LOCUS       sequence-466366-        4558 bp DNA     circular SYN 24-MAR-2025
DEFINITION  AiE3104m is an enhancer sequence, designed to drive AAV-mediated 
            transgene expression in specific populations of brain cells.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 4558)
  AUTHORS   Ben-Simon Y, Hooper M, Narayan S, Daigle T, Dwivedi D, Way SW, Oster
            A, Stafford DA, Mich JK, Taormina MJ, Martinez RA, Opitz-Araya X, 
            Roth JR, Allen S, Ayala A, Bakken TE, Barcelli T, Barta S, Bendrick 
            J, Bertagnolli D, Bowlus J, Boyer G, Brouner K, Casian B, Casper T, 
            Chakka AB, Chakrabarty R, Chance RK, Chavan S, Departee M, Donadio 
            N, Dotson N, Egdorf T, Gabitto M, Garcia J, Gary A, Gasperini M, 
            Goldy J, Gore BB, Graybuck L, Greisman N, Haeseleer F, Halterman C, 
            Helback O, Hockemeyer D, Huang C, Huff S, Hunker A, Johansen N, 
            Juneau Z, Kalmbach B, Khem S, Kussick E, Kutsal R, Larsen R, Lee C, 
            Lee AY, Leibly M, Lenz GH, Liang E, Lusk N, Malone J, Mollenkopf T, 
            Morin E, Newman D, Ng L, Ngo K, Omstead V, Oyama A, Pham T, Pom CA, 
            Potekhina L, Ransford S, Rette D, Rimorin C, Rocha D, Ruiz A, 
            Sanchez REA, Sedeno-Cortes A, Sevigny JP, Shapovalova N, Shulga L, 
            Sigler AR, Siverts LA, Somasundaram S, Stewart K, Szelenyi E, Tieu 
            M, Trader C, van Velthoven CTJ, Walker M, Weed N, Wirthlin M, Wood 
            T, Wynalda B, Yao Z, Zhou T, Ariza J, Dee N, Reding M, Ronellenfitch
            K, Mufti S, Sunkin SM, Smith KA, Esposito L, Waters J, Thyagarajan 
            B, Yao S, Lein ES, Zeng H, Levi BP, Ngai J, Ting J, Tasic B
  TITLE     A suite of enhancer AAVs and transgenic mouse lines for genetic 
            access to cortical cell types.
  JOURNAL   bioRxiv [Preprint]. 2024 Sep 26:2024.06.10.597244. doi: 
            10.1101/2024.06.10.597244.
  PUBMED    38915722
REFERENCE   2  (bases 1 to 4558)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Mar 24, 2025 from SnapGene Server 7.0.3
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "bioRxiv 
            [Preprint]. 2024 Sep 26:2024.06.10.597244. doi: 
            10.1101/2024.06.10.597244."
FEATURES             Location/Qualifiers
     source          1..4558
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     regulatory      301..310
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             307..1023
                     /codon_start=1
                     /product="monomeric optimized variant of EYFP, identical to
                     mVenus but with L68V (Kremers et al., 2006)"
                     /label=SYFP2
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KLICTTGKLPVPWPTLVTTLGYGVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIK
                     ANFKIRHNIEDGGVQLADHYQQNTPIGDGPVLLPDNHYLSYQSKLSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(352..373)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(613..632)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     960..981
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     primer_bind     complement(1116..1136)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     polyA_signal    1323..1434
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     repeat_region   1552..1692
                     /label=AAV2 ITR
                     /note="inverted terminal repeat of adeno-associated virus 
                     serotype 2"
     repeat_region   1552..1681
                     /label=AAV2 ITR
     rep_origin      1767..2222
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1854..1873)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2064..2085
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(2239..2258)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     2358..2380
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(2418..2436)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        2504..2608
                     /gene="bla"
                     /label=AmpR promoter
     CDS             2609..3469
                     /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(2827..2846)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      3640..4228
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     4129..4148
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     repeat_region   4290..4419
                     /label=AAV2 ITR (alternate)
                     /note="Functional equivalent of wild-type AAV2 ITR"
ORIGIN
        1 cctgagtcat cttccatggt ctggcaaggc ctctgttctc atctgtgcaa tcaaatctca
       61 aactgatttc tctctttggt tttcttcttc ttcttttttt ggcatgggag aaaataactt
      121 ctgtattctt tttttaggag agtgagaaaa ggaatatcat tctatttctc agaattgcat
      181 atagcatttc aaaaagtgac gccggcggag ctcgggctgg gcataaaagt cagggcagag
      241 ccatctattg cttacatttg cttctgggat ccagatcttt cgaagctagc gctaccggtc
      301 gccaccatgg tgagcaaggg cgaggagctg ttcaccgggg tggtgcccat cctggtcgag
      361 ctggacggcg acgtaaacgg ccacaagttc agcgtgtccg gcgagggcga gggcgatgcc
      421 acctacggca agctgaccct gaagctgatc tgcaccaccg gcaagctgcc cgtgccctgg
      481 cccaccctcg tgaccaccct gggctacggc gtgcagtgct tcgcccgcta ccccgaccac
      541 atgaagcagc acgacttctt caagtccgcc atgcccgaag gctacgtcca ggagcgcacc
      601 atcttcttca aggacgacgg caactacaag acccgcgccg aggtgaagtt cgagggcgac
      661 accctggtga accgcatcga gctgaagggc atcgacttca aggaggacgg caacatcctg
      721 gggcacaagc tggagtacaa ctacaacagc cacaacgtct atatcaccgc cgacaagcag
      781 aagaacggca tcaaggccaa cttcaagatc cgccacaaca tcgaggacgg cggcgtgcag
      841 ctcgccgacc actaccagca gaacaccccc atcggcgacg gccccgtgct gctgcccgac
      901 aaccactacc tgagctacca gtccaagctg agcaaagacc ccaacgagaa gcgcgatcac
      961 atggtcctgc tggagttcgt gaccgccgcc gggatcactc tcggcatgga cgagctgtac
     1021 aagtaagtcg acggcgcgcc gcggccgcga attcgatatc ataatcaacc tctggattac
     1081 aaaatttgtg aaagattgac tggtattctt aactatgttg ctccttttac gctatgtgga
     1141 tacgctgctt taatgccttt gtatcatgct attgcttccc gtatggcttt cattttctcc
     1201 tccttgtata aatcctggtt agttcttgcc acggcggaac tcatcgccgc ctgccttgcc
     1261 cgctgctgga caggggctcg gctgttgggc actgacaatt ccgtggctcg agagatcttc
     1321 gactgtgcct tctagttgcc agccatctgt tgtttgcccc tcccccgtgc cttccttgac
     1381 cctggaaggt gccactccca ctgtcctttc ctaataaaat gaggaaattg catcgcattg
     1441 tctgagtagg tgtcattcta ttctgggggg tggggtgggg caggacagca agggggagga
     1501 ttgggaagac aatagcaggc atgagatctc acgtgcggac cgagcggccg caggaacccc
     1561 tagtgatgga gttggccact ccctctctgc gcgctcgctc gctcactgag gccgggcgac
     1621 caaaggtcgc ccgacgcccg ggctttgccc gggcggcctc agtgagcgag cgagcgcgca
     1681 gctgcctgca ggggcgcctg atgcggtatt ttctccttac gcatctgtgc ggtatttcac
     1741 accgcatacg tcaaagcaac catagtacgc gccctgtagc ggcgcattaa gcgcggcggg
     1801 tgtggtggtt acgcgcagcg tgaccgctac acttgccagc gccttagcgc ccgctccttt
     1861 cgctttcttc ccttcctttc tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg
     1921 ggggctccct ttagggttcc gatttagtgc tttacggcac ctcgacccca aaaaacttga
     1981 tttgggtgat ggttcacgta gtgggccatc gccctgatag acggtttttc gccctttgac
     2041 gttggagtcc acgttcttta atagtggact cttgttccaa actggaacaa cactcaactc
     2101 tatctcgggc tattcttttg atttataagg gattttgccg atttcggtct attggttaaa
     2161 aaatgagctg atttaacaaa aatttaacgc gaattttaac aaaatattaa cgtttacaat
     2221 tttatggtgc actctcagta caatctgctc tgatgccgca tagttaagcc agccccgaca
     2281 cccgccaaca cccgctgacg cgccctgacg ggcttgtctg ctcccggcat ccgcttacag
     2341 acaagctgtg accgtctccg ggagctgcat gtgtcagagg ttttcaccgt catcaccgaa
     2401 acgcgcgaga cgaaagggcc tcgtgatacg cctattttta taggttaatg tcatgataat
     2461 aatggtttct tagacgtcag gtggcacttt tcggggaaat gtgcgcggaa cccctatttg
     2521 tttatttttc taaatacatt caaatatgta tccgctcatg agacaataac cctgataaat
     2581 gcttcaataa tattgaaaaa ggaagagtat gagtattcaa catttccgtg tcgcccttat
     2641 tccctttttt gcggcatttt gccttcctgt ttttgctcac ccagaaacgc tggtgaaagt
     2701 aaaagatgct gaagatcagt tgggtgcacg agtgggttac atcgaactgg atctcaacag
     2761 cggtaagatc cttgagagtt ttcgccccga agaacgtttt ccaatgatga gcacttttaa
     2821 agttctgcta tgtggcgcgg tattatcccg tattgacgcc gggcaagagc aactcggtcg
     2881 ccgcatacac tattctcaga atgacttggt tgagtactca ccagtcacag aaaagcatct
     2941 tacggatggc atgacagtaa gagaattatg cagtgctgcc ataaccatga gtgataacac
     3001 tgcggccaac ttacttctga caacgatcgg aggaccgaag gagctaaccg cttttttgca
     3061 caacatgggg gatcatgtaa ctcgccttga tcgttgggaa ccggagctga atgaagccat
     3121 accaaacgac gagcgtgaca ccacgatgcc tgtagcaatg gcaacaacgt tgcgcaaact
     3181 attaactggc gaactactta ctctagcttc ccggcaacaa ttaatagact ggatggaggc
     3241 ggataaagtt gcaggaccac ttctgcgctc ggcccttccg gctggctggt ttattgctga
     3301 taaatctgga gccggtgagc gtgggtctcg cggtatcatt gcagcactgg ggccagatgg
     3361 taagccctcc cgtatcgtag ttatctacac gacggggagt caggcaacta tggatgaacg
     3421 aaatagacag atcgctgaga taggtgcctc actgattaag cattggtaac tgtcagacca
     3481 agtttactca tatatacttt agattgattt aaaacttcat ttttaattta aaaggatcta
     3541 ggtgaagatc ctttttgata atctcatgac caaaatccct taacgtgagt tttcgttcca
     3601 ctgagcgtca gaccccgtag aaaagatcaa aggatcttct tgagatcctt tttttctgcg
     3661 cgtaatctgc tgcttgcaaa caaaaaaacc accgctacca gcggtggttt gtttgccgga
     3721 tcaagagcta ccaactcttt ttccgaaggt aactggcttc agcagagcgc agataccaaa
     3781 tactgttctt ctagtgtagc cgtagttagg ccaccacttc aagaactctg tagcaccgcc
     3841 tacatacctc gctctgctaa tcctgttacc agtggctgct gccagtggcg ataagtcgtg
     3901 tcttaccggg ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac
     3961 ggggggttcg tgcacacagc ccagcttgga gcgaacgacc tacaccgaac tgagatacct
     4021 acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc
     4081 ggtaagcggc agggtcggaa caggagagcg cacgagggag cttccagggg gaaacgcctg
     4141 gtatctttat agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg
     4201 ctcgtcaggg gggcggagcc tatggaaaaa cgccagcaac gcggcctttt tacggttcct
     4261 ggccttttgc tggccttttg ctcacatgtc ctgcaggcag ctgcgcgctc gctcgctcac
     4321 tgaggccgcc cgggcgtcgg gcgacctttg gtcgcccggc ctcagtgagc gagcgagcgc
     4381 gcagagaggg agtggccaac tccatcacta ggggttcctg cggccgcacg cgttctgtgg
     4441 taaagagaag ggtcagtgag gaaagccttg ctaataaatg gcctcctagt gacaatgggt
     4501 tattacctct ttctgaaccc ttaggcagag accaggttgg agccaagatt aaaggctt
//
