LOCUS       sequence-261604-        6266 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Double floxed mScarlet under the control of Ef1a promoter.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6266)
  AUTHORS   Marshel JH, Kim YS, Machado TA, Quirin S, Benson B, Kadmon J, Raja 
            C, Chibukhchyan A, Ramakrishnan C, Inoue M, Shane JC, McKnight DJ, 
            Yoshizawa S, Kato HE, Ganguli S, Deisseroth K
  TITLE     Cortical layer-specific critical dynamics triggering perception.
  JOURNAL   Science. 2019 Aug 9;365(6453). pii: science.aaw5202. doi: 
            10.1126/science.aaw5202. Epub 2019 Jul 18.
  PUBMED    31320556
REFERENCE   2  (bases 1 to 6266)
  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: "Science."; 
            date: "2019-08-9"; volume: "365(6453). pii: science.aaw5202. doi"; 
            pages: " 10.1126/science.aaw5202. Epub 2019 Jul 18"
COMMENT     Sequence Label: pAAV-Ef1a-DIO mScarlet
FEATURES             Location/Qualifiers
     source          1..6266
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     repeat_region   1..130
                     /label=AAV2 ITR (alternate)
                     /note="Functional equivalent of wild-type AAV2 ITR"
     promoter        231..1409
                     /label=EF-1-alpha promoter
                     /note="strong constitutive promoter for human elongation 
                     factor EF-1-alpha"
     intron          462..1400
                     /label=EF-1-alpha intron A
                     /note="intron upstream of the start codon of human 
                     EF-1-alpha"
     primer_bind     1357..1377
                     /label=EF1a-F
                     /note="Human elongation factor-1a promoter, forward primer"
     protein_bind    complement(1416..1449)
                     /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(1500..1533)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     CDS             complement(1545..2240)
                     /codon_start=1
                     /product="bright monomeric red fluorescent protein evolved 
                     from a synthetic template (Bindels et al., 2016)"
                     /label=mScarlet
                     /translation="MVSKGEAVIKEFMRFKVHMEGSMNGHEFEIEGEGEGRPYEGTQTA
                     KLKVTKGGPLPFSWDILSPQFMYGSRAFTKHPADIPDYYKQSFPEGFKWERVMNFEDGG
                     AVTVTQDTSLEDGTLIYKVKLRGTNFPPDGPVMQKKTMGWEASTERLYPEDGVLKGDIK
                     MALRLKDGGRYLADFKTTYKAKKPVQMPGAYNVDRKLDITSHNEDYTVVEQYERSEGRH
                     STGGMDELYK"
     primer_bind     complement(1820..1839)
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     primer_bind     2089..2107
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     regulatory      2237..2246
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     protein_bind    2251..2284
                     /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    2335..2368
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     misc_feature    2393..2981
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(2446..2466)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2864..2875)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    3013..3489
                     /label=hGH poly(A) signal
                     /note="human growth hormone polyadenylation signal"
     primer_bind     complement(3212..3231)
                     /label=hGH-PA-R
                     /note="Human growth hormone terminator, reverse primer"
     repeat_region   3529..3669
                     /label=AAV2 ITR
                     /note="inverted terminal repeat of adeno-associated virus 
                     serotype 2"
     repeat_region   3529..3658
                     /label=AAV2 ITR
     rep_origin      3744..4199
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3831..3850)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4041..4062
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(4216..4235)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     4335..4357
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(4395..4413)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        4481..4585
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(4586..4654,4655..5446)
                     /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(4804..4823)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      5617..6205
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     6106..6125
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 cctgcaggca gctgcgcgct cgctcgctca ctgaggccgc ccgggcgtcg ggcgaccttt
       61 ggtcgcccgg cctcagtgag cgagcgagcg cgcagagagg gagtggccaa ctccatcact
      121 aggggttcct gcggccgcac gcgtaagctt tgcaaagatg gataaagttt taaacagaga
      181 ggaatctttg cagctaatgg accttctagg tcttgaaagg agtgggaatt ggctccggtg
      241 cccgtcagtg ggcagagcgc acatcgccca cagtccccga gaagttgggg ggaggggtcg
      301 gcaattgaac cggtgcctag agaaggtggc gcggggtaaa ctgggaaagt gatgtcgtgt
      361 actggctccg cctttttccc gagggtgggg gagaaccgta tataagtgca gtagtcgccg
      421 tgaacgttct ttttcgcaac gggtttgccg ccagaacaca ggtaagtgcc gtgtgtggtt
      481 cccgcgggcc tggcctcttt acgggttatg gcccttgcgt gccttgaatt acttccacct
      541 ggctgcagta cgtgattctt gatcccgagc ttcgggttgg aagtgggtgg gagagttcga
      601 ggccttgcgc ttaaggagcc ccttcgcctc gtgcttgagt tgaggcctgg cctgggcgct
      661 ggggccgccg cgtgcgaatc tggtggcacc ttcgcgcctg tctcgctgct ttcgataagt
      721 ctctagccat ttaaaatttt tgatgacctg ctgcgacgct ttttttctgg caagatagtc
      781 ttgtaaatgc gggccaagat ctgcacactg gtatttcggt ttttggggcc gcgggcggcg
      841 acggggcccg tgcgtcccag cgcacatgtt cggcgaggcg gggcctgcga gcgcggccac
      901 cgagaatcgg acgggggtag tctcaagctg gccggcctgc tctggtgcct ggcctcgcgc
      961 cgccgtgtat cgccccgccc tgggcggcaa ggctggcccg gtcggcacca gttgcgtgag
     1021 cggaaagatg gccgcttccc ggccctgctg cagggagctc aaaatggagg acgcggcgct
     1081 cgggagagcg ggcgggtgag tcacccacac aaaggaaaag ggcctttccg tcctcagccg
     1141 tcgcttcatg tgactccacg gagtaccggg cgccgtccag gcacctcgat tagttctcga
     1201 gcttttggag tacgtcgtct ttaggttggg gggaggggtt ttatgcgatg gagtttcccc
     1261 acactgagtg ggtggagact gaagttaggc cagcttggca cttgatgtaa ttctccttgg
     1321 aatttgccct ttttgagttt ggatcttggt tcattctcaa gcctcagaca gtggttcaaa
     1381 gtttttttct tccatttcag gtgtcgtgag gatccataac ttcgtatagg atactttata
     1441 cgaagttatg cagaatggta gctggattgt agctgctatt agcaatatga aacctcttaa
     1501 taacttcgta tagcatacat tatacgaagt tatggcgcgc cttacttgta cagctcgtcc
     1561 atgccgccgg tggagtggcg gccctcggag cgttcgtact gttccaccac ggtgtagtcc
     1621 tcgttgtggg aggtgatgtc caacttgcgg tccacgttgt aggcgccggg catctgcacg
     1681 ggcttcttgg ccttgtaggt ggtcttgaag tccgccaggt agcgcccgcc gtccttcagg
     1741 cgcagggcca tcttaatgtc gcccttcagc acgccgtcct cggggtacaa ccgctcggtg
     1801 gacgcttccc agcccattgt cttcttctgc attacggggc cgtcaggagg gaagttggtg
     1861 ccgcggagct tcaccttgta gatcagggtg ccgtcctcca gggaggtgtc ctgggtcacg
     1921 gtcacggcgc cgccgtcctc gaagttcatc acgcgctccc acttgaagcc ctcggggaag
     1981 gactgcttat agtagtcggg gatgtcggcg gggtgcttgg tgaaggccct ggagccgtac
     2041 atgaactgag gggacaggat gtcccaggag aagggcaggg ggccaccctt ggtcaccttc
     2101 agcttggcgg tctgggtgcc ctcgtagggg cggccctcgc cctcgccctc gatctcgaac
     2161 tcgtggccgt tcatggagcc ctccatgtgc accttgaacc gcatgaactc cttgatcact
     2221 gcctcgccct tgctcaccat ggtggctagc ataacttcgt ataaagtatc ctatacgaag
     2281 ttatttgcct taacccagaa attatcactg ttattcttta gaatggtgca aagaataact
     2341 tcgtataatg tatgctatac gaagttatga attcgatatc aagcttatcg ataatcaacc
     2401 tctggattac aaaatttgtg aaagattgac tggtattctt aactatgttg ctccttttac
     2461 gctatgtgga tacgctgctt taatgccttt gtatcatgct attgcttccc gtatggcttt
     2521 cattttctcc tccttgtata aatcctggtt gctgtctctt tatgaggagt tgtggcccgt
     2581 tgtcaggcaa cgtggcgtgg tgtgcactgt gtttgctgac gcaaccccca ctggttgggg
     2641 cattgccacc acctgtcagc tcctttccgg gactttcgct ttccccctcc ctattgccac
     2701 ggcggaactc atcgccgcct gccttgcccg ctgctggaca ggggctcggc tgttgggcac
     2761 tgacaattcc gtggtgttgt cggggaaatc atcgtccttt ccttggctgc tcgcctatgt
     2821 tgccacctgg attctgcgcg ggacgtcctt ctgctacgtc ccttcggccc tcaatccagc
     2881 ggaccttcct tcccgcggcc tgctgccggc tctgcggcct cttccgcgtc ttcgccttcg
     2941 ccctcagacg agtcggatct ccctttgggc cgcctccccg catcgatacc gagcgctgct
     3001 cgagagatct acgggtggca tccctgtgac ccctccccag tgcctctcct ggccctggaa
     3061 gttgccactc cagtgcccac cagccttgtc ctaataaaat taagttgcat cattttgtct
     3121 gactaggtgt ccttctataa tattatgggg tggagggggg tggtatggag caaggggcaa
     3181 gttgggaaga caacctgtag ggcctgcggg gtctattggg aaccaagctg gagtgcagtg
     3241 gcacaatctt ggctcactgc aatctccgcc tcctgggttc aagcgattct cctgcctcag
     3301 cctcccgagt tgttgggatt ccaggcatgc atgaccaggc tcagctaatt tttgtttttt
     3361 tggtagagac ggggtttcac catattggcc aggctggtct ccaactccta atctcaggtg
     3421 atctacccac cttggcctcc caaattgctg ggattacagg cgtgaaccac tgctcccttc
     3481 cctgtccttc tgattttgta ggtaaccacg tgcggaccga gcggccgcag gaacccctag
     3541 tgatggagtt ggccactccc tctctgcgcg ctcgctcgct cactgaggcc gggcgaccaa
     3601 aggtcgcccg acgcccgggc tttgcccggg cggcctcagt gagcgagcga gcgcgcagct
     3661 gcctgcaggg gcgcctgatg cggtattttc tccttacgca tctgtgcggt atttcacacc
     3721 gcatacgtca aagcaaccat agtacgcgcc ctgtagcggc gcattaagcg cggcgggtgt
     3781 ggtggttacg cgcagcgtga ccgctacact tgccagcgcc ttagcgcccg ctcctttcgc
     3841 tttcttccct tcctttctcg ccacgttcgc cggctttccc cgtcaagctc taaatcgggg
     3901 gctcccttta gggttccgat ttagtgcttt acggcacctc gaccccaaaa aacttgattt
     3961 gggtgatggt tcacgtagtg ggccatcgcc ctgatagacg gtttttcgcc ctttgacgtt
     4021 ggagtccacg ttctttaata gtggactctt gttccaaact ggaacaacac tcaactctat
     4081 ctcgggctat tcttttgatt tataagggat tttgccgatt tcggtctatt ggttaaaaaa
     4141 tgagctgatt taacaaaaat ttaacgcgaa ttttaacaaa atattaacgt ttacaatttt
     4201 atggtgcact ctcagtacaa tctgctctga tgccgcatag ttaagccagc cccgacaccc
     4261 gccaacaccc gctgacgcgc cctgacgggc ttgtctgctc ccggcatccg cttacagaca
     4321 agctgtgacc gtctccggga gctgcatgtg tcagaggttt tcaccgtcat caccgaaacg
     4381 cgcgagacga aagggcctcg tgatacgcct atttttatag gttaatgtca tgataataat
     4441 ggtttcttag acgtcaggtg gcacttttcg gggaaatgtg cgcggaaccc ctatttgttt
     4501 atttttctaa atacattcaa atatgtatcc gctcatgaga caataaccct gataaatgct
     4561 tcaataatat tgaaaaagga agagtatgag tattcaacat ttccgtgtcg cccttattcc
     4621 cttttttgcg gcattttgcc ttcctgtttt tgctcaccca gaaacgctgg tgaaagtaaa
     4681 agatgctgaa gatcagttgg gtgcacgagt gggttacatc gaactggatc tcaacagcgg
     4741 taagatcctt gagagttttc gccccgaaga acgttttcca atgatgagca cttttaaagt
     4801 tctgctatgt ggcgcggtat tatcccgtat tgacgccggg caagagcaac tcggtcgccg
     4861 catacactat tctcagaatg acttggttga gtactcacca gtcacagaaa agcatcttac
     4921 ggatggcatg acagtaagag aattatgcag tgctgccata accatgagtg ataacactgc
     4981 ggccaactta cttctgacaa cgatcggagg accgaaggag ctaaccgctt ttttgcacaa
     5041 catgggggat catgtaactc gccttgatcg ttgggaaccg gagctgaatg aagccatacc
     5101 aaacgacgag cgtgacacca cgatgcctgt agcaatggca acaacgttgc gcaaactatt
     5161 aactggcgaa ctacttactc tagcttcccg gcaacaatta atagactgga tggaggcgga
     5221 taaagttgca ggaccacttc tgcgctcggc ccttccggct ggctggttta ttgctgataa
     5281 atctggagcc ggtgagcgtg ggtctcgcgg tatcattgca gcactggggc cagatggtaa
     5341 gccctcccgt atcgtagtta tctacacgac ggggagtcag gcaactatgg atgaacgaaa
     5401 tagacagatc gctgagatag gtgcctcact gattaagcat tggtaactgt cagaccaagt
     5461 ttactcatat atactttaga ttgatttaaa acttcatttt taatttaaaa ggatctaggt
     5521 gaagatcctt tttgataatc tcatgaccaa aatcccttaa cgtgagtttt cgttccactg
     5581 agcgtcagac cccgtagaaa agatcaaagg atcttcttga gatccttttt ttctgcgcgt
     5641 aatctgctgc ttgcaaacaa aaaaaccacc gctaccagcg gtggtttgtt tgccggatca
     5701 agagctacca actctttttc cgaaggtaac tggcttcagc agagcgcaga taccaaatac
     5761 tgttcttcta gtgtagccgt agttaggcca ccacttcaag aactctgtag caccgcctac
     5821 atacctcgct ctgctaatcc tgttaccagt ggctgctgcc agtggcgata agtcgtgtct
     5881 taccgggttg gactcaagac gatagttacc ggataaggcg cagcggtcgg gctgaacggg
     5941 gggttcgtgc acacagccca gcttggagcg aacgacctac accgaactga gatacctaca
     6001 gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca ggtatccggt
     6061 aagcggcagg gtcggaacag gagagcgcac gagggagctt ccagggggaa acgcctggta
     6121 tctttatagt cctgtcgggt ttcgccacct ctgacttgag cgtcgatttt tgtgatgctc
     6181 gtcagggggg cggagcctat ggaaaaacgc cagcaacgcg gcctttttac ggttcctggc
     6241 cttttgctgg ccttttgctc acatgt
//
