LOCUS       sequence-402611-        3207 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Thermotoga petrophila (T. pe) fluoride riboswitch, W1D4.
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: pJBL831
FEATURES             Location/Qualifiers
     source          1..3207
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        16..50
                     /label=J23119(SpeI) promoter
                     /note="bacterial promoter (Registry of Standard Biological 
                     Parts BBa_J23119) modified to end with an SpeI site"
     CDS             join(150..152,153..866)
                     /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             150..863
                     /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(180..208)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     primer_bind     803..823
                     /label=GFP-F
                     /note="GFP, forward primer. Does NOT anneal to EGFP"
     terminator      899..970
                     /label=rrnB T1 terminator
                     /note="transcription terminator T1 from the E. coli rrnB 
                     gene"
     terminator      986..1013
                     /label=T7Te terminator
                     /note="phage T7 early transcription terminator"
     CDS             1169..1828
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(1235..1254)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     terminator      1849..1943
                     /label=lambda t0 terminator
                     /note="transcription terminator from phage lambda"
     primer_bind     complement(2350..2367)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2484..3029)
                     /direction=LEFT
                     /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     complement(2564..2583)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 gaattctaaa gatctttgac agctagctca gtcctaggta taatactagt aacgggcgat
       61 gaagctcgcc caaactgccc tgaagagggc tgatggcttc tactggcttg atcagtagaa
      121 gccattttct tttgtaggag gaaggatcta tgagcaaagg agaagaactt ttcactggag
      181 ttgtcccaat tcttgttgaa ttagatggtg atgttaatgg gcacaaattt tctgtccgtg
      241 gagagggtga aggtgatgct acaaacggaa aactcaccct taaatttatt tgcactactg
      301 gaaaactacc tgttccgtgg ccaacacttg tcactactct gacctatggt gttcaatgct
      361 tttcccgtta tccggatcac atgaaacggc atgacttttt caagagtgcc atgcccgaag
      421 gttatgtaca ggaacgcact atatctttca aagatgacgg gacctacaag acgcgtgctg
      481 aagtcaagtt tgaaggtgat acccttgtta atcgtatcga gttaaagggt attgatttta
      541 aagaagatgg aaacattctt ggacacaaac tcgagtacaa ctttaactca cacaatgtat
      601 acatcacggc agacaaacaa aagaatggaa tcaaagctaa cttcaaaatt cgccacaacg
      661 ttgaagatgg ttccgttcaa ctagcagacc attatcaaca aaatactcca attggcgatg
      721 gccctgtcct tttaccagac aaccattacc tgtcgacaca atctgtcctt tcgaaagatc
      781 ccaacgaaaa gcgtgaccac atggtccttc ttgagtttgt aactgctgct gggattacac
      841 atggcatgga tgagctctac aaataaggat ccaaactcga gtaaggatct ccaggcatca
      901 aataaaacga aaggctcagt cgaaagactg ggcctttcgt tttatctgtt gtttgtcggt
      961 gaacgctctc tactagagtc acactggctc accttcgggt gggcctttct gcgtttatac
     1021 ctagggtacg gttttgggat ccttactcga gtctagactg cagttgatcg ggcacgtaag
     1081 aggttccaac tttcaccata atgaaataag atcactaccg ggcgtatttt ttgagttatc
     1141 gagattttca ggagctaagg aagctaaaat ggagaaaaaa atcactggat ataccaccgt
     1201 tgatatatcc caatggcatc gtaaagaaca ttttgaggca tttcagtcag ttgctcaatg
     1261 tacctataac cagaccgttc agctggatat tacggccttt ttaaagaccg taaagaaaaa
     1321 taagcacaag ttttatccgg cctttattca cattcttgcc cgcctgatga atgctcatcc
     1381 ggaatttcgt atggcaatga aagacggtga gctggtgata tgggatagtg ttcacccttg
     1441 ttacaccgtt ttccatgagc aaactgaaac gttttcatcg ctctggagtg aataccacga
     1501 cgatttccgg cagtttctac acatatattc gcaagatgtg gcgtgttacg gtgaaaacct
     1561 ggcctatttc cctaaagggt ttattgagaa tatgtttttc gtctcagcca atccctgggt
     1621 gagtttcacc agttttgatt taaacgtggc caatatggac aacttcttcg cccccgtttt
     1681 caccatgggc aaatattata cgcaaggcga caaggtgctg atgccgctgg cgattcaggt
     1741 tcatcatgcc gtttgtgatg gcttccatgt cggcagaatg cttaatgaat tacaacagta
     1801 ctgcgatgag tggcagggcg gggcgtaatt tgatatcgag ctcgcttgga ctcctgttga
     1861 tagatccagt aatgacctca gaactccatc tggatttgtt cagaacgctc ggttgccgcc
     1921 gggcgttttt tattggtgag aatccaagcc tccgatcaac gtctcatttt cgccaaaagt
     1981 tggcccaggg cttcccggta tcaacaggga caccaggatt tatttattct gcgaagtgat
     2041 cttccgtcac aggtatttat tcggcgcaaa gtgcgtcggg tgatgctgcc aacttactga
     2101 tttagtgtat gatggtgttt ttgaggtgct ccagtggctt ctgtttctat cagctgtccc
     2161 tcctgttcag ctactgacgg ggtggtgcgt aacggcaaaa gcaccgccgg acatcagcgc
     2221 tagcggagtg tatactggct tactatgttg gcactgatga gggtgtcagt gaagtgcttc
     2281 atgtggcagg agaaaaaagg ctgcaccggt gcgtcagcag aatatgtgat acaggatata
     2341 ttccgcttcc tcgctcactg actcgctacg ctcggtcgtt cgactgcggc gagcggaaat
     2401 ggcttacgaa cggggcggag atttcctgga agatgccagg aagatactta acagggaagt
     2461 gagagggccg cggcaaagcc gtttttccat aggctccgcc cccctgacaa gcatcacgaa
     2521 atctgacgct caaatcagtg gtggcgaaac ccgacaggac tataaagata ccaggcgttt
     2581 ccccctggcg gctccctcgt gcgctctcct gttcctgcct ttcggtttac cggtgtcatt
     2641 ccgctgttat ggccgcgttt gtctcattcc acgcctgaca ctcagttccg ggtaggcagt
     2701 tcgctccaag ctggactgta tgcacgaacc ccccgttcag tccgaccgct gcgccttatc
     2761 cggtaactat cgtcttgagt ccaacccgga aagacatgca aaagcaccac tggcagcagc
     2821 cactggtaat tgatttagag gagttagtct tgaagtcatg cgccggttaa ggctaaactg
     2881 aaaggacaag ttttggtgac tgcgctcctc caagccagtt acctcggttc aaagagttgg
     2941 tagctcagag aaccttcgaa aaaccgccct gcaaggcggt tttttcgttt tcagagcaag
     3001 agattacgcg cagaccaaaa cgatctcaag aagatcatct tattaatcag ataaaatatt
     3061 tctagatttc agtgcaattt atctcttcaa atgtagcacc tgaagtcagc cccatacgat
     3121 ataagttgta attctcatgt ttgacagctt atcatcgata agcttccgat ggcgcgccga
     3181 gaggctttac actttatgct tccggct
//
