LOCUS       sequence-238932-        6601 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  siRNA.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6601)
  TITLE     Oka Lab plasmids
REFERENCE   2  (bases 1 to 6601)
  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"
COMMENT     Sequence Label: AV5-siRNA-dsRed
FEATURES             Location/Qualifiers
     source          1..6601
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     repeat_region   69..198
                     /label=AAV2 ITR
     promoter        426..739
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for mouse U6 snRNA (Das 
                     et al., 1988)"
     primer_bind     658..678
                     /label=mU6-F
                     /note="Mouse U6 promoter, forward primer"
     primer_bind     755..771
                     /label=pBluescriptKS
                     /note="For pBluescript vector"
     primer_bind     756..772
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     protein_bind    complement(814..847)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     enhancer        963..1266
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        1267..1470
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     1421..1441
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     regulatory      1509..1518
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             1515..2192
                     /codon_start=1
                     /product="rapidly maturing tetrameric variant of DsRed 
                     fluorescent protein (Bevis and Glick, 2002)"
                     /label=DsRed-Express
                     /note="mammalian codon-optimized"
                     /translation="MASSEDVIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGTQTAK
                     LKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGV
                     VTVTQDSSLQDGSFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHK
                     ALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERAEGRHH
                     LFL"
     primer_bind     complement(1645..1663)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     complement(1695..1715)
                     /label=DsRed1-N
                     /note="DsRed1, reverse primer"
     primer_bind     1913..1932
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     primer_bind     2107..2130
                     /label=DsRed1-C
                     /note="DsRed1, forward primer"
     misc_feature    2206..2794
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(2259..2279)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(2677..2688)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    2802..3424
                     /label=hGH poly(A) signal
                     /note="human growth hormone polyadenylation signal"
     primer_bind     complement(3001..3020)
                     /label=hGH-PA-R
                     /note="Human growth hormone terminator, reverse primer"
     promoter        complement(3726..3744)
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     complement(3727..3744)
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     primer_bind     complement(3762..3778)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3762..3778)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(3775..3797)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    3786..3802
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     promoter        complement(join(3810..3816,3817..3834,3835..3840))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    3855..3876
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     rep_origin      complement(4164..4752)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4244..4263)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4923..5714,5715..5783))
                     /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     5546..5565
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5784..5888)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(5966..6421)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(6103..6124)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     6315..6334
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     6547..6569
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     6561..6578
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     6562..6578
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     join(6585..6601,1..3)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        join(6585..6601,1..2)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
ORIGIN
        1 gggcgaattg ggcccggcgc gccgacgtcg catgctcctc tagactcgat cgaggaattc
       61 ggtaccccct gcgcgctcgc tcgctcactg aggccgcccg ggcaaagccc gggcgtcggg
      121 cgacctttgg tcgcccggcc tcagtgagcg agcgagcgcg cagagaggga gtggccaact
      181 ccatcactag gggttccttg tagttaatga ttaacccgcc atgctactta tctacgtagc
      241 catgctctag agtggagtcg tgacgtgaat tacgtcatag ggttagggag gtcctgtatt
      301 agaggtcacg tgagtgtttt gcgacatttt gcgacaccat gtggtcacgc tgggtattta
      361 agcccgagtg agcacgcagg gtctccatac gcgccgtcga cgagctcaga tctccccgct
      421 ctagagatcc gacgccgcca tctctaggcc cgcgccggcc ccctcgcaca gacttgtggg
      481 agaagctcgg ctactcccct gccccggtta atttgcatat aatatttcct agtaactata
      541 gaggcttaat gtgcgataaa agacagataa tctgttcttt ttaatactag ctacatttta
      601 catgataggc ttggatttct ataagagata caaatactaa attattattt taaaaaacag
      661 cacaaaagga aactcaccct aactgtaaag taattgtgtg ttttgagact ataaatatcc
      721 cttggagaaa agccttgtta acgcgcggtg accctcgagg tcgacggtat cgataagctc
      781 gcttcacgag attccagcag gtcgagggac ctaataactt cgtatagcat acattatacg
      841 aagttatatt aagggttcca agcttaagcg gccgcgtgga taaccgtatt accgccatgc
      901 attagttatt aatagtaatc aattacgggg tcattagttc atagcccata tatggagttc
      961 cgcgttacat aacttacggt aaatggcccg cctggctgac cgcccaacga cccccgccca
     1021 ttgacgtcaa taatgacgta tgttcccata gtaacgccaa tagggacttt ccattgacgt
     1081 caatgggtgg agtatttacg gtaaactgcc cacttggcag tacatcaagt gtatcatatg
     1141 ccaagtacgc cccctattga cgtcaatgac ggtaaatggc ccgcctggca ttatgcccag
     1201 tacatgacct tatgggactt tcctacttgg cagtacatct acgtattagt catcgctatt
     1261 accatggtga tgcggttttg gcagtacatc aatgggcgtg gatagcggtt tgactcacgg
     1321 ggatttccaa gtctccaccc cattgacgtc aatgggagtt tgttttggca ccaaaatcaa
     1381 cgggactttc caaaatgtcg taacaactcc gccccattga cgcaaatggg cggtaggcgt
     1441 gtacggtggg aggtctatat aagcagagct ggtttagtga accgtcagat ccgctagcgc
     1501 taccggtcgc caccatggcc tcctccgagg acgtcatcaa ggagttcatg cgcttcaagg
     1561 tgcgcatgga gggctccgtg aacggccacg agttcgagat cgagggcgag ggcgagggcc
     1621 gcccctacga gggcacccag accgccaagc tgaaggtgac caagggcggc cccctgccct
     1681 tcgcctggga catcctgtcc ccccagttcc agtacggctc caaggtgtac gtgaagcacc
     1741 ccgccgacat ccccgactac aagaagctgt ccttccccga gggcttcaag tgggagcgcg
     1801 tgatgaactt cgaggacggc ggcgtggtga ccgtgaccca ggactcctcc ctgcaggacg
     1861 gctccttcat ctacaaggtg aagttcatcg gcgtgaactt cccctccgac ggccccgtaa
     1921 tgcagaagaa gactatgggc tgggaggcct ccaccgagcg cctgtacccc cgcgacggcg
     1981 tgctgaaggg cgagatccac aaggccctga agctgaagga cggcggccac tacctggtgg
     2041 agttcaagtc catctacatg gccaagaagc ccgtgcagct gcccggctac tactacgtgg
     2101 actccaagct ggacatcacc tcccacaacg aggactacac catcgtggag cagtacgagc
     2161 gcgccgaggg ccgccaccac ctgttcctgt aggaattcta tcgataatca acctctggat
     2221 tacaaaattt gtgaaagatt gactggtatt cttaactatg ttgctccttt tacgctatgt
     2281 ggatacgctg ctttaatgcc tttgtatcat gctattgctt cccgtatggc tttcattttc
     2341 tcctccttgt ataaatcctg gttgctgtct ctttatgagg agttgtggcc cgttgtcagg
     2401 caacgtggcg tggtgtgcac tgtgtttgct gacgcaaccc ccactggttg gggcattgcc
     2461 accacctgtc agctcctttc cgggactttc gctttccccc tccctattgc cacggcggaa
     2521 ctcatcgccg cctgccttgc ccgctgctgg acaggggctc ggctgttggg cactgacaat
     2581 tccgtggtgt tgtcggggaa atcatcgtcc tttccttggc tgctcgcctg tgttgccacc
     2641 tggattctgc gcgggacgtc cttctgctac gtcccttcgg ccctcaatcc agcggacctt
     2701 ccttcccgcg gcctgctgcc ggctctgcgg cctcttccgc gtcttcgcct tcgccctcag
     2761 acgagtcgga tctccctttg ggccgcctcc ccgcatcgat agggtggcat ccctgtgacc
     2821 cctccccagt gcctctcctg gccctggaag ttgccactcc agtgcccacc agccttgtcc
     2881 taataaaatt aagttgcatc attttgtctg actaggtgtc cttctataat attatggggt
     2941 ggaggggggt ggtatggagc aaggggcaag ttgggaagac aacctgtagg gcctgcgggg
     3001 tctattggga accaagctgg agtgcagtgg cacaatcttg gctcactgca atctccgcct
     3061 cctgggttca agcgattctc ctgcctcagc ctcccgagtt gttgggattc caggcatgca
     3121 tgaccaggct cagctaattt ttgttttttt ggtagagacg gggtttcacc atattggcca
     3181 ggctggtctc caactcctaa tctcaggtga tctacccacc ttggcctccc aaattgctgg
     3241 gattacaggc gtgaaccact gctcccttcc ctgtccttct gattttaaaa taactatacc
     3301 agcaggagga cgtccagaca cagcataggc tacctggcca tgcccaaccg gtgggacatt
     3361 tgagttgctt gcttggcact gtcctctcat gcgttgggtc cactcagtag atgcctgttg
     3421 aattgggctg cagacgcgtg tctagaggag catgcgcgtc ggcgcgtcgc tctagagcat
     3481 ggctacgtag ataagtagca tggcgggtta atcattaact acaaggaacc cctagtgatg
     3541 gagttggcca ctccctctct gcgcgctcgc tcgctcactg aggccgggcg accaaaggtc
     3601 gcccgacgcc cgggctttgc ccgggcggcc tcagtgagcg agcgagcgcg ccaggggttc
     3661 gaaatcgata agcttggatc gatccggaga gctcgtcgac ggcgcgccat gcatagcttg
     3721 agtattctat agtgtcacct aaatagcttg gcgtaatcat ggtcatagct gtttcctgtg
     3781 tgaaattgtt atccgctcac aattccacac aacatacgag ccggaagcat aaagtgtaaa
     3841 gcctggggtg cctaatgagt gagctaactc acattaattg cgttgcgctc actgcccgct
     3901 ttccagtcgg gaaacctgtc gtgccagctg cattaatgaa tcggccaacg cgcggggaga
     3961 ggcggtttgc gtattgggcg ctcttccgct tcctcgctca ctgactcgct gcgctcggtc
     4021 gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt atccacagaa
     4081 tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc caggaaccgt
     4141 aaaaaggccg cgttgctggc gtttttccat aggctccgcc cccctgacga gcatcacaaa
     4201 aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt
     4261 ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg
     4321 tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg taggtatctc
     4381 agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc
     4441 gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta
     4501 tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt aggcggtgct
     4561 acagagttct tgaagtggtg gcctaactac ggctacacta gaagaacagt atttggtatc
     4621 tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg atccggcaaa
     4681 caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac gcgcagaaaa
     4741 aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca gtggaacgaa
     4801 aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac ctagatcctt
     4861 ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac ttggtctgac
     4921 agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt tcgttcatcc
     4981 atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt accatctggc
     5041 cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt atcagcaata
     5101 aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc cgcctccatc
     5161 cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa tagtttgcgc
     5221 aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg tatggcttca
     5281 ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt gtgcaaaaaa
     5341 gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc agtgttatca
     5401 ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt aagatgcttt
     5461 tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg gcgaccgagt
     5521 tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac tttaaaagtg
     5581 ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc gctgttgaga
     5641 tccagttcga tgtaacccac tcgtgcaccc aactgatctt cagcatcttt tactttcacc
     5701 agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg aataagggcg
     5761 acacggaaat gttgaatact catactcttc ctttttcaat attattgaag catttatcag
     5821 ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa acaaataggg
     5881 gttccgcgca catttccccg aaaagtgcca cctgatgcgg tgtgaaatac cgcacagatg
     5941 cgtaaggaga aaataccgca tcaggaaatt gtaagcgtta atattttgtt aaaattcgcg
     6001 ttaaattttt gttaaatcag ctcatttttt aaccaatagg ccgaaatcgg caaaatccct
     6061 tataaatcaa aagaatagac cgagataggg ttgagtgttg ttccagtttg gaacaagagt
     6121 ccactattaa agaacgtgga ctccaacgtc aaagggcgaa aaaccgtcta tcagggcgat
     6181 ggcccactac gtgaaccatc accctaatca agttttttgg ggtcgaggtg ccgtaaagca
     6241 ctaaatcgga accctaaagg gagcccccga tttagagctt gacggggaaa gccggcgaac
     6301 gtggcgagaa aggaagggaa gaaagcgaaa ggagcgggcg ctagggcgct ggcaagtgta
     6361 gcggtcacgc tgcgcgtaac caccacaccc gccgcgctta atgcgccgct acagggcgcg
     6421 tccattcgcc attcaggctg cgcaactgtt gggaagggcg atcggtgcgg gcctcttcgc
     6481 tattacgcca gctggcgaaa gggggatgtg ctgcaaggcg attaagttgg gtaacgccag
     6541 ggttttccca gtcacgacgt tgtaaaacga cggccagtga attgtaatac gactcactat
     6601 a
//
