LOCUS       sequence-122579-        3126 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  RNA-IN S3 variant 5' UTR sequence controlling expression of 
            superfolder GFP (UTR sequence from Mutalik et al., Nat. Chem. Biol.,
            2012).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 3126)
  AUTHORS   Watters KE, Abbott TR, Lucks JB
  TITLE     Simultaneous characterization of cellular RNA structure and function
            with in-cell SHAPE-Seq.
  JOURNAL   Nucleic Acids Res. 2015 Sep 8. pii: gkv879.
  PUBMED    26350218
REFERENCE   2  (bases 1 to 3126)
  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"; journalName: "Nucleic 
            Acids Res. 2015 Sep 8. pii: gkv879."
COMMENT     Sequence Label: pJBL-RNAINS3
FEATURES             Location/Qualifiers
     source          1..3126
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        11..45
                     /label=J23119(SpeI) promoter
                     /note="bacterial promoter (Registry of Standard Biological 
                     Parts BBa_J23119) modified to end with an SpeI site"
     CDS             join(88..90,91..804)
                     /codon_start=1
                     /product="Cycle 3 GFP (Crameri et al., 1996)"
                     /label=Cycle 3 GFP
                     /note="mammalian codon-optimized"
                     /translation="ASKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLK
                     FICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDG
                     TYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKA
                     NFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLE
                     FVTAAGITHGMDELYK"
     primer_bind     complement(118..146)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     primer_bind     741..761
                     /label=GFP-F
                     /note="GFP, forward primer. Does NOT anneal to EGFP"
     terminator      837..908
                     /label=rrnB T1 terminator
                     /note="transcription terminator T1 from the E. coli rrnB 
                     gene"
     terminator      924..951
                     /label=T7Te terminator
                     /note="phage T7 early transcription terminator"
     CDS             1088..1747
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(1154..1173)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     terminator      1768..1862
                     /label=lambda t0 terminator
                     /note="transcription terminator from phage lambda"
     primer_bind     complement(2269..2286)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2403..2948)
                     /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(2483..2502)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 gaattcgaat ttgacagcta gctcagtcct aggtataata ctagtgggaa aaatcaataa
       61 ggagacaaca agatgtgcga actcgatgct agcaaaggag aagaactttt cactggagtt
      121 gtcccaattc ttgttgaatt agatggtgat gttaatgggc acaaattttc tgtccgtgga
      181 gagggtgaag gtgatgctac aaacggaaaa ctcaccctta aatttatttg cactactgga
      241 aaactacctg ttccgtggcc aacacttgtc actactctga cctatggtgt tcaatgcttt
      301 tcccgttatc cggatcacat gaaacggcat gactttttca agagtgccat gcccgaaggt
      361 tatgtacagg aacgcactat atctttcaaa gatgacggga cctacaagac gcgtgctgaa
      421 gtcaagtttg aaggtgatac ccttgttaat cgtatcgagt taaagggtat tgattttaaa
      481 gaagatggaa acattcttgg acacaaactc gagtacaact ttaactcaca caatgtatac
      541 atcacggcag acaaacaaaa gaatggaatc aaagctaact tcaaaattcg ccacaacgtt
      601 gaagatggtt ccgttcaact agcagaccat tatcaacaaa atactccaat tggcgatggc
      661 cctgtccttt taccagacaa ccattacctg tcgacacaat ctgtcctttc gaaagatccc
      721 aacgaaaagc gtgaccacat ggtccttctt gagtttgtaa ctgctgctgg gattacacat
      781 ggcatggatg agctctacaa ataaggatcc aaactcgagt aaggatctcc aggcatcaaa
      841 taaaacgaaa ggctcagtcg aaagactggg cctttcgttt tatctgttgt ttgtcggtga
      901 acgctctcta ctagagtcac actggctcac cttcgggtgg gcctttctgc gtttatacct
      961 agggtacggg ttttgcctgc agttgatcgg gcacgtaaga ggttccaact ttcaccataa
     1021 tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag gagctaagga
     1081 agctaaaatg gagaaaaaaa tcactggata taccaccgtt gatatatccc aatggcatcg
     1141 taaagaacat tttgaggcat ttcagtcagt tgctcaatgt acctataacc agaccgttca
     1201 gctggatatt acggcctttt taaagaccgt aaagaaaaat aagcacaagt tttatccggc
     1261 ctttattcac attcttgccc gcctgatgaa tgctcatccg gaatttcgta tggcaatgaa
     1321 agacggtgag ctggtgatat gggatagtgt tcacccttgt tacaccgttt tccatgagca
     1381 aactgaaacg ttttcatcgc tctggagtga ataccacgac gatttccggc agtttctaca
     1441 catatattcg caagatgtgg cgtgttacgg tgaaaacctg gcctatttcc ctaaagggtt
     1501 tattgagaat atgtttttcg tctcagccaa tccctgggtg agtttcacca gttttgattt
     1561 aaacgtggcc aatatggaca acttcttcgc ccccgttttc accatgggca aatattatac
     1621 gcaaggcgac aaggtgctga tgccgctggc gattcaggtt catcatgccg tttgtgatgg
     1681 cttccatgtc ggcagaatgc ttaatgaatt acaacagtac tgcgatgagt ggcagggcgg
     1741 ggcgtaattt gatatcgagc tcgcttggac tcctgttgat agatccagta atgacctcag
     1801 aactccatct ggatttgttc agaacgctcg gttgccgccg ggcgtttttt attggtgaga
     1861 atccaagcct ccgatcaacg tctcattttc gccaaaagtt ggcccagggc ttcccggtat
     1921 caacagggac accaggattt atttattctg cgaagtgatc ttccgtcaca ggtatttatt
     1981 cggcgcaaag tgcgtcgggt gatgctgcca acttactgat ttagtgtatg atggtgtttt
     2041 tgaggtgctc cagtggcttc tgtttctatc agctgtccct cctgttcagc tactgacggg
     2101 gtggtgcgta acggcaaaag caccgccgga catcagcgct agcggagtgt atactggctt
     2161 actatgttgg cactgatgag ggtgtcagtg aagtgcttca tgtggcagga gaaaaaaggc
     2221 tgcaccggtg cgtcagcaga atatgtgata caggatatat tccgcttcct cgctcactga
     2281 ctcgctacgc tcggtcgttc gactgcggcg agcggaaatg gcttacgaac ggggcggaga
     2341 tttcctggaa gatgccagga agatacttaa cagggaagtg agagggccgc ggcaaagccg
     2401 tttttccata ggctccgccc ccctgacaag catcacgaaa tctgacgctc aaatcagtgg
     2461 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggcgg ctccctcgtg
     2521 cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg gccgcgtttg
     2581 tctcattcca cgcctgacac tcagttccgg gtaggcagtt cgctccaagc tggactgtat
     2641 gcacgaaccc cccgttcagt ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc
     2701 caacccggaa agacatgcaa aagcaccact ggcagcagcc actggtaatt gatttagagg
     2761 agttagtctt gaagtcatgc gccggttaag gctaaactga aaggacaagt tttggtgact
     2821 gcgctcctcc aagccagtta cctcggttca aagagttggt agctcagaga accttcgaaa
     2881 aaccgccctg caaggcggtt ttttcgtttt cagagcaaga gattacgcgc agaccaaaac
     2941 gatctcaaga agatcatctt attaatcaga taaaatattt ctagatttca gtgcaattta
     3001 tctcttcaaa tgtagcacct gaagtcagcc ccatacgata taagttgtaa ttctcatgtt
     3061 tgacagctta tcatcgataa gcttccgatg gcgcgccgag aggctttaca ctttatgctt
     3121 ccggct
//
