LOCUS       sequence-403409-        3207 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Thermotoga petrophila (T. pe) fluoride riboswitch, 
            pseudoknot/terminator overlap from B. ce.
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: pJBL815
FEATURES             Location/Qualifiers
     source          1..3207
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(311..328)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(445..990)
                     /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(525..544)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     promoter        1184..1218
                     /label=J23119(SpeI) promoter
                     /note="bacterial promoter (Registry of Standard Biological 
                     Parts BBa_J23119) modified to end with an SpeI site"
     CDS             join(1318..1320,1321..2034)
                     /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             1318..2031
                     /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(1348..1376)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     primer_bind     1971..1991
                     /label=GFP-F
                     /note="GFP, forward primer. Does NOT anneal to EGFP"
     terminator      2067..2138
                     /label=rrnB T1 terminator
                     /note="transcription terminator T1 from the E. coli rrnB 
                     gene"
     terminator      2154..2181
                     /label=T7Te terminator
                     /note="phage T7 early transcription terminator"
     CDS             2337..2996
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(2403..2422)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     terminator      3017..3111
                     /label=lambda t0 terminator
                     /note="transcription terminator from phage lambda"
ORIGIN
        1 tcttccgtca caggtattta ttcggcgcaa agtgcgtcgg gtgatgctgc caacttactg
       61 atttagtgta tgatggtgtt tttgaggtgc tccagtggct tctgtttcta tcagctgtcc
      121 ctcctgttca gctactgacg gggtggtgcg taacggcaaa agcaccgccg gacatcagcg
      181 ctagcggagt gtatactggc ttactatgtt ggcactgatg agggtgtcag tgaagtgctt
      241 catgtggcag gagaaaaaag gctgcaccgg tgcgtcagca gaatatgtga tacaggatat
      301 attccgcttc ctcgctcact gactcgctac gctcggtcgt tcgactgcgg cgagcggaaa
      361 tggcttacga acggggcgga gatttcctgg aagatgccag gaagatactt aacagggaag
      421 tgagagggcc gcggcaaagc cgtttttcca taggctccgc ccccctgaca agcatcacga
      481 aatctgacgc tcaaatcagt ggtggcgaaa cccgacagga ctataaagat accaggcgtt
      541 tccccctggc ggctccctcg tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat
      601 tccgctgtta tggccgcgtt tgtctcattc cacgcctgac actcagttcc gggtaggcag
      661 ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgaccgc tgcgccttat
      721 ccggtaacta tcgtcttgag tccaacccgg aaagacatgc aaaagcacca ctggcagcag
      781 ccactggtaa ttgatttaga ggagttagtc ttgaagtcat gcgccggtta aggctaaact
      841 gaaaggacaa gttttggtga ctgcgctcct ccaagccagt tacctcggtt caaagagttg
      901 gtagctcaga gaaccttcga aaaaccgccc tgcaaggcgg ttttttcgtt ttcagagcaa
      961 gagattacgc gcagaccaaa acgatctcaa gaagatcatc ttattaatca gataaaatat
     1021 ttctagattt cagtgcaatt tatctcttca aatgtagcac ctgaagtcag ccccatacga
     1081 tataagttgt aattctcatg tttgacagct tatcatcgat aagcttccga tggcgcgccg
     1141 agaggcttta cactttatgc ttccggctga attctaaaga tctttgacag ctagctcagt
     1201 cctaggtata atactagtaa cgggcgatgg agttcgccca aactgccctg aagagggctg
     1261 atgactccta ctggcttgat cagtaggagt cattttcttt tgtaggagga aggatctatg
     1321 agcaaaggag aagaactttt cactggagtt gtcccaattc ttgttgaatt agatggtgat
     1381 gttaatgggc acaaattttc tgtccgtgga gagggtgaag gtgatgctac aaacggaaaa
     1441 ctcaccctta aatttatttg cactactgga aaactacctg ttccgtggcc aacacttgtc
     1501 actactctga cctatggtgt tcaatgcttt tcccgttatc cggatcacat gaaacggcat
     1561 gactttttca agagtgccat gcccgaaggt tatgtacagg aacgcactat atctttcaaa
     1621 gatgacggga cctacaagac gcgtgctgaa gtcaagtttg aaggtgatac ccttgttaat
     1681 cgtatcgagt taaagggtat tgattttaaa gaagatggaa acattcttgg acacaaactc
     1741 gagtacaact ttaactcaca caatgtatac atcacggcag acaaacaaaa gaatggaatc
     1801 aaagctaact tcaaaattcg ccacaacgtt gaagatggtt ccgttcaact agcagaccat
     1861 tatcaacaaa atactccaat tggcgatggc cctgtccttt taccagacaa ccattacctg
     1921 tcgacacaat ctgtcctttc gaaagatccc aacgaaaagc gtgaccacat ggtccttctt
     1981 gagtttgtaa ctgctgctgg gattacacat ggcatggatg agctctacaa ataaggatcc
     2041 aaactcgagt aaggatctcc aggcatcaaa taaaacgaaa ggctcagtcg aaagactggg
     2101 cctttcgttt tatctgttgt ttgtcggtga acgctctcta ctagagtcac actggctcac
     2161 cttcgggtgg gcctttctgc gtttatacct agggtacggt tttgggatcc ttactcgagt
     2221 ctagactgca gttgatcggg cacgtaagag gttccaactt tcaccataat gaaataagat
     2281 cactaccggg cgtatttttt gagttatcga gattttcagg agctaaggaa gctaaaatgg
     2341 agaaaaaaat cactggatat accaccgttg atatatccca atggcatcgt aaagaacatt
     2401 ttgaggcatt tcagtcagtt gctcaatgta cctataacca gaccgttcag ctggatatta
     2461 cggccttttt aaagaccgta aagaaaaata agcacaagtt ttatccggcc tttattcaca
     2521 ttcttgcccg cctgatgaat gctcatccgg aatttcgtat ggcaatgaaa gacggtgagc
     2581 tggtgatatg ggatagtgtt cacccttgtt acaccgtttt ccatgagcaa actgaaacgt
     2641 tttcatcgct ctggagtgaa taccacgacg atttccggca gtttctacac atatattcgc
     2701 aagatgtggc gtgttacggt gaaaacctgg cctatttccc taaagggttt attgagaata
     2761 tgtttttcgt ctcagccaat ccctgggtga gtttcaccag ttttgattta aacgtggcca
     2821 atatggacaa cttcttcgcc cccgttttca ccatgggcaa atattatacg caaggcgaca
     2881 aggtgctgat gccgctggcg attcaggttc atcatgccgt ttgtgatggc ttccatgtcg
     2941 gcagaatgct taatgaatta caacagtact gcgatgagtg gcagggcggg gcgtaatttg
     3001 atatcgagct cgcttggact cctgttgata gatccagtaa tgacctcaga actccatctg
     3061 gatttgttca gaacgctcgg ttgccgccgg gcgtttttta ttggtgagaa tccaagcctc
     3121 cgatcaacgt ctcattttcg ccaaaagttg gcccagggct tcccggtatc aacagggaca
     3181 ccaggattta tttattctgc gaagtga
//
