LOCUS       sequence-341506-        7310 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Cre-dependent AAV virus.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7310)
  AUTHORS   Yao S, Wang Q, Hirokawa KE, Ouellette B, Ahmed R, Bomben J, Brouner 
            K, Casal L, Caldejon S, Cho A, Dotson NI, Daigle TL, Egdorf T, 
            Enstrom R, Gary A, Gelfand E, Gorham M, Griffin F, Gu H, Hancock N, 
            Howard R, Kuan L, Lambert S, Lee EK, Luviano J, Mace K, Maxwell M, 
            Mortrud MT, Naeemi M, Nayan C, Ngo NK, Nguyen T, North K, Ransford 
            S, Ruiz A, Seid S, Swapp J, Taormina MJ, Wakeman W, Zhou T, Nicovich
            PR, Williford A, Potekhina L, McGraw M, Ng L, Groblewski PA, Tasic 
            B, Mihalas S, Harris JA, Cetin A, Zeng H
  TITLE     A whole-brain monosynaptic input connectome to neuron classes in 
            mouse visual cortex.
  JOURNAL   Nat Neurosci. 2023 Feb;26(2):350-364. doi: 
            10.1038/s41593-022-01219-x. Epub 2022 Dec 22.
  PUBMED    36550293
REFERENCE   2  (bases 1 to 7310)
  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"; doi: 
            "10.1038/s41593-022-01219-x"; journalName: "Nat Neurosci"; date: 
            "2023-02"; volume: "26"; issue: "2"; pages: "350-364"
COMMENT     Sequence Label: AiP5004 pAAV-Syn-DIO-TVA-dTom-SAD-B19G
FEATURES             Location/Qualifiers
     source          1..7310
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     repeat_region   7..136
                     /label=AAV2 ITR (alternate)
                     /note="Functional equivalent of wild-type AAV2 ITR"
     promoter        164..611
                     /label=hSyn promoter
                     /note="human synapsin I promoter; confers neuron-specific 
                     expression (Kugler et al., 2003)"
     regulatory      618..627
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     protein_bind    633..666
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     protein_bind    717..750
                     /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)."
     CDS             complement(2331..2387)
                     /codon_start=1
                     /product="2A peptide from porcine teschovirus-1 
                     polyprotein"
                     /label=P2A
                     /note="Eukaryotic ribosomes fail to insert a peptide bond 
                     between the Gly and Pro residues, yielding separate 
                     polypeptides."
                     /translation="ATNFSLLKQAGDVEENPGP"
     CDS             complement(2397..3098)
                     /codon_start=1
                     /product="dimeric variant of DsRed fluorescent protein 
                     (Shaner et al., 2004)"
                     /label=dTomato
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEEVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYEGTQTA
                     KLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMNFEDGG
                     LVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVLKGEIH
                     QALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYERSEGRH
                     HLFLYGMDELYK"
     primer_bind     complement(2480..2503)
                     /label=DsRed1-C
                     /note="DsRed1, forward primer"
     primer_bind     complement(2678..2697)
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     primer_bind     2947..2965
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     CDS             complement(3099..3155)
                     /codon_start=1
                     /product="2A peptide from porcine teschovirus-1 
                     polyprotein"
                     /label=P2A
                     /note="Eukaryotic ribosomes fail to insert a peptide bond 
                     between the Gly and Pro residues, yielding separate 
                     polypeptides."
                     /translation="ATNFSLLKQAGDVEENPGP"
     protein_bind    complement(3638..3671)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     protein_bind    complement(3722..3755)
                     /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)."
     misc_feature    3757..4345
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3810..3830)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4228..4239)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    4353..4577
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     repeat_region   4579..4719
                     /label=AAV2 ITR
                     /note="inverted terminal repeat of adeno-associated virus 
                     serotype 2"
     repeat_region   4579..4708
                     /label=AAV2 ITR
     rep_origin      4794..5249
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(4881..4900)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5091..5112
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(5266..5285)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     5385..5407
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(5445..5463)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        5531..5635
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5636..5704,5705..6496)
                     /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(5854..5873)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      6667..7255
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     7156..7175
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 acatgtcctg caggcagctg cgcgctcgct cgctcactga ggccgcccgg gcgtcgggcg
       61 acctttggtc gcccggcctc agtgagcgag cgagcgcgca gagagggagt ggccaactcc
      121 atcactaggg gttcctgcta gactgcagag ggccctgcgt atgagtgcaa gtgggtttta
      181 ggaccaggat gaggcggggt gggggtgcct acctgacgac cgaccccgac ccactggaca
      241 agcacccaac ccccattccc caaattgcgc atcccctatc agagaggggg aggggaaaca
      301 ggatgcggcg aggcgcgtgc gcactgccag cttcagcacc gcggacagtg ccttcgcccc
      361 cgcctggcgg cgcgcgccac cgccgcctca gcactgaagg cgcgctgacg tcactcgccg
      421 gtcccccgca aactcccctt cccggccacc ttggtcgcgt ccgcgccgcc gccggcccag
      481 ccggaccgca ccacgcgagg cgcgagatag gggggcacgg gcgcgaccat ctgcgctgcg
      541 gcgccggcga ctcagcgctg cctcagtctg cggtgggcag cggaggagtc gtgtcgtgcc
      601 tgagagcgca gtcagccgcc accatggtta atataacttc gtataatgta tgctatacga
      661 agttatgcag aatggtagct ggattgtagc tgctattagc aatatgaaac ctcttaataa
      721 cttcgtataa agtatcctat acgaagttat ggtacctaca gtctggtctc acccccactc
      781 ttgtgtgatt cccatgaaga tatgatcttc ccgctttggg gagtgactga cacctccctc
      841 cctgtccctc tgagattgtg ttgcgtaggt tctgatcgat tgactcttct acaacatgtc
      901 atcaggaaaa ttatcaacat caaggcagtc agggcccctg cactcagtaa tacatacttc
      961 ccccagttcg ggagacccaa gtcaactcct gagacctgat tgtgcacatc gggaaggtga
     1021 acttcaacaa aatcctcagc ctcgtcaccg tccttgaaaa cggtagacgg gtctgccagg
     1081 gggtgcacaa gggggataac cgaggattcc aacaactcca tatgttgctg gaggagggat
     1141 gattgcatct ctgggattaa gacattgccg tcaggtccta atattatacc attgaaaaac
     1201 accccgttca catgaggatg acacctcccc ccaactctta aacacccttt tgaagggagg
     1261 atctcattcc aagttctgac tgacttgtag tgagcatcgg cttccatcaa ggtcttgttg
     1321 aatatggtat atgcttttcc aaacccaggg acaagttttc ttaaatgact gagacgtctg
     1381 aaactcactg acttggttgt catgatggac tctagtgcat ccagacactc ctctctcttc
     1441 ctgaccaact cctctacaac aaggtgctca atttcgtctg agcgaaagtc gtgcaggttc
     1501 accaacttat cgggagggca ccatttggtt tcatttgatg tttgcatcga gacccatgtt
     1561 ccatccataa gtctaagtcc tagaactcca cataacttga gtttgcatgc tccttttaaa
     1621 gacttatata ggcctctttc atctacaaag ccgcaagtct cactcccttt ggatgctctc
     1681 ttccctctac tattggtaaa aatgtcacaa gacatcccta gtctcggatt ctcgggcatc
     1741 caaatggtgt aatcgtggtt agtggagcag taggtagaag acaccgctac tcctgagcac
     1801 ttcccgctag ggaagaccct cgagtgaagg gatctgtcat atgggtccaa atctgccaca
     1861 cttggagata tgataacgag agactccttg gtggttttta cagttcgaag ccagcggtag
     1921 tcagggtacg gattgtgtag agactcttca tatctggggt caccggccat cttccagttg
     1981 tacgcggctc tacatgcatc tggtgttggg cggaaatgct ttcttttgaa cgtggttgtg
     2041 acataaccaa cgaagttagt gtaggtttca gcctccgtca caacgcctgt gcaagtgaac
     2101 ccgttcactt ttatggctaa gatgtatcca actttaagtt ccatgtagga gaaccctgac
     2161 aggttggtgc atccttcgtc ctccactacc aaattgtttg ggcagctgag gtgatgtatg
     2221 tcaatcggac tccagggacc aagcttgtct ggtatcgtgt aaatagggaa tttcccaaaa
     2281 cacaatggaa aaaccagaag gggtacaaac aggagagcct gaggaaccat gggtccaggg
     2341 ttctcctcca cgtctccagc ctgcttcagc aggctgaagt tagtagctcc ggatcccttg
     2401 tacagctcgt ccatgccgta caggaacagg tggtggcggc cctcggagcg ctcgtactgt
     2461 tccacgatgg tgtagtcctc gttgtgggag gtgatgtcca gcttggtgtc cacgtagtag
     2521 tagccgggca gttgcacggg cttcttggcc atgtagatgg tcttgaactc caccaggtag
     2581 tggccgccgt ccttcagctt cagggcctgg tggatctcgc ccttcagcac gccgtcgcgg
     2641 gggtacaggc gctcggtgga ggcctcccag cccatggtct tcttctgcat tacggggccg
     2701 tcggggggga agttggtgcc gcgcatcttc accttgtaga tcagcgtgcc gtcctgcagg
     2761 gaggagtcct gggtcacggt caccagaccg ccgtcctcga agttcatcac gcgctcccac
     2821 ttgaagccct cggggaagga cagcttcttg taatcgggga tgtcggcggg gtgcttcacg
     2881 tacgccttgg agccgtacat gaactggggg gacaggatgt cccaggcgaa gggcaggggg
     2941 ccgcccttgg tcaccttcag cttggcggtc tgggtgccct cgtaggggcg gccctcgccc
     3001 tcgccctcga tctcgaactc gtggccgttc atggagccct ccatgcgcac cttgaagcgc
     3061 atgaactctt tgatgacctc ctcgcccttg ctcaccatgg gtccagggtt ctcctccacg
     3121 tctccagcct gcttcagcag gctgaagtta gtagctccgg atccggagaa caagtctgcc
     3181 tggctcttgt caggcaccag cagctccttg gatgcgcttt caagactgaa gatgtcagac
     3241 ctgctttttg ctttggactt cccccatgca gcgataccac ccacagctac caggcagcac
     3301 aggagcactg cagtgatcag catccacatg cggccgtgat tcctggctgg cagagcacgt
     3361 ccaggagcag gggcagtggg agcctctgtg ccgttgtccg tgggcaccgc ggggatcgcg
     3421 ctggtcccgc agccccactc gtcccgcccg tcgtcgcagt cggggtgtcc gtcgcacagc
     3481 cagtcctgcg ggtaacactc cccgtgggca ccgggcggct ccgagcagcg gaactgaccg
     3541 ggggggcaac gggacaaaga accgttaccg gacccgttac cggtcacgtt accgggcagc
     3601 agcagcagca gcagcgcggg cagcagccgc gcacctaata acttcgtata gcatacatta
     3661 tacgaagtta tttgccttaa cccagaaatt atcactgtta ttctttagaa tggtgcaaag
     3721 aataacttcg tataggatac tttatacgaa gttatgaatc aacctctgga ttacaaaatt
     3781 tgtgaaagat tgactggtat tcttaactat gttgctcctt ttacgctatg tggatacgct
     3841 gctttaatgc ctttgtatca tgctattgct tcccgtatgg ctttcatttt ctcctccttg
     3901 tataaatcct ggttgctgtc tctttatgag gagttgtggc ccgttgtcag gcaacgtggc
     3961 gtggtgtgca ctgtgtttgc tgacgcaacc cccactggtt ggggcattgc caccacctgt
     4021 cagctccttt ccgggacttt cgctttcccc ctccctattg ccacggcgga actcatcgcc
     4081 gcctgccttg cccgctgctg gacaggggct cggctgttgg gcactgacaa ttccgtggtg
     4141 ttgtcgggga agctgacgtc ctttccatgg ctgctcgcct gtgttgccac ctggattctg
     4201 cgcgggacgt ccttctgcta cgtcccttcg gccctcaatc cagcggacct tccttcccgc
     4261 ggcctgctgc cggctctgcg gcctcttccg cgtcttcgcc ttcgccctca gacgagtcgg
     4321 atctcccttt gggccgcctc cccgcctgga tcctgtgcct tctagttgcc agccatctgt
     4381 tgtttgcccc tcccccgtgc cttccttgac cctggaaggt gccactccca ctgtcctttc
     4441 ctaataaaat gaggaaattg catcgcattg tctgagtagg tgtcattcta ttctgggggg
     4501 tggggtgggg caggacagca agggggagga ttgggaagac aatagcaggc atgctgggga
     4561 tgcggtgggc tctatggcag gaacccctag tgatggagtt ggccactccc tctctgcgcg
     4621 ctcgctcgct cactgaggcc gggcgaccaa aggtcgcccg acgcccgggc tttgcccggg
     4681 cggcctcagt gagcgagcga gcgcgcagct gcctgcaggg gcgcctgatg cggtattttc
     4741 tccttacgca tctgtgcggt atttcacacc gcatacgtca aagcaaccat agtacgcgcc
     4801 ctgtagcggc gcattaagcg cggcgggtgt ggtggttacg cgcagcgtga ccgctacact
     4861 tgccagcgcc ctagcgcccg ctcctttcgc tttcttccct tcctttctcg ccacgttcgc
     4921 cggctttccc cgtcaagctc taaatcgggg gctcccttta gggttccgat ttagtgcttt
     4981 acggcacctc gaccccaaaa aacttgattt gggtgatggt tcacgtagtg ggccatcgcc
     5041 ctgatagacg gtttttcgcc ctttgacgtt ggagtccacg ttctttaata gtggactctt
     5101 gttccaaact ggaacaacac tcaaccctat ctcgggctat tcttttgatt tataagggat
     5161 tttgccgatt tcggcctatt ggttaaaaaa tgagctgatt taacaaaaat ttaacgcgaa
     5221 ttttaacaaa atattaacgt ttacaatttt atggtgcact ctcagtacaa tctgctctga
     5281 tgccgcatag ttaagccagc cccgacaccc gccaacaccc gctgacgcgc cctgacgggc
     5341 ttgtctgctc ccggcatccg cttacagaca agctgtgacc gtctccggga gctgcatgtg
     5401 tcagaggttt tcaccgtcat caccgaaacg cgcgagacga aagggcctcg tgatacgcct
     5461 atttttatag gttaatgtca tgataataat ggtttcttag acgtcaggtg gcacttttcg
     5521 gggaaatgtg cgcggaaccc ctatttgttt atttttctaa atacattcaa atatgtatcc
     5581 gctcatgaga caataaccct gataaatgct tcaataatat tgaaaaagga agagtatgag
     5641 tattcaacat ttccgtgtcg cccttattcc cttttttgcg gcattttgcc ttcctgtttt
     5701 tgctcaccca gaaacgctgg tgaaagtaaa agatgctgaa gatcagttgg gtgcacgagt
     5761 gggttacatc gaactggatc tcaacagcgg taagatcctt gagagttttc gccccgaaga
     5821 acgttttcca atgatgagca cttttaaagt tctgctatgt ggcgcggtat tatcccgtat
     5881 tgacgccggg caagagcaac tcggtcgccg catacactat tctcagaatg acttggttga
     5941 gtactcacca gtcacagaaa agcatcttac ggatggcatg acagtaagag aattatgcag
     6001 tgctgccata accatgagtg ataacactgc ggccaactta cttctgacaa cgatcggagg
     6061 accgaaggag ctaaccgctt ttttgcacaa catgggggat catgtaactc gccttgatcg
     6121 ttgggaaccg gagctgaatg aagccatacc aaacgacgag cgtgacacca cgatgcctgt
     6181 agcaatggca acaacgttgc gcaaactatt aactggcgaa ctacttactc tagcttcccg
     6241 gcaacaatta atagactgga tggaggcgga taaagttgca ggaccacttc tgcgctcggc
     6301 ccttccggct ggctggttta ttgctgataa atctggagcc ggtgagcgtg ggtctcgcgg
     6361 tatcattgca gcactggggc cagatggtaa gccctcccgt atcgtagtta tctacacgac
     6421 ggggagtcag gcaactatgg atgaacgaaa tagacagatc gctgagatag gtgcctcact
     6481 gattaagcat tggtaactgt cagaccaagt ttactcatat atactttaga ttgatttaaa
     6541 acttcatttt taatttaaaa ggatctaggt gaagatcctt tttgataatc tcatgaccaa
     6601 aatcccttaa cgtgagtttt cgttccactg agcgtcagac cccgtagaaa agatcaaagg
     6661 atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa aaaaaccacc
     6721 gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc cgaaggtaac
     6781 tggcttcagc agagcgcaga taccaaatac tgtccttcta gtgtagccgt agttaggcca
     6841 ccacttcaag aactctgtag caccgcctac atacctcgct ctgctaatcc tgttaccagt
     6901 ggctgctgcc agtggcgata agtcgtgtct taccgggttg gactcaagac gatagttacc
     6961 ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc acacagccca gcttggagcg
     7021 aacgacctac accgaactga gatacctaca gcgtgagcta tgagaaagcg ccacgcttcc
     7081 cgaagggaga aaggcggaca ggtatccggt aagcggcagg gtcggaacag gagagcgcac
     7141 gagggagctt ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacct
     7201 ctgacttgag cgtcgatttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc
     7261 cagcaacgcg gcctttttac ggttcctggc cttttgctgg ccttttgctc
//
