LOCUS       sequence-147995-        7399 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  AAV expression of mammalian codon optimized ChIEF for optogenetic 
            excitation..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7399)
  AUTHORS   Jurgens CW, Bell KA, McQuiston AR, Guido W
  TITLE     Optogenetic stimulation of the corticothalamic pathway affects relay
            cells and GABAergic neurons differently in the mouse visual 
            thalamus.
  JOURNAL   PLoS One. 2012;7(9):e45717. doi: 10.1371/journal.pone.0045717. Epub 
            2012 Sep 20.
  PUBMED    23029198
REFERENCE   2  (bases 1 to 7399)
  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: "PLoS One.";
            date: "2012"; volume: "7(9):e45717. doi"; pages: " 
            10.1371/journal.pone.0045717. Epub 2012 Sep 20"
COMMENT     Sequence Label: pACAGW-oChiEFtdTomato-AAV
FEATURES             Location/Qualifiers
     source          1..7399
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     repeat_region   38..167
                     /label=AAV2 ITR
     promoter        478..734
                     /label=chicken beta-actin promoter
                     /note="contains a 21-bp deletion relative to the standard 
                     chicken beta-actin promoter"
     primer_bind     1013..1035
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     1097..1116
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     CDS             2248..3678
                     /codon_start=1
                     /product="tandem dimeric (pseudo-monomeric) derivative of 
                     DsRed (Shaner et al., 2004)"
                     /label=tdTomato
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEEVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYEGTQTA
                     KLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMNFEDGG
                     LVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVLKGEIH
                     QALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYERSEGRH
                     HLFLGHGTGSTGSGSSGTASSEDNNMAVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPY
                     EGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVM
                     NFEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGV
                     LKGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYE
                     RSEGRHHLFLYGMDELYK"
     intron          3692..3824
                     /label=chimeric intron
                     /note="chimera between introns from human beta-globin and 
                     immunoglobulin heavy chain genes"
     primer_bind     3807..3826
                     /label=pMT2-F
                     /note="Synthetic intron, forward primer"
     misc_feature    3880..4468
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3933..3953)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4351..4362)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    4511..4632
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4522..4541)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     4576..4595
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     repeat_region   4794..4923
                     /label=AAV2 ITR
     rep_origin      complement(5160..5748)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5240..5259)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5919..6710,6711..6779))
                     /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     6542..6561
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6780..6884)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(6910..7365)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(7047..7068)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     7259..7278
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
ORIGIN
        1 agggcgatcg gtgcgggcct cttcgctatt acgccagctg cgcgctcgct cgctcactga
       61 ggccgcccgg gcaaagcccg ggcgtcgggc gacctttggt cgcccggcct cagtgagcga
      121 gcgagcgcgc agagagggag tggccaactc catcactagg ggttccttgt agttaatgat
      181 taacccgcca tgctacttat ctacgtagcc atgctctagg aagagtacca ttgacgtcaa
      241 taatgacgta tgttcccata gtaacgccaa tagggacttt ccattgacgt caatgggtgg
      301 agtatttacg gtaaactgcc cacttggcag tacatcaagt gtatcatatg ccaagtacgc
      361 cccctattga cgtcaatgac ggtaaatggc ccgcctggca ttatgcccag tacatgacct
      421 tatgggactt tcctacttgg cagtacatct acgtattagt catcgctatt accatggtcg
      481 aggtgagccc cacgttctgc ttcactctcc ccatctcccc cccctcccca cccccaattt
      541 tgtatttatt tattttttaa ttattttgtg cagcgatggg ggcggggggg gggggggggc
      601 ggggcgaggg gcggggcggg gcgaggcgga gaggtgcggc ggcagccaat cagagcggcg
      661 cgctccgaaa gtttcctttt atggcgaggc ggcggcggcg gcggccctat aaaaagcgaa
      721 gcgcgcggcg ggcgggagtc gctgcgcgct gccttcgccc cgtgccccgc tccgccgccg
      781 cctcgcgccg cccgccccgg ctctgactga ccgcgttact cccacaggtg agcgggcggg
      841 acggcccttc tcctccgggc tgtaattagc gcttggttta atgacggctt gtttcttttc
      901 tgtggctgcg tgaaagcctt gaggggctcc gggagggccc tttgtgcggg gggagcggct
      961 cggggctgtc cgcgggggga cggctgcctt cgggggggac ggggcagggc ggggttcggc
     1021 ttctggcgtg tgaccggcgg ctctagagcc tctgctaacc atgttcatgc cttcttcttt
     1081 ttcctacagc tcctgggcaa cgtgctggtt attgtgctgt ctcatcattt tggcaaagaa
     1141 ttggatcggg atccaccggt gaccatggtg agcagaagac cctggctgct ggccctggcc
     1201 ctggccgtgg ccctggccgc cggcagcgcc ggcgccagca ccggcagcga cgccaccgtg
     1261 cccgtggcca cccaggacgg ccccgactac gtgttccaca gagcccacga gagaatgctg
     1321 ttccagacca gctacaccct ggagaacaac ggcagcgtga tctgcatccc caacaacggc
     1381 cagtgcttct gcctggcctg gctgaagagt aacggcacca acgccgagaa gctggccgcc
     1441 aacatcctgc agtggatcac cttcgccctg agcgccctgt gcctgatgtt ctacggctac
     1501 cagacctgga agagtacctg cggctgggag gagatctacg tggccaccat cgagatgatc
     1561 aagttcatca tagagtactt ccacgagttc gacgagcccg ccgtgatcta cagcagcaac
     1621 ggcaacaaga ccgtgtggct gagatacgcc gagtggctgc tgacctgccc cgtggtcctg
     1681 atccacctga gcaacctgac cggcctggcc aacgactaca acaagagaac catgggcctg
     1741 ctggtgagcg acatcggcac catcgtgtgg ggcaccaccg ccgccctgag caagggctac
     1801 gtgagagtga tcttcttcct gatgggcctg tgctacggca tctacacctt cttcaacgcc
     1861 gccaaggtgt acatcgaggc ctaccacacc gtgcccaagg gcagatgcag acaggtggtg
     1921 accggcatgg cctggctgtt cttcgtgagc tggggcatgt tccccatcct gttcatcctg
     1981 ggccccgagg gcttcggcgt gctgagcgtg tacggcagca ccgtgggcca caccatcatc
     2041 gacctgatga gcaagaactg ctggggcctg ctgggccact acctgagagt gctgatccac
     2101 gagcacatcc tgatccacgg cgacatcaga aagaccacca agctgaacat cggcggcacc
     2161 gagatcgagg tggagaccct ggtggaggac gaggccgagg ccggcgccgt gaacaagggc
     2221 accggcaagt acgagagcag catcgatatg gtgagcaagg gcgaggaggt catcaaagag
     2281 ttcatgcgct tcaaggtgcg catggagggc tccatgaacg gccacgagtt cgagatcgag
     2341 ggcgagggcg agggccgccc ctacgagggc acccagaccg ccaagctgaa ggtgaccaag
     2401 ggcggccccc tgcccttcgc ctgggacatc ctgtcccccc agttcatgta cggctccaag
     2461 gcgtacgtga agcaccccgc cgacatcccc gattacaaga agctgtcctt ccccgagggc
     2521 ttcaagtggg agcgcgtgat gaacttcgag gacggcggtc tggtgaccgt gacccaggac
     2581 tcctccctgc aggacggcac gctgatctac aaggtgaaga tgcgcggcac caacttcccc
     2641 cccgacggcc ccgtaatgca gaagaagacc atgggctggg aggcctccac cgagcgcctg
     2701 tacccccgcg acggcgtgct gaagggcgag atccaccagg ccctgaagct gaaggacggc
     2761 ggccactacc tggtggagtt caagaccatc tacatggcca agaagcccgt gcaactgccc
     2821 ggctactact acgtggacac caagctggac atcacctccc acaacgagga ctacaccatc
     2881 gtggaacagt acgagcgctc cgagggccgc caccacctgt tcctggggca tggcaccggc
     2941 agcaccggca gcggcagctc cggcaccgcc tcctccgagg acaacaacat ggccgtcatc
     3001 aaagagttca tgcgcttcaa ggtgcgcatg gagggctcca tgaacggcca cgagttcgag
     3061 atcgagggcg agggcgaggg ccgcccctac gagggcaccc agaccgccaa gctgaaggtg
     3121 accaagggcg gccccctgcc cttcgcctgg gacatcctgt ccccccagtt catgtacggc
     3181 tccaaggcgt acgtgaagca ccccgccgac atccccgatt acaagaagct gtccttcccc
     3241 gagggcttca agtgggagcg cgtgatgaac ttcgaggacg gcggtctggt gaccgtgacc
     3301 caggactcct ccctgcagga cggcacgctg atctacaagg tgaagatgcg cggcaccaac
     3361 ttcccccccg acggccccgt aatgcagaag aagaccatgg gctgggaggc ctccaccgag
     3421 cgcctgtacc cccgcgacgg cgtgctgaag ggcgagatcc accaggccct gaagctgaag
     3481 gacggcggcc actacctggt ggagttcaag accatctaca tggccaagaa gcccgtgcaa
     3541 ctgcccggct actactacgt ggacaccaag ctggacatca cctcccacaa cgaggactac
     3601 accatcgtgg aacagtacga gcgctccgag ggccgccacc acctgttcct gtacggcatg
     3661 gacgagctgt acaagtagct cgaggccgca ggtaagtatc aaggttacaa gacaggttta
     3721 aggagaccaa tagaaactgg gcttgtcgag acagagaaga ctcttgcgtt tctgataggc
     3781 acctattggt cttactgaca tccactttgc ctttctctcc acaggtgtcg agtggagctc
     3841 gcgactagtc gattcgaatt cgatatcaag cttatcgata atcaacctct ggattacaaa
     3901 atttgtgaaa gattgactgg tattcttaac tatgttgctc cttttacgct atgtggatac
     3961 gctgctttaa tgcctttgta tcatgctatt gcttcccgta tggctttcat tttctcctcc
     4021 ttgtataaat cctggttgct gtctctttat gaggagttgt ggcccgttgt caggcaacgt
     4081 ggcgtggtgt gcactgtgtt tgctgacgca acccccactg gttggggcat tgccaccacc
     4141 tgtcagctcc tttccgggac tttcgctttc cccctcccta ttgccacggc ggaactcatc
     4201 gccgcctgcc ttgcccgctg ctggacaggg gctcggctgt tgggcactga caattccgtg
     4261 gtgttgtcgg ggaaatcatc gtcctttcct tggctgctcg cctgtgttgc cacctggatt
     4321 ctgcgcggga cgtccttctg ctacgtccct tcggccctca atccagcgga ccttccttcc
     4381 cgcggcctgc tgccggctct gcggcctctt ccgcgtcttc gccttcgccc tcagacgagt
     4441 cggatctccc tttgggccgc ctccccgcat cgataccgtc gacccgggcg gccgcttcga
     4501 gcagacatga taagatacat tgatgagttt ggacaaacca caactagaat gcagtgaaaa
     4561 aaatgcttta tttgtgaaat ttgtgatgct attgctttat ttgtaaccat tataagctgc
     4621 aataaacaag ttaacaacaa caattgcatt cattttatgt ttcaggttca gggggagatg
     4681 tgggaggttt tttaaagcaa gtaaaacctc tacaaatgtg gtaaaatcga taaggatctt
     4741 cctagagcat ggctacgtag ataagtagca tggcgggtta atcattaact acaaggaacc
     4801 cctagtgatg gagttggcca ctccctctct gcgcgctcgc tcgctcactg aggccgggcg
     4861 accaaaggtc gcccgacgcc cgggctttgc ccgggcggcc tcagtgagcg agcgagcgcg
     4921 cagctgcatt aatgaatcgg ccaacgcgcg gggagaggcg gtttgcgtat tgggcgctct
     4981 tccgcttcct cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg agcggtatca
     5041 gctcactcaa aggcggtaat acggttatcc acagaatcag gggataacgc aggaaagaac
     5101 atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa aggccgcgtt gctggcgttt
     5161 ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg
     5221 cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc
     5281 tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc
     5341 gtggcgcttt ctcatagctc acgctgtagg tatctcagtt cggtgtaggt cgttcgctcc
     5401 aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac
     5461 tatcgtcttg agtccaaccc ggtaagacac gacttatcgc cactggcagc agccactggt
     5521 aacaggatta gcagagcgag gtatgtaggc ggtgctacag agttcttgaa gtggtggcct
     5581 aactacggct acactagaag aacagtattt ggtatctgcg ctctgctgaa gccagttacc
     5641 ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg tagcggtggt
     5701 ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga agatcctttg
     5761 atcttttcta cggggtctga cgctcagtgg aacgaaaact cacgttaagg gattttggtc
     5821 atgagattat caaaaaggat cttcacctag atccttttaa attaaaaatg aagttttaaa
     5881 tcaatctaaa gtatatatga gtaaacttgg tctgacagtt accaatgctt aatcagtgag
     5941 gcacctatct cagcgatctg tctatttcgt tcatccatag ttgcctgact ccccgtcgtg
     6001 tagataacta cgatacggga gggcttacca tctggcccca gtgctgcaat gataccgcga
     6061 gacccacgct caccggctcc agatttatca gcaataaacc agccagccgg aagggccgag
     6121 cgcagaagtg gtcctgcaac tttatccgcc tccatccagt ctattaattg ttgccgggaa
     6181 gctagagtaa gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat tgctacaggc
     6241 atcgtggtgt cacgctcgtc gtttggtatg gcttcattca gctccggttc ccaacgatca
     6301 aggcgagtta catgatcccc catgttgtgc aaaaaagcgg ttagctcctt cggtcctccg
     6361 atcgttgtca gaagtaagtt ggccgcagtg ttatcactca tggttatggc agcactgcat
     6421 aattctctta ctgtcatgcc atccgtaaga tgcttttctg tgactggtga gtactcaacc
     6481 aagtcattct gagaatagtg tatgcggcga ccgagttgct cttgcccggc gtcaatacgg
     6541 gataataccg cgccacatag cagaacttta aaagtgctca tcattggaaa acgttcttcg
     6601 gggcgaaaac tctcaaggat cttaccgctg ttgagatcca gttcgatgta acccactcgt
     6661 gcacccaact gatcttcagc atcttttact ttcaccagcg tttctgggtg agcaaaaaca
     6721 ggaaggcaaa atgccgcaaa aaagggaata agggcgacac ggaaatgttg aatactcata
     6781 ctcttccttt ttcaatatta ttgaagcatt tatcagggtt attgtctcat gagcggatac
     6841 atatttgaat gtatttagaa aaataaacaa ataggggttc cgcgcacatt tccccgaaaa
     6901 gtgccaccta aattgtaagc gttaatattt tgttaaaatt cgcgttaaat ttttgttaaa
     6961 tcagctcatt ttttaaccaa taggccgaaa tcggcaaaat cccttataaa tcaaaagaat
     7021 agaccgagat agggttgagt gttgttccag tttggaacaa gagtccacta ttaaagaacg
     7081 tggactccaa cgtcaaaggg cgaaaaaccg tctatcaggg cgatggccca ctacgtgaac
     7141 catcacccta atcaagtttt ttggggtcga ggtgccgtaa agcactaaat cggaacccta
     7201 aagggagccc ccgatttaga gcttgacggg gaaagccggc gaacgtggcg agaaaggaag
     7261 ggaagaaagc gaaaggagcg ggcgctaggg cgctggcaag tgtagcggtc acgctgcgcg
     7321 taaccaccac acccgccgcg cttaatgcgc cgctacaggg cgcgtcccat tcgccattca
     7381 ggctgcgcaa ctgttggga
//
