LOCUS       sequence-416806-        9806 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses Optimal lambda HA-Optimal Firefly luciferase.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 9806)
  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 9806)
  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_Opt-lambda-HAramp-FLuc100
FEATURES             Location/Qualifiers
     source          1..9806
                     /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"
     regulatory      2622..2631
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             2628..2693
                     /codon_start=1
                     /product="N-terminal RNA-binding domain from the lambda 
                     bacteriophage antiterminator protein N (Baron-Benhamou et 
                     al., 2004)"
                     /label=lambda N peptide
                     /translation="MDAQTRRRERRAEKQAQWKAAN"
     CDS             2718..2744
                     /codon_start=1
                     /product="HA (human influenza hemagglutinin) epitope tag"
                     /label=HA
                     /translation="YPYDVPDYA"
     misc_feature    6196..6784
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(6249..6269)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(6667..6678)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             6859..7092
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     primer_bind     complement(7211..7229)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        7297..7401
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(7402..7470,7471..8262)
                     /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(7620..7639)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      8433..9021
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     8922..8941
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     9175..9192
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    9432..9453
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(9468..9473,9474..9491,9492..9498)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    9506..9522
                     /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     9511..9533
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     9530..9546
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     9530..9546
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     9596..9615
                     /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 cgccaccatg gacgctcaga
     2641 ctcggcgacg ggagcggcgg gctgagaaac aggctcagtg gaaagctgct aacggcggct
     2701 caccaccaca catggcttac ccatacgacg tgccagacta cgctccacca tcactgaact
     2761 cagctgacat tcagcactca ggaggcggtg gatcaggtgg actgcaggag gacgccaaaa
     2821 acattaaaaa aggcccggct ccattctacc cgctggagga cggtactgct ggcgagcagc
     2881 tgcacaaagc tatgaaacga tacgcactag ttccgggtac tattgctttc actgacgctc
     2941 acatcgaggt ggacatcact tacgctgagt acttcgagat gagcgttcgg ttggccgagg
     3001 ctatgaaacg atacggcctg aacactaacc accgaatcgt ggtgtgctca gagaactcat
     3061 tacagttctt catgccggtg ttgggcgcct tattcatcgg cgttgctgtt gccccagcca
     3121 acgacattta caacgagcga gagttgttaa actcaatggg catttcacag ccaactgtgg
     3181 tgttcgtttc aaaaaaaggc ttgcagaaaa ttttgaacgt gcagaaaaaa ttaccaatca
     3241 tccagaaaat tattatcatg gacagcaaaa ctgactacca gggtttccag agcatgtaca
     3301 ctttcgttac ttcacacttg ccaccgggtt tcaacgagta cgacttcgtg ccagagagct
     3361 tcgaccgaga caaaactatt gccctgatca tgaactcatc aggctcaact ggtctgccga
     3421 aaggtgttgc tctgccgcac cggactgcct gcgtgcgatt ctcacacgcc cgggacccaa
     3481 ttttcggcaa ccagatcatt ccggacactg ccattttaag cgttgttcca ttccaccacg
     3541 gtttcggcat gttcactact ctgggttact tcatatgcgg tttccgagtt gtgttaatgt
     3601 accggttcga ggaggagctg ttcctgcgaa gcttgcagga ctacaaaatt cagtcagctc
     3661 tgctggtgcc aactctgttc agcttcttcg ccaaaagcac tctgattgac aaatacgact
     3721 tatcaaactt acacgagatt gcttcaggtg gcgctccgtt atcaaaagag gttggcgagg
     3781 ccgttgccaa acgattccac ctgccaggta tccgacaggg ttacggtttg actgagacta
     3841 cttcagctat tctgattact ccggagggtg acgacaaacc gggcgctgtg ggtaaagttg
     3901 ttccattctt cgaggctaaa gttgtggacc tggacactgg taaaactctg ggcgttaacc
     3961 agcgaggcga gctgtgcgtg cgaggtccga tgattatgag cggttacgtg aacaacccgg
     4021 aggctactaa cgccttgatt gacaaagacg gttggttaca cagcggtgac atcgcttact
     4081 gggacgagga cgagcacttc ttcatcgttg accggctgaa atcactgatt aaatacaaag
     4141 gctaccaggt ggctccggct gagttggagt caatcttgtt acagcaccca aacatcttcg
     4201 acgctggtgt ggctggtctg ccggacgacg acgccggtga gttaccagcc gccgttgttg
     4261 ttttggagca cggtaaaact atgactgaga aagagatcgt ggactacgtt gccagccagg
     4321 ttactactgc taaaaaattg cggggtggcg ttgtgttcgt cgacgaggtt ccgaaaggtt
     4381 taactggcaa attggacgct cgaaaaatcc gagagatcct gatcaaagcc aaaaaaggcg
     4441 gcaaaatcgc cgtgtaagct agctaggcgg actgttactg agctgcgttt tacacccttt
     4501 ctttgacaaa acctaacttg cgcagaaaaa aaaaaaataa gagacaacat tggcatggct
     4561 ttgttttttt aaattttttt taaagttttt tttttttttt ttttttttta agtttttttg
     4621 ttttgttttg gcgcttttga ctcaggattt aaaaactgga acggtgaagg cgacagcagt
     4681 tggttggagc aaacatcccc caaagttcta caaatgtggc tgaggacttt gtacattgtt
     4741 ttgttttttt tttttttggt tttgtctttt tttaatagtc attccaagta tccatgaaat
     4801 aagtggttac aggaagtccc tcaccctccc aaaagccacc cccactccta agaggaggat
     4861 ggtcgcgtcc atgccctgag tccaccccgg ggaaggtgac aaccggtaac ctacaaacgg
     4921 gtggaggatc accccacccg acacttcaca atcaaggggt acaatacaca agggtggagg
     4981 aacaccccac cctccagaca cattacacag aaatccaatc aaacagaagc accatcaggg
     5041 cttctgctac caaatttatc tcaaaaaact acaacaagga atcaccatca gggattccct
     5101 gtgcaatata cgtcaaacga gggccacgac gggaggacga tcacgcctcc cgaatatcgg
     5161 catgtctggc tttcgaattc agtgcgtgga gcatcagccc acgcagccaa tcagagtcga
     5221 atacaagtcg actttcgcga agagcatcag ccttcgcgcc attcttacac aaaccacact
     5281 ctcccctaca ggaacagcat cagcgttcct gcccagtacc caactcaaga aaatttatgt
     5341 ccccatgcag catcagcgca tgggccccaa gaatacatcc ccaacaaaat cacatccgag
     5401 caccaacagg gctcggagtg ttgtttcttg tccaactgga caaaccctcc atggaccatc
     5461 aggccatgga ctctcaccaa caagacaaaa actactcttc tcgaagcagc atcagcgctt
     5521 cgaaacactc gagcatacat tgtgcctatt tcttgggtgg acgatcacgc cacccatgct
     5581 ctcacgaatt tcaaaacacg gacaaggacg agcaccacca gggctcgtcg ttccacgtcc
     5641 aatacgatta cttacctttc gggatcacga tcacggatcc cgcagctaca tcacttccac
     5701 tcaggacatt caagcatgca cgatcacggc atgctccaca agtctcaacc acagaaacta
     5761 ccaaatgggt tcagcaccag cgaacccact cctacctcaa acctcttccc acaaaactgg
     5821 caagcaggat caccgcttgc ccattccaac ataccaaatc aaaaacaatt actggtacag
     5881 catcagcgta ccagcccaca tctctcacta ctatcaaaaa ccaaaccgtt cagcaacagc
     5941 gaacggtaca cacggaaaaa tcaactggtt tacaaatacg aaagacgatc acgctttcgt
     6001 ccagcgcaaa ctattacgaa aaacatccga cgggaagagc aacagccttc ccgcggcgga
     6061 aaacctcaca aaaacacgac aaacggatgc acgaacacgg catccgccga caacccacaa
     6121 acttacaacc aggcaaacgg tgcaggatca ccgcaccgta catcaaacac ctcagatctc
     6181 atatcgatag atcctaatca acctctggat tacaaaattt gtgaaagatt gactggtatt
     6241 cttaactatg ttgctccttt tacgctatgt ggatacgctg ctttaatgcc tttgtatcat
     6301 gctattgctt cccgtatggc tttcattttc tcctccttgt ataaatcctg gttgctgtct
     6361 ctttatgagg agttgtggcc cgttgtcagg caacgtggcg tggtgtgcac tgtgtttgct
     6421 gacgcaaccc ccactggttg gggcattgcc accacctgtc agctcctttc cgggactttc
     6481 gctttccccc tccctattgc cacggcggaa ctcatcgccg cctgccttgc ccgctgctgg
     6541 acaggggctc ggctgttggg cactgacaat tccgtggtgt tgtcggggaa atcatcgtcc
     6601 tttccttggc tgctcgcctg tgttgccacc tggattctgc gcgggacgtc cttctgctac
     6661 gtcccttcgg ccctcaatcc agcggacctt ccttcccgcg gcctgctgcc ggctctgcgg
     6721 cctcttccgc gtcttcgcct tcgccctcag acgagtcgga tctccctttg ggccgcctcc
     6781 ccgcctgaga tcctttaaga ccaatgactt acaaggcagc tgtagatctt agccactttt
     6841 taaaagaaaa ggggggactg gaagggctaa ttcactccca acgaagacaa gatctgcttt
     6901 ttgcttgtac tgggtctctc tggttagacc agatctgagc ctgggagctc tctggctaac
     6961 tagggaaccc actgcttaag cctcaataaa gcttgccttg agtgcttcaa gtagtgtgtg
     7021 cccgtctgtt gtgtgactct ggtaactaga gatccctcag acccttttag tcagtgtgga
     7081 aaatctctag cagtagtagt tcatgtcatc ttattattca gtatttataa cttgcaaaga
     7141 aatgaatatc agagagtgag aggcccgggt taattaagga aagggctaga tcattcttga
     7201 agacgaaagg gcctcgtgat acgcctattt ttataggtta atgtcatgat aataatggtt
     7261 tcttagacgt caggtggcac ttttcgggga aatgtgcgcg gaacccctat ttgtttattt
     7321 ttctaaatac attcaaatat gtatccgctc atgagacaat aaccctgata aatgcttcaa
     7381 taatattgaa aaaggaagag tatgagtatt caacatttcc gtgtcgccct tattcccttt
     7441 tttgcggcat tttgccttcc tgtttttgct cacccagaaa cgctggtgaa agtaaaagat
     7501 gctgaagatc agttgggtgc acgagtgggt tacatcgaac tggatctcaa cagcggtaag
     7561 atccttgaga gttttcgccc cgaagaacgt tttccaatga tgagcacttt taaagttctg
     7621 ctatgtggcg cggtattatc ccgtgttgac gccgggcaag agcaactcgg tcgccgcata
     7681 cactattctc agaatgactt ggttgagtac tcaccagtca cagaaaagca tcttacggat
     7741 ggcatgacag taagagaatt atgcagtgct gccataacca tgagtgataa cactgcggcc
     7801 aacttacttc tgacaacgat cggaggaccg aaggagctaa ccgctttttt gcacaacatg
     7861 ggggatcatg taactcgcct tgatcgttgg gaaccggagc tgaatgaagc cataccaaac
     7921 gacgagcgtg acaccacgat gcctgtagca atggcaacaa cgttgcgcaa actattaact
     7981 ggcgaactac ttactctagc ttcccggcaa caattaatag actggatgga ggcggataaa
     8041 gttgcaggac cacttctgcg ctcggccctt ccggctggct ggtttattgc tgataaatct
     8101 ggagccggtg agcgtgggtc tcgcggtatc attgcagcac tggggccaga tggtaagccc
     8161 tcccgtatcg tagttatcta cacgacgggg agtcaggcaa ctatggatga acgaaataga
     8221 cagatcgctg agataggtgc ctcactgatt aagcattggt aactgtcaga ccaagtttac
     8281 tcatatatac tttagattga tttaaaactt catttttaat ttaaaaggat ctaggtgaag
     8341 atcctttttg ataatctcat gaccaaaatc ccttaacgtg agttttcgtt ccactgagcg
     8401 tcagaccccg tagaaaagat caaaggatct tcttgagatc ctttttttct gcgcgtaatc
     8461 tgctgcttgc aaacaaaaaa accaccgcta ccagcggtgg tttgtttgcc ggatcaagag
     8521 ctaccaactc tttttccgaa ggtaactggc ttcagcagag cgcagatacc aaatactgtt
     8581 cttctagtgt agccgtagtt aggccaccac ttcaagaact ctgtagcacc gcctacatac
     8641 ctcgctctgc taatcctgtt accagtggct gctgccagtg gcgataagtc gtgtcttacc
     8701 gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
     8761 tcgtgcacac agcccagctt ggagcgaacg acctacaccg aactgagata cctacagcgt
     8821 gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaagc
     8881 ggcagggtcg gaacaggaga gcgcacgagg gagcttccag ggggaaacgc ctggtatctt
     8941 tatagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttttgtg atgctcgtca
     9001 ggggggcgga gcctatggaa aaacgccagc aacgcggcct ttttacggtt cctggccttt
     9061 tgctggcctt ttgctcacat gttctttcct gcgttatccc ctgattctgt ggataaccgt
     9121 attaccgcct ttgagtgagc tgataccgct cgccgcagcc gaacgaccga gcgcagcgag
     9181 tcagtgagcg aggaagcgga agagcgccca atacgcaaac cgcctctccc cgcgcgttgg
     9241 ccgattcatt aatgcagcaa gctcatggct gactaatttt ttttatttat gcagaggccg
     9301 aggccgcctc ggcctctgag ctattccaga agtagtgagg aggctttttt ggaggcctag
     9361 gcttttgcaa aaagctcccc gtggcacgac aggtttcccg actggaaagc gggcagtgag
     9421 cgcaacgcaa ttaatgtgag ttagctcact cattaggcac cccaggcttt acactttatg
     9481 cttccggctc gtatgttgtg tggaattgtg agcggataac aatttcacac aggaaacagc
     9541 tatgacatga ttacgaattt cacaaataaa gcattttttt cactgcattc tagttgtggt
     9601 ttgtccaaac tcatcaatgt atcttatcat gtctggatca actggataac tcaagctaac
     9661 caaaatcatc ccaaacttcc caccccatac cctattacca ctgccaatta cctgtggttt
     9721 catttactct aaacctgtga ttcctctgaa ttattttcat tttaaagaaa ttgtatttgt
     9781 taaatatgta ctacaaactt agtagt
//
