LOCUS       sequence-416800-        9625 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses Optimal Firefly with 3'UTR MS2 hairpins.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 9625)
  AUTHORS   Barrington CL, Galindo G, Koch AL, Horton ER, Morrison EJ, Tisa S, 
            Stasevich TJ, Rissland OS
  TITLE     Synonymous codon usage regulates translation initiation.
  JOURNAL   Cell Rep. 2023 Dec 26;42(12):113413. doi: 
            10.1016/j.celrep.2023.113413. Epub 2023 Dec 12.
  PUBMED    38096059
REFERENCE   2  (bases 1 to 9625)
  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: "Cell Rep.";
            date: "2023-12-26"; volume: "42(12):113413. doi"; pages: " 
            10.1016/j.celrep.2023.113413. Epub 2023 Dec 12"
COMMENT     Sequence Label: pUB_FLuc100---MS2
FEATURES             Location/Qualifiers
     source          1..9625
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     LTR             1..634
                     /label=3' LTR
                     /note="3' long terminal repeat (LTR) from HIV-1"
     misc_feature    681..806
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1303..1536
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1721..1765
                     /codon_start=1
                     /product="antigenic peptide corresponding to amino acids 
                     655 to 669 of the HIV envelope protein gp41 (Lutje Hulsik 
                     et al., 2013)"
                     /label=gp41 peptide
                     /note="recognized by the 2H10 single-chain llama nanobody"
                     /translation="KNEQELLELDKWASL"
     misc_feature    2058..2175
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        2218..2616
                     /label=UbC promoter
                     /note="human ubiquitin C promoter"
     misc_feature    6015..6603
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(6068..6088)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(6486..6497)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             6678..6911
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     primer_bind     complement(7030..7048)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        7116..7220
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(7221..7289,7290..8081)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     complement(7439..7458)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      8252..8840
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     8741..8760
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     8994..9011
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    9251..9272
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(9287..9292,9293..9310,9311..9317)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    9325..9341
                     /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)."
     primer_bind     9330..9352
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     9349..9365
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     9349..9365
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     9415..9434
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
ORIGIN
        1 tggaagggct aattcactcc caaagaagac aagatatcct tgatctgtgg atctaccaca
       61 cacaaggcta cttccctgat tagcagaact acacaccagg gccaggggtc agatatccac
      121 tgacctttgg atggtgctac aagctagtac cagttgagcc agataaggta gaagaggcca
      181 ataaaggaga gaacaccagc ttgttacacc ctgtgagcct gcatgggatg gatgacccgg
      241 agagagaagt gttagagtgg aggtttgaca gccgcctagc atttcatcac gtggcccgag
      301 agctgcatcc ggagtacttc aagaactgct gatatcgagc ttgctacaag ggactttccg
      361 ctggggactt tccagggagg cgtggcctgg gcgggactgg ggagtggcga gccctcagat
      421 cctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga
      481 gcctgggagc tctctggcta actagggaac ccactgctta agcctcaata aagcttgcct
      541 tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta gagatccctc
      601 agaccctttt agtcagtgtg gaaaatctct agcagtggcg cccgaacagg gacttgaaag
      661 cgaaagggaa accagaggag ctctctcgac gcaggactcg gcttgctgaa gcgcgcacgg
      721 caagaggcga ggggcggcga ctggtgagta cgccaaaaat tttgactagc ggaggctaga
      781 aggagagaga tgggtgcgag agcgtcagta ttaagcgggg gagaattaga tcgcgatggg
      841 aaaaaattcg gttaaggcca gggggaaaga aaaaatataa attaaaacat atagtatggg
      901 caagcaggga gctagaacga ttcgcagtta atcctggcct gttagaaaca tcagaaggct
      961 gtagacaaat actgggacag ctacaaccat cccttcagac aggatcagaa gaacttagat
     1021 cattatataa tacagtagca accctctatt gtgtgcatca aaggatagag ataaaagaca
     1081 ccaaggaagc tttagacaag atagaggaag agcaaaacaa aagtaagacc accgcacagc
     1141 aagcggccgg ccgctgatct tcagacctgg aggaggagat atgagggaca attggagaag
     1201 tgaattatat aaatataaag tagtaaaaat tgaaccatta ggagtagcac ccaccaaggc
     1261 aaagagaaga gtggtgcaga gagaaaaaag agcagtggga ataggagctt tgttccttgg
     1321 gttcttggga gcagcaggaa gcactatggg cgcagcgtca atgacgctga cggtacaggc
     1381 cagacaatta ttgtctggta tagtgcagca gcagaacaat ttgctgaggg ctattgaggc
     1441 gcaacagcat ctgttgcaac tcacagtctg gggcatcaag cagctccagg caagaatcct
     1501 ggctgtggaa agatacctaa aggatcaaca gctcctgggg atttggggtt gctctggaaa
     1561 actcatttgc accactgctg tgccttggaa tgctagttgg agtaataaat ctctggaaca
     1621 gatttggaat cacacgacct ggatggagtg ggacagagaa attaacaatt acacaagctt
     1681 aatacactcc ttaattgaag aatcgcaaaa ccagcaagaa aagaatgaac aagaattatt
     1741 ggaattagat aaatgggcaa gtttgtggaa ttggtttaac ataacaaatt ggctgtggta
     1801 tataaaatta ttcataatga tagtaggagg cttggtaggt ttaagaatag tttttgctgt
     1861 actttctata gtgaatagag ttaggcaggg atattcacca ttatcgtttc agacccacct
     1921 cccaaccccg aggggacccg acaggcccga aggaatagaa gaagaaggtg gagagagaga
     1981 cagagacaga tccattcgat tagtgaacgg atctcgacgg tatcgccgaa ttcacaaatg
     2041 gcagtattca tccacaattt taaaagaaaa ggggggattg gggggtacag tgcaggggaa
     2101 agaatagtag acataatagc aacagacata caaactaaag aattacaaaa acaaattaca
     2161 aaaattcaaa attttcgggt ttattacagg gacagcagag atccagtttg gactagtggc
     2221 ctccgcgccg ggttttggcg cctcccgcgg gcgcccccct cctcacggcg agcgctgcca
     2281 cgtcagacga agggcgcagc gagcgtcctg atccttccgc ccggacgctc aggacagcgg
     2341 cccgctgctc ataagactcg gccttagaac cccagtatca gcagaaggac attttaggac
     2401 gggacttggg tgactctagg gcactggttt tctttccaga gagcggaaca ggcgaggaaa
     2461 agtagtccct tctcggcgat tctgcggagg gatctccgtg gggcggtgaa cgccgatgat
     2521 tatataagga cgcgccgggt gtggcacagc tagttccgtc gcagccggga tttgggtcgc
     2581 ggttcttgtt tgtggatcgc tgtgatcgtc acttggcggc cgcatggagg acgccaaaaa
     2641 cattaaaaaa ggcccggctc cattctaccc gctggaggac ggtactgctg gcgagcagct
     2701 gcacaaagct atgaaacgat acgcactagt tccgggtact attgctttca ctgacgctca
     2761 catcgaggtg gacatcactt acgctgagta cttcgagatg agcgttcggt tggccgaggc
     2821 tatgaaacga tacggcctga acactaacca ccgaatcgtg gtgtgctcag agaactcatt
     2881 acagttcttc atgccggtgt tgggcgcctt attcatcggc gttgctgttg ccccagccaa
     2941 cgacatttac aacgagcgag agttgttaaa ctcaatgggc atttcacagc caactgtggt
     3001 gttcgtttca aaaaaaggct tgcagaaaat tttgaacgtg cagaaaaaat taccaatcat
     3061 ccagaaaatt attatcatgg acagcaaaac tgactaccag ggtttccaga gcatgtacac
     3121 tttcgttact tcacacttgc caccgggttt caacgagtac gacttcgtgc cagagagctt
     3181 cgaccgagac aaaactattg ccctgatcat gaactcatca ggctcaactg gtctgccgaa
     3241 aggtgttgct ctgccgcacc ggactgcctg cgtgcgattc tcacacgccc gggacccaat
     3301 tttcggcaac cagatcattc cggacactgc cattttaagc gttgttccat tccaccacgg
     3361 tttcggcatg ttcactactc tgggttactt catatgcggt ttccgagttg tgttaatgta
     3421 ccggttcgag gaggagctgt tcctgcgaag cttgcaggac tacaaaattc agtcagctct
     3481 gctggtgcca actctgttca gcttcttcgc caaaagcact ctgattgaca aatacgactt
     3541 atcaaactta cacgagattg cttcaggtgg cgctccgtta tcaaaagagg ttggcgaggc
     3601 cgttgccaaa cgattccacc tgccaggtat ccgacagggt tacggtttga ctgagactac
     3661 ttcagctatt ctgattactc cggagggtga cgacaaaccg ggcgctgtgg gtaaagttgt
     3721 tccattcttc gaggctaaag ttgtggacct ggacactggt aaaactctgg gcgttaacca
     3781 gcgaggcgag ctgtgcgtgc gaggtccgat gattatgagc ggttacgtga acaacccgga
     3841 ggctactaac gccttgattg acaaagacgg ttggttacac agcggtgaca tcgcttactg
     3901 ggacgaggac gagcacttct tcatcgttga ccggctgaaa tcactgatta aatacaaagg
     3961 ctaccaggtg gctccggctg agttggagtc aatcttgtta cagcacccaa acatcttcga
     4021 cgctggtgtg gctggtctgc cggacgacga cgccggtgag ttaccagccg ccgttgttgt
     4081 tttggagcac ggtaaaacta tgactgagaa agagatcgtg gactacgttg ccagccaggt
     4141 tactactgct aaaaaattgc ggggtggcgt tgtgttcgtc gacgaggttc cgaaaggttt
     4201 aactggcaaa ttggacgctc gaaaaatccg agagatcctg atcaaagcca aaaaaggcgg
     4261 caaaatcgcc gtgtaagcta gctaggcgga ctgttactga gctgcgtttt acaccctttc
     4321 tttgacaaaa cctaacttgc gcagaaaaaa aaaaaataag agacaacatt ggcatggctt
     4381 tgttttttta aatttttttt aaagtttttt tttttttttt ttttttttaa gtttttttgt
     4441 tttgttttgg cgcttttgac tcaggattta aaaactggaa cggtgaaggc gacagcagtt
     4501 ggttggagca aacatccccc aaagttctac aaatgtggct gaggactttg tacattgttt
     4561 tgtttttttt ttttttggtt ttgtcttttt ttaatagtca ttccaagtat ccatgaaata
     4621 agtggttaca ggaagtccct caccctccca aaagccaccc ccactcctaa gaggaggatg
     4681 gtcgcgtcca tgccctgagt ccaccccggg gaaggtgaca accggtaacc tacaaacggg
     4741 tggaggatca ccccacccga cacttcacaa tcaaggggta caatacacaa gggtggagga
     4801 acaccccacc ctccagacac attacacaga aatccaatca aacagaagca ccatcagggc
     4861 ttctgctacc aaatttatct caaaaaacta caacaaggaa tcaccatcag ggattccctg
     4921 tgcaatatac gtcaaacgag ggccacgacg ggaggacgat cacgcctccc gaatatcggc
     4981 atgtctggct ttcgaattca gtgcgtggag catcagccca cgcagccaat cagagtcgaa
     5041 tacaagtcga ctttcgcgaa gagcatcagc cttcgcgcca ttcttacaca aaccacactc
     5101 tcccctacag gaacagcatc agcgttcctg cccagtaccc aactcaagaa aatttatgtc
     5161 cccatgcagc atcagcgcat gggccccaag aatacatccc caacaaaatc acatccgagc
     5221 accaacaggg ctcggagtgt tgtttcttgt ccaactggac aaaccctcca tggaccatca
     5281 ggccatggac tctcaccaac aagacaaaaa ctactcttct cgaagcagca tcagcgcttc
     5341 gaaacactcg agcatacatt gtgcctattt cttgggtgga cgatcacgcc acccatgctc
     5401 tcacgaattt caaaacacgg acaaggacga gcaccaccag ggctcgtcgt tccacgtcca
     5461 atacgattac ttacctttcg ggatcacgat cacggatccc gcagctacat cacttccact
     5521 caggacattc aagcatgcac gatcacggca tgctccacaa gtctcaacca cagaaactac
     5581 caaatgggtt cagcaccagc gaacccactc ctacctcaaa cctcttccca caaaactggc
     5641 aagcaggatc accgcttgcc cattccaaca taccaaatca aaaacaatta ctggtacagc
     5701 atcagcgtac cagcccacat ctctcactac tatcaaaaac caaaccgttc agcaacagcg
     5761 aacggtacac acggaaaaat caactggttt acaaatacga aagacgatca cgctttcgtc
     5821 cagcgcaaac tattacgaaa aacatccgac gggaagagca acagccttcc cgcggcggaa
     5881 aacctcacaa aaacacgaca aacggatgca cgaacacggc atccgccgac aacccacaaa
     5941 cttacaacca ggcaaacggt gcaggatcac cgcaccgtac atcaaacacc tcagatctca
     6001 tatcgataga tcctaatcaa cctctggatt acaaaatttg tgaaagattg actggtattc
     6061 ttaactatgt tgctcctttt acgctatgtg gatacgctgc tttaatgcct ttgtatcatg
     6121 ctattgcttc ccgtatggct ttcattttct cctccttgta taaatcctgg ttgctgtctc
     6181 tttatgagga gttgtggccc gttgtcaggc aacgtggcgt ggtgtgcact gtgtttgctg
     6241 acgcaacccc cactggttgg ggcattgcca ccacctgtca gctcctttcc gggactttcg
     6301 ctttccccct ccctattgcc acggcggaac tcatcgccgc ctgccttgcc cgctgctgga
     6361 caggggctcg gctgttgggc actgacaatt ccgtggtgtt gtcggggaaa tcatcgtcct
     6421 ttccttggct gctcgcctgt gttgccacct ggattctgcg cgggacgtcc ttctgctacg
     6481 tcccttcggc cctcaatcca gcggaccttc cttcccgcgg cctgctgccg gctctgcggc
     6541 ctcttccgcg tcttcgcctt cgccctcaga cgagtcggat ctccctttgg gccgcctccc
     6601 cgcctgagat cctttaagac caatgactta caaggcagct gtagatctta gccacttttt
     6661 aaaagaaaag gggggactgg aagggctaat tcactcccaa cgaagacaag atctgctttt
     6721 tgcttgtact gggtctctct ggttagacca gatctgagcc tgggagctct ctggctaact
     6781 agggaaccca ctgcttaagc ctcaataaag cttgccttga gtgcttcaag tagtgtgtgc
     6841 ccgtctgttg tgtgactctg gtaactagag atccctcaga cccttttagt cagtgtggaa
     6901 aatctctagc agtagtagtt catgtcatct tattattcag tatttataac ttgcaaagaa
     6961 atgaatatca gagagtgaga ggcccgggtt aattaaggaa agggctagat cattcttgaa
     7021 gacgaaaggg cctcgtgata cgcctatttt tataggttaa tgtcatgata ataatggttt
     7081 cttagacgtc aggtggcact tttcggggaa atgtgcgcgg aacccctatt tgtttatttt
     7141 tctaaataca ttcaaatatg tatccgctca tgagacaata accctgataa atgcttcaat
     7201 aatattgaaa aaggaagagt atgagtattc aacatttccg tgtcgccctt attccctttt
     7261 ttgcggcatt ttgccttcct gtttttgctc acccagaaac gctggtgaaa gtaaaagatg
     7321 ctgaagatca gttgggtgca cgagtgggtt acatcgaact ggatctcaac agcggtaaga
     7381 tccttgagag ttttcgcccc gaagaacgtt ttccaatgat gagcactttt aaagttctgc
     7441 tatgtggcgc ggtattatcc cgtgttgacg ccgggcaaga gcaactcggt cgccgcatac
     7501 actattctca gaatgacttg gttgagtact caccagtcac agaaaagcat cttacggatg
     7561 gcatgacagt aagagaatta tgcagtgctg ccataaccat gagtgataac actgcggcca
     7621 acttacttct gacaacgatc ggaggaccga aggagctaac cgcttttttg cacaacatgg
     7681 gggatcatgt aactcgcctt gatcgttggg aaccggagct gaatgaagcc ataccaaacg
     7741 acgagcgtga caccacgatg cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg
     7801 gcgaactact tactctagct tcccggcaac aattaataga ctggatggag gcggataaag
     7861 ttgcaggacc acttctgcgc tcggcccttc cggctggctg gtttattgct gataaatctg
     7921 gagccggtga gcgtgggtct cgcggtatca ttgcagcact ggggccagat ggtaagccct
     7981 cccgtatcgt agttatctac acgacgggga gtcaggcaac tatggatgaa cgaaatagac
     8041 agatcgctga gataggtgcc tcactgatta agcattggta actgtcagac caagtttact
     8101 catatatact ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga
     8161 tcctttttga taatctcatg accaaaatcc cttaacgtga gttttcgttc cactgagcgt
     8221 cagaccccgt agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct
     8281 gctgcttgca aacaaaaaaa ccaccgctac cagcggtggt ttgtttgccg gatcaagagc
     8341 taccaactct ttttccgaag gtaactggct tcagcagagc gcagatacca aatactgttc
     8401 ttctagtgta gccgtagtta ggccaccact tcaagaactc tgtagcaccg cctacatacc
     8461 tcgctctgct aatcctgtta ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg
     8521 ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt
     8581 cgtgcacaca gcccagcttg gagcgaacga cctacaccga actgagatac ctacagcgtg
     8641 agctatgaga aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg
     8701 gcagggtcgg aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt
     8761 atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag
     8821 gggggcggag cctatggaaa aacgccagca acgcggcctt tttacggttc ctggcctttt
     8881 gctggccttt tgctcacatg ttctttcctg cgttatcccc tgattctgtg gataaccgta
     8941 ttaccgcctt tgagtgagct gataccgctc gccgcagccg aacgaccgag cgcagcgagt
     9001 cagtgagcga ggaagcggaa gagcgcccaa tacgcaaacc gcctctcccc gcgcgttggc
     9061 cgattcatta atgcagcaag ctcatggctg actaattttt tttatttatg cagaggccga
     9121 ggccgcctcg gcctctgagc tattccagaa gtagtgagga ggcttttttg gaggcctagg
     9181 cttttgcaaa aagctccccg tggcacgaca ggtttcccga ctggaaagcg ggcagtgagc
     9241 gcaacgcaat taatgtgagt tagctcactc attaggcacc ccaggcttta cactttatgc
     9301 ttccggctcg tatgttgtgt ggaattgtga gcggataaca atttcacaca ggaaacagct
     9361 atgacatgat tacgaatttc acaaataaag catttttttc actgcattct agttgtggtt
     9421 tgtccaaact catcaatgta tcttatcatg tctggatcaa ctggataact caagctaacc
     9481 aaaatcatcc caaacttccc accccatacc ctattaccac tgccaattac ctgtggtttc
     9541 atttactcta aacctgtgat tcctctgaat tattttcatt ttaaagaaat tgtatttgtt
     9601 aaatatgtac tacaaactta gtagt
//
