LOCUS       sequence-423728-        6449 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Fluorescent reporter system, NMD negative control. No intron in 
            5'UTR.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6449)
  AUTHORS   Kolakada D, Campbell AE, Galvis LB, Li Z, Lore M, Jagannathan S
  TITLE     A system of reporters for comparative investigation of 
            EJC-independent and EJC-enhanced nonsense-mediated mRNA decay.
  JOURNAL   Nucleic Acids Res. 2024 Feb 20:gkae121. doi: 10.1093/nar/gkae121.
  PUBMED    38375914
REFERENCE   2  (bases 1 to 6449)
  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. 2024 Feb 20:gkae121. doi: 10.1093/nar/gkae121."
COMMENT     Sequence Label: ARTX_ctrl
FEATURES             Location/Qualifiers
     source          1..6449
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      1..589
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     490..509
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     743..760
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    877..898
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(913..918,919..936,937..943)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    951..967
                     /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     956..978
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     975..991
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     975..991
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     1010..1030
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        1012..1030
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     polyA_signal    1049..1170
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     protein_bind    complement(1183..1216)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     primer_bind     1430..1449
                     /label=rbglobpA-R
                     /note="Rabbit beta-globin polyA, reverse primer. Also 
                     called rb-glob-pA-term-R"
     polyA_signal    1448..1503
                     /label=beta-globin poly(A) signal
                     /note="rabbit beta-globin polyadenylation signal (Gil and 
                     Proudfoot, 1987)"
     primer_bind     1549..1568
                     /label=Bglob-pA-R
                     /note="Rabbit beta-globin polyA region, reverse primer"
     CDS             complement(join(1645..2358,2359..2361,2362..2364))
                     /codon_start=1
                     /product="enhanced GFP with monomerizing A206K mutation 
                     (Zacharias et al., 2002)"
                     /label=mEGFP
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLSHGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNIYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLL
                     EFRTAAGITHGMDELYK"
     primer_bind     2039..2058
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     2298..2319
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     regulatory      2361..2370
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     primer_bind     complement(2397..2421)
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     enhancer        2529..2832
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        2833..3036
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     2987..3007
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     regulatory      3070..3079
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             3079..3108
                     /codon_start=1
                     /product="Myc (human c-Myc proto-oncogene) epitope tag"
                     /label=Myc
                     /translation="EQKLISEEDL"
     CDS             3109..3807
                     /codon_start=1
                     /product="far-red-shifted derivative of red fluorescent 
                     protein from Entacmaea quadricolor, also known as Katushka 
                     (Shcherbo et al., 2007)"
                     /label=TurboFP635
                     /note="mammalian codon-optimized"
                     /translation="GEDSVLITENMHMKLYMEGTVNDHHFKCTSEGEGKPYEGTQTMKI
                     KVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVL
                     TATQDTSLQNGCLIYNVKINGVNFPSNGPVMQKKTLGWEASTEMLYPADSGLRGHSQMA
                     LKLVGGGYLHCSLKTTYRSKKPAKNLKMPGFYFVDRRLERIKEADKETYVEQHEMAVAR
                     YCDLPSKLGHS"
     polyA_signal    3874..3995
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     polyA_signal    4091..4202
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     primer_bind     4191..4208
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     CDS             complement(4344..4943)
                     /codon_start=1
                     /gene="pac from Streptomyces alboniger"
                     /product="puromycin N-acetyltransferase"
                     /label=PuroR
                     /note="confers resistance to puromycin"
                     /translation="MTEYKPTVRLATRDDVPRAVRTLAAAFADYPATRHTVDPDRHIER
                     VTELQELFLTRVGLDIGKVWVADDGAAVAVWTTPESVEAGAVFAEIGPRMAELSGSRLA
                     AQQQMEGLLAPHRPKEPAWFLATVGVSPDHQGKGLGSAVVLPGVEAAERAGVPAFLETS
                     APRNLPFYERLGFTVTADVEVPEGPRTWCMTRKPGA"
     primer_bind     complement(4427..4447)
                     /label=Puro-F
                     /note="Puromycin resistance gene, forward primer"
     primer_bind     4924..4943
                     /label=Puro-R
                     /note="Puromycin resistance gene, reverse primer. Also 
                     called puro-variant-R"
     protein_bind    complement(4948..4981)
                     /label=lox2272
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (AAGTATCC) (Shaw et al., 2021). lox2272 sites are 
                     compatible with each other, but incompatible with loxP or 
                     loxN sites (Lee and Saito, 1988)."
     polyA_signal    5193..5241
                     /label=HSV TK poly(A) signal
                     /note="herpes simplex virus thymidine kinase 
                     polyadenylation signal (Cole and Stacy, 1985)"
     promoter        5314..5418
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5419..5487,5488..6279)
                     /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     complement(5637..5656)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
ORIGIN
        1 ttgagatcct ttttttctgc gcgtaatctg ctgcttgcaa acaaaaaaac caccgctacc
       61 agcggtggtt tgtttgccgg atcaagagct accaactctt tttccgaagg taactggctt
      121 cagcagagcg cagataccaa atactgttct tctagtgtag ccgtagttag gccaccactt
      181 caagaactct gtagcaccgc ctacatacct cgctctgcta atcctgttac cagtggctgc
      241 tgccagtggc gataagtcgt gtcttaccgg gttggactca agacgatagt taccggataa
      301 ggcgcagcgg tcgggctgaa cggggggttc gtgcacacag cccagcttgg agcgaacgac
      361 ctacaccgaa ctgagatacc tacagcgtga gctatgagaa agcgccacgc ttcccgaagg
      421 gagaaaggcg gacaggtatc cggtaagcgg cagggtcgga acaggagagc gcacgaggga
      481 gcttccaggg ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc acctctgact
      541 tgagcgtcga tttttgtgat gctcgtcagg ggggcggagc ctatggaaaa acgccagcaa
      601 cgcggccttt ttacggttcc tggccttttg ctggcctttt gctcacatgt tctttcctgc
      661 gttatcccct gattctgtgg ataaccgtat taccgccttt gagtgagctg ataccgctcg
      721 ccgcagccga acgaccgagc gcagcgagtc agtgagcgag gaagcggaag agcgcccaat
      781 acgcaaaccg cctctccccg cgcgttggcc gattcattaa tgcagctggc acgacaggtt
      841 tcccgactgg aaagcgggca gtgagcgcaa cgcaattaat gtgagttagc tcactcatta
      901 ggcaccccag gctttacact ttatgcttcc ggctcgtatg ttgtgtggaa ttgtgagcgg
      961 ataacaattt cacacaggaa acagctatga ccatgattac gccaagcgcg caattaaccc
     1021 tcactaaagg gaacaaaagc tgggtaccta agatacattg atgagtttgg acaaaccaca
     1081 actagaatgc agtgaaaaaa atgctttatt tgtgaaattt gtgatgctat tgctttattt
     1141 gtaaccatta taagctgcaa taaacaagtt gacggtatcg taataacttc gtatagcata
     1201 cattatacga agttatatgg atccatatgc tagctcgacg ctcaggtcga gggatcttca
     1261 taagagaaga gggacagcta tgactgggag taaggaatgg acagcagggg gctgtttcat
     1321 atactgatga cctctttata gccacctttg ttcatggcag ccagcatatg gcatatgttg
     1381 ccaaactcta aaccaaatac tcattctgat gttttaaatg atttgccctc ccatatgtcc
     1441 ttccgagtga gagacacaaa aaattccaac acactattgc aatgaaaata aatttccttt
     1501 attagccaga agtcagatgc tcaaggggct tcatgatgtc cccataattt ttggcagagg
     1561 gaaaaagatc tcagtggtat ttgtgagcca gggcattggc cacaccagcc accaccttct
     1621 gataggcagc ctgcacctga gtgtttactt gtacagctcg tccatgccgt gagtgatccc
     1681 ggcggcggtg cggaactcca gcaggaccat gtgatcgcgc ttctcgttgg ggtctttgct
     1741 cagcttggac tgggtgctca ggtagtggtt gtcgggcagc agcacggggc cgtcgccgat
     1801 gggggtgttc tgctggtagt ggtcggcgag ctgcacgctg ccgtcctcga tgttgtggcg
     1861 gatcttgaag ttcaccttga tgccgttctt ctgcttgtcg gccatgatat agatgttgtg
     1921 gctgttgaag ttgtactcca gcttgtgccc caggatgttg ccgtcctcct tgaagtcgat
     1981 gcccttcagc tcgatgcggt tcaccagggt gtcgccctcg aacttcacct cggcgcgggt
     2041 cttgtagttg ccgtcgtcct tgaagaagat ggtgcgctcc tggacgtagc cttcgggcat
     2101 ggcggacttg aagaagtcgt gctgcttcat gtggtcgggg tagcggctga agcactgcac
     2161 gccgtggctc agggtggtca cgagggtggg ccagggcacg ggcagcttgc cggtggtgca
     2221 gatgaacttc agggtcagct tgccgtaggt ggcatcgccc tcgccctcgc cggacacgct
     2281 gaacttgtgg ccgtttacgt cgccgtccag ctcgaccagg atgggcacca ccccggtgaa
     2341 cagctcctcg cccttgctca ccatggtggc gaccacgatc ctcatcctgt ctctgcgatc
     2401 tgacggttca ctaaacgagc tctgcttata taggcctccc accgtacacg ccacctcgac
     2461 atactcagta gttattaata gtaatcaatt acggggtcat tagttcatag cgaggctgca
     2521 gtctaccgcg ttacataact tacggtaaat ggcccgcctg gctgaccgcc caacgacccc
     2581 cgcccattga cgtcaataat gacgtatgtt cccatagtaa cgccaatagg gactttccat
     2641 tgacgtcaat gggtggagta tttacggtaa actgcccact tggcagtaca tcaagtgtat
     2701 catatgccaa gtacgccccc tattgacgtc aatgacggta aatggcccgc ctggcattat
     2761 gcccagtaca tgaccttatg ggactttcct acttggcagt acatctacgt attagtcatc
     2821 gctattacca tggtgatgcg gttttggcag tacatcaatg ggcgtggata gcggtttgac
     2881 tcacggggat ttccaagtct ccaccccatt gacgtcaatg ggagtttgtt ttggcaccaa
     2941 aatcaacggg actttccaaa atgtcgtaac aactccgccc cattgacgca aatgggcggt
     3001 aggcgtgtac ggtgggaggt ctatataagc agagctggtt tagtgaaccg tcagataccg
     3061 gtcgccaccg ccaccatgga acaaaagctg atttctgaag aagacttggg tgaggatagc
     3121 gtgctgatca ccgagaacat gcacatgaaa ctgtacatgg agggcaccgt gaacgaccac
     3181 cacttcaagt gcacatccga gggcgaaggc aagccctacg agggcaccca gaccatgaag
     3241 atcaaggtgg tcgagggcgg ccctctcccc ttcgccttcg acatcctggc taccagcttc
     3301 atgtacggca gcaaaacctt tatcaaccac acccagggca tccccgactt ctttaagcag
     3361 tccttccctg agggcttcac atgggagagg atcaccacat acgaagacgg gggcgtgctg
     3421 accgctaccc aggacaccag cctccagaac ggctgcctca tctacaacgt caagatcaac
     3481 ggggtgaact tcccatccaa cggccctgtg atgcagaaga aaacactcgg ctgggaggcc
     3541 agcaccgaga tgctgtaccc cgctgacagc ggcctgagag gccatagcca gatggccctg
     3601 aagctcgtgg gcgggggcta cctgcactgc tccctcaaga ccacatacag atccaagaaa
     3661 cccgctaaga acctcaagat gcccggcttc tacttcgtgg acaggagact ggaaagaatc
     3721 aaggaggccg acaaagagac ctacgtcgag cagcacgaga tggctgtggc tcgctactgc
     3781 gacctgccta gcaaactggg gcacagcctc gagggtggtt ctggtggttc tgcctaaggt
     3841 ggttctggtg gttctgaatt aattgttgtt gttaacttgt ttattgcagc ttataatggt
     3901 tacaaataaa gcaatagcat cacaaatttc acaaataaag catttttttc actgcattct
     3961 agttgtggtt tgtccaaact catcaatgta tcttaacgcg aaactagtgc tattgtcttc
     4021 ccaatcctcc cccttgctgt cctgccccac cccacccccc agaatagaat gacacctact
     4081 cagacaatgc gatgcaattt cctcatttta ttaggaaagg acagtgggag tggcaccttc
     4141 cagggtcaag gaaggcacgg gggaggggca aacaacagat ggctggcaac tagaaggcac
     4201 agtcgaggct gatcagcgag ctctagagtc ggtgggcctc gggggcgggt gcggggtcgg
     4261 cggggccgcc ccgggtggct tcggtcggag ccatggggtc gtgcgctcct ttcggtcggg
     4321 cgctgcgggt cgtggggcgg gcgtcaggca ccgggcttgc gggtcatgca ccaggtgcgc
     4381 ggtccttcgg gcacctcgac gtcggcggtg acggtgaagc cgagccgctc gtagaagggg
     4441 aggttgcggg gcgcggaggt ctccaggaag gcgggcaccc cggcgcgctc ggccgcctcc
     4501 actccgggga gcacgacggc gctgcccaga cccttgccct ggtggtcggg cgacacgccg
     4561 acggtggcca ggaaccacgc gggctccttg ggccggtgcg gcgccaggag gccttccatc
     4621 tgttgctgcg cggccagccg ggaaccgctc aactcggcca tgcgcgggcc gatctcggcg
     4681 aacaccgccc ccgcttcgac gctctccggc gtggtccaga ccgccaccgc ggcgccgtcg
     4741 tccgcgaccc acaccttgcc gatgtcgagc ccgacgcgcg tgaggaagag ttcttgcagc
     4801 tcggtgaccc gctcgatgtg gcggtccggg tcgacggtgt ggcgcgtggc ggggtagtcg
     4861 gcgaacgcgg cggcgagggt gcgtacggcc cgggggacgt cgtcgcgggt ggcgaggcgc
     4921 accgtgggct tgtactcggt catggtgata acttcgtata ggatacttta tacgaagtta
     4981 tttattctcg aatgggggac cccgtcccta acccacgggg ccagtggcta tggcagggcc
     5041 tgccgccccg acgttggctg cgagccctgg gccttcaccc gaacttgggg ggtggggtgg
     5101 ggaaaaggaa gaaacgcggg cgtattggcc ccaatggggt ctcggtgggg tatcgacaga
     5161 gtgccagccc tgggaccgaa ccccgcgttt atgaacaaac gacccaacac ccgtgcgttt
     5221 tattctgtct ttttattgcc gtcatagcgc gggttccttc cggtattgtc tccttccgtg
     5281 tttattaagc ttggcacttt tcggggaaat gtgcgcggaa cccctatttg tttatttttc
     5341 taaatacatt caaatatgta tccgctcatg agacaataac cctgataaat gcttcaataa
     5401 tattgaaaaa ggaagagtat gagtattcaa catttccgtg tcgcccttat tccctttttt
     5461 gcggcatttt gccttcctgt ttttgctcac ccagaaacgc tggtgaaagt aaaagatgct
     5521 gaagatcagt tgggtgcacg agtgggttac atcgaactgg atctcaacag cggtaagatc
     5581 cttgagagtt ttcgccccga agaacgtttt ccaatgatga gcacttttaa agttctgcta
     5641 tgtggcgcgg tattatcccg tattgacgcc gggcaagagc aactcggtcg ccgcatacac
     5701 tattctcaga atgacttggt tgagtactca ccagtcacag aaaagcatct tacggatggc
     5761 atgacagtaa gagaattatg cagtgctgcc ataaccatga gtgataacac tgcggccaac
     5821 ttacttctga caacgatcgg aggaccgaag gagctaaccg cttttttgca caacatgggg
     5881 gatcatgtaa ctcgccttga tcgttgggaa ccggagctga atgaagccat accaaacgac
     5941 gagcgtgaca ccacgatgcc tgtagcaatg gcaacaacgt tgcgcaaact attaactggc
     6001 gaactactta ctctagcttc ccggcaacaa ttaatagact ggatggaggc ggataaagtt
     6061 gcaggaccac ttctgcgctc ggcccttccg gctggctggt ttattgctga taaatctgga
     6121 gccggtgagc gtgggtctcg cggtatcatt gcagcactgg ggccagatgg taagccctcc
     6181 cgtatcgtag ttatctacac gacggggagt caggcaacta tggatgaacg aaatagacag
     6241 atcgctgaga taggtgcctc actgattaag cattggtaac tgtcagacca agtttactca
     6301 tatatacttt agattgattt aaaacttcat ttttaattta aaaggatcta ggtgaagatc
     6361 ctttttgata atctcatgac caaaatccct taacgtgagt tttcgttcca ctgagcgtca
     6421 gaccccgtag aaaagatcaa aggatcttc
//
