LOCUS       sequence-213556-        7656 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Cation channelrhodopsin CoChR fused to mRuby2 fluorophore and 
            targeted to the neuronal soma and proximal dendrites.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7656)
  AUTHORS   Mardinly AR, Oldenburg IA, Pegard NC, Sridharan S, Lyall EH, Chesnov
            K, Brohawn SG, Waller L, Adesnik H
  TITLE     Precise multimodal optical control of neural ensemble activity.
  JOURNAL   Nat Neurosci. 2018 Apr 30. pii: 10.1038/s41593-018-0139-8. doi: 
            10.1038/s41593-018-0139-8.
  PUBMED    29713079
REFERENCE   2  (bases 1 to 7656)
  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"; journalName: "Nat 
            Neurosci. 2018 Apr 30. pii: 10.1038/s41593-018-0139-8. doi: 
            10.1038/s41593-018-0139-8."
COMMENT     Sequence Label: pCAG-CoChR-mRuby2-ST
FEATURES             Location/Qualifiers
     source          1..7656
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        5..384
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        386..661
                     /label=chicken beta-actin promoter
     intron          662..1678
                     /label=chimeric intron
                     /note="chimera between introns from chicken beta-actin and 
                     rabbit beta-globin"
     primer_bind     1602..1624
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     1686..1705
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     CDS             1739..2602
                     /codon_start=1
                     /product="high-photocurrent channelrhodopsin from 
                     Chloromonas oogama (Shemesh et al., 2017)"
                     /label=CoChR
                     /translation="MLGNGSAIVPIDQCFCLAWTDSLGSDTEQLVANILQWFAFGFSIL
                     ILMFYAYQTWRATCGWEEVYVCCVELTKVIIEFFHEFDDPSMLYLANGHRVQWLRYAEW
                     LLTCPVILIHLSNLTGLKDDYSKRTMRLLVSDVGTIVWGATSAMSTGYVKVIFFVLGCI
                     YGANTFFHAAKVYIESYHVVPKGRPRTVVRIMAWLFFLSWGMFPVLFVVGPEGFDAISV
                     YGSTIGHTIIDLMSKNCWGLLGHYLRVLIHQHIIIYGDIRKKTKINVAGEEMEVETMVD
                     QEDEETV"
     CDS             2618..3328
                     /codon_start=1
                     /product="monomeric red fluorescent protein derived from 
                     mRuby, with improved photophysical properties (Lam et al., 
                     2012)"
                     /label=mRuby2
                     /translation="MVSKGEELIKENMRMKVVMEGSVNGHQFKCTGEGEGNPYMGTQTM
                     RIKVIEGGPLPFAFDILATSFMYGSRTFIKYPKGIPDFFKQSFPEGFTWERVTRYEDGG
                     VVTVMQDTSLEDGCLVYHVQVRGVNFPSNGPVMQKKTKGWEPNTEMMYPADGGLRGYTH
                     MALKVDGGGHLSCSFVTTYRSKKTVGNIKMPGIHAVDHRLERLEESDNEMFVVQREHAV
                     AKFAGLGGGMDELYK"
     intron          3552..3684
                     /label=chimeric intron
                     /note="chimera between introns from human beta-globin and 
                     immunoglobulin heavy chain genes"
     primer_bind     3667..3686
                     /label=pMT2-F
                     /note="Synthetic intron, forward primer"
     misc_feature    3693..4281
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3746..3766)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4164..4175)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     primer_bind     complement(4308..4325)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    4314..4425
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     primer_bind     complement(4521..4541)
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        complement(4521..4539)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(4560..4576)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4678..4697)
                     /label=Bglob-pA-R
                     /note="Rabbit beta-globin polyA region, reverse primer"
     polyA_signal    4743..4798
                     /label=beta-globin poly(A) signal
                     /note="rabbit beta-globin polyadenylation signal (Gil and 
                     Proudfoot, 1987)"
     primer_bind     complement(4797..4816)
                     /label=rbglobpA-R
                     /note="Rabbit beta-globin polyA, reverse primer. Also 
                     called rb-glob-pA-term-R"
     primer_bind     complement(5159..5175)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     protein_bind    5183..5199
                     /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(5207..5213,5214..5231,5232..5237))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5252..5273
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        5332..5527
                     /label=SV40 promoter
                     /note="SV40 early promoter"
     rep_origin      5378..5513
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     polyA_signal    5533..5667
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(5570..5589)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     5624..5643
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(5735..5752)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(5906..6494)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5986..6005)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(6665..7456,7457..7525))
                     /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     7288..7307
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(7526..7630)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 ggtcgacatt gattattgac tagttattaa tagtaatcaa ttacggggtc attagttcat
       61 agcccatata tggagttccg cgttacataa cttacggtaa atggcccgcc tggctgaccg
      121 cccaacgacc cccgcccatt gacgtcaata atgacgtatg ttcccatagt aacgccaata
      181 gggactttcc attgacgtca atgggtggag tatttacggt aaactgccca cttggcagta
      241 catcaagtgt atcatatgcc aagtacgccc cctattgacg tcaatgacgg taaatggccc
      301 gcctggcatt atgcccagta catgacctta tgggactttc ctacttggca gtacatctac
      361 gtattagtca tcgctattac catggtcgag gtgagcccca cgttctgctt cactctcccc
      421 atctcccccc cctccccacc cccaattttg tatttattta ttttttaatt attttgtgca
      481 gcgatggggg cggggggggg gggggcgcgc gccagggggg gcgggggggg gggggggggg
      541 ggggggggcg gggcggagag gtgcggcggc agccaatcag agcggcgcgc tccgaaagtt
      601 tccttttatg gcgaggcggc ggcggcggcg gccctataaa aagcgaagcg cgcggcgggc
      661 gggagtcgct gcgcgctgcc ttcgccccgt gccccgctcc gccgccgcct cgcgccgccc
      721 gccccggctc tgactgaccg cgttactccc acaggtgagc gggcgggacg gcccttctcc
      781 tccgggctgt aattagcgct tggtttaatg acggcttgtt tcttttctgt ggctgcgtga
      841 aagccttgag gggctccggg agggcccttt gtgcgggggg agcggctcgg ggggtgcgtg
      901 cgtgtgtgtg tgcgtgggga gcgccgcgtg cggctccgcg ctgcccggcg gctgtgagcg
      961 ctgcgggcgc ggcgcggggc tttgtgcgct ccgcagtgtg cgcgagggga gcgcggccgg
     1021 gggcggtgcc ccgcggtgcg gggggggctg cgaggggaac aaaggctgcg tgcggggtgt
     1081 gtgcgtgggg gggtgagcag ggggtgtggg cgcgtcggtc gggctgcaac cccccctgca
     1141 cccccctccc cgagttgctg agcacggccc ggcttcgggt gcggggctcc gtacggggcg
     1201 tggcgcgggg ctcgccgtgc cgggcggggg gtggcggcag gtgggggtgc cgggcggggc
     1261 ggggccgcct cgggccgggg agggctcggg ggaggggcgc ggcggccccc ggagcgccgg
     1321 cggctgtcga ggcgcggcga gccgcagcca ttgcctttta tggtaatcgt gcgagagggc
     1381 gcagggactt cctttgtccc aaatctgtgc ggagccgaaa tctgggaggc gccgccgcac
     1441 cccctctagc gggcgcgggg cgaagcggtg cggcgccggc aggaaggaaa tgggcgggga
     1501 gggccttcgt gcgtcgccgc gccgccgtcc ccttctccct ctccagcctc ggggctgtcc
     1561 gcggggggac ggctgccttc gggggggacg gggcagggcg gggttcggct tctggcgtgt
     1621 gaccggcggc tctagagcct ctgctaacca tgttcatgcc ttcttctttt tcctacagct
     1681 cctgggcaac gtgctggtta ttgtgctgtc tcatcatttt ggcaaagaat tcggtaccat
     1741 gctgggaaac ggcagcgcca ttgtgcctat cgaccagtgc ttttgcctgg cttggaccga
     1801 cagcctggga agcgatacag agcagctggt ggccaacatc ctccagtggt tcgccttcgg
     1861 cttcagcatc ctgatcctga tgttctacgc ctaccagact tggagagcca cttgcggttg
     1921 ggaggaggtc tacgtctgtt gcgtcgagct gaccaaggtc atcatcgagt tcttccacga
     1981 gttcgacgac cccagcatgc tgtacctggc taacggacac cgagtccagt ggctgagata
     2041 cgcagagtgg ctgctgactt gtcccgtcat cctgatccac ctgagcaacc tgaccggcct
     2101 gaaggacgac tacagcaagc ggaccatgag gctgctggtg tcagacgtgg gaaccatcgt
     2161 gtggggagct acaagcgcca tgagcacagg ctacgtcaag gtcatcttct tcgtgctggg
     2221 ttgcatctac ggcgccaaca ccttcttcca cgccgccaag gtgtatatcg agagctacca
     2281 cgtggtgcca aagggcagac ctagaaccgt cgtgcggatc atggcttggc tgttcttcct
     2341 gtcttggggc atgttccccg tgctgttcgt cgtgggacca gaaggattcg acgccatcag
     2401 cgtgtacggc tctaccattg gccacaccat catcgacctc atgagcaaga attgttgggg
     2461 cctgctggga cactatctga gagtgctgat ccaccagcac atcatcatct acggcgacat
     2521 ccggaagaag accaagatca acgtggccgg cgaggagatg gaagtggaga ccatggtgga
     2581 ccaggaggac gaggagacag tggcggccgc accggtaatg gtgtctaagg gcgaagagct
     2641 gatcaaggaa aatatgcgta tgaaggtggt catggaaggt tcggtcaacg gccaccaatt
     2701 caaatgcaca ggtgaaggag aaggcaatcc gtacatggga actcaaacca tgaggatcaa
     2761 agtcatcgag ggaggacccc tgccatttgc ctttgacatt cttgccacgt cgttcatgta
     2821 tggcagccgt acttttatca agtacccgaa aggcattcct gatttcttta aacagtcctt
     2881 tcctgagggt tttacttggg aaagagttac gagatacgaa gatggtggag tcgtcaccgt
     2941 catgcaggac accagccttg aggatggctg tctcgtttac cacgtccaag tcagaggggt
     3001 aaactttccc tccaatggtc ccgtgatgca gaagaagacc aagggttggg agcctaatac
     3061 agagatgatg tatccagcag atggtggtct gaggggatac actcatatgg cactgaaagt
     3121 tgatggtggt ggccatctgt cttgctcttt cgtaacaact tacaggtcaa aaaagaccgt
     3181 cgggaacatc aagatgcccg gtatccatgc cgttgatcac cgcctggaaa ggttagagga
     3241 aagtgacaat gaaatgttcg tagtacaacg cgaacacgca gttgccaagt tcgccgggct
     3301 tggtggtggg atggacgagc tgtacaaggc cctagagcag tcccagccca tcctcaacac
     3361 caaggagatg gccccgcaga gcaagcctcc agaggagctg gagatgagca gcatgcccag
     3421 ccccgtggcc cctctgcccg ctcgcacgga gggcgtcatc gacatgcgga gcatgtccag
     3481 cattgacagc ttcatcagct gtgccacgga cttccctgaa gccaccagat tctaaggact
     3541 cgaggccgca ggtaagtatc aaggttacaa gacaggttta aggagaccaa tagaaactgg
     3601 gcttgtcgag acagagaaga ctcttgcgtt tctgataggc acctattggt cttactgaca
     3661 tccactttgc ctttctctcc acaggtgtcg acaatcaacc tctggattac aaaatttgtg
     3721 aaagattgac tggtattctt aactatgttg ctccttttac gctatgtgga tacgctgctt
     3781 taatgccttt gtatcatgct attgcttccc gtatggcttt cattttctcc tccttgtata
     3841 aatcctggtt gctgtctctt tatgaggagt tgtggcccgt tgtcaggcaa cgtggcgtgg
     3901 tgtgcactgt gtttgctgac gcaaccccca ctggttgggg cattgccacc acctgtcagc
     3961 tcctttccgg gactttcgct ttccccctcc ctattgccac ggcggaactc atcgccgcct
     4021 gccttgcccg ctgctggaca ggggctcggc tgttgggcac tgacaattcc gtggtgttgt
     4081 cggggaagct gacgtccttt ccatggctgc tcgcctgtgt tgccacctgg attctgcgcg
     4141 ggacgtcctt ctgctacgtc ccttcggccc tcaatccagc ggaccttcct tcccgcggcc
     4201 tgctgccggc tctgcggcct cttccgcgtc ttcgccttcg ccctcagacg agtcggatct
     4261 ccctttgggc cgcctccccg cctggaattc gagctcggta cgatcagcct cgactgtgcc
     4321 ttctagttgc cagccatctg ttgtttgccc ctcccccgtg ccttccttga ccctggaagg
     4381 tgccactccc actgtccttt cctaataaaa tgaggaaatt gcatcgcatt gtctgagtag
     4441 gtgtcattct attctggggg gtggggtggg gcaggacagc aagggggagg attgggaaga
     4501 caatagccca gcttttgttc cctttagtga gggttaattg cgcgcttggc gtaatcatgg
     4561 tcatagctgt ttcctgtgtg aaattgttat ccgctaattc actcctcagg tgcaggctgc
     4621 ctatcagaag gtggtggctg gtgtggccaa tgccctggct cacaaatacc actgagatct
     4681 ttttccctct gccaaaaatt atggggacat catgaagccc cttgagcatc tgacttctgg
     4741 ctaataaagg aaatttattt tcattgcaat agtgtgttgg aattttttgt gtctctcact
     4801 cggaaggaca tatgggaggg caaatcattt aaaacatcag aatgagtatt tggtttagag
     4861 tttggcaaca tatgcccata tgctggctgc catgaacaaa ggttggctat aaagaggtca
     4921 tcagtatatg aaacagcccc ctgctgtcca ttccttattc catagaaaag ccttgacttg
     4981 aggttagatt ttttttatat tttgttttgt gttatttttt tctttaacat ccctaaaatt
     5041 ttccttacat gttttactag ccagattttt cctcctctcc tgactactcc cagtcatagc
     5101 tgtccctctt ctcttatgga gatccctcga cctgcagccc aagcttggcg taatcatggt
     5161 catagctgtt tcctgtgtga aattgttatc cgctcacaat tccacacaac atacgagccg
     5221 gaagcataaa gtgtaaagcc tggggtgcct aatgagtgag ctaactcaca ttaattgcgt
     5281 tgcgctcact gcccgctttc cagtcgggaa acctgtcgtg ccagcggatc cgcatctcaa
     5341 ttagtcagca accatagtcc cgcccctaac tccgcccatc ccgcccctaa ctccgcccag
     5401 ttccgcccat tctccgcccc atggctgact aatttttttt atttatgcag aggccgaggc
     5461 cgcctcggcc tctgagctat tccagaagta gtgaggaggc ttttttggag gcctaggctt
     5521 ttgcaaaaag ctaacttgtt tattgcagct tataatggtt acaaataaag caatagcatc
     5581 acaaatttca caaataaagc atttttttca ctgcattcta gttgtggttt gtccaaactc
     5641 atcaatgtat cttatcatgt ctggatccgc tgcattaatg aatcggccaa cgcgcgggga
     5701 gaggcggttt gcgtattggg cgctcttccg cttcctcgct cactgactcg ctgcgctcgg
     5761 tcgttcggct gcggcgagcg gtatcagctc actcaaaggc ggtaatacgg ttatccacag
     5821 aatcagggga taacgcagga aagaacatgt gagcaaaagg ccagcaaaag gccaggaacc
     5881 gtaaaaaggc cgcgttgctg gcgtttttcc ataggctccg cccccctgac gagcatcaca
     5941 aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg actataaaga taccaggcgt
     6001 ttccccctgg aagctccctc gtgcgctctc ctgttccgac cctgccgctt accggatacc
     6061 tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca tagctcacgc tgtaggtatc
     6121 tcagttcggt gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc
     6181 ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc caacccggta agacacgact
     6241 tatcgccact ggcagcagcc actggtaaca ggattagcag agcgaggtat gtaggcggtg
     6301 ctacagagtt cttgaagtgg tggcctaact acggctacac tagaagaaca gtatttggta
     6361 tctgcgctct gctgaagcca gttaccttcg gaaaaagagt tggtagctct tgatccggca
     6421 aacaaaccac cgctggtagc ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa
     6481 aaaaaggatc tcaagaagat cctttgatct tttctacggg gtctgacgct cagtggaacg
     6541 aaaactcacg ttaagggatt ttggtcatga gattatcaaa aaggatcttc acctagatcc
     6601 ttttaaatta aaaatgaagt tttaaatcaa tctaaagtat atatgagtaa acttggtctg
     6661 acagttacca atgcttaatc agtgaggcac ctatctcagc gatctgtcta tttcgttcat
     6721 ccatagttgc ctgactcccc gtcgtgtaga taactacgat acgggagggc ttaccatctg
     6781 gccccagtgc tgcaatgata ccgcgagacc cacgctcacc ggctccagat ttatcagcaa
     6841 taaaccagcc agccggaagg gccgagcgca gaagtggtcc tgcaacttta tccgcctcca
     6901 tccagtctat taattgttgc cgggaagcta gagtaagtag ttcgccagtt aatagtttgc
     6961 gcaacgttgt tgccattgct acaggcatcg tggtgtcacg ctcgtcgttt ggtatggctt
     7021 cattcagctc cggttcccaa cgatcaaggc gagttacatg atcccccatg ttgtgcaaaa
     7081 aagcggttag ctccttcggt cctccgatcg ttgtcagaag taagttggcc gcagtgttat
     7141 cactcatggt tatggcagca ctgcataatt ctcttactgt catgccatcc gtaagatgct
     7201 tttctgtgac tggtgagtac tcaaccaagt cattctgaga atagtgtatg cggcgaccga
     7261 gttgctcttg cccggcgtca atacgggata ataccgcgcc acatagcaga actttaaaag
     7321 tgctcatcat tggaaaacgt tcttcggggc gaaaactctc aaggatctta ccgctgttga
     7381 gatccagttc gatgtaaccc actcgtgcac ccaactgatc ttcagcatct tttactttca
     7441 ccagcgtttc tgggtgagca aaaacaggaa ggcaaaatgc cgcaaaaaag ggaataaggg
     7501 cgacacggaa atgttgaata ctcatactct tcctttttca atattattga agcatttatc
     7561 agggttattg tctcatgagc ggatacatat ttgaatgtat ttagaaaaat aaacaaatag
     7621 gggttccgcg cacatttccc cgaaaagtgc cacctg
//
