LOCUS       sequence-209435-        7614 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses beta-globin reporter with premature termination codon 
            (PTC39); enables detection of 5'-3' decay intermediates (xrFrag) and
            allows detection via northern blot (4H binding sites).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7614)
  AUTHORS   Boehm V, Gerbracht JV, Marx MC, Gehring NH
  TITLE     Interrogating the degradation pathways of unstable mRNAs with 
            XRN1-resistant sequences.
  JOURNAL   Nat Commun. 2016 Dec 5;7:13691. doi: 10.1038/ncomms13691.
  PUBMED    27917860
REFERENCE   2  (bases 1 to 7614)
  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: "Nat 
            Commun."; date: "2016-12-5"; volume: "7:13691. doi"; pages: " 
            10.1038/ncomms13691"
COMMENT     Sequence Label: pCI-globin_del5UTR_PTC39-xrRNA-4H
FEATURES             Location/Qualifiers
     source          1..7614
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        138..517
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        518..729
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     680..700
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     726..750
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     intron          890..1022
                     /label=chimeric intron
                     /note="chimera between introns from human beta-globin and 
                     immunoglobulin heavy chain genes"
     primer_bind     1005..1024
                     /label=pMT2-F
                     /note="Synthetic intron, forward primer"
     promoter        1067..1085
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     polyA_signal    3318..3439
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3329..3348)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3383..3402
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     rep_origin      3625..4080
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3712..3731)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3922..3943
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        4197..4554
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     enhancer        4197..4388
                     /label=SV40 enhancer
                     /note="enhancer for the SV40 early promoter (Herr, 1993)"
     primer_bind     complement(4220..4240)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     rep_origin      4405..4540
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     CDS             4605..5399
                     /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(4659..4678)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     5269..5288
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    5463..5511
                     /note="synthetic polyadenylation signal"
     primer_bind     complement(5552..5571)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     5671..5693
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(5731..5749)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        5817..5921
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5922..5990,5991..6782)
                     /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(6140..6159)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      6953..7541
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     7442..7461
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 tcaatattgg ccattagcca tattattcat tggttatata gcataaatca atattggcta
       61 ttggccattg catacgttgt atctatatca taatatgtac atttatattg gctcatgtcc
      121 aatatgaccg ccatgttggc attgattatt gactagttat taatagtaat caattacggg
      181 gtcattagtt catagcccat atatggagtt ccgcgttaca taacttacgg taaatggccc
      241 gcctggctga ccgcccaacg acccccgccc attgacgtca ataatgacgt atgttcccat
      301 agtaacgcca atagggactt tccattgacg tcaatgggtg gagtatttac ggtaaactgc
      361 ccacttggca gtacatcaag tgtatcatat gccaagtccg ccccctattg acgtcaatga
      421 cggtaaatgg cccgcctggc attatgccca gtacatgacc ttacgggact ttcctacttg
      481 gcagtacatc tacgtattag tcatcgctat taccatggtg atgcggtttt ggcagtacac
      541 caatgggcgt ggatagcggt ttgactcacg gggatttcca agtctccacc ccattgacgt
      601 caatgggagt ttgttttggc accaaaatca acgggacttt ccaaaatgtc gtaacaactg
      661 cgatcgcccg ccccgttgac gcaaatgggc ggtaggcgtg tacggtggga ggtctatata
      721 agcagagctc gtttagtgaa ccgtcagatc actagaagct ttattgcggt agtttatcac
      781 agttaaattg ctaacgcagt cagtgcttct gacacaacag tctcgaactt aagctgcagt
      841 gactctctta aggtagcctt gcagaagttg gtcgtgaggc actgggcagg taagtatcaa
      901 ggttacaaga caggtttaag gagaccaata gaaactgggc ttgtcgagac agagaagact
      961 cttgcgtttc tgataggcac ctattggtct tactgacatc cactttgcct ttctctccac
     1021 aggtgtccac tcccagttca attacagctc ttaaggctag agtacttaat acgactcact
     1081 ataggctagc accatggtgc acctgactcc tgaggagaag tctgccgtta ctgccctgtg
     1141 gggcaaggtg aacgtggatg aagttggtgg tgaggccctg ggcaggttgg tatcaaggtt
     1201 acaagacagg tttaaggaga ccaatagaaa ctgggcatgt ggagacagag aagactcttg
     1261 ggtttctgat aggcactgac tctctctgcc tattggtcta ttttcccacc cttaggctgc
     1321 tggtggtcta cccttggacc tagaggttct ttgagtcctt tggggatctg tccactcctg
     1381 atgctgttat gggcaaccct aaggtgaagg ctcatggcaa gaaagtgctc ggtgccttta
     1441 gtgatggcct ggctcacctg gacaacctca agggcacctt tgccacactg agtgagctgc
     1501 actgtgacaa gctgcacgtg gatcctgaga acttcagggt gagtctatgg gacccttgat
     1561 gttttctttc cccttctttt ctatggttaa gttcatgtca taggaagggg ataagtaaca
     1621 gggtacagtt tagaatggga aacagacgaa tgattgcatc agtgtggaag tctcaggatc
     1681 gttttagttt cttttatttg ctgttcataa caattgtttt cttttgttta attcttgctt
     1741 tctttttttt tcttctccgc aatttttact attatactta atgccttaac attgtgtata
     1801 acaaaaggaa atatctctga gatacattaa gtaacttaaa aaaaaacttt acacagtctg
     1861 cctagtacat tactatttgg aatatatgtg tgcttatttg catattcata atctccctac
     1921 tttattttct tttattttta attgatacat aatcattata catatttatg ggttaaagtg
     1981 taatgtttta atatgtgtac acatattgac caaatcaggg taattttgca tttgtaattt
     2041 taaaaaatgc tttcttcttt taatatactt ttttgtttat cttatttcta atactttccc
     2101 taatctcttt ctttcagggc aataatgata caatgtatca tgcctctttg caccattcta
     2161 aagaataaca gtgataattt ctgggttaag gcaatagcaa tatttctgca tataaatatt
     2221 tctgcatata aattgtaact gatgtaagag gtttcatatt gctaatagca gctacaatcc
     2281 agctaccatt ctgcttttat tttatggttg ggataaggct ggattattct gagtccaagc
     2341 taggcccttt tgctaatcat gttcatacct cttatcttcc tcccacagct cctgggcaac
     2401 gtgctggtct gtgtgctggc ccatcacttt ggcaaagaat tcaccccacc agtgcaggct
     2461 gcctatcaga aagtggtggc tggtgtggct aatgccctgg cccacaagta tcactaagct
     2521 cgctttcttg ctgtccaatt tctctcgagg tgagcaaggg cgaggagctg ttcaccgggg
     2581 tggtgcccat cctggtggac ttgatagtca ggccagccgg ttaggctgcc accgaaggtt
     2641 ggtagacggt gctgcctgcg accaacccca ggaggactgg gttaccaaag ctgattctcc
     2701 acggttggaa agcctcccag aaccgtctcg gaagaggagt ccctgccaac aatggagatg
     2761 aagcccgtgt cagatcgcga aagcgccact tcgccgagga gtgcaatctg tgaggcccca
     2821 ggaggactgg gtaaacagtc gagcacccca ccagtgcagg ctgcctatca gaaagtggtg
     2881 gctggtgtgg ctaatgccct ggcccacaag tatcactaag ctcgctttct tgctgtccaa
     2941 tttgtcgagc accccaccag tgcaggctgc ctatcagaaa gtggtggctg gtgtggctaa
     3001 tgccctggcc cacaagtatc actaagctcg ctttcttgct gtccaatttg tcgagcaccc
     3061 caccagtgca ggctgcctat cagaaagtgg tggctggtgt ggctaatgcc ctggcccaca
     3121 agtatcacta agctcgcttt cttgctgtcc aatttgtcga gcaccccacc agtgcaggct
     3181 gcctatcaga aagtggtggc tggtgtggct aatgccctgg cccacaagta tcactaagct
     3241 cgctttcttg ctgtccaatt tgtcgacccg ggcggccgct tccctttagt gagggttaat
     3301 gcttcgagca gacatgataa gatacattga tgagtttgga caaaccacaa ctagaatgca
     3361 gtgaaaaaaa tgctttattt gtgaaatttg tgatgctatt gctttatttg taaccattat
     3421 aagctgcaat aaacaagtta acaacaacaa ttgcattcat tttatgtttc aggttcaggg
     3481 ggagatgtgg gaggtttttt aaagcaagta aaacctctac aaatgtggta aaatccgata
     3541 aggatcgatc cgggctggcg taatagcgaa gaggcccgca ccgatcgccc ttcccaacag
     3601 ttgcgcagcc tgaatggcga atggacgcgc cctgtagcgg cgcattaagc gcggcgggtg
     3661 tggtggttac gcgcagcgtg accgctacac ttgccagcgc cctagcgccc gctcctttcg
     3721 ctttcttccc ttcctttctc gccacgttcg ccggctttcc ccgtcaagct ctaaatcggg
     3781 ggctcccttt agggttccga tttagtgctt tacggcacct cgaccccaaa aaacttgatt
     3841 agggtgatgg ttcacgtagt gggccatcgc cctgatagac ggtttttcgc cctttgacgt
     3901 tggagtccac gttctttaat agtggactct tgttccaaac tggaacaaca ctcaacccta
     3961 tctcggtcta ttcttttgat ttataaggga ttttgccgat ttcggcctat tggttaaaaa
     4021 atgagctgat ttaacaaaaa tttaacgcga attttaacaa aatattaacg cttacaattt
     4081 cctgatgcgg tattttctcc ttacgcatct gtgcggtatt tcacaccgca tacgcggatc
     4141 tgcgcagcac catggcctga aataacctct gaaagaggaa cttggttagg taccttctga
     4201 ggcggaaaga accagctgtg gaatgtgtgt cagttagggt gtggaaagtc cccaggctcc
     4261 ccagcaggca gaagtatgca aagcatgcat ctcaattagt cagcaaccag gtgtggaaag
     4321 tccccaggct ccccagcagg cagaagtatg caaagcatgc atctcaatta gtcagcaacc
     4381 atagtcccgc ccctaactcc gcccatcccg cccctaactc cgcccagttc cgcccattct
     4441 ccgccccatg gctgactaat tttttttatt tatgcagagg ccgaggccgc ctcggcctct
     4501 gagctattcc agaagtagtg aggaggcttt tttggaggcc taggcttttg caaaaagctt
     4561 gattcttctg acacaacagt ctcgaactta aggctagagc caccatgatt gaacaagatg
     4621 gattgcacgc aggttctccg gccgcttggg tggagaggct attcggctat gactgggcac
     4681 aacagacaat cggctgctct gatgccgccg tgttccggct gtcagcgcag gggcgcccgg
     4741 ttctttttgt caagaccgac ctgtccggtg ccctgaatga actgcaggac gaggcagcgc
     4801 ggctatcgtg gctggccacg acgggcgttc cttgcgcagc tgtgctcgac gttgtcactg
     4861 aagcgggaag ggactggctg ctattgggcg aagtgccggg gcaggatctc ctgtcatctc
     4921 accttgctcc tgccgagaaa gtatccatca tggctgatgc aatgcggcgg ctgcatacgc
     4981 ttgatccggc tacctgccca ttcgaccacc aagcgaaaca tcgcatcgag cgagcacgta
     5041 ctcggatgga agccggtctt gtcgatcagg atgatctgga cgaagagcat caggggctcg
     5101 cgccagccga actgttcgcc aggctcaagg cgcgcatgcc cgacggcgag gatctcgtcg
     5161 tgacccatgg cgatgcctgc ttgccgaata tcatggtgga aaatggccgc ttttctggat
     5221 tcatcgactg tggccggctg ggtgtggcgg accgctatca ggacatagcg ttggctaccc
     5281 gtgatattgc tgaagagctt ggcggcgaat gggctgaccg cttcctcgtg ctttacggta
     5341 tcgccgctcc cgattcgcag cgcatcgcct tctatcgcct tcttgacgag ttcttctgag
     5401 cgggactctg gggttcgaaa tgaccgacca agcgacgccc aacctgccat cacgatggcc
     5461 gcaataaaat atctttattt tcattacatc tgtgtgttgg ttttttgtgt gaatcgatag
     5521 cgataaggat ccgcgtatgg tgcactctca gtacaatctg ctctgatgcc gcatagttaa
     5581 gccagccccg acacccgcca acacccgctg acgcgccctg acgggcttgt ctgctcccgg
     5641 catccgctta cagacaagct gtgaccgtct ccgggagctg catgtgtcag aggttttcac
     5701 cgtcatcacc gaaacgcgcg agacgaaagg gcctcgtgat acgcctattt ttataggtta
     5761 atgtcatgat aataatggtt tcttagacgt caggtggcac ttttcgggga aatgtgcgcg
     5821 gaacccctat ttgtttattt ttctaaatac attcaaatat gtatccgctc atgagacaat
     5881 aaccctgata aatgcttcaa taatattgaa aaaggaagag tatgagtatt caacatttcc
     5941 gtgtcgccct tattcccttt tttgcggcat tttgccttcc tgtttttgct cacccagaaa
     6001 cgctggtgaa agtaaaagat gctgaagatc agttgggtgc acgagtgggt tacatcgaac
     6061 tggatctcaa cagcggtaag atccttgaga gttttcgccc cgaagaacgt tttccaatga
     6121 tgagcacttt taaagttctg ctatgtggcg cggtattatc ccgtattgac gccgggcaag
     6181 agcaactcgg tcgccgcata cactattctc agaatgactt ggttgagtac tcaccagtca
     6241 cagaaaagca tcttacggat ggcatgacag taagagaatt atgcagtgct gccataacca
     6301 tgagtgataa cactgcggcc aacttacttc tgacaacgat cggaggaccg aaggagctaa
     6361 ccgctttttt gcacaacatg ggggatcatg taactcgcct tgatcgttgg gaaccggagc
     6421 tgaatgaagc cataccaaac gacgagcgtg acaccacgat gcctgtagca atggcaacaa
     6481 cgttgcgcaa actattaact ggcgaactac ttactctagc ttcccggcaa caattaatag
     6541 actggatgga ggcggataaa gttgcaggac cacttctgcg ctcggccctt ccggctggct
     6601 ggtttattgc tgataaatct ggagccggtg agcgtgggtc tcgcggtatc attgcagcac
     6661 tggggccaga tggtaagccc tcccgtatcg tagttatcta cacgacgggg agtcaggcaa
     6721 ctatggatga acgaaataga cagatcgctg agataggtgc ctcactgatt aagcattggt
     6781 aactgtcaga ccaagtttac tcatatatac tttagattga tttaaaactt catttttaat
     6841 ttaaaaggat ctaggtgaag atcctttttg ataatctcat gaccaaaatc ccttaacgtg
     6901 agttttcgtt ccactgagcg tcagaccccg tagaaaagat caaaggatct tcttgagatc
     6961 ctttttttct gcgcgtaatc tgctgcttgc aaacaaaaaa accaccgcta ccagcggtgg
     7021 tttgtttgcc ggatcaagag ctaccaactc tttttccgaa ggtaactggc ttcagcagag
     7081 cgcagatacc aaatactgtt cttctagtgt agccgtagtt aggccaccac ttcaagaact
     7141 ctgtagcacc gcctacatac ctcgctctgc taatcctgtt accagtggct gctgccagtg
     7201 gcgataagtc gtgtcttacc gggttggact caagacgata gttaccggat aaggcgcagc
     7261 ggtcgggctg aacggggggt tcgtgcacac agcccagctt ggagcgaacg acctacaccg
     7321 aactgagata cctacagcgt gagctatgag aaagcgccac gcttcccgaa gggagaaagg
     7381 cggacaggta tccggtaagc ggcagggtcg gaacaggaga gcgcacgagg gagcttccag
     7441 ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg ccacctctga cttgagcgtc
     7501 gatttttgtg atgctcgtca ggggggcgga gcctatggaa aaacgccagc aacgcggcct
     7561 ttttacggtt cctggccttt tgctggcctt ttgctcacat ggctcgacag atct
//
