LOCUS       sequence-490838-        6733 bp    DNA     circular SYN 27-OCT-2025
DEFINITION  modulADAR sensor against sythetic target transcript (syn GluR-B 
            stemloop).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6733)
  AUTHORS   Kolber NS, K. Kaseniit E, Lanz TV, Robinson WH, Gao XJ
  TITLE     Sequence-Independent RNA Sensing in Living Mammalian Cells
  JOURNAL   bioRxiv 2025.09.18.677213
REFERENCE   2  (bases 1 to 6733)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Oct 27, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "bioRxiv 
            2025.09.18.677213"
COMMENT     Sequence Label: EK0656 SFFV-mCherry-SGc(70587.os4)cSG-EGFP-(3x...
FEATURES             Location/Qualifiers
     source          1..6733
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        176..583
                     /label=SFFV promoter
                     /note="spleen focus-forming virus long terminal repeat 
                     (LTR) promoter"
     regulatory      591..600
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             597..1304
                     /codon_start=1
                     /product="monomeric derivative of DsRed fluorescent protein
                     (Shaner et al., 2004)"
                     /label=mCherry
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEG
                     TQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNF
                     EDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALK
                     GEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERA
                     EGRHSTGGMDELYK"
     primer_bind     complement(742..760)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     1010..1029
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     CDS             1350..1415
                     /codon_start=1
                     /product="2A peptide from foot-and-mouth disease virus 
                     polyprotein"
                     /label=F2A
                     /note="Eukaryotic ribosomes fail to insert a peptide bond 
                     between the Gly and Pro residues, yielding separate 
                     polypeptides."
                     /translation="VKQTLNFDLLKLAGDVESNPGP"
     CDS             1614..1679
                     /codon_start=1
                     /product="2A peptide from foot-and-mouth disease virus 
                     polyprotein"
                     /label=F2A
                     /note="Eukaryotic ribosomes fail to insert a peptide bond 
                     between the Gly and Pro residues, yielding separate 
                     polypeptides."
                     /translation="VKQTLNFDLLKLAGDVESNPGP"
     CDS             join(1686..1688,1689..2399)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="VSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLK
                     FICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDG
                     NYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV
                     NFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLE
                     FVTAAGITLGMDELYK"
     CDS             2486..2515
                     /codon_start=1
                     /product="Myc (human c-Myc proto-oncogene) epitope tag"
                     /label=Myc
                     /translation="EQKLISEEDL"
     primer_bind     complement(2571..2588)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    2577..2801
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     primer_bind     complement(2973..2992)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     protein_bind    3124..3171
                     /label=FRT
                     /bound_moiety="FLP recombinase from the Saccharomyces 
                     cerevisiae 2u plasmid"
                     /note="FLP-mediated recombination occurs in the 8-bp core 
                     sequence TCTAGAAA (Turan and Bode, 2011)."
     CDS             3179..4201
                     /codon_start=1
                     /product="hygromycin B phosphotransferase"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="KKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRGY
                     VLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLPE
                     TELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQT
                     VMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMFG
                     DSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDGN
                     FDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAKE
                     "
     CDS             3179..4201
                     /codon_start=1
                     /gene="aph(4)-Ia"
                     /product="aminoglycoside phosphotransferase from E. coli"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="KKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRGY
                     VLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLPE
                     TELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQT
                     VMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMFG
                     DSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDGN
                     FDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAKE
                     "
     polyA_signal    4331..4452
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4368..4387)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4422..4441
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(4501..4517)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4501..4517)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(4514..4536)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    4525..4541
                     /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(4549..4555,4556..4573,4574..4579))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4594..4615
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4732..4749)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4903..5491)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4983..5002)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5662..6453,6454..6522))
                     /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     6285..6304
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6523..6627)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(6702..6721)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
ORIGIN
        1 agtatctgct ccctgcttgt gtgttggagg tcgctgagta gtgcgcgagc aaaatttaag
       61 ctacaacaag gcaaggcttg accgacaatt gccgataaaa taaaagattt tatttagtct
      121 ccagaaaaag gggggaatga aagaccccac ctgtaggttt ggcaagctag ctgcagtaac
      181 gccattttgc aaggcatgga aaaataccaa accaagaata gagaagttca gatcaagggc
      241 gggtacatga aaatagctaa cgttgggcca aacaggatat ctgcggtgag cagtttcggc
      301 cccggcccgg ggccaagaac agatggtcac cgcagtttcg gccccggccc gaggccaaga
      361 acagatggtc cccagatatg gcccaaccct cagcagtttc ttaagaccca tcagatgttt
      421 ccaggctccc ccaaggacct gaaatgaccc tgcgccttat ttgaattaac caatcagcct
      481 gcttctcgct tctgttcgcg cgcttctgct tcccgagctc tataaaagag ctcacaaccc
      541 ctcactcggc gcgccagtcc tccgacagac tgagtcgccc gggaagcttc gccaccatgg
      601 tgagcaaggg cgaggaggat aacatggcca tcatcaagga gttcatgcgc ttcaaggtgc
      661 acatggaggg ctccgtgaac ggccacgagt tcgagatcga gggcgagggc gagggccgcc
      721 cctacgaggg cacccagacc gccaagctga aggtgaccaa gggtggcccc ctgcccttcg
      781 cctgggacat cctgtcccct cagttcatgt acggctccaa ggcctacgtg aagcaccccg
      841 ccgacattcc cgactacttg aagctgtcct tccccgaggg cttcaagtgg gagcgcgtga
      901 tgaacttcga ggacggcggc gtggtgaccg tgacccagga ctcctccctg caggacggcg
      961 agttcatcta caaggtgaag ctgcgcggca ccaacttccc ctccgacggc cccgtaatgc
     1021 agaagaagac catgggctgg gaggcctcct ccgagcggat gtaccccgag gacggcgccc
     1081 tgaagggcga gatcaagcag aggctgaagc tgaaggacgg cggccactac gacgctgagg
     1141 tcaagaccac ctacaaggcc aagaagcccg tgcagctgcc cggcgcctac aacgtcaaca
     1201 tcaagttgga catcacctcc cacaacgagg actacaccat cgtggaacag tacgaacgcg
     1261 ccgagggccg ccactccacc ggcggcatgg acgagctgta caagagcgac gcgttggaag
     1321 ccagacacaa acagaaaatt gtggctccgg tgaaacagac tttgaatttt gaccttctga
     1381 agctggcggg agacgtcgag tccaaccccg gtcccggtac cggatccacc aagtcgacac
     1441 ggatgagtgt ttccttctat ccgcgtcatt gttccgttta ggtgggtgga atagtaatac
     1501 aaagtatccc acctacccag acgtgggcct tacgtaccga tagaccactg gtgcaaatag
     1561 agagctatac cggtactagt gaggcacggc ataagcaaaa gatcgtagcc ccagtaaagc
     1621 aaacactcaa cttcgatcta ctcaaactcg caggtgatgt ggaatctaat ccaggaccct
     1681 cgagtgtctc aaagggcgag gaacttttta cgggcgttgt tccgatcctc gtcgaattgg
     1741 acggggacgt taatgggcat aaattctcag ttagtggtga gggtgagggg gacgcgacat
     1801 atgggaaact tacgctgaag ttcatatgta ccaccggaaa attgccagtg ccgtggccta
     1861 ctctcgtcac caccctgaca tatggtgttc agtgttttag ccggtatcca gaccatatga
     1921 aacagcacga tttttttaaa tccgctatgc ctgaaggtta cgtacaggag cgaacgatat
     1981 tttttaaaga cgacggaaac tacaaaacta gagccgaggt aaaattcgag ggtgacactc
     2041 tcgtgaaccg gatcgaactg aagggcatag attttaagga ggatggcaat atactgggcc
     2101 acaagctcga atacaactat aattctcata atgtctatat catggcggac aaacagaaaa
     2161 acggcatcaa ggtaaacttt aaaatccgac acaatattga ggacggctct gtccagcttg
     2221 cggaccatta ccaacagaac acgccgatag gggatggtcc agtacttctc cctgataatc
     2281 actatttgtc tactcagtca gctcttagca aggacccaaa cgaaaaacgg gatcacatgg
     2341 tccttcttga gttcgtcact gcggctggga taacactcgg gatggacgaa ctgtataagt
     2401 aggccggagg gcccacgtac accatcaggg tacgtctcag acaccatcag ggtctgtctg
     2461 gtacagcatc agcgtaccat ggcccgaaca aaaactcatc tcagaagagg atctgaatag
     2521 cgccgtcgac catcatcata atcatcattg agtttaaacc cgctgatcag cctcgactgt
     2581 gccttctagt tgccagccat ctgttgtttg cccctccccc gtgccttcct tgaccctgga
     2641 aggtgccact cccactgtcc tttcctaata aaatgaggaa attgcatcgc attgtctgag
     2701 taggtgtcat tctattctgg ggggtggggt ggggcaggac agcaaggggg aggattggga
     2761 agacaatagc aggcatgctg gggatgcggt gggctctatg gagatctatc gatgttctgg
     2821 ggatgcggtg ggctctatgg cttctgaggc ggaaagaacc agctggggct ctagggggta
     2881 tccccacgcg ccctgtagcg gcgcattaag cgcggcgggt gtggtggtta cgcgcagcgt
     2941 gaccgctaca cttgccagcg ccctagcgcc cgctcctttc gctttcttcc cttcctttct
     3001 cgccacgttc gccggctttc cccgtcaagc tctaaatcgg gggctccctt tagggttccg
     3061 atttagtgct ttacggcacc tcgaccccaa aaaacttgat tagggtgatg gttcacgtac
     3121 ctagaagttc ctattccgaa gttcctattc tctagaaagt ataggaactt ccttggccaa
     3181 aaagcctgaa ctcaccgcga cgtctgtcga gaagtttctg atcgaaaagt tcgacagcgt
     3241 ctccgacctg atgcagctct cggagggcga agaatctcgt gctttcagct tcgatgtagg
     3301 agggcgtgga tatgtcctgc gggtaaatag ctgcgccgat ggtttctaca aagatcgtta
     3361 tgtttatcgg cactttgcat cggccgcgct cccgattccg gaagtgcttg acattgggga
     3421 attcagcgag agcctgacct attgcatctc ccgccgtgca cagggtgtca cgttgcaaga
     3481 cctgcctgaa accgaactgc ccgctgttct gcagccggtc gcggaggcca tggatgcgat
     3541 cgctgcggcc gatcttagcc agacgagcgg gttcggccca ttcggaccgc aaggaatcgg
     3601 tcaatacact acatggcgtg atttcatatg cgcgattgct gatccccatg tgtatcactg
     3661 gcaaactgtg atggacgaca ccgtcagtgc gtccgtcgcg caggctctcg atgagctgat
     3721 gctttgggcc gaggactgcc ccgaagtccg gcacctcgtg cacgcggatt tcggctccaa
     3781 caatgtcctg acggacaatg gccgcataac agcggtcatt gactggagcg aggcgatgtt
     3841 cggggattcc caatacgagg tcgccaacat cttcttctgg aggccgtggt tggcttgtat
     3901 ggagcagcag acgcgctact tcgagcggag gcatccggag cttgcaggat cgccgcggct
     3961 ccgggcgtat atgctccgca ttggtcttga ccaactctat cagagcttgg ttgacggcaa
     4021 tttcgatgat gcagcttggg cgcagggtcg atgcgacgca atcgtccgat ccggagccgg
     4081 gactgtcggg cgtacacaaa tcgcccgcag aagcgcggcc gtctggaccg atggctgtgt
     4141 agaagtactc gccgatagtg gaaaccgacg ccccagcact cgtccgaggg caaaggaata
     4201 gcacgtacta cgagatttcg attccaccgc cgccttctat gaaaggttgg gcttcggaat
     4261 cgttttccgg gacgccggct ggatgatcct ccagcgcggg gatctcatgc tggagttctt
     4321 cgcccacccc aacttgttta ttgcagctta taatggttac aaataaagca atagcatcac
     4381 aaatttcaca aataaagcat ttttttcact gcattctagt tgtggtttgt ccaaactcat
     4441 caatgtatct tatcatgtct gtataccgtc gacctctagc tagagcttgg cgtaatcatg
     4501 gtcatagctg tttcctgtgt gaaattgtta tccgctcaca attccacaca acatacgagc
     4561 cggaagcata aagtgtaaag cctggggtgc ctaatgagtg agctaactca cattaattgc
     4621 gttgcgctca ctgcccgctt tccagtcggg aaacctgtcg tgccagctgc attaatgaat
     4681 cggccaacgc gcggggagag gcggtttgcg tattgggcgc tcttccgctt cctcgctcac
     4741 tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta tcagctcact caaaggcggt
     4801 aatacggtta tccacagaat caggggataa cgcaggaaag aacatgtgag caaaaggcca
     4861 gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg tttttccata ggctccgccc
     4921 ccctgacgag catcacaaaa atcgacgctc aagtcagagg tggcgaaacc cgacaggact
     4981 ataaagatac caggcgtttc cccctggaag ctccctcgtg cgctctcctg ttccgaccct
     5041 gccgcttacc ggatacctgt ccgcctttct cccttcggga agcgtggcgc tttctcatag
     5101 ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc tccaagctgg gctgtgtgca
     5161 cgaacccccc gttcagcccg accgctgcgc cttatccggt aactatcgtc ttgagtccaa
     5221 cccggtaaga cacgacttat cgccactggc agcagccact ggtaacagga ttagcagagc
     5281 gaggtatgta ggcggtgcta cagagttctt gaagtggtgg cctaactacg gctacactag
     5341 aagaacagta tttggtatct gcgctctgct gaagccagtt accttcggaa aaagagttgg
     5401 tagctcttga tccggcaaac aaaccaccgc tggtagcggt ggtttttttg tttgcaagca
     5461 gcagattacg cgcagaaaaa aaggatctca agaagatcct ttgatctttt ctacggggtc
     5521 tgacgctcag tggaacgaaa actcacgtta agggattttg gtcatgagat tatcaaaaag
     5581 gatcttcacc tagatccttt taaattaaaa atgaagtttt aaatcaatct aaagtatata
     5641 tgagtaaact tggtctgaca gttaccaatg cttaatcagt gaggcaccta tctcagcgat
     5701 ctgtctattt cgttcatcca tagttgcctg actccccgtc gtgtagataa ctacgatacg
     5761 ggagggctta ccatctggcc ccagtgctgc aatgataccg cgagacccac gctcaccggc
     5821 tccagattta tcagcaataa accagccagc cggaagggcc gagcgcagaa gtggtcctgc
     5881 aactttatcc gcctccatcc agtctattaa ttgttgccgg gaagctagag taagtagttc
     5941 gccagttaat agtttgcgca acgttgttgc cattgctaca ggcatcgtgg tgtcacgctc
     6001 gtcgtttggt atggcttcat tcagctccgg ttcccaacga tcaaggcgag ttacatgatc
     6061 ccccatgttg tgcaaaaaag cggttagctc cttcggtcct ccgatcgttg tcagaagtaa
     6121 gttggccgca gtgttatcac tcatggttat ggcagcactg cataattctc ttactgtcat
     6181 gccatccgta agatgctttt ctgtgactgg tgagtactca accaagtcat tctgagaata
     6241 gtgtatgcgg cgaccgagtt gctcttgccc ggcgtcaata cgggataata ccgcgccaca
     6301 tagcagaact ttaaaagtgc tcatcattgg aaaacgttct tcggggcgaa aactctcaag
     6361 gatcttaccg ctgttgagat ccagttcgat gtaacccact cgtgcaccca actgatcttc
     6421 agcatctttt actttcacca gcgtttctgg gtgagcaaaa acaggaaggc aaaatgccgc
     6481 aaaaaaggga ataagggcga cacggaaatg ttgaatactc atactcttcc tttttcaata
     6541 ttattgaagc atttatcagg gttattgtct catgagcgga tacatatttg aatgtattta
     6601 gaaaaataaa caaatagggg ttccgcgcac atttccccga aaagtgccac ctgacgtcga
     6661 cggatcggga gatctcccga tcccctatgg tgcactctca gtacaatctg ctctgatgcc
     6721 gcatagttaa gcc
//
