
     4681 atctgacttc tggctaataa aggaaattta ttttcattgc aatagtgtgt tggaattttt
     4741 tgtgtctctc actcggaagg acatatggga gggcaaatca tttaaaacat cagaatgagt
     4801 atttggttta gagtttggca acatatgccc atatgctggc tgccatgaac aaaggttggc
     4861 tataaagagg tcatcagtat atgaaacagc cccctgctgt ccattcctta ttccatagaa
     4921 aagccttgac ttgaggttag atttttttta tattttgttt tgtgttattt ttttctttaa
     4981 catccctaaa attttcctta catgttttac tagccagatt tttcctcctc tcctgactac
     5041 tcccagtcat agctgtccct cttctcttat ggagatccct cgacctgcag cccaagcttg
     5101 gcgtaatcat ggtcatagct gtttcctgtg tgaaattgtt atccgctcac aattccacac
     5161 aacatacgag ccggaagcat aaagtgtaaa gcctggggtg cctaatgagt gagctaactc
     5221 acattaattg cgttgcgctc actgcccgct ttccagtcgg gaaacctgtc gtgccagcgg
     5281 atccgcatct caattagtca gcaaccatag tcccgcccct aactccgccc atcccgcccc
     5341 taactccgcc cagttccgcc cattctccgc cccatggctg actaattttt tttatttatg
     5401 cagaggccga ggccgcctcg gcctctgagc tattccagaa gtagtgagga ggcttttttg
     5461 gaggcctagg cttttgcaaa aagctaactt gtttattgca gcttataatg gttacaaata
     5521 aagcaatagc atcacaaatt tcacaaataa agcatttttt tcactgcatt ctagttgtgg
     5581 tttgtccaaa ctcatcaatg tatcttatca tgtctggatc cgctgcatta atgaatcggc
     5641 caacgcgcgg ggagaggcgg tttgcgtatt gggcgctctt ccgcttcctc gctcactgac
     5701 tcgctgcgct cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa ggcggtaata
     5761 cggttatcca cagaatcagg ggataacgca ggaaagaaca tgtgagcaaa aggccagcaa
     5821 aaggccagga accgtaaaaa ggccgcgttg ctggcgtttt tccataggct ccgcccccct
     5881 gacgagcatc acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggactataa
     5941 agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg
     6001 cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca
     6061 cgctgtaggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa
     6121 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg
     6181 gtaagacacg acttatcgcc actggcagca gccactggta acaggattag cagagcgagg
     6241 tatgtaggcg gtgctacaga gttcttgaag tggtggccta actacggcta cactagaaga
     6301 acagtatttg gtatctgcgc tctgctgaag ccagttacct tcggaaaaag agttggtagc
     6361 tcttgatccg gcaaacaaac caccgctggt agcggtggtt tttttgtttg caagcagcag
     6421 attacgcgca gaaaaaaagg atctcaagaa gatcctttga tcttttctac ggggtctgac
     6481 gctcagtgga acgaaaactc acgttaaggg attttggtca tgagattatc aaaaaggatc
     6541 ttcacctaga tccttttaaa ttaaaaatga agttttaaat caatctaaag tatatatgag
     6601 taaacttggt ctgacagtta ccaatgctta atcagtgagg cacctatctc agcgatctgt
     6661 ctatttcgtt catccatagt tgcctgactc cccgtcgtgt agataactac gatacgggag
     6721 ggcttaccat ctggccccag tgctgcaatg ataccgcgag acccacgctc accggctcca
     6781 gatttatcag caataaacca gccagccgga agggccgagc gcagaagtgg tcctgcaact
     6841 ttatccgcct ccatccagtc tattaattgt tgccgggaag ctagagtaag tagttcgcca
     6901 gttaatagtt tgcgcaacgt tgttgccatt gctacaggca tcgtggtgtc acgctcgtcg
     6961 tttggtatgg cttcattcag ctccggttcc caacgatcaa ggcgagttac atgatccccc
     7021 atgttgtgca aaaaagcggt tagctccttc ggtcctccga tcgttgtcag aagtaagttg
     7081 gccgcagtgt tatcactcat ggttatggca gcactgcata attctcttac tgtcatgcca
     7141 tccgtaagat gcttttctgt gactggtgag tactcaacca agtcattctg agaatagtgt
     7201 atgcggcgac cgagttgctc ttgcccggcg tcaatacggg ataataccgc gccacatagc
     7261 agaactttaa aagtgctcat cattggaaaa cgttcttcgg ggcgaaaact ctcaaggatc
     7321 ttaccgctgt tgagatccag ttcgatgtaa cccactcgtg cacccaactg atcttcagca
     7381 tcttttactt tcaccagcgt ttctgggtga gcaaaaacag gaaggcaaaa tgccgcaaaa
     7441 aagggaataa gggcgacacg gaaatgttga atactcatac tcttcctttt tcaatattat
     7501 tgaagcattt atcagggtta ttgtctcatg agcggataca tatttgaatg tatttagaaa
     7561 aataaacaaa taggggttcc gcgcacattt ccccgaaaag tgccacctg
//
