LOCUS       sequence-183060-        7071 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  AAV expression of ChR2(H134R)-tdTomato under the Syn promoter.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7071)
  AUTHORS   Shepherd
  TITLE     Shepherd Lab _ Syn-ChR-tdTomato plasmid
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7071)
  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: 
            "Unpublished"
COMMENT     Sequence Label: Syn-ChR-tdTomato
FEATURES             Location/Qualifiers
     source          1..7071
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     misc_feature    9..597
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(62..82)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(480..491)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    617..1093
                     /label=hGH poly(A) signal
                     /note="human growth hormone polyadenylation signal"
     primer_bind     complement(816..835)
                     /label=hGH-PA-R
                     /note="Human growth hormone terminator, reverse primer"
     repeat_region   1139..1279
                     /label=AAV2 ITR
                     /note="inverted terminal repeat of adeno-associated virus 
                     serotype 2"
     repeat_region   1139..1268
                     /label=AAV2 ITR
     rep_origin      1354..1809
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1441..1460)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1651..1672
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(1826..1845)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     1945..1967
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(2005..2023)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        2091..2195
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(2196..2264,2265..3056)
                     /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(2414..2433)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      3227..3815
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     3716..3735
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     repeat_region   3877..4006
                     /label=AAV2 ITR (alternate)
                     /note="Functional equivalent of wild-type AAV2 ITR"
     promoter        4217..4664
                     /label=hSyn promoter
                     /note="human synapsin I promoter; confers neuron-specific 
                     expression (Kugler et al., 2003)"
     regulatory      4677..4686
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             4683..5609
                     /codon_start=1
                     /product="H134R mutant of an N-terminal fragment of 
                     channelrhodopsin-2 from the alga Chlamydomonas reinhardtii 
                     (Nagel et al., 2005)"
                     /label=ChR2(H134R)
                     /note="blue light-activated cation channel"
                     /translation="MDYGGALSAVGRELLFVTNPVVVNGSVLVPEDQCYCAGWIESRGT
                     NGAQTASNVLQWLAAGFSILLLMFYAYQTWKSTCGWEEIYVCAIEMVKVILEFFFEFKN
                     PSMLYLATGHRVQWLRYAEWLLTCPVILIRLSNLTGLSNDYSRRTMGLLVSDIGTIVWG
                     ATSAMATGYVKVIFFCLGLCYGANTFFHAAKAYIEGYHTVPKGRCRQVVTGMAWLFFVS
                     WGMFPILFILGPEGFGVLSVYGSTVGHTIIDLMSKNCWGLLGHYLRVLIHEHILIHGDI
                     RKTTKLNIGGTEIEVETLVEDEAEAGAV"
     CDS             5628..7055
                     /codon_start=1
                     /product="tandem dimeric (pseudo-monomeric) derivative of 
                     DsRed (Shaner et al., 2004)"
                     /label=tdTomato
                     /note="mammalian codon-optimized"
                     /translation="VSKGEEVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYEGTQTAK
                     LKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGL
                     VTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVLKGEIHQ
                     ALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYERSEGRHH
                     LFLGHGIGSTGSGSSGTASSEDNNMAVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYE
                     GTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMN
                     FEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVL
                     KGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYER
                     SEGRHHLFLYGMDELYK"
ORIGIN
        1 ttatcgataa tcaacctctg gattacaaaa tttgtgaaag attgactggt attcttaact
       61 atgttgctcc ttttacgcta tgtggatacg ctgctttaat gcctttgtat catgctattg
      121 cttcccgtat ggctttcatt ttctcctcct tgtataaatc ctggttgctg tctctttatg
      181 aggagttgtg gcccgttgtc aggcaacgtg gcgtggtgtg cactgtgttt gctgacgcaa
      241 cccccactgg ttggggcatt gccaccacct gtcagctcct ttccgggact ttcgctttcc
      301 ccctccctat tgccacggcg gaactcatcg ccgcctgcct tgcccgctgc tggacagggg
      361 ctcggctgtt gggcactgac aattccgtgg tgttgtcggg gaaatcatcg tcctttcctt
      421 ggctgctcgc ctatgttgcc acctggattc tgcgcgggac gtccttctgc tacgtccctt
      481 cggccctcaa tccagcggac cttccttccc gcggcctgct gccggctctg cggcctcttc
      541 cgcgtcttcg ccttcgccct cagacgagtc ggatctccct ttgggccgcc tccccgcatc
      601 gataccggct cgagacgggt ggcatccctg tgacccctcc ccagtgcctc tcctggccct
      661 ggaagttgcc actccagtgc ccaccagcct tgtcctaata aaattaagtt gcatcatttt
      721 gtctgactag gtgtccttct ataatattat ggggtggagg ggggtggtat ggagcaaggg
      781 gcaagttggg aagacaacct gtagggcctg cggggtctat tgggaaccaa gctggagtgc
      841 agtggcacaa tcttggctca ctgcaatctc cgcctcctgg gttcaagcga ttctcctgcc
      901 tcagcctccc gagttgttgg gattccaggc atgcatgacc aggctcagct aatttttgtt
      961 tttttggtag agacggggtt tcaccatatt ggccaggctg gtctccaact cctaatctca
     1021 ggtgatctac ccaccttggc ctcccaaatt gctgggatta caggcgtgaa ccactgctcc
     1081 cttccctgtc cttctcgagc tgattttgta ggtaaccacg tgcggaccga gcggccgcag
     1141 gaacccctag tgatggagtt ggccactccc tctctgcgcg ctcgctcgct cactgaggcc
     1201 gggcgaccaa aggtcgcccg acgcccgggc tttgcccggg cggcctcagt gagcgagcga
     1261 gcgcgcagct gcctgcaggg gcgcctgatg cggtattttc tccttacgca tctgtgcggt
     1321 atttcacacc gcatacgtca aagcaaccat agtacgcgcc ctgtagcggc gcattaagcg
     1381 cggcgggtgt ggtggttacg cgcagcgtga ccgctacact tgccagcgcc ttagcgcccg
     1441 ctcctttcgc tttcttccct tcctttctcg ccacgttcgc cggctttccc cgtcaagctc
     1501 taaatcgggg gctcccttta gggttccgat ttagtgcttt acggcacctc gaccccaaaa
     1561 aacttgattt gggtgatggt tcacgtagtg ggccatcgcc ctgatagacg gtttttcgcc
     1621 ctttgacgtt ggagtccacg ttctttaata gtggactctt gttccaaact ggaacaacac
     1681 tcaactctat ctcgggctat tcttttgatt tataagggat tttgccgatt tcggtctatt
     1741 ggttaaaaaa tgagctgatt taacaaaaat ttaacgcgaa ttttaacaaa atattaacgt
     1801 ttacaatttt atggtgcact ctcagtacaa tctgctctga tgccgcatag ttaagccagc
     1861 cccgacaccc gccaacaccc gctgacgcgc cctgacgggc ttgtctgctc ccggcatccg
     1921 cttacagaca agctgtgacc gtctccggga gctgcatgtg tcagaggttt tcaccgtcat
     1981 caccgaaacg cgcgagacga aagggcctcg tgatacgcct atttttatag gttaatgtca
     2041 tgataataat ggtttcttag acgtcaggtg gcacttttcg gggaaatgtg cgcggaaccc
     2101 ctatttgttt atttttctaa atacattcaa atatgtatcc gctcatgaga caataaccct
     2161 gataaatgct tcaataatat tgaaaaagga agagtatgag tattcaacat ttccgtgtcg
     2221 cccttattcc cttttttgcg gcattttgcc ttcctgtttt tgctcaccca gaaacgctgg
     2281 tgaaagtaaa agatgctgaa gatcagttgg gtgcacgagt gggttacatc gaactggatc
     2341 tcaacagcgg taagatcctt gagagttttc gccccgaaga acgttttcca atgatgagca
     2401 cttttaaagt tctgctatgt ggcgcggtat tatcccgtat tgacgccggg caagagcaac
     2461 tcggtcgccg catacactat tctcagaatg acttggttga gtactcacca gtcacagaaa
     2521 agcatcttac ggatggcatg acagtaagag aattatgcag tgctgccata accatgagtg
     2581 ataacactgc ggccaactta cttctgacaa cgatcggagg accgaaggag ctaaccgctt
     2641 ttttgcacaa catgggggat catgtaactc gccttgatcg ttgggaaccg gagctgaatg
     2701 aagccatacc aaacgacgag cgtgacacca cgatgcctgt agcaatggca acaacgttgc
     2761 gcaaactatt aactggcgaa ctacttactc tagcttcccg gcaacaatta atagactgga
     2821 tggaggcgga taaagttgca ggaccacttc tgcgctcggc ccttccggct ggctggttta
     2881 ttgctgataa atctggagcc ggtgagcgtg ggtctcgcgg tatcattgca gcactggggc
     2941 cagatggtaa gccctcccgt atcgtagtta tctacacgac ggggagtcag gcaactatgg
     3001 atgaacgaaa tagacagatc gctgagatag gtgcctcact gattaagcat tggtaactgt
     3061 cagaccaagt ttactcatat atactttaga ttgatttaaa acttcatttt taatttaaaa
     3121 ggatctaggt gaagatcctt tttgataatc tcatgaccaa aatcccttaa cgtgagtttt
     3181 cgttccactg agcgtcagac cccgtagaaa agatcaaagg atcttcttga gatccttttt
     3241 ttctgcgcgt aatctgctgc ttgcaaacaa aaaaaccacc gctaccagcg gtggtttgtt
     3301 tgccggatca agagctacca actctttttc cgaaggtaac tggcttcagc agagcgcaga
     3361 taccaaatac tgttcttcta gtgtagccgt agttaggcca ccacttcaag aactctgtag
     3421 caccgcctac atacctcgct ctgctaatcc tgttaccagt ggctgctgcc agtggcgata
     3481 agtcgtgtct taccgggttg gactcaagac gatagttacc ggataaggcg cagcggtcgg
     3541 gctgaacggg gggttcgtgc acacagccca gcttggagcg aacgacctac accgaactga
     3601 gatacctaca gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca
     3661 ggtatccggt aagcggcagg gtcggaacag gagagcgcac gagggagctt ccagggggaa
     3721 acgcctggta tctttatagt cctgtcgggt ttcgccacct ctgacttgag cgtcgatttt
     3781 tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc cagcaacgcg gcctttttac
     3841 ggttcctggc cttttgctgg ccttttgctc acatgtcctg caggcagctg cgcgctcgct
     3901 cgctcactga ggccgcccgg gcgtcgggcg acctttggtc gcccggcctc agtgagcgag
     3961 cgagcgcgca gagagggagt ggccaactcc atcactaggg gttcctgcgg ccgcacgcgt
     4021 tgcaaagatg gataaagttt taaacagaga ggaatctttg cagctaatgg accttctagg
     4081 tcttgaaagg agtgggaatt ggctccggtg cccgtcagtg ggcagagcgc acatcgccca
     4141 cagtccccga gaagttgggg ggaggggtcg gcagcaaatg gttaattaat ctagactgca
     4201 gagggccctg cgtatgagtg caagtgggtt ttaggaccag gatgaggcgg ggtgggggtg
     4261 cctacctgac gaccgacccc gacccactgg acaagcaccc aacccccatt ccccaaattg
     4321 cgcatcccct atcagagagg gggaggggaa acaggatgcg gcgaggcgcg tgcgcactgc
     4381 cagcttcagc accgcggaca gtgccttcgc ccccgcctgg cggcgcgcgc caccgccgcc
     4441 tcagcactga aggcgcgctg acgtcactcg ccggtccccc gcaaactccc cttcccggcc
     4501 accttggtcg cgtccgcgcc gccgccggcc cagccggacc gcaccacgcg aggcgcgaga
     4561 taggggggca cgggcgcgac catctgcgct gcggcgccgg cgactcagcg ctgcctcagt
     4621 ctgcggtggg cagcggagga gtcgtgtcgt gcctgagagc gcagtcgaga ggatccgcca
     4681 ccatggacta tggcggcgct ttgtctgccg tcggacgcga acttttgttc gttactaatc
     4741 ctgtggtggt gaacgggtcc gtcctggtcc ctgaggatca atgttactgt gccggatgga
     4801 ttgaatctcg cggcacgaac ggcgctcaga ccgcgtcaaa tgtcctgcag tggcttgcag
     4861 caggattcag cattttgctg ctgatgttct atgcctacca aacctggaaa tctacatgcg
     4921 gctgggagga gatctatgtg tgcgccattg aaatggttaa ggtgattctc gagttctttt
     4981 ttgagtttaa gaatccctct atgctctacc ttgccacagg acaccgggtg cagtggctgc
     5041 gctatgcaga gtggctgctc acttgtcctg tcatccttat cagactgagc aacctcaccg
     5101 gcctgagcaa cgactacagc aggagaacca tgggactcct tgtctcagac atcgggacta
     5161 tcgtgtgggg ggctaccagc gccatggcaa ccggctatgt taaagtcatc ttcttttgtc
     5221 ttggattgtg ctatggcgcg aacacatttt ttcacgccgc caaagcatat atcgagggtt
     5281 atcatactgt gccaaagggt cggtgccgcc aggtcgtgac cggcatggca tggctgtttt
     5341 tcgtgagctg gggtatgttc ccaattctct tcattttggg gcccgaaggt tttggcgtcc
     5401 tgagcgtcta tggctccacc gtaggtcaca cgattattga tctgatgagt aaaaattgtt
     5461 gggggttgtt gggacactac ctgcgcgtcc tgatccacga gcacatattg attcacggag
     5521 atatccgcaa aaccaccaaa ctgaacatcg gcggaacgga gatcgaggtc gagactctcg
     5581 tcgaagacga agccgaggcc ggagccgtgg cggcaccggt agtagcagtg agcaagggcg
     5641 aggaggtcat caaagagttc atgcgcttca aggtgcgcat ggagggctcc atgaacggcc
     5701 acgagttcga gatcgagggc gagggcgagg gccgccccta cgagggcacc cagaccgcca
     5761 agctgaaggt gaccaagggc ggccccctgc ccttcgcctg ggacatcctg tccccccagt
     5821 tcatgtacgg ctccaaggcg tacgtgaagc accccgccga catccccgat tacaagaagc
     5881 tgtccttccc cgagggcttc aagtgggagc gcgtgatgaa cttcgaggac ggcggtctgg
     5941 tgaccgtgac ccaggactcc tccctgcagg acggcacgct gatctacaag gtgaagatgc
     6001 gcggcaccaa cttccccccc gacggccccg taatgcagaa gaagaccatg ggctgggagg
     6061 cctccaccga gcgcctgtac ccccgcgacg gcgtgctgaa gggcgagatc caccaggccc
     6121 tgaagctgaa ggacggcggc cactacctgg tggagttcaa gaccatctac atggccaaga
     6181 agcccgtgca actgcccggc tactactacg tggacaccaa gctggacatc acctcccaca
     6241 acgaggacta caccatcgtg gaacagtacg agcgctccga gggccgccac cacctgttcc
     6301 tggggcatgg catcggcagc accggcagcg gcagctccgg caccgcctcc tccgaggaca
     6361 acaacatggc cgtcatcaaa gagttcatgc gcttcaaggt gcgcatggag ggctccatga
     6421 acggccacga gttcgagatc gagggcgagg gcgagggccg cccctacgag ggcacccaga
     6481 ccgccaagct gaaggtgacc aagggcggcc ccctgccctt cgcctgggac atcctgtccc
     6541 cccagttcat gtacggctcc aaggcgtacg tgaagcaccc cgccgacatc cccgattaca
     6601 agaagctgtc cttccccgag ggcttcaagt gggagcgcgt gatgaacttc gaggacggcg
     6661 gtctggtgac cgtgacccag gactcctccc tgcaggacgg cacgctgatc tacaaggtga
     6721 agatgcgcgg caccaacttc ccccccgacg gccccgtaat gcagaagaag accatgggct
     6781 gggaggcctc caccgagcgc ctgtaccccc gcgacggcgt gctgaagggc gagatccacc
     6841 aggccctgaa gctgaaggac ggcggccact acctggtgga gttcaagacc atctacatgg
     6901 ccaagaagcc cgtgcaactg cccggctact actacgtgga caccaagctg gacatcacct
     6961 cccacaacga ggactacacc atcgtggaac agtacgagcg ctccgagggc cgccaccacc
     7021 tgttcctgta cggcatggac gagctgtaca agtaagaatt ccgtacaaag c
//
