LOCUS       sequence-243953-        6576 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 6576)
  TITLE     Oka Lab plasmids
REFERENCE   2  (bases 1 to 6576)
  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..6576
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        102..405
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        406..609
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     560..580
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     regulatory      648..657
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             654..1331
                     /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(784..802)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     complement(834..854)
                     /label=DsRed1-N
                     /note="DsRed1, reverse primer"
     primer_bind     1052..1071
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     primer_bind     1246..1269
                     /label=DsRed1-C
                     /note="DsRed1, forward primer"
     misc_feature    1345..1933
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(1398..1418)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(1816..1827)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     polyA_signal    1941..2563
                     /label=hGH poly(A) signal
                     /note="human growth hormone polyadenylation signal"
     primer_bind     complement(2140..2159)
                     /label=hGH-PA-R
                     /note="Human growth hormone terminator, reverse primer"
     repeat_region   2660..2789
                     /label=AAV2 ITR
     promoter        complement(2860..2878)
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     complement(2861..2878)
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     primer_bind     complement(2896..2912)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2896..2912)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(2909..2931)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    2920..2936
                     /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(2944..2950,2951..2968,2969..2974))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    2989..3010
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     rep_origin      complement(3298..3886)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3378..3397)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4057..4848,4849..4917))
                     /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     4680..4699
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(4918..5022)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(5100..5555)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5237..5258)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     5449..5468
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5681..5703
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     5695..5712
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     5696..5712
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5719..5738
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        5719..5737
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     promoter        6142..6454
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for mouse U6 snRNA (Das 
                     et al., 1988)"
     primer_bind     6373..6393
                     /label=mU6-F
                     /note="Mouse U6 promoter, forward primer"
     primer_bind     6470..6486
                     /label=pBluescriptKS
                     /note="For pBluescript vector"
     primer_bind     6471..6487
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     protein_bind    complement(6529..6562)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
ORIGIN
        1 gcttaagcgg ccgcgtggat aaccgtatta ccgccatgca ttagttatta atagtaatca
       61 attacggggt cattagttca tagcccatat atggagttcc gcgttacata acttacggta
      121 aatggcccgc ctggctgacc gcccaacgac ccccgcccat tgacgtcaat aatgacgtat
      181 gttcccatag taacgccaat agggactttc cattgacgtc aatgggtgga gtatttacgg
      241 taaactgccc acttggcagt acatcaagtg tatcatatgc caagtacgcc ccctattgac
      301 gtcaatgacg gtaaatggcc cgcctggcat tatgcccagt acatgacctt atgggacttt
      361 cctacttggc agtacatcta cgtattagtc atcgctatta ccatggtgat gcggttttgg
      421 cagtacatca atgggcgtgg atagcggttt gactcacggg gatttccaag tctccacccc
      481 attgacgtca atgggagttt gttttggcac caaaatcaac gggactttcc aaaatgtcgt
      541 aacaactccg ccccattgac gcaaatgggc ggtaggcgtg tacggtggga ggtctatata
      601 agcagagctg gtttagtgaa ccgtcagatc cgctagcgct accggtcgcc accatggcct
      661 cctccgagga cgtcatcaag gagttcatgc gcttcaaggt gcgcatggag ggctccgtga
      721 acggccacga gttcgagatc gagggcgagg gcgagggccg cccctacgag ggcacccaga
      781 ccgccaagct gaaggtgacc aagggcggcc ccctgccctt cgcctgggac atcctgtccc
      841 cccagttcca gtacggctcc aaggtgtacg tgaagcaccc cgccgacatc cccgactaca
      901 agaagctgtc cttccccgag ggcttcaagt gggagcgcgt gatgaacttc gaggacggcg
      961 gcgtggtgac cgtgacccag gactcctccc tgcaggacgg ctccttcatc tacaaggtga
     1021 agttcatcgg cgtgaacttc ccctccgacg gccccgtaat gcagaagaag actatgggct
     1081 gggaggcctc caccgagcgc ctgtaccccc gcgacggcgt gctgaagggc gagatccaca
     1141 aggccctgaa gctgaaggac ggcggccact acctggtgga gttcaagtcc atctacatgg
     1201 ccaagaagcc cgtgcagctg cccggctact actacgtgga ctccaagctg gacatcacct
     1261 cccacaacga ggactacacc atcgtggagc agtacgagcg cgccgagggc cgccaccacc
     1321 tgttcctgta ggaattctat cgataatcaa cctctggatt acaaaatttg tgaaagattg
     1381 actggtattc ttaactatgt tgctcctttt acgctatgtg gatacgctgc tttaatgcct
     1441 ttgtatcatg ctattgcttc ccgtatggct ttcattttct cctccttgta taaatcctgg
     1501 ttgctgtctc tttatgagga gttgtggccc gttgtcaggc aacgtggcgt ggtgtgcact
     1561 gtgtttgctg acgcaacccc cactggttgg ggcattgcca ccacctgtca gctcctttcc
     1621 gggactttcg ctttccccct ccctattgcc acggcggaac tcatcgccgc ctgccttgcc
     1681 cgctgctgga caggggctcg gctgttgggc actgacaatt ccgtggtgtt gtcggggaaa
     1741 tcatcgtcct ttccttggct gctcgcctgt gttgccacct ggattctgcg cgggacgtcc
     1801 ttctgctacg tcccttcggc cctcaatcca gcggaccttc cttcccgcgg cctgctgccg
     1861 gctctgcggc ctcttccgcg tcttcgcctt cgccctcaga cgagtcggat ctccctttgg
     1921 gccgcctccc cgcatcgata gggtggcatc cctgtgaccc ctccccagtg cctctcctgg
     1981 ccctggaagt tgccactcca gtgcccacca gccttgtcct aataaaatta agttgcatca
     2041 ttttgtctga ctaggtgtcc ttctataata ttatggggtg gaggggggtg gtatggagca
     2101 aggggcaagt tgggaagaca acctgtaggg cctgcggggt ctattgggaa ccaagctgga
     2161 gtgcagtggc acaatcttgg ctcactgcaa tctccgcctc ctgggttcaa gcgattctcc
     2221 tgcctcagcc tcccgagttg ttgggattcc aggcatgcat gaccaggctc agctaatttt
     2281 tgtttttttg gtagagacgg ggtttcacca tattggccag gctggtctcc aactcctaat
     2341 ctcaggtgat ctacccacct tggcctccca aattgctggg attacaggcg tgaaccactg
     2401 ctcccttccc tgtccttctg attttaaaat aactatacca gcaggaggac gtccagacac
     2461 agcataggct acctggccat gcccaaccgg tgggacattt gagttgcttg cttggcactg
     2521 tcctctcatg cgttgggtcc actcagtaga tgcctgttga attgggctgc agacgcgtgt
     2581 ctagaggagc atgcgcgtcg gcgcgttcta gagcatggct acgtagataa gtagcatggc
     2641 gggttaatca ttaactacaa ggaaccccta gtgatggagt tggccactcc ctctctgcgc
     2701 gctcgctcgc tcactgaggc cgggcgacca aaggtcgccc gacgcccggg ctttgcccgg
     2761 gcggcctcag tgagcgagcg agcgcgcagg gttcgaaatc gataagcttg gatcgatccg
     2821 gagagctcgt cgacggcgcg ccatgcatag cttgagtatt ctatagtgtc acctaaatag
     2881 cttggcgtaa tcatggtcat agctgtttcc tgtgtgaaat tgttatccgc tcacaattcc
     2941 acacaacata cgagccggaa gcataaagtg taaagcctgg ggtgcctaat gagtgagcta
     3001 actcacatta attgcgttgc gctcactgcc cgctttccag tcgggaaacc tgtcgtgcca
     3061 gctgcattaa tgaatcggcc aacgcgcggg gagaggcggt ttgcgtattg ggcgctcttc
     3121 cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag cggtatcagc
     3181 tcactcaaag gcggtaatac ggttatccac agaatcaggg gataacgcag gaaagaacat
     3241 gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc tggcgttttt
     3301 ccataggctc cgcccccctg acgagcatca caaaaatcga cgctcaagtc agaggtggcg
     3361 aaacccgaca ggactataaa gataccaggc gtttccccct ggaagctccc tcgtgcgctc
     3421 tcctgttccg accctgccgc ttaccggata cctgtccgcc tttctccctt cgggaagcgt
     3481 ggcgctttct catagctcac gctgtaggta tctcagttcg gtgtaggtcg ttcgctccaa
     3541 gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta
     3601 tcgtcttgag tccaacccgg taagacacga cttatcgcca ctggcagcag ccactggtaa
     3661 caggattagc agagcgaggt atgtaggcgg tgctacagag ttcttgaagt ggtggcctaa
     3721 ctacggctac actagaagaa cagtatttgg tatctgcgct ctgctgaagc cagttacctt
     3781 cggaaaaaga gttggtagct cttgatccgg caaacaaacc accgctggta gcggtggttt
     3841 ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag atcctttgat
     3901 cttttctacg gggtctgacg ctcagtggaa cgaaaactca cgttaaggga ttttggtcat
     3961 gagattatca aaaaggatct tcacctagat ccttttaaat taaaaatgaa gttttaaatc
     4021 aatctaaagt atatatgagt aaacttggtc tgacagttac caatgcttaa tcagtgaggc
     4081 acctatctca gcgatctgtc tatttcgttc atccatagtt gcctgactcc ccgtcgtgta
     4141 gataactacg atacgggagg gcttaccatc tggccccagt gctgcaatga taccgcgaga
     4201 cccacgctca ccggctccag atttatcagc aataaaccag ccagccggaa gggccgagcg
     4261 cagaagtggt cctgcaactt tatccgcctc catccagtct attaattgtt gccgggaagc
     4321 tagagtaagt agttcgccag ttaatagttt gcgcaacgtt gttgccattg ctacaggcat
     4381 cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc tccggttccc aacgatcaag
     4441 gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt agctccttcg gtcctccgat
     4501 cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg gttatggcag cactgcataa
     4561 ttctcttact gtcatgccat ccgtaagatg cttttctgtg actggtgagt actcaaccaa
     4621 gtcattctga gaatagtgta tgcggcgacc gagttgctct tgcccggcgt caatacggga
     4681 taataccgcg ccacatagca gaactttaaa agtgctcatc attggaaaac gttcttcggg
     4741 gcgaaaactc tcaaggatct taccgctgtt gagatccagt tcgatgtaac ccactcgtgc
     4801 acccaactga tcttcagcat cttttacttt caccagcgtt tctgggtgag caaaaacagg
     4861 aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa tactcatact
     4921 cttccttttt caatattatt gaagcattta tcagggttat tgtctcatga gcggatacat
     4981 atttgaatgt atttagaaaa ataaacaaat aggggttccg cgcacatttc cccgaaaagt
     5041 gccacctgat gcggtgtgaa ataccgcaca gatgcgtaag gagaaaatac cgcatcagga
     5101 aattgtaagc gttaatattt tgttaaaatt cgcgttaaat ttttgttaaa tcagctcatt
     5161 ttttaaccaa taggccgaaa tcggcaaaat cccttataaa tcaaaagaat agaccgagat
     5221 agggttgagt gttgttccag tttggaacaa gagtccacta ttaaagaacg tggactccaa
     5281 cgtcaaaggg cgaaaaaccg tctatcaggg cgatggccca ctacgtgaac catcacccta
     5341 atcaagtttt ttggggtcga ggtgccgtaa agcactaaat cggaacccta aagggagccc
     5401 ccgatttaga gcttgacggg gaaagccggc gaacgtggcg agaaaggaag ggaagaaagc
     5461 gaaaggagcg ggcgctaggg cgctggcaag tgtagcggtc acgctgcgcg taaccaccac
     5521 acccgccgcg cttaatgcgc cgctacaggg cgcgtccatt cgccattcag gctgcgcaac
     5581 tgttgggaag ggcgatcggt gcgggcctct tcgctattac gccagctggc gaaaggggga
     5641 tgtgctgcaa ggcgattaag ttgggtaacg ccagggtttt cccagtcacg acgttgtaaa
     5701 acgacggcca gtgaattgta atacgactca ctatagggcg aattgggccc ggcgcgccga
     5761 cgcgcatgct cctctagcta gactcgatcg aggaattcgg taccccctgc gcgctcgctc
     5821 gctcactgag gccgcccggg caaagcccgg gcggcctcag tgagcgagcg agcgcgcaga
     5881 gagggagtgg ccaactccat cactaggggt tccttgtagt taatgattaa cccgccatgc
     5941 tacttatcta cgtagccatg ctctagagtg gagtcgtgac gtgaattacg tcatagggtt
     6001 agggaggtcc tgtattagag gtcacgtgag tgttttgcga cattttgcga caccatgtgg
     6061 tcacgctggg tatttaagcc cgagtgagca cgcagggtct ccatacgcgc cgtcgacgag
     6121 ctcagatctc cccgctctag agatccgacg cgccatctct aggcccgcgc cggccccctc
     6181 gcacagactt gtgggagaag ctcggctact cccctgcccc ggttaatttg catataatat
     6241 ttcctagtaa ctatagaggc ttaatgtgcg ataaaagaca gataatctgt tctttttaat
     6301 actagctaca ttttacatga taggcttgga tttctataag agatacaaat actaaattat
     6361 tattttaaaa aacagcacaa aaggaaactc accctaactg taaagtaatt gtgtgttttg
     6421 agactataaa tatcccttgg agaaaagcct tgttaacgcg cggtgaccct cgaggtcgac
     6481 ggtatcgata agctcgcttc acgagattcc agcaggtcga gggacctaat aacttcgtat
     6541 agcatacatt atacgaagtt atattaaggg ttccaa
//
