LOCUS       pAAV-hSyn-roxSTO        7777 bp    DNA     circular SYN 04-AUG-2021
DEFINITION  .
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  recombinant plasmid
REFERENCE   1  (bases 1 to 7777)
  AUTHORS   HHMI-Janelia
  TITLE     Direct Submission
  JOURNAL   Exported Mar 11, 2025 from SnapGene 8.0.2
            https://www.snapgene.com
FEATURES             Location/Qualifiers
     source          1..7777
                     /mol_type="other DNA"
                     /organism="recombinant plasmid"
     repeat_region   1..130
                     /label=AAV2 ITR (alternate)
                     /note="Functional equivalent of wild-type AAV2 ITR"
                     /note="color: #ffcc99"
     promoter        175..622
                     /label=hSyn promoter
                     /note="human synapsin I promoter; confers neuron-specific 
                     expression (Kugler et al., 2003)"
                     /note="color: #ffffff; direction: RIGHT"
     misc_feature    636..667
                     /label=Rox
                     /note="Rox site:TAACTTTAAATAATGCCAATTATTTAAAGTTA, Sequence 
                     took from the original paper (8/4/21 HY)
                     Nucleic Acids Res. 2004; 32(20): 6086–6095.
                     Published online 2004 Nov 18. doi: 10.1093/nar/gkh941
                     PMCID: PMC534624
                     PMID: 15550568
                     DNA recombination with a heterospecific Cre homolog 
                     identified from comparison of the pac-c1 regions of 
                     P1-related phages
                     Brian Sauer1,2,* and Jeffrey McDermott1
                     https://www.ncbi.nlm.nih.gov/pmc/articles/PMC534624/"
                     /note="color: #ff00ff; direction: RIGHT"
     polyA_signal    834..968
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
                     /note="color: #a6acb3"
     polyA_signal    1088..1222
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
                     /note="color: #a6acb3"
     polyA_signal    1342..1476
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
                     /note="color: #a6acb3"
     misc_feature    1505..1536
                     /label=Rox
                     /note="Rox site:TAACTTTAAATAATGCCAATTATTTAAAGTTA, Sequence 
                     took from the original paper (8/4/21 HY)
                     Nucleic Acids Res. 2004; 32(20): 6086–6095.Published online
                     2004 Nov 18. doi: 10.1093/nar/gkh941PMCID: PMC534624PMID: 
                     15550568DNA recombination with a heterospecific Cre homolog
                     identified from comparison of the pac-c1 regions of 
                     P1-related phagesBrian Sauer1,2,* and Jeffrey 
                     McDermott1https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5346
                     24/"
                     /note="color: #ff00ff; direction: RIGHT"
     CDS             1544..3879
                     /codon_start=1
                     /label=NaChBac
                     /note="color: #00ffff"
                     /translation="MKMEARQKQNSFTSKMQKIVNHRAFTFTVIALILFNALIVGIETY
                     PRIYADHKWLFYRIDLVLLWIFTIEIAMRFLASNPKSAFFRSSWNWFDFLIVAAGHIFA
                     GAQFVTVLRILRVLRVLRAISVVPSLRRLVDALVMTIPALGNILILMSIFFYIFAVIGT
                     MLFQHVSPEYFGNLQLSLLTLFQVVTLESWASGVMRPIFAEVPWSWLYFVSFVLIGTFI
                     IFNLFIGVIVNNVEKAELTDNEEDGEADGLKQEISALRKDVAELKSLLKQLKDIGSGEG
                     RGSLLTCGDVEENPGPADPATMVSKGEEVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRP
                     YEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERV
                     MNFEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDG
                     VLKGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQY
                     ERSEGRHHLFLGHGTGSTGSGSSGTASSEDNNMAVIKEFMRFKVRMEGSMNGHEFEIEG
                     EGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEG
                     FKWERVMNFEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTER
                     LYPRDGVLKGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDY
                     TIVEQYERSEGRHHLFLYGMDELYK"
     CDS             2381..2434
                     /codon_start=1
                     /product="2A peptide from Thosea asigna virus capsid 
                     protein"
                     /label=T2A
                     /note="Eukaryotic ribosomes fail to insert a peptide bond 
                     between the Gly and Pro residues, yielding separate 
                     polypeptides."
                     /note="color: #cc99b2
                     Cleavage site after base 2431"
                     /translation="EGRGSLLTCGDVEENPGP"
     regulatory      2444..2453
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /note="color: #a6acb3"
                     /regulatory_class="other"
     CDS             2450..3879
                     /codon_start=1
                     /product="tandem dimeric (pseudo-monomeric) derivative of 
                     DsRed (Shaner et al., 2004)"
                     /label=tdTomato
                     /note="mammalian codon-optimized"
                     /note="color: #ff0000"
                     /translation="MVSKGEEVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYEGTQTA
                     KLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMNFEDGG
                     LVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVLKGEIH
                     QALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYERSEGRH
                     HLFLGHGTGSTGSGSSGTASSEDNNMAVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPY
                     EGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVM
                     NFEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGV
                     LKGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYE
                     RSEGRHHLFLYGMDELYK"
     misc_feature    3904..4492
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
                     /note="color: #ffffff"
     CDS             complement(4375..4386)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /note="color: #cc99b2
                     Cleavage site after base 4374"
                     /translation="IEGR"
     polyA_signal    4524..5000
                     /label=hGH poly(A) signal
                     /note="human growth hormone polyadenylation signal"
                     /note="color: #a6acb3"
     repeat_region   5040..5180
                     /label=AAV2 ITR
                     /note="inverted terminal repeat of adeno-associated virus 
                     serotype 2"
                     /note="color: #ffe4c4"
     repeat_region   5040..5169
                     /label=AAV2 ITR
                     /note="color: #a6acb3"
     rep_origin      5255..5710
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
                     /note="color: #ffff00"
     promoter        5992..6096
                     /gene="bla"
                     /label=AmpR promoter
                     /note="color: #ffffff; direction: RIGHT"
     CDS             join(6097..6165,6166..6957)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /note="This feature has 2 segments:
                        1: 6097 .. 6165 / #ccffcc / signal sequence
                        2: 6166 .. 6957 / #ccffcc
                     Cleavage site after base 6165"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     rep_origin      7128..7716
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
                     /note="color: #ffff00"
ORIGIN
        1 cctgcaggca gctgcgcgct cgctcgctca ctgaggccgc ccgggcgtcg ggcgaccttt
       61 ggtcgcccgg cctcagtgag cgagcgagcg cgcagagagg gagtggccaa ctccatcact
      121 aggggttcct gcggccgcac gcgtgtgtct agactgcaga gggccctgcg tatgagtgca
      181 agtgggtttt aggaccagga tgaggcgggg tgggggtgcc tacctgacga ccgaccccga
      241 cccactggac aagcacccaa cccccattcc ccaaattgcg catcccctat cagagagggg
      301 gaggggaaac aggatgcggc gaggcgcgtg cgcactgcca gcttcagcac cgcggacagt
      361 gccttcgccc ccgcctggcg gcgcgcgcca ccgccgcctc agcactgaag gcgcgctgac
      421 gtcactcgcc ggtcccccgc aaactcccct tcccggccac cttggtcgcg tccgcgccgc
      481 cgccggccca gccggaccgc accacgcgag gcgcgagata ggggggcacg ggcgcgacca
      541 tctgcgctgc ggcgccggcg actcagcgct gcctcagtct gcggtgggca gcggaggagt
      601 cgtgtcgtgc ctgagagcgc agtcgagaag gtacctaact ttaaataatt ggcattattt
      661 aaagttatcg cgatgaataa atgaaagctt gcagatctgc gactctagag gatctgcgac
      721 tctagaggat cataatcagc cataccacat ttgtagaggt tttacttgct ttaaaaaacc
      781 tcccacacct ccccctgaac ctgaaacata aaatgaatgc aattgttgtt gttaacttgt
      841 ttattgcagc ttataatggt tacaaataaa gcaatagcat cacaaatttc acaaataaag
      901 catttttttc actgcattct agttgtggtt tgtccaaact catcaatgta tcttatcatg
      961 tctggatctg cgactctaga ggatcataat cagccatacc acatttgtag aggttttact
     1021 tgctttaaaa aacctcccac acctccccct gaacctgaaa cataaaatga atgcaattgt
     1081 tgttgttaac ttgtttattg cagcttataa tggttacaaa taaagcaata gcatcacaaa
     1141 tttcacaaat aaagcatttt tttcactgca ttctagttgt ggtttgtcca aactcatcaa
     1201 tgtatcttat catgtctgga tctgcgactc tagaggatca taatcagcca taccacattt
     1261 gtagaggttt tacttgcttt aaaaaacctc ccacacctcc ccctgaacct gaaacataaa
     1321 atgaatgcaa ttgttgttgt taacttgttt attgcagctt ataatggtta caaataaagc
     1381 aatagcatca caaatttcac aaataaagca tttttttcac tgcattctag ttgtggtttg
     1441 tccaaactca tcaatgtatc ttatcatgtc tggatcccca tcaagctgat ccggaaccct
     1501 taattaactt taaataattg gcattattta aagttaggca gccatgaaaa tggaagcacg
     1561 ccagaaacag aactcattca cgtcaaagat gcagaaaatt gtcaaccata gagcgtttac
     1621 tttcaccgtc attgccctga tcctctttaa tgcactgatc gtgggaatcg aaacatatcc
     1681 gaggatctac gcggaccaca agtggctctt ttatcggatt gacctcgtcc tgctttggat
     1741 cttcaccatc gagatcgcga tgaggttttt ggcgtcgaac ccaaagtcgg ccttcttccg
     1801 cagctcgtgg aattggtttg attttctgat tgtcgcggct gggcatatct tcgcgggagc
     1861 ccagttcgtg acagtattgc gaatccttag agtgctgcgg gtactcaggg cgatctccgt
     1921 cgtcccctcc ctgcgcagac tcgtagatgc gctggtgatg acgattccgg cgttgggcaa
     1981 tatcttgatc ttgatgtcca tcttcttcta tatctttgca gtgatcggga caatgctctt
     2041 ccagcacgta tcgcctgaat actttgggaa cctccagctt tcgttgctga cgctgttcca
     2101 agtggtgacc ttggagagct gggccagcgg tgtaatgcgg cccatttttg cagaggtgcc
     2161 ctggtcatgg ctctactttg tctcgtttgt cctgattggt acttttatca ttttcaatct
     2221 tttcatcgga gtcattgtga acaacgtgga aaaggcggag cttacggaca atgaggaaga
     2281 tggggaggcc gacggactta aacaggagat ttcagcattg cgaaaggatg tagccgaact
     2341 gaagagcttg ctcaaacaac ttaaggatat cggcagtgga gagggcagag gaagtctgct
     2401 aacatgcggt gacgtcgagg agaatcctgg cccagcggat cccgccacca tggtgagcaa
     2461 gggcgaggag gtcatcaaag agttcatgcg cttcaaggtg cgcatggagg gctccatgaa
     2521 cggccacgag ttcgagatcg agggcgaggg cgagggccgc ccctacgagg gcacccagac
     2581 cgccaagctg aaggtgacca agggcggccc cctgcccttc gcctgggaca tcctgtcccc
     2641 ccagttcatg tacggctcca aggcgtacgt gaagcacccc gccgacatcc ccgattacaa
     2701 gaagctgtcc ttccccgagg gcttcaagtg ggagcgcgtg atgaacttcg aggacggcgg
     2761 tctggtgacc gtgacccagg actcctccct gcaggacggc acgctgatct acaaggtgaa
     2821 gatgcgcggc accaacttcc cccccgacgg ccccgtaatg cagaagaaga ccatgggctg
     2881 ggaggcctcc accgagcgcc tgtacccccg cgacggcgtg ctgaagggcg agatccacca
     2941 ggccctgaag ctgaaggacg gcggccacta cctggtggag ttcaagacca tctacatggc
     3001 caagaagccc gtgcaactgc ccggctacta ctacgtggac accaagctgg acatcacctc
     3061 ccacaacgag gactacacca tcgtggaaca gtacgagcgc tccgagggcc gccaccacct
     3121 gttcctgggg catggcaccg gcagcaccgg cagcggcagc tccggcaccg cctcctccga
     3181 ggacaacaac atggccgtca tcaaagagtt catgcgcttc aaggtgcgca tggagggctc
     3241 catgaacggc cacgagttcg agatcgaggg cgagggcgag ggccgcccct acgagggcac
     3301 ccagaccgcc aagctgaagg tgaccaaggg cggccccctg cccttcgcct gggacatcct
     3361 gtccccccag ttcatgtacg gctccaaggc gtacgtgaag caccccgccg acatccccga
     3421 ttacaagaag ctgtccttcc ccgagggctt caagtgggag cgcgtgatga acttcgagga
     3481 cggcggtctg gtgaccgtga cccaggactc ctccctgcag gacggcacgc tgatctacaa
     3541 ggtgaagatg cgcggcacca acttcccccc cgacggcccc gtaatgcaga agaagaccat
     3601 gggctgggag gcctccaccg agcgcctgta cccccgcgac ggcgtgctga agggcgagat
     3661 ccaccaggcc ctgaagctga aggacggcgg ccactacctg gtggagttca agaccatcta
     3721 catggccaag aagcccgtgc aactgcccgg ctactactac gtggacacca agctggacat
     3781 cacctcccac aacgaggact acaccatcgt ggaacagtac gagcgctccg agggccgcca
     3841 ccacctgttc ctgtacggca tggacgagct gtacaagtag aattcgatat caagcttatc
     3901 gataatcaac ctctggatta caaaatttgt gaaagattga ctggtattct taactatgtt
     3961 gctcctttta cgctatgtgg atacgctgct ttaatgcctt tgtatcatgc tattgcttcc
     4021 cgtatggctt tcattttctc ctccttgtat aaatcctggt tgctgtctct ttatgaggag
     4081 ttgtggcccg ttgtcaggca acgtggcgtg gtgtgcactg tgtttgctga cgcaaccccc
     4141 actggttggg gcattgccac cacctgtcag ctcctttccg ggactttcgc tttccccctc
     4201 cctattgcca cggcggaact catcgccgcc tgccttgccc gctgctggac aggggctcgg
     4261 ctgttgggca ctgacaattc cgtggtgttg tcggggaaat catcgtcctt tccttggctg
     4321 ctcgcctatg ttgccacctg gattctgcgc gggacgtcct tctgctacgt cccttcggcc
     4381 ctcaatccag cggaccttcc ttcccgcggc ctgctgccgg ctctgcggcc tcttccgcgt
     4441 cttcgccttc gccctcagac gagtcggatc tccctttggg ccgcctcccc gcatcgatac
     4501 cgagcgctgc tcgagagatc tacgggtggc atccctgtga cccctcccca gtgcctctcc
     4561 tggccctgga agttgccact ccagtgccca ccagccttgt cctaataaaa ttaagttgca
     4621 tcattttgtc tgactaggtg tccttctata atattatggg gtggaggggg gtggtatgga
     4681 gcaaggggca agttgggaag acaacctgta gggcctgcgg ggtctattgg gaaccaagct
     4741 ggagtgcagt ggcacaatct tggctcactg caatctccgc ctcctgggtt caagcgattc
     4801 tcctgcctca gcctcccgag ttgttgggat tccaggcatg catgaccagg ctcagctaat
     4861 ttttgttttt ttggtagaga cggggtttca ccatattggc caggctggtc tccaactcct
     4921 aatctcaggt gatctaccca ccttggcctc ccaaattgct gggattacag gcgtgaacca
     4981 ctgctccctt ccctgtcctt ctgattttgt aggtaaccac gtgcggaccg agcggccgca
     5041 ggaaccccta gtgatggagt tggccactcc ctctctgcgc gctcgctcgc tcactgaggc
     5101 cgggcgacca aaggtcgccc gacgcccggg ctttgcccgg gcggcctcag tgagcgagcg
     5161 agcgcgcagc tgcctgcagg ggcgcctgat gcggtatttt ctccttacgc atctgtgcgg
     5221 tatttcacac cgcatacgtc aaagcaacca tagtacgcgc cctgtagcgg cgcattaagc
     5281 gcggcgggtg tggtggttac gcgcagcgtg accgctacac ttgccagcgc cttagcgccc
     5341 gctcctttcg ctttcttccc ttcctttctc gccacgttcg ccggctttcc ccgtcaagct
     5401 ctaaatcggg ggctcccttt agggttccga tttagtgctt tacggcacct cgaccccaaa
     5461 aaacttgatt tgggtgatgg ttcacgtagt gggccatcgc cctgatagac ggtttttcgc
     5521 cctttgacgt tggagtccac gttctttaat agtggactct tgttccaaac tggaacaaca
     5581 ctcaactcta tctcgggcta ttcttttgat ttataaggga ttttgccgat ttcggtctat
     5641 tggttaaaaa atgagctgat ttaacaaaaa tttaacgcga attttaacaa aatattaacg
     5701 tttacaattt tatggtgcac tctcagtaca atctgctctg atgccgcata gttaagccag
     5761 ccccgacacc cgccaacacc cgctgacgcg ccctgacggg cttgtctgct cccggcatcc
     5821 gcttacagac aagctgtgac cgtctccggg agctgcatgt gtcagaggtt ttcaccgtca
     5881 tcaccgaaac gcgcgagacg aaagggcctc gtgatacgcc tatttttata ggttaatgtc
     5941 atgataataa tggtttctta gacgtcaggt ggcacttttc ggggaaatgt gcgcggaacc
     6001 cctatttgtt tatttttcta aatacattca aatatgtatc cgctcatgag acaataaccc
     6061 tgataaatgc ttcaataata ttgaaaaagg aagagtatga gtattcaaca tttccgtgtc
     6121 gcccttattc ccttttttgc ggcattttgc cttcctgttt ttgctcaccc agaaacgctg
     6181 gtgaaagtaa aagatgctga agatcagttg ggtgcacgag tgggttacat cgaactggat
     6241 ctcaacagcg gtaagatcct tgagagtttt cgccccgaag aacgttttcc aatgatgagc
     6301 acttttaaag ttctgctatg tggcgcggta ttatcccgta ttgacgccgg gcaagagcaa
     6361 ctcggtcgcc gcatacacta ttctcagaat gacttggttg agtactcacc agtcacagaa
     6421 aagcatctta cggatggcat gacagtaaga gaattatgca gtgctgccat aaccatgagt
     6481 gataacactg cggccaactt acttctgaca acgatcggag gaccgaagga gctaaccgct
     6541 tttttgcaca acatggggga tcatgtaact cgccttgatc gttgggaacc ggagctgaat
     6601 gaagccatac caaacgacga gcgtgacacc acgatgcctg tagcaatggc aacaacgttg
     6661 cgcaaactat taactggcga actacttact ctagcttccc ggcaacaatt aatagactgg
     6721 atggaggcgg ataaagttgc aggaccactt ctgcgctcgg cccttccggc tggctggttt
     6781 attgctgata aatctggagc cggtgagcgt gggtctcgcg gtatcattgc agcactgggg
     6841 ccagatggta agccctcccg tatcgtagtt atctacacga cggggagtca ggcaactatg
     6901 gatgaacgaa atagacagat cgctgagata ggtgcctcac tgattaagca ttggtaactg
     6961 tcagaccaag tttactcata tatactttag attgatttaa aacttcattt ttaatttaaa
     7021 aggatctagg tgaagatcct ttttgataat ctcatgacca aaatccctta acgtgagttt
     7081 tcgttccact gagcgtcaga ccccgtagaa aagatcaaag gatcttcttg agatcctttt
     7141 tttctgcgcg taatctgctg cttgcaaaca aaaaaaccac cgctaccagc ggtggtttgt
     7201 ttgccggatc aagagctacc aactcttttt ccgaaggtaa ctggcttcag cagagcgcag
     7261 ataccaaata ctgttcttct agtgtagccg tagttaggcc accacttcaa gaactctgta
     7321 gcaccgccta catacctcgc tctgctaatc ctgttaccag tggctgctgc cagtggcgat
     7381 aagtcgtgtc ttaccgggtt ggactcaaga cgatagttac cggataaggc gcagcggtcg
     7441 ggctgaacgg ggggttcgtg cacacagccc agcttggagc gaacgaccta caccgaactg
     7501 agatacctac agcgtgagct atgagaaagc gccacgcttc ccgaagggag aaaggcggac
     7561 aggtatccgg taagcggcag ggtcggaaca ggagagcgca cgagggagct tccaggggga
     7621 aacgcctggt atctttatag tcctgtcggg tttcgccacc tctgacttga gcgtcgattt
     7681 ttgtgatgct cgtcaggggg gcggagccta tggaaaaacg ccagcaacgc ggccttttta
     7741 cggttcctgg ccttttgctg gccttttgct cacatgt
//
