LOCUS       sequence-13408-e        7226 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Cre-dependent viral expression of ArchT-tdTomato for neuronal 
            inhibition.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7226)
  AUTHORS   Han X, Chow BY, Zhou H, Klapoetke NC, Chuong A, Rajimehr R, Yang A, 
            Baratta MV, Winkle J, Desimone R, Boyden ES
  TITLE     A high-light sensitivity optical neural silencer: development and 
            application to optogenetic control of non-human primate cortex.
  JOURNAL   Front Syst Neurosci. 2011;5:18. Epub 2011 Apr 13.
  PUBMED    21811444
REFERENCE   2  (bases 1 to 7226)
  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: "Front Syst 
            Neurosci."; date: "2011"; volume: "5"; pages: "18. Epub 2011 Apr 13"
COMMENT     Sequence Label: pAAV-FLEX-ArchT-tdTomato
FEATURES             Location/Qualifiers
     source          1..7226
                     /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        2901..3178
                     /label=chicken beta-actin promoter
     primer_bind     3458..3480
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     3542..3561
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     protein_bind    3596..3629
                     /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    3692..3725
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     CDS             complement(3746..5173)
                     /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
                     LFLGHGTGSTGSGSSGTASSEDNNMAVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYE
                     GTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMN
                     FEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVL
                     KGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYER
                     SEGRHHLFLYGMDELYK"
     regulatory      5923..5932
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     protein_bind    complement(5949..5982)
                     /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(6053..6086)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     misc_feature    6128..6716
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(6181..6201)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(6599..6610)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    6759..6880
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(6770..6789)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     6824..6843
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     repeat_region   7042..7171
                     /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 ccattgacgt caataatgac gtatgttccc atagtaacgc caatagggac
     2701 tttccattga cgtcaatggg tggagtattt acggtaaact gcccacttgg cagtacatca
     2761 agtgtatcat atgccaagta cgccccctat tgacgtcaat gacggtaaat ggcccgcctg
     2821 gcattatgcc cagtacatga ccttatggga ctttcctact tggcagtaca tctacgtatt
     2881 agtcatcgct attaccatgg tcgaggtgag ccccacgttc tgcttcactc tccccatctc
     2941 ccccccctcc ccacccccaa ttttgtattt atttattttt taattatttt gtgcagcgat
     3001 gggggcgggg gggggggggg ggcgcgcgcc aggcggggcg gggcggggcg aggggcgggg
     3061 cggggcgagg cggagaggtg cggcggcagc caatcagagc ggcgcgctcc gaaagtttcc
     3121 ttttatggcg aggcggcggc ggcggcggcc ctataaaaag cgaagcgcgc ggcgggcggg
     3181 agtcgctgcg acgctgcctt cgccccgtgc cccgctccgc cgccgcctcg cgccgcccgc
     3241 cccggctctg actgaccgcg ttactcccac aggtgagcgg gcgggacggc ccttctcctc
     3301 cgggctgtaa ttagcgcttg gtttaatgac ggcttgtttc ttttctgtgg ctgcgtgaaa
     3361 gccttgaggg gctccgggag ggccctttgt gcggggggag cggctcgggg ctgtccgcgg
     3421 ggggacggct gccttcgggg gggacggggc agggcggggt tcggcttctg gcgtgtgacc
     3481 ggcggctcta gagcctctgc taaccatgtt catgccttct tctttttcct acagctcctg
     3541 ggcaacgtgc tggttattgt gctgtctcat cattttggca aagaattgga tccccataac
     3601 ttcgtataaa gtatcctata cgaagttata tcaaaatagg aagaccaatg cttcaccatc
     3661 gacccgaatt gccaagcatc accatcgacc cataacttcg tataatgtat gctatacgaa
     3721 gttatactag gatccccctc gagttttact tgtacagctc gtccatgccg tacaggaaca
     3781 ggtggtggcg gccctcggag cgctcgtact gttccacgat ggtgtagtcc tcgttgtggg
     3841 aggtgatgtc cagcttggtg tccacgtagt agtagccggg cagttgcacg ggcttcttgg
     3901 ccatgtagat ggtcttgaac tccaccaggt agtggccgcc gtccttcagc ttcagggcct
     3961 ggtggatctc gcccttcagc acgccgtcgc gggggtacag gcgctcggtg gaggcctccc
     4021 agcccatggt cttcttctgc attacggggc cgtcgggggg gaagttggtg ccgcgcatct
     4081 tcaccttgta gatcagcgtg ccgtcctgca gggaggagtc ctgggtcacg gtcaccagac
     4141 cgccgtcctc gaagttcatc acgcgctccc acttgaagcc ctcggggaag gacagcttct
     4201 tgtaatcggg gatgtcggcg gggtgcttca cgtacgcctt ggagccgtac atgaactggg
     4261 gggacaggat gtcccaggcg aagggcaggg ggccgccctt ggtcaccttc agcttggcgg
     4321 tctgggtgcc ctcgtagggg cggccctcgc cctcgccctc gatctcgaac tcgtggccgt
     4381 tcatggagcc ctccatgcgc accttgaagc gcatgaactc tttgatgacg gccatgttgt
     4441 tgtcctcgga ggaggcggtg ccggagctgc cgctgccggt gctgccggtg ccatgcccca
     4501 ggaacaggtg gtggcggccc tcggagcgct cgtactgttc cacgatggtg tagtcctcgt
     4561 tgtgggaggt gatgtccagc ttggtgtcca cgtagtagta gccgggcagt tgcacgggct
     4621 tcttggccat gtagatggtc ttgaactcca ccaggtagtg gccgccgtcc ttcagcttca
     4681 gggcctggtg gatctcgccc ttcagcacgc cgtcgcgggg gtacaggcgc tcggtggagg
     4741 cctcccagcc catggtcttc ttctgcatta cggggccgtc gggggggaag ttggtgccgc
     4801 gcatcttcac cttgtagatc agcgtgccgt cctgcaggga ggagtcctgg gtcacggtca
     4861 ccagaccgcc gtcctcgaag ttcatcacgc gctcccactt gaagccctcg gggaaggaca
     4921 gcttcttgta atcggggatg tcggcggggt gcttcacgta cgccttggag ccgtacatga
     4981 actgggggga caggatgtcc caggcgaagg gcagggggcc gcccttggtc accttcagct
     5041 tggcggtctg ggtgccctcg taggggcggc cctcgccctc gccctcgatc tcgaactcgt
     5101 ggccgttcat ggagccctcc atgcgcacct tgaagcgcat gaactctttg atgacctcct
     5161 cgcccttgct cactaccggt cggggctcgg gggcctcggt gtcgcccagg atggccctgc
     5221 tcctcagcag gatgaagccg aagcccactt tggcggtcac gtccagcacc atgaacagca
     5281 gggtctcgat tcccagtccc accactccag ctccctcggt tccgatgatc cacaggatgg
     5341 ggtaggcggt ccacagcacc agcaccaggg cggtcagggt gttgaaggtg ctagccacct
     5401 ctggtcccct ctccttagca gcagccctca ggctggtagc caggaagtac agcaccacga
     5461 tcatgcagat ggtgctgaac agccaccagc tgtacctagc cagtggggtg tggctcaggg
     5521 cgccgatcag gccggtcacg atcatcaggg cgtccactcc caccagggtt ccgatgctca
     5581 ccctgtccac cttagccagc agggccaggt cgagcagaag caaaggggtg gtgaacagcc
     5641 agtcggcgta tctggcgtag tagatgtcca gcacctcgcc ggccacggtc acctcggtca
     5701 ggccgatgcc gaagaacatg ctcaggtagg cggcgctggc gatgccgggc accaggattg
     5761 tgatgctgta gtactccctg gcctccttgt cggtcacgcc ccagcccttc acgatgaagt
     5821 agaaggtgcc gatcagcatc agcagggttc cgattcccag ccacagggtc tctggccttc
     5881 cgtcgcccag caggtcgtat cctgcctgca gagcgatggg gtccatggtg gcggtaccga
     5941 attctagtat aacttcgtat aggatacttt atacgaagtt atcattggga ttcttcctat
     6001 tttgatccaa gcatcaccat cgaccctcta gtccagatct caccatcgac ccataacttc
     6061 gtatagcata cattatacga agttatgtcc ctcgaagagg ttcgaattcg atatcaagct
     6121 tatcgataat caacctctgg attacaaaat ttgtgaaaga ttgactggta ttcttaacta
     6181 tgttgctcct tttacgctat gtggatacgc tgctttaatg cctttgtatc atgctattgc
     6241 ttcccgtatg gctttcattt tctcctcctt gtataaatcc tggttgctgt ctctttatga
     6301 ggagttgtgg cccgttgtca ggcaacgtgg cgtggtgtgc actgtgtttg ctgacgcaac
     6361 ccccactggt tggggcattg ccaccacctg tcagctcctt tccgggactt tcgctttccc
     6421 cctccctatt gccacggcgg aactcatcgc cgcctgcctt gcccgctgct ggacaggggc
     6481 tcggctgttg ggcactgaca attccgtggt gttgtcgggg aaatcatcgt cctttccttg
     6541 gctgctcgcc tgtgttgcca cctggattct gcgcgggacg tccttctgct acgtcccttc
     6601 ggccctcaat ccagcggacc ttccttcccg cggcctgctg ccggctctgc ggcctcttcc
     6661 gcgtcttcgc cttcgccctc agacgagtcg gatctccctt tgggccgcct ccccgcatcg
     6721 ataccgtcga cccgggcggc cgcttcgagc agacatgata agatacattg atgagtttgg
     6781 acaaaccaca actagaatgc agtgaaaaaa atgctttatt tgtgaaattt gtgatgctat
     6841 tgctttattt gtaaccatta taagctgcaa taaacaagtt aacaacaaca attgcattca
     6901 ttttatgttt caggttcagg gggagatgtg ggaggttttt taaagcaagt aaaacctcta
     6961 caaatgtggt aaaatcgata aggatcttcc tagagcatgg ctacgtagat aagtagcatg
     7021 gcgggttaat cattaactac aaggaacccc tagtgatgga gttggccact ccctctctgc
     7081 gcgctcgctc gctcactgag gccgggcgac caaaggtcgc ccgacgcccg ggctttgccc
     7141 gggcggcctc agtgagcgag cgagcgcgca gctgcattaa tgaatcggcc aacgcgcggg
     7201 gagaggcggt ttgcgtattg ggcgct
//
