LOCUS       sequence-174139-        7368 bp    DNA     linear   UNA 14-APR-2025
DEFINITION  Cre-dependent viral expression of ChR2-tdTomato for neuronal 
            excitation.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      natural DNA sequence
  ORGANISM  unspecified
REFERENCE   1  (bases 1 to 7368)
  AUTHORS   Atasoy D, Aponte Y, Su HH, Sternson SM
  TITLE     A FLEX switch targets Channelrhodopsin-2 to multiple cell types for 
            imaging and long-range circuit mapping.
  JOURNAL   J Neurosci. 2008 Jul 9. 28(28):7025-30.
  PUBMED    18614669
REFERENCE   2  (bases 1 to 7368)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Apr 14, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "J Neurosci.
            2008 Jul 9. 28(28):7025-30."
COMMENT     Sequence Label: AAV-FLEX-rev-ChR2-tdtomato
FEATURES             Location/Qualifiers
     source          1..7368
                     /mol_type="genomic DNA"
                     /organism="unspecified"
     primer_bind     364..386
                     /label=pCAGGS-5
                     /note="Chimeric intron in CAG promoter, forward primer"
     primer_bind     448..467
                     /label=pCAG-F
                     /note="Rabbit beta-globin intron, for pCAG plasmids, 
                     forward primer"
     protein_bind    502..535
                     /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    598..631
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     CDS             complement(645..2072)
                     /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"
     CDS             complement(2085..3011)
                     /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
                     PSMLYLATGHRVQWLRYAEWLLTCPVILIHLSNLTGLSNDYSRRTMGLLVSDIGTIVWG
                     ATSAMATGYVKVIFFCLGLCYGANTFFHAAKAYIEGYHTVPKGRCRQVVTGMAWLFFVS
                     WGMFPILFILGPEGFGVLSVYGSTVGHTIIDLMSKNCWGLLGHYLRVLIHEHILIHGDI
                     RKTTKLNIGGTEIEVETLVEDEAEAGAV"
     CDS             complement(2085..3011)
                     /codon_start=1
                     /product="N-terminal fragment of channelrhodopsin-2 from 
                     the alga Chlamydomonas reinhardtii (Nagel et al., 2003)"
                     /label=ChR2
                     /note="blue light-activated cation channel"
                     /translation="MDYGGALSAVGRELLFVTNPVVVNGSVLVPEDQCYCAGWIESRGT
                     NGAQTASNVLQWLAAGFSILLLMFYAYQTWKSTCGWEEIYVCAIEMVKVILEFFFEFKN
                     PSMLYLATGHRVQWLRYAEWLLTCPVILIHLSNLTGLSNDYSRRTMGLLVSDIGTIVWG
                     ATSAMATGYVKVIFFCLGLCYGANTFFHAAKAYIEGYHTVPKGRCRQVVTGMAWLFFVS
                     WGMFPILFILGPEGFGVLSVYGSTVGHTIIDLMSKNCWGLLGHYLRVLIHEHILIHGDI
                     RKTTKLNIGGTEIEVETLVEDEAEAGAV"
     regulatory      3008..3017
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     protein_bind    complement(3047..3080)
                     /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(3151..3184)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     misc_feature    3226..3814
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3279..3299)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(3697..3708)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    3857..3978
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3868..3887)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3922..3941
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     repeat_region   4140..4269
                     /label=AAV2 ITR
     rep_origin      complement(4506..5094)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4586..4605)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5265..6056,6057..6125))
                     /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     5888..5907
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6126..6230)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(6256..6711)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(6393..6414)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     6605..6624
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     repeat_region   6783..6912
                     /label=AAV2 ITR
ORIGIN
        1 tcagagcggc gcgctccgaa agtttccttt tatggcgagg cggcggcggc ggcggcccta
       61 taaaaagcga agcgcgcggc gggcgggagt cgctgcgcgc tgccttcgcc ccgtgccccg
      121 ctccgccgcc gcctcgcgcc gcccgccccg gctctgactg accgcgttac tcccacaggt
      181 gagcgggcgg gacggccctt ctcctccggg ctgtaattag cgcttggttt aatgacggct
      241 tgtttctttt ctgtggctgc gtgaaagcct tgaggggctc cgggagggcc ctttgtgcgg
      301 ggggagcggc tcggggctgt ccgcgggggg acggctgcct tcggggggga cggggcaggg
      361 cggggttcgg cttctggcgt gtgaccggcg gctctagagc ctctgctaac catgttcatg
      421 ccttcttctt tttcctacag ctcctgggca acgtgctggt tattgtgctg tctcatcatt
      481 ttggcaaaga attggatccc cataacttcg tataaagtat cctatacgaa gttatatcaa
      541 aataggaaga ccaatgcttc accatcgacc cgaattgcca agcatcacca tcgacccata
      601 acttcgtata atgtatgcta tacgaagtta tactagggat ccccttactt gtacagctcg
      661 tccatgccgt acaggaacag gtggtggcgg ccctcggagc gctcgtactg ttccacgatg
      721 gtgtagtcct cgttgtggga ggtgatgtcc agcttggtgt ccacgtagta gtagccgggc
      781 agttgcacgg gcttcttggc catgtagatg gtcttgaact ccaccaggta gtggccgccg
      841 tccttcagct tcagggcctg gtggatctcg cccttcagca cgccgtcgcg ggggtacagg
      901 cgctcggtgg aggcctccca gcccatggtc ttcttctgca ttacggggcc gtcggggggg
      961 aagttggtgc cgcgcatctt caccttgtag atcagcgtgc cgtcctgcag ggaggagtcc
     1021 tgggtcacgg tcaccagacc gccgtcctcg aagttcatca cgcgctccca cttgaagccc
     1081 tcggggaagg acagcttctt gtaatcgggg atgtcggcgg ggtgcttcac gtacgccttg
     1141 gagccgtaca tgaactgggg ggacaggatg tcccaggcga agggcagggg gccgcccttg
     1201 gtcaccttca gcttggcggt ctgggtgccc tcgtaggggc ggccctcgcc ctcgccctcg
     1261 atctcgaact cgtggccgtt catggagccc tccatgcgca ccttgaagcg catgaactct
     1321 ttgatgacgg ccatgttgtt gtcctcggag gaggcggtgc cggagctgcc gctgccggtg
     1381 ctgccgatgc catgccccag gaacaggtgg tggcggccct cggagcgctc gtactgttcc
     1441 acgatggtgt agtcctcgtt gtgggaggtg atgtccagct tggtgtccac gtagtagtag
     1501 ccgggcagtt gcacgggctt cttggccatg tagatggtct tgaactccac caggtagtgg
     1561 ccgccgtcct tcagcttcag ggcctggtgg atctcgccct tcagcacgcc gtcgcggggg
     1621 tacaggcgct cggtggaggc ctcccagccc atggtcttct tctgcattac ggggccgtcg
     1681 ggggggaagt tggtgccgcg catcttcacc ttgtagatca gcgtgccgtc ctgcagggag
     1741 gagtcctggg tcacggtcac cagaccgccg tcctcgaagt tcatcacgcg ctcccacttg
     1801 aagccctcgg ggaaggacag cttcttgtaa tcggggatgt cggcggggtg cttcacgtac
     1861 gccttggagc cgtacatgaa ctggggggac aggatgtccc aggcgaaggg cagggggccg
     1921 cccttggtca ccttcagctt ggcggtctgg gtgccctcgt aggggcggcc ctcgccctcg
     1981 ccctcgatct cgaactcgtg gccgttcatg gagccctcca tgcgcacctt gaagcgcatg
     2041 aactctttga tgacctcctc gcccttgctc acggccgcgg ctggcacggc tccggcctcg
     2101 gcttcgtctt cgacgagagt ctcgacctcg atctccgttc cgccgatgtt cagtttggtg
     2161 gttttgcgga tatctccgtg aatcaatatg tgctcgtgga tcaggacgcg caggtagtgt
     2221 cccaacaacc cccaacaatt tttactcatc agatcaataa tcgtgtgacc tacggtggag
     2281 ccatagacgc tcaggacgcc aaaaccttcg ggccccaaaa tgaagagaat tgggaacata
     2341 ccccagctca cgaaaaacag ccatgccatg ccggtcacga cctggcggca ccgacccttt
     2401 ggcacagtat gataaccctc gatatatgct ttggcggcgt gaaaaaatgt gttcgcgcca
     2461 tagcacaatc caagacaaaa gaagatgact ttaacatagc cggttgccat ggcgctggta
     2521 gccccccaca cgatagtccc gatgtctgag acaaggagtc ccatggttct cctgctgtag
     2581 tcgttgctca ggccggtgag gttgctcagg tggataagga tgacaggaca agtgagcagc
     2641 cactctgcat agcgcagcca ctgcacccgg tgtcctgtgg caaggtagag catagaggga
     2701 ttcttaaact caaaaaagaa ctcgagaatc accttaacca tttcaatggc gcacacatag
     2761 atctcctccc agccgcatgt agatttccag gtttggtagg catagaacat cagcagcaaa
     2821 atgctgaatc ctgctgcaag ccactgcagg acatttgacg cggtctgagc gccgttcgtg
     2881 ccgcgagatt caatccatcc ggcacagtaa cattgatcct cagggaccag gacggacccg
     2941 ttcaccacca caggattagt aacgaacaaa agttcgcgtc cgacggcaga caaagcgccg
     3001 ccatagtcca tggtggcgct aggggcccgc ggtaccgaat tctagtataa cttcgtatag
     3061 gatactttat acgaagttat cattgggatt cttcctattt tgatccaagc atcaccatcg
     3121 accctctagt ccagatctca ccatcgaccc ataacttcgt atagcataca ttatacgaag
     3181 ttatgtccct cgaagaggtt cgaattcgat atcaagctta tcgataatca acctctggat
     3241 tacaaaattt gtgaaagatt gactggtatt cttaactatg ttgctccttt tacgctatgt
     3301 ggatacgctg ctttaatgcc tttgtatcat gctattgctt cccgtatggc tttcattttc
     3361 tcctccttgt ataaatcctg gttgctgtct ctttatgagg agttgtggcc cgttgtcagg
     3421 caacgtggcg tggtgtgcac tgtgtttgct gacgcaaccc ccactggttg gggcattgcc
     3481 accacctgtc agctcctttc cgggactttc gctttccccc tccctattgc cacggcggaa
     3541 ctcatcgccg cctgccttgc ccgctgctgg acaggggctc ggctgttggg cactgacaat
     3601 tccgtggtgt tgtcggggaa atcatcgtcc tttccttggc tgctcgcctg tgttgccacc
     3661 tggattctgc gcgggacgtc cttctgctac gtcccttcgg ccctcaatcc agcggacctt
     3721 ccttcccgcg gcctgctgcc ggctctgcgg cctcttccgc gtcttcgcct tcgccctcag
     3781 acgagtcgga tctccctttg ggccgcctcc ccgcatcgat accgtcgacc cgggcggccg
     3841 cttcgagcag acatgataag atacattgat gagtttggac aaaccacaac tagaatgcag
     3901 tgaaaaaaat gctttatttg tgaaatttgt gatgctattg ctttatttgt aaccattata
     3961 agctgcaata aacaagttaa caacaacaat tgcattcatt ttatgtttca ggttcagggg
     4021 gagatgtggg aggtttttta aagcaagtaa aacctctaca aatgtggtaa aatcgataag
     4081 gatcttccta gagcatggct acgtagataa gtagcatggc gggttaatca ttaactacaa
     4141 ggaaccccta gtgatggagt tggccactcc ctctctgcgc gctcgctcgc tcactgaggc
     4201 cgggcgacca aaggtcgccc gacgcccggg ctttgcccgg gcggcctcag tgagcgagcg
     4261 agcgcgcagc tgcattaatg aatcggccaa cgcgcgggga gaggcggttt gcgtattggg
     4321 cgctcttccg cttcctcgct cactgactcg ctgcgctcgg tcgttcggct gcggcgagcg
     4381 gtatcagctc actcaaaggc ggtaatacgg ttatccacag aatcagggga taacgcagga
     4441 aagaacatgt gagcaaaagg ccagcaaaag gccaggaacc gtaaaaaggc cgcgttgctg
     4501 gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaatcgacg ctcaagtcag
     4561 aggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg aagctccctc
     4621 gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt tctcccttcg
     4681 ggaagcgtgg cgctttctca tagctcacgc tgtaggtatc tcagttcggt gtaggtcgtt
     4741 cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg cgccttatcc
     4801 ggtaactatc gtcttgagtc caacccggta agacacgact tatcgccact ggcagcagcc
     4861 actggtaaca ggattagcag agcgaggtat gtaggcggtg ctacagagtt cttgaagtgg
     4921 tggcctaact acggctacac tagaagaaca gtatttggta tctgcgctct gctgaagcca
     4981 gttaccttcg gaaaaagagt tggtagctct tgatccggca aacaaaccac cgctggtagc
     5041 ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa aaaaaggatc tcaagaagat
     5101 cctttgatct tttctacggg gtctgacgct cagtggaacg aaaactcacg ttaagggatt
     5161 ttggtcatga gattatcaaa aaggatcttc acctagatcc ttttaaatta aaaatgaagt
     5221 tttaaatcaa tctaaagtat atatgagtaa acttggtctg acagttacca atgcttaatc
     5281 agtgaggcac ctatctcagc gatctgtcta tttcgttcat ccatagttgc ctgactcccc
     5341 gtcgtgtaga taactacgat acgggagggc ttaccatctg gccccagtgc tgcaatgata
     5401 ccgcgagacc cacgctcacc ggctccagat ttatcagcaa taaaccagcc agccggaagg
     5461 gccgagcgca gaagtggtcc tgcaacttta tccgcctcca tccagtctat taattgttgc
     5521 cgggaagcta gagtaagtag ttcgccagtt aatagtttgc gcaacgttgt tgccattgct
     5581 acaggcatcg tggtgtcacg ctcgtcgttt ggtatggctt cattcagctc cggttcccaa
     5641 cgatcaaggc gagttacatg atcccccatg ttgtgcaaaa aagcggttag ctccttcggt
     5701 cctccgatcg ttgtcagaag taagttggcc gcagtgttat cactcatggt tatggcagca
     5761 ctgcataatt ctcttactgt catgccatcc gtaagatgct tttctgtgac tggtgagtac
     5821 tcaaccaagt cattctgaga atagtgtatg cggcgaccga gttgctcttg cccggcgtca
     5881 atacgggata ataccgcgcc acatagcaga actttaaaag tgctcatcat tggaaaacgt
     5941 tcttcggggc gaaaactctc aaggatctta ccgctgttga gatccagttc gatgtaaccc
     6001 actcgtgcac ccaactgatc ttcagcatct tttactttca ccagcgtttc tgggtgagca
     6061 aaaacaggaa ggcaaaatgc cgcaaaaaag ggaataaggg cgacacggaa atgttgaata
     6121 ctcatactct tcctttttca atattattga agcatttatc agggttattg tctcatgagc
     6181 ggatacatat ttgaatgtat ttagaaaaat aaacaaatag gggttccgcg cacatttccc
     6241 cgaaaagtgc cacctaaatt gtaagcgtta atattttgtt aaaattcgcg ttaaattttt
     6301 gttaaatcag ctcatttttt aaccaatagg ccgaaatcgg caaaatccct tataaatcaa
     6361 aagaatagac cgagataggg ttgagtgttg ttccagtttg gaacaagagt ccactattaa
     6421 agaacgtgga ctccaacgtc aaagggcgaa aaaccgtcta tcagggcgat ggcccactac
     6481 gtgaaccatc accctaatca agttttttgg ggtcgaggtg ccgtaaagca ctaaatcgga
     6541 accctaaagg gagcccccga tttagagctt gacggggaaa gccggcgaac gtggcgagaa
     6601 aggaagggaa gaaagcgaaa ggagcgggcg ctagggcgct ggcaagtgta gcggtcacgc
     6661 tgcgcgtaac caccacaccc gccgcgctta atgcgccgct acagggcgcg tcccattcgc
     6721 cattcaggct gcgcaactgt tgggaagggc gatcggtgcg ggcctcttcg ctattacgcc
     6781 agctgcgcgc tcgctcgctc actgaggccg cccgggcaaa gcccgggcgt cgggcgacct
     6841 ttggtcgccc ggcctcagtg agcgagcgag cgcgcagaga gggagtggcc aactccatca
     6901 ctaggggttc cttgtagtta atgattaacc cgccatgcta cttatctacg tagccatgct
     6961 ctaggaagag taccattgac gtcaataatg acgtatgttc ccatagtaac gccaataggg
     7021 actttccatt gacgtcaatg ggtggagtat ttacggtaaa ctgcccactt ggcagtacat
     7081 caagtgtatc atatgccaag tacgccccct attgacgtca atgacggtaa atggcccgcc
     7141 tggcattatg cccagtacat gaccttatgg gactttccta cttggcagta catctacgta
     7201 ttagtcatcg ctattaccat ggtcgaggtg agccccacgt tctgcttcac tctccccatc
     7261 tcccccccct ccccaccccc aattttgtat ttatttattt tttaattatt ttgtgcagcg
     7321 atgggggcgg gggggggggg ggggcgcggc ggggcggggc ggggggag
//
