LOCUS       sequence-416816-        8037 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses SM(FLAG)-nonoptimal Firefly - 3'UTR malat1 triple helix.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8037)
  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 8037)
  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: pcDNA3.1_SM-FLuc0-malat1
FEATURES             Location/Qualifiers
     source          1..8037
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        complement(100..204)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(279..298)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        470..849
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        850..1053
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     1004..1024
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     1098..1117
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        1098..1116
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     regulatory      1142..1151
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             1151..1174
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             1178..1201
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             1205..1228
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             1733..1756
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             1763..1786
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             1799..1822
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             1829..1852
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             2045..2068
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             2072..2095
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             2099..2122
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     rep_origin      4139..4567
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(4226..4245)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4436..4457
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(4576..4596)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        4581..4910
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      4761..4896
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     4823..4842
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             4977..5771
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(5031..5050)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     5641..5660
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    5945..6066
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(5982..6001)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     6036..6055
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(6115..6131)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(6115..6131)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(6128..6150)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    6139..6155
                     /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)."
     promoter        complement(join(6163..6169,6170..6187,6188..6193))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6208..6229
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(6346..6363)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(6517..7105)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(6597..6616)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(7276..8037,1..30,31..99))
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     7899..7918
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
ORIGIN
        1 atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa
       61 aaagggaata agggcgacac ggaaatgttg aatactcata ctcttccttt ttcaatatta
      121 ttgaagcatt tatcagggtt attgtctcat gagcggatac atatttgaat gtatttagaa
      181 aaataaacaa ataggggttc cgcgcacatt tccccgaaaa gtgccacctg acgtcgacgg
      241 atcgggagat ctcccgatcc cctatggtgc actctcagta caatctgctc tgatgccgca
      301 tagttaagcc agtatctgct ccctgcttgt gtgttggagg tcgctgagta gtgcgcgagc
      361 aaaatttaag ctacaacaag gcaaggcttg accgacaatt gcatgaagaa tctgcttagg
      421 gttaggcgtt ttgcgctgct tcgcgatgta cgggccagat atacgcgttg acattgatta
      481 ttgactagtt attaatagta atcaattacg gggtcattag ttcatagccc atatatggag
      541 ttccgcgtta cataacttac ggtaaatggc ccgcctggct gaccgcccaa cgacccccgc
      601 ccattgacgt caataatgac gtatgttccc atagtaacgc caatagggac tttccattga
      661 cgtcaatggg tggagtattt acggtaaact gcccacttgg cagtacatca agtgtatcat
      721 atgccaagta cgccccctat tgacgtcaat gacggtaaat ggcccgcctg gcattatgcc
      781 cagtacatga ccttatggga ctttcctact tggcagtaca tctacgtatt agtcatcgct
      841 attaccatgg tgatgcggtt ttggcagtac atcaatgggc gtggatagcg gtttgactca
      901 cggggatttc caagtctcca ccccattgac gtcaatggga gtttgttttg gcaccaaaat
      961 caacgggact ttccaaaatg tcgtaacaac tccgccccat tgacgcaaat gggcggtagg
     1021 cgtgtacggt gggaggtcta tataagcaga gctctctggc taactagaga acccactgct
     1081 tactggctta tcgaaattaa tacgactcac tatagggaga cccaagctgg ctagcgcggc
     1141 cgccaccatg gactacaagg acgacgacga caaaggtgac tacaaagatg atgacgataa
     1201 aggcgactat aaggacgatg acgacaaggg cggaaactca ctgatcaagg aaaacatgcg
     1261 gatgaaggtg gtgatggagg gctccgtgaa tggtcaccag ttcaagtgca ccggagaggg
     1321 agagggaaac ccgtacatgg gaactcagac catgcgcatt aaggtcatcg aaggaggtcc
     1381 gctgccgttc gctttcgata tcctggccac ttcgttcgga ggagggtcgc gcacgttcat
     1441 caagtacccg aagggaatcc cggacttctt taagcagtca ttcccggaag gattcacttg
     1501 ggaacgggtg acccggtatg aagatggagg tgtggtgact gtcatgcaag atacttcgct
     1561 ggaggatggg tgcctcgtgt accacgtcca agtccgcgga gtgaatttcc cgtccaacgg
     1621 accagtgatg cagaaaaaga cgaagggttg ggaacctaat actgaaatga tgtaccccgc
     1681 agacggaggg ctgaggggct acacccacat ggcgctgaag gtcgacggag gagattacaa
     1741 ggatgacgac gataagcaac aagattacaa agacgatgat gacaagggcc agcagggcga
     1801 ctacaaggac gacgacgaca agcagcagga ctacaaagat gacgatgata aaggaggagg
     1861 acatctgtcc tgttcgttcg tgaccaccta cagatcaaag aaaaccgtgg gaaacatcaa
     1921 gatgccgggc attcatgccg tcgaccaccg cctggagcgg ctcgaagaat cagacaatga
     1981 gatgttcgtc gtgcaaagag aacatgccgt ggccaagttc gcgggactgg gaggcggtgg
     2041 aggcgattac aaagacgatg atgacaaggg tgactataaa gacgacgatg acaaagggga
     2101 ttacaaggat gatgatgata agggaggcgg tggatcaggt ggaggaggtt cactgcagga
     2161 agatgcgaag aatataaaga agggacccgc gcctttttat cccctagaag atggaaccgc
     2221 gggagaacaa ctacataagg caatgaagag atatgcacta gtacctggaa caatagcatt
     2281 tacagatgca catatagaag tcgatataac gtatgcggaa tattttgaaa tgtccgtccg
     2341 tctcgcagaa gcgatgaaga gatatgggct aaatacaaat catagaatag tcgtatgtag
     2401 tgaaaattct cttcaatttt ttatgcctgt cctcggggcg ctatttatag gagtcgcagt
     2461 cgcgcccgcg aatgatatat ataatgaacg tgaactcctc aatagtatgg gaatatcgca
     2521 acctaccgta gtatttgtat ccaagaaggg gctccaaaag atactcaatg tccaaaagaa
     2581 gctccccata atccaaaaga tcataataat ggattctaag acggattatc aaggatttca
     2641 atcgatgtat acgtttgtca catctcatct acctcccgga tttaatgaat atgattttgt
     2701 ccctgaatcc tttgataggg ataagacaat agcactaata atgaattcct ctggatctac
     2761 cggacttcct aagggggtcg cacttcctca tagaaccgca tgtgtcagat tttcgcatgc
     2821 gagagatcct atatttggca atcaaataat acctgataca gcgatactta gtgtcgtccc
     2881 ttttcatcat gggtttggaa tgtttactac actcggatat ttcatatgtg gatttcgcgt
     2941 cgtcctcatg tatagatttg aagaagaact ctttctaagg tcccttcaag attataagat
     3001 acaaagtgcg ctcctcgtcc ctaccctatt ctcctttttt gcaaagagta cccttataga
     3061 taagtatgat ctttctaatc tacatgaaat agcatctggg ggagcgcccc tctctaagga
     3121 agtcggggaa gcggtagcaa agaggtttca tctacctggg ataaggcaag gatatgggct
     3181 cacagaaacc acaagtgcga tactaataac acccgaaggg gatgataagc ctggagcggt
     3241 cgggaaggta gtaccctttt ttgaagcgaa ggtcgtagat cttgataccg ggaagacgct
     3301 tggagtcaat caaagagggg aactctgtgt cagaggacct atgataatgt ccggatatgt
     3361 aaataatccc gaagcgacca atgcgctaat agataaggat ggatggctac attctggaga
     3421 tatagcgtat tgggatgaag atgaacattt ttttatagtt gaccgcctaa agtctctcat
     3481 aaagtataag gggtatcaag tagcacccgc agaacttgaa tccatactac tccaacatcc
     3541 caatatattt gatgcagggg tcgcaggact tcccgatgat gatgcggggg aacttcccgc
     3601 agcggtcgtc gtcctcgaac atggaaagac gatgacggaa aaggaaatag tagattatgt
     3661 cgcaagtcaa gtaacaaccg cgaagaagct tcgcggagga gtcgtatttg tcgacgaagt
     3721 acccaagggg cttaccggaa agctcgatgc aagaaagata agagaaatac tcataaaggc
     3781 aaagaagggg ggaaagatag cagtataagg taccgagctc ggatccacta gtccagtgtg
     3841 gtggaattct gcagatatcc agcacagtgg cggccgctcg agtctagagg gcccgtttaa
     3901 acccgctgat cagcctcgac gattcgtcag tagggttgta aaggtttttc ttttcctgag
     3961 aaaacaacct tttgttttct caggttttgc tttttggcct ttccctagct ttaaaaaaaa
     4021 aaagcaaaag acgctggtgg ctggcactcc tggtttccag gacggggttc aagtccctgc
     4081 ggtgtctttg cttcttctga ggcggaaaga accagctggg gctctagggg gtatccccac
     4141 gcgccctgta gcggcgcatt aagcgcggcg ggtgtggtgg ttacgcgcag cgtgaccgct
     4201 acacttgcca gcgccctagc gcccgctcct ttcgctttct tcccttcctt tctcgccacg
     4261 ttcgccggct ttccccgtca agctctaaat cgggggctcc ctttagggtt ccgatttagt
     4321 gctttacggc acctcgaccc caaaaaactt gattagggtg atggttcacg tagtgggcca
     4381 tcgccctgat agacggtttt tcgccctttg acgttggagt ccacgttctt taatagtgga
     4441 ctcttgttcc aaactggaac aacactcaac cctatctcgg tctattcttt tgatttataa
     4501 gggattttgc cgatttcggc ctattggtta aaaaatgagc tgatttaaca aaaatttaac
     4561 gcgaattaat tctgtggaat gtgtgtcagt tagggtgtgg aaagtcccca ggctccccag
     4621 caggcagaag tatgcaaagc atgcatctca attagtcagc aaccaggtgt ggaaagtccc
     4681 caggctcccc agcaggcaga agtatgcaaa gcatgcatct caattagtca gcaaccatag
     4741 tcccgcccct aactccgccc atcccgcccc taactccgcc cagttccgcc cattctccgc
     4801 cccatggctg actaattttt tttatttatg cagaggccga ggccgcctct gcctctgagc
     4861 tattccagaa gtagtgagga ggcttttttg gaggcctagg cttttgcaaa aagctcccgg
     4921 gagcttgtat atccattttc ggatctgatc aagagacagg atgaggatcg tttcgcatga
     4981 ttgaacaaga tggattgcac gcaggttctc cggccgcttg ggtggagagg ctattcggct
     5041 atgactgggc acaacagaca atcggctgct ctgatgccgc cgtgttccgg ctgtcagcgc
     5101 aggggcgccc ggttcttttt gtcaagaccg acctgtccgg tgccctgaat gaactgcagg
     5161 acgaggcagc gcggctatcg tggctggcca cgacgggcgt tccttgcgca gctgtgctcg
     5221 acgttgtcac tgaagcggga agggactggc tgctattggg cgaagtgccg gggcaggatc
     5281 tcctgtcatc tcaccttgct cctgccgaga aagtatccat catggctgat gcaatgcggc
     5341 ggctgcatac gcttgatccg gctacctgcc cattcgacca ccaagcgaaa catcgcatcg
     5401 agcgagcacg tactcggatg gaagccggtc ttgtcgatca ggatgatctg gacgaagagc
     5461 atcaggggct cgcgccagcc gaactgttcg ccaggctcaa ggcgcgcatg cccgacggcg
     5521 aggatctcgt cgtgacccat ggcgatgcct gcttgccgaa tatcatggtg gaaaatggcc
     5581 gcttttctgg attcatcgac tgtggccggc tgggtgtggc ggaccgctat caggacatag
     5641 cgttggctac ccgtgatatt gctgaagagc ttggcggcga atgggctgac cgcttcctcg
     5701 tgctttacgg tatcgccgct cccgattcgc agcgcatcgc cttctatcgc cttcttgacg
     5761 agttcttctg agcgggactc tggggttcga aatgaccgac caagcgacgc ccaacctgcc
     5821 atcacgagat ttcgattcca ccgccgcctt ctatgaaagg ttgggcttcg gaatcgtttt
     5881 ccgggacgcc ggctggatga tcctccagcg cggggatctc atgctggagt tcttcgccca
     5941 ccccaacttg tttattgcag cttataatgg ttacaaataa agcaatagca tcacaaattt
     6001 cacaaataaa gcattttttt cactgcattc tagttgtggt ttgtccaaac tcatcaatgt
     6061 atcttatcat gtctgtatac cgtcgacctc tagctagagc ttggcgtaat catggtcata
     6121 gctgtttcct gtgtgaaatt gttatccgct cacaattcca cacaacatac gagccggaag
     6181 cataaagtgt aaagcctggg gtgcctaatg agtgagctaa ctcacattaa ttgcgttgcg
     6241 ctcactgccc gctttccagt cgggaaacct gtcgtgccag ctgcattaat gaatcggcca
     6301 acgcgcgggg agaggcggtt tgcgtattgg gcgctcttcc gcttcctcgc tcactgactc
     6361 gctgcgctcg gtcgttcggc tgcggcgagc ggtatcagct cactcaaagg cggtaatacg
     6421 gttatccaca gaatcagggg ataacgcagg aaagaacatg tgagcaaaag gccagcaaaa
     6481 ggccaggaac cgtaaaaagg ccgcgttgct ggcgtttttc cataggctcc gcccccctga
     6541 cgagcatcac aaaaatcgac gctcaagtca gaggtggcga aacccgacag gactataaag
     6601 ataccaggcg tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgtcgct
     6661 taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg
     6721 ctgtaggtat ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc
     6781 ccccgttcag cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt
     6841 aagacacgac ttatcgccac tggcagcagc cactggtaac aggattagca gagcgaggta
     6901 tgtaggcggt gctacagagt tcttgaagtg gtggcctaac tacggctaca ctagaagaac
     6961 agtatttggt atctgcgctc tgctgaagcc agttaccttc ggaaaaagag ttggtagctc
     7021 ttgatccggc aaacaaacca ccgctggtag cggtggtttt tttgtttgca agcagcagat
     7081 tacgcgcaga aaaaaaggat ctcaagaaga tcctttgatc ttttctacgg ggtctgacgc
     7141 tcagtggaac gaaaactcac gttaagggat tttggtcatg agattatcaa aaaggatctt
     7201 cacctagatc cttttaaatt aaaaatgaag ttttaaatca atctaaagta tatatgagta
     7261 aacttggtct gacagttacc aatgcttaat cagtgaggca cctatctcag cgatctgtct
     7321 atttcgttca tccatagttg cctgactccc cgtcgtgtag ataactacga tacgggaggg
     7381 cttaccatct ggccccagtg ctgcaatgat accgcgagac ccacgctcac cggctccaga
     7441 tttatcagca ataaaccagc cagccggaag ggccgagcgc agaagtggtc ctgcaacttt
     7501 atccgcctcc atccagtcta ttaattgttg ccgggaagct agagtaagta gttcgccagt
     7561 taatagtttg cgcaacgttg ttgccattgc tacaggcatc gtggtgtcac gctcgtcgtt
     7621 tggtatggct tcattcagct ccggttccca acgatcaagg cgagttacat gatcccccat
     7681 gttgtgcaaa aaagcggtta gctccttcgg tcctccgatc gttgtcagaa gtaagttggc
     7741 cgcagtgtta tcactcatgg ttatggcagc actgcataat tctcttactg tcatgccatc
     7801 cgtaagatgc ttttctgtga ctggtgagta ctcaaccaag tcattctgag aatagtgtat
     7861 gcggcgaccg agttgctctt gcccggcgtc aatacgggat aataccgcgc cacatagcag
     7921 aactttaaaa gtgctcatca ttggaaaacg ttcttcgggg cgaaaactct caaggatctt
     7981 accgctgttg agatccagtt cgatgtaacc cactcgtgca cccaactgat cttcagc
//
