LOCUS       sequence-403412-        3207 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Thermotoga petrophila (T. pe) fluoride riboswitch, D4.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 3207)
  AUTHORS   Hertz LM, White EN, Kuznedelov K, Cheng L, Yu AM, Kakkaramadam R, 
            Severinov K, Chen A, Lucks JB
  TITLE     The effect of pseudoknot base pairing on cotranscriptional 
            structural switching of the fluoride riboswitch.
  JOURNAL   Nucleic Acids Res. 2024 May 8;52(8):4466-4482. doi: 
            10.1093/nar/gkae231.
  PUBMED    38567721
REFERENCE   2  (bases 1 to 3207)
  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"; doi: "10"; journalName: 
            "Nucleic Acids Res"; date: "2024-05-8- 8"; volume: "52"; issue: "8";
            pages: "4466-4482"
COMMENT     Sequence Label: pJBL830
FEATURES             Location/Qualifiers
     source          1..3207
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     terminator      complement(401..495)
                     /label=lambda t0 terminator
                     /note="transcription terminator from phage lambda"
     CDS             complement(516..1175)
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     1090..1109
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     terminator      complement(1331..1358)
                     /label=T7Te terminator
                     /note="phage T7 early transcription terminator"
     terminator      complement(1374..1445)
                     /label=rrnB T1 terminator
                     /note="transcription terminator T1 from the E. coli rrnB 
                     gene"
     CDS             complement(join(1478..2191,2192..2194))
                     /codon_start=1
                     /product="GFP variant that folds robustly even when fused 
                     to poorly folded proteins (Pedelacq et al., 2006)"
                     /label=superfolder GFP
                     /note="mammalian codon-optimized"
                     /translation="MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLK
                     FICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDG
                     TYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKA
                     NFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLE
                     FVTAAGITHGMDELYK"
     CDS             complement(1481..2194)
                     /codon_start=1
                     /product="GFP variant that folds robustly even when fused 
                     to poorly folded proteins (Nager et al., 2011)"
                     /label=superfolder GFP
                     /translation="MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLK
                     FICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDG
                     TYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKA
                     NFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLE
                     FVTAAGITHGMDELYK"
     primer_bind     complement(1521..1541)
                     /label=GFP-F
                     /note="GFP, forward primer. Does NOT anneal to EGFP"
     primer_bind     2136..2164
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     promoter        complement(2294..2328)
                     /label=J23119(SpeI) promoter
                     /note="bacterial promoter (Registry of Standard Biological 
                     Parts BBa_J23119) modified to end with an SpeI site"
     rep_origin      2522..3067
                     /direction=RIGHT
                     /label=p15A ori
                     /note="Plasmids containing the medium-copy-number p15A 
                     origin of replication can be propagated in E. coli cells 
                     that contain a second plasmid with the ColE1 origin.
                     "
     primer_bind     2968..2987
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     3184..3201
                     /label=L4440
                     /note="L4440 vector, forward primer"
ORIGIN
        1 gaatatatcc tgtatcacat attctgctga cgcaccggtg cagccttttt tctcctgcca
       61 catgaagcac ttcactgaca ccctcatcag tgccaacata gtaagccagt atacactccg
      121 ctagcgctga tgtccggcgg tgcttttgcc gttacgcacc accccgtcag tagctgaaca
      181 ggagggacag ctgatagaaa cagaagccac tggagcacct caaaaacacc atcatacact
      241 aaatcagtaa gttggcagca tcacccgacg cactttgcgc cgaataaata cctgtgacgg
      301 aagatcactt cgcagaataa ataaatcctg gtgtccctgt tgataccggg aagccctggg
      361 ccaacttttg gcgaaaatga gacgttgatc ggaggcttgg attctcacca ataaaaaacg
      421 cccggcggca accgagcgtt ctgaacaaat ccagatggag ttctgaggtc attactggat
      481 ctatcaacag gagtccaagc gagctcgata tcaaattacg ccccgccctg ccactcatcg
      541 cagtactgtt gtaattcatt aagcattctg ccgacatgga agccatcaca aacggcatga
      601 tgaacctgaa tcgccagcgg catcagcacc ttgtcgcctt gcgtataata tttgcccatg
      661 gtgaaaacgg gggcgaagaa gttgtccata ttggccacgt ttaaatcaaa actggtgaaa
      721 ctcacccagg gattggctga gacgaaaaac atattctcaa taaacccttt agggaaatag
      781 gccaggtttt caccgtaaca cgccacatct tgcgaatata tgtgtagaaa ctgccggaaa
      841 tcgtcgtggt attcactcca gagcgatgaa aacgtttcag tttgctcatg gaaaacggtg
      901 taacaagggt gaacactatc ccatatcacc agctcaccgt ctttcattgc catacgaaat
      961 tccggatgag cattcatcag gcgggcaaga atgtgaataa aggccggata aaacttgtgc
     1021 ttatttttct ttacggtctt taaaaaggcc gtaatatcca gctgaacggt ctggttatag
     1081 gtacattgag caactgactg aaatgcctca aaatgttctt tacgatgcca ttgggatata
     1141 tcaacggtgg tatatccagt gatttttttc tccattttag cttccttagc tcctgaaaat
     1201 ctcgataact caaaaaatac gcccggtagt gatcttattt cattatggtg aaagttggaa
     1261 cctcttacgt gcccgatcaa ctgcagtcta gactcgagta aggatcccaa aaccgtaccc
     1321 taggtataaa cgcagaaagg cccacccgaa ggtgagccag tgtgactcta gtagagagcg
     1381 ttcaccgaca aacaacagat aaaacgaaag gcccagtctt tcgactgagc ctttcgtttt
     1441 atttgatgcc tggagatcct tactcgagtt tggatcctta tttgtagagc tcatccatgc
     1501 catgtgtaat cccagcagca gttacaaact caagaaggac catgtggtca cgcttttcgt
     1561 tgggatcttt cgaaaggaca gattgtgtcg acaggtaatg gttgtctggt aaaaggacag
     1621 ggccatcgcc aattggagta ttttgttgat aatggtctgc tagttgaacg gaaccatctt
     1681 caacgttgtg gcgaattttg aagttagctt tgattccatt cttttgtttg tctgccgtga
     1741 tgtatacatt gtgtgagtta aagttgtact cgagtttgtg tccaagaatg tttccatctt
     1801 ctttaaaatc aatacccttt aactcgatac gattaacaag ggtatcacct tcaaacttga
     1861 cttcagcacg cgtcttgtag gtcccgtcat ctttgaaaga tatagtgcgt tcctgtacat
     1921 aaccttcggg catggcactc ttgaaaaagt catgccgttt catgtgatcc ggataacggg
     1981 aaaagcattg aacaccatag gtcagagtag tgacaagtgt tggccacgga acaggtagtt
     2041 ttccagtagt gcaaataaat ttaagggtga gttttccgtt tgtagcatca ccttcaccct
     2101 ctccacggac agaaaatttg tgcccattaa catcaccatc taattcaaca agaattggga
     2161 caactccagt gaaaagttct tctcctttgc tcatagatcc ttcctcctac aaaagaaaat
     2221 ggcttctact gatcaagcca gtagaagcca tcagccctct tcagggcagt ttgggcgggc
     2281 ttcatcgccc gttactagta ttatacctag gactgagcta gctgtcaaag atctttagaa
     2341 ttcagccgga agcataaagt gtaaagcctc tcggcgcgcc atcggaagct tatcgatgat
     2401 aagctgtcaa acatgagaat tacaacttat atcgtatggg gctgacttca ggtgctacat
     2461 ttgaagagat aaattgcact gaaatctaga aatattttat ctgattaata agatgatctt
     2521 cttgagatcg ttttggtctg cgcgtaatct cttgctctga aaacgaaaaa accgccttgc
     2581 agggcggttt ttcgaaggtt ctctgagcta ccaactcttt gaaccgaggt aactggcttg
     2641 gaggagcgca gtcaccaaaa cttgtccttt cagtttagcc ttaaccggcg catgacttca
     2701 agactaactc ctctaaatca attaccagtg gctgctgcca gtggtgcttt tgcatgtctt
     2761 tccgggttgg actcaagacg atagttaccg gataaggcgc agcggtcgga ctgaacgggg
     2821 ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag tgtcaggcgt
     2881 ggaatgagac aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac
     2941 aggagagcgc acgagggagc cgccaggggg aaacgcctgg tatctttata gtcctgtcgg
     3001 gtttcgccac cactgatttg agcgtcagat ttcgtgatgc ttgtcagggg ggcggagcct
     3061 atggaaaaac ggctttgccg cggccctctc acttccctgt taagtatctt cctggcatct
     3121 tccaggaaat ctccgccccg ttcgtaagcc atttccgctc gccgcagtcg aacgaccgag
     3181 cgtagcgagt cagtgagcga ggaagcg
//
