LOCUS       sequence-208350-        9113 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses wild type TPI reporter; contains partial IL6 3' UTR; 
            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 9113)
  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 9113)
  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-TPI_WT-IL6_3UTR-xrRNA-4H
FEATURES             Location/Qualifiers
     source          1..9113
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     enhancer        77..380
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        381..592
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     543..563
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     589..613
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     intron          753..885
                     /label=chimeric intron
                     /note="chimera between introns from human beta-globin and 
                     immunoglobulin heavy chain genes"
     primer_bind     868..887
                     /label=pMT2-F
                     /note="Synthetic intron, forward primer"
     promoter        930..948
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     polyA_signal    4680..4801
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4691..4710)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     4745..4764
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     rep_origin      4987..5442
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5074..5093)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5284..5305
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        5559..5916
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     enhancer        5559..5750
                     /label=SV40 enhancer
                     /note="enhancer for the SV40 early promoter (Herr, 1993)"
     primer_bind     complement(5582..5602)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     rep_origin      5767..5902
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     CDS             5967..6761
                     /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(6021..6040)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     6631..6650
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    6825..6873
                     /note="synthetic polyadenylation signal"
     primer_bind     complement(6914..6933)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     7033..7055
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(7093..7111)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        7179..7283
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(7284..7352,7353..8144)
                     /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(7502..7521)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      8315..8903
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     8804..8823
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
ORIGIN
        1 ggcattgatt attgactagt tattaatagt aatcaattac ggggtcatta gttcatagcc
       61 catatatgga gttccgcgtt acataactta cggtaaatgg cccgcctggc tgaccgccca
      121 acgacccccg cccattgacg tcaataatga cgtatgttcc catagtaacg ccaataggga
      181 ctttccattg acgtcaatgg gtggagtatt tacggtaaac tgcccacttg gcagtacatc
      241 aagtgtatca tatgccaagt ccgcccccta ttgacgtcaa tgacggtaaa tggcccgcct
      301 ggcattatgc ccagtacatg accttacggg actttcctac ttggcagtac atctacgtat
      361 tagtcatcgc tattaccatg gtgatgcggt tttggcagta caccaatggg cgtggatagc
      421 ggtttgactc acggggattt ccaagtctcc accccattga cgtcaatggg agtttgtttt
      481 ggcaccaaaa tcaacgggac tttccaaaat gtcgtaacaa ctgcgatcgc ccgccccgtt
      541 gacgcaaatg ggcggtaggc gtgtacggtg ggaggtctat ataagcagag ctcgtttagt
      601 gaaccgtcag atcactagaa gctttattgc ggtagtttat cacagttaaa ttgctaacgc
      661 agtcagtgct tctgacacaa cagtctcgaa cttaagctgc agtgactctc ttaaggtagc
      721 cttgcagaag ttggtcgtga ggcactgggc aggtaagtat caaggttaca agacaggttt
      781 aaggagacca atagaaactg ggcttgtcga gacagagaag actcttgcgt ttctgatagg
      841 cacctattgg tcttactgac atccactttg cctttctctc cacaggtgtc cactcccagt
      901 tcaattacag ctcttaaggc tagagtactt aatacgactc actataggct agcgcctcgg
      961 ctccagcacc atggcgccct ccaggaagtt cttcgttggg ggaaactgga agatgaacgg
     1021 gcggaagcag agtctggggg agctcatcgg cactctgaac gcggccaagg tgccggccga
     1081 caccggtaag ccctcgccga ggaggggtct ggccgggccg gggccggggc cggggcagga
     1141 gtggcagcgc cctctcccga ggccccgagg ccccgaggcc ggtatccgcg cggacctgat
     1201 gcagggctgt gggacgaggg ccgctggggt ccgggcaggg gcctcgcagc cgcagccccg
     1261 tcggtgcgtc gagggggcag ggcggagcac atgatgcccc ttggactatg gggcaggtaa
     1321 ggacgttttc ttcccttcgg caacctgaac gactcccgcc ttccacggaa gggaccgagc
     1381 ccgtgccaaa caggctgagc gatttgggag tgaggagcca tcctaccgct ttccccaacc
     1441 tggaaacagc aaagcgcaag gcctctgagt cagttaggtc tctgccaccc acgggcaaag
     1501 gatgctctcc tccatcctcc ttcctccctc caccgaaatc ggagagccgc gggcctgatc
     1561 caaagaggca tccccttctc gttcattccc cagaggcctc aatacaaacc ccaggagttg
     1621 gcccctctcc ttttgctaca aatccttgcc ttgcaaaggg gaggtgagga tgggctattt
     1681 tagaagggaa gcagggttgc tccctggaga atgctgagtc tgtgaggtgc ctatgccgag
     1741 aataggtcga ggaaattgga gccccagctg ttaaaagagc agagggcagg gtgagggccg
     1801 tggcctctca ggggtatctg gaaggctctt cgagttgagt gcagacccag cctgggctgg
     1861 aaaatggaca aaggtcatct tgctggggtg aaaaggggga gagcagaacc aagaagaaga
     1921 gggtgagggc tggggggctc cagggcactg gttaggaatt gtggggaatg aaggctttct
     1981 ttagtctcat ccccctgtgg taccatcttg tcctcagagg tggtttgtgc tccccctact
     2041 gcctatatcg acttcgcccg gcagaagcta gatcccaaga ttgctgtggc tgcgcagaac
     2101 tgctacaaag tgactaatgg ggcttttact ggggagatca ggtgagatcg aggtggagag
     2161 gggtgtgtgg gacccttccc tcactttcct cgttgagggg aaagccacag ggtgggctcc
     2221 ctgctgaacc ttggcttcat ctcttccttt agccctggca tgatcaaaga ctgcggagcc
     2281 acgtgggtgg tcctggggca ctcagagaga aggcatgtct ttggggagtc agatgaggtt
     2341 agtagccaag agagaagata agggatgtct ttttccaaga aggatgtctc accaagtctg
     2401 tttctcaaca gctgattggg cagaaagtgg cccatgctct ggcagaggga ctcggagtaa
     2461 tcgcctgcat tggggagaag ctagatgaaa gggaagctgg catcactgag aaggttgttt
     2521 tcgagcagac aaaggtcatc gcaggtatct ctggagaaag ggacctttga gcctatccag
     2581 ggccacagag actcagaggg tagggtcagg ccctggagcc tgtcttggtc cccatgctga
     2641 tccagaaaag gaaaaagggg agggggagtg acaatctttg cttggggcct atgacttctc
     2701 cagccccaag gtagatgcca cctggaaatc ccccaatgtc cactaggggg cagtaggcca
     2761 ccgttcttcg tactccggag aacctggctg gagagctctt tcttgttcac ccttccctcc
     2821 atctgtatct ctgccctgca gataacgtga aggactggag caaggtcgtc ctggcctatg
     2881 agcctgtgtg ggccattggt actggcaaga ctgcaacacc ccaacaggta accgggccca
     2941 ggagccctgc cctcatccca gcctgcctca ataggtttgg acagacacag cccacatggg
     3001 gcaacccctt atttcaaaga cacagagacc ttgaacccag agacagtgac ttgtccaagg
     3061 gcatccagtc cagggcctgg cttggatcag agccctggta ctctgactca gtcagaaacc
     3121 acactaagtg tccactggtg ccagtgattt ttcctcttag agaggcagaa aaggtcttac
     3181 ttaggccagc ttcttgttct aggcccagga agtacacgag aagctccgag gatggctgaa
     3241 gtccaacgtc tctgatgcgg tggctcagag cacccgtatc atttatggag gtgagtggct
     3301 ttggttcccg gctgaggtgg agtgggctga ggactagact gagccctcgg acatggaggt
     3361 ggggatgggg cagactcatc ccattcttga ccaagccctt gttctgctcc cttcccaggc
     3421 tctgtgactg gggcaacctg caaggagctg gccagccagc ctgatgtgga tggcttcctt
     3481 gtgggtggtg cttccctcaa gcccgaattc gtggacatca tcaatgccaa acaatgagcc
     3541 ccatccatct tccctaccct tcctgccaag ccagggactc gagcatgggc acctcagatt
     3601 gttgttgtta atgggcattc cttcttctgg tcagaaacct gtccactggg cacagaactt
     3661 atgttgttct ctatggagaa ctaaaagtat gagcgttagg acactatttt aattattttt
     3721 aatttattaa tatttaaata tgtgaagctg agttaattta tgtaagtcat atttatattt
     3781 ttaagaagta ccacttgaaa cattttatgt attagttttg aaataataat ggaaagtggc
     3841 tatgcagttt gaatatcctt tgtttcagag ccagatcatt tcttggaaag tgtaggctta
     3901 cctcagtcga ggtgagcaag ggcgaggagc tgttcaccgg ggtggtgccc atcctggtgg
     3961 acttgatagt caggccagcc ggttaggctg ccaccgaagg ttggtagacg gtgctgcctg
     4021 cgaccaaccc caggaggact gggttaccaa agctgattct ccacggttgg aaagcctccc
     4081 agaaccgtct cggaagagga gtccctgcca acaatggaga tgaagcccgt gtcagatcgc
     4141 gaaagcgcca cttcgccgag gagtgcaatc tgtgaggccc caggaggact gggtaaacag
     4201 tcgagcaccc caccagtgca ggctgcctat cagaaagtgg tggctggtgt ggctaatgcc
     4261 ctggcccaca agtatcacta agctcgcttt cttgctgtcc aatttgtcga gcaccccacc
     4321 agtgcaggct gcctatcaga aagtggtggc tggtgtggct aatgccctgg cccacaagta
     4381 tcactaagct cgctttcttg ctgtccaatt tgtcgagcac cccaccagtg caggctgcct
     4441 atcagaaagt ggtggctggt gtggctaatg ccctggccca caagtatcac taagctcgct
     4501 ttcttgctgt ccaatttgtc gagcacccca ccagtgcagg ctgcctatca gaaagtggtg
     4561 gctggtgtgg ctaatgccct ggcccacaag tatcactaag ctcgctttct tgctgtccaa
     4621 tttgtcgacc cgggcggccg cttcccttta gtgagggtta atgcttcgag cagacatgat
     4681 aagatacatt gatgagtttg gacaaaccac aactagaatg cagtgaaaaa aatgctttat
     4741 ttgtgaaatt tgtgatgcta ttgctttatt tgtaaccatt ataagctgca ataaacaagt
     4801 taacaacaac aattgcattc attttatgtt tcaggttcag ggggagatgt gggaggtttt
     4861 ttaaagcaag taaaacctct acaaatgtgg taaaatccga taaggatcga tccgggctgg
     4921 cgtaatagcg aagaggcccg caccgatcgc ccttcccaac agttgcgcag cctgaatggc
     4981 gaatggacgc gccctgtagc ggcgcattaa gcgcggcggg tgtggtggtt acgcgcagcg
     5041 tgaccgctac acttgccagc gccctagcgc ccgctccttt cgctttcttc ccttcctttc
     5101 tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg ggggctccct ttagggttcc
     5161 gatttagtgc tttacggcac ctcgacccca aaaaacttga ttagggtgat ggttcacgta
     5221 gtgggccatc gccctgatag acggtttttc gccctttgac gttggagtcc acgttcttta
     5281 atagtggact cttgttccaa actggaacaa cactcaaccc tatctcggtc tattcttttg
     5341 atttataagg gattttgccg atttcggcct attggttaaa aaatgagctg atttaacaaa
     5401 aatttaacgc gaattttaac aaaatattaa cgcttacaat ttcctgatgc ggtattttct
     5461 ccttacgcat ctgtgcggta tttcacaccg catacgcgga tctgcgcagc accatggcct
     5521 gaaataacct ctgaaagagg aacttggtta ggtaccttct gaggcggaaa gaaccagctg
     5581 tggaatgtgt gtcagttagg gtgtggaaag tccccaggct ccccagcagg cagaagtatg
     5641 caaagcatgc atctcaatta gtcagcaacc aggtgtggaa agtccccagg ctccccagca
     5701 ggcagaagta tgcaaagcat gcatctcaat tagtcagcaa ccatagtccc gcccctaact
     5761 ccgcccatcc cgcccctaac tccgcccagt tccgcccatt ctccgcccca tggctgacta
     5821 atttttttta tttatgcaga ggccgaggcc gcctcggcct ctgagctatt ccagaagtag
     5881 tgaggaggct tttttggagg cctaggcttt tgcaaaaagc ttgattcttc tgacacaaca
     5941 gtctcgaact taaggctaga gccaccatga ttgaacaaga tggattgcac gcaggttctc
     6001 cggccgcttg ggtggagagg ctattcggct atgactgggc acaacagaca atcggctgct
     6061 ctgatgccgc cgtgttccgg ctgtcagcgc aggggcgccc ggttcttttt gtcaagaccg
     6121 acctgtccgg tgccctgaat gaactgcagg acgaggcagc gcggctatcg tggctggcca
     6181 cgacgggcgt tccttgcgca gctgtgctcg acgttgtcac tgaagcggga agggactggc
     6241 tgctattggg cgaagtgccg gggcaggatc tcctgtcatc tcaccttgct cctgccgaga
     6301 aagtatccat catggctgat gcaatgcggc ggctgcatac gcttgatccg gctacctgcc
     6361 cattcgacca ccaagcgaaa catcgcatcg agcgagcacg tactcggatg gaagccggtc
     6421 ttgtcgatca ggatgatctg gacgaagagc atcaggggct cgcgccagcc gaactgttcg
     6481 ccaggctcaa ggcgcgcatg cccgacggcg aggatctcgt cgtgacccat ggcgatgcct
     6541 gcttgccgaa tatcatggtg gaaaatggcc gcttttctgg attcatcgac tgtggccggc
     6601 tgggtgtggc ggaccgctat caggacatag cgttggctac ccgtgatatt gctgaagagc
     6661 ttggcggcga atgggctgac cgcttcctcg tgctttacgg tatcgccgct cccgattcgc
     6721 agcgcatcgc cttctatcgc cttcttgacg agttcttctg agcgggactc tggggttcga
     6781 aatgaccgac caagcgacgc ccaacctgcc atcacgatgg ccgcaataaa atatctttat
     6841 tttcattaca tctgtgtgtt ggttttttgt gtgaatcgat agcgataagg atccgcgtat
     6901 ggtgcactct cagtacaatc tgctctgatg ccgcatagtt aagccagccc cgacacccgc
     6961 caacacccgc tgacgcgccc tgacgggctt gtctgctccc ggcatccgct tacagacaag
     7021 ctgtgaccgt ctccgggagc tgcatgtgtc agaggttttc accgtcatca ccgaaacgcg
     7081 cgagacgaaa gggcctcgtg atacgcctat ttttataggt taatgtcatg ataataatgg
     7141 tttcttagac gtcaggtggc acttttcggg gaaatgtgcg cggaacccct atttgtttat
     7201 ttttctaaat acattcaaat atgtatccgc tcatgagaca ataaccctga taaatgcttc
     7261 aataatattg aaaaaggaag agtatgagta ttcaacattt ccgtgtcgcc cttattccct
     7321 tttttgcggc attttgcctt cctgtttttg ctcacccaga aacgctggtg aaagtaaaag
     7381 atgctgaaga tcagttgggt gcacgagtgg gttacatcga actggatctc aacagcggta
     7441 agatccttga gagttttcgc cccgaagaac gttttccaat gatgagcact tttaaagttc
     7501 tgctatgtgg cgcggtatta tcccgtattg acgccgggca agagcaactc ggtcgccgca
     7561 tacactattc tcagaatgac ttggttgagt actcaccagt cacagaaaag catcttacgg
     7621 atggcatgac agtaagagaa ttatgcagtg ctgccataac catgagtgat aacactgcgg
     7681 ccaacttact tctgacaacg atcggaggac cgaaggagct aaccgctttt ttgcacaaca
     7741 tgggggatca tgtaactcgc cttgatcgtt gggaaccgga gctgaatgaa gccataccaa
     7801 acgacgagcg tgacaccacg atgcctgtag caatggcaac aacgttgcgc aaactattaa
     7861 ctggcgaact acttactcta gcttcccggc aacaattaat agactggatg gaggcggata
     7921 aagttgcagg accacttctg cgctcggccc ttccggctgg ctggtttatt gctgataaat
     7981 ctggagccgg tgagcgtggg tctcgcggta tcattgcagc actggggcca gatggtaagc
     8041 cctcccgtat cgtagttatc tacacgacgg ggagtcaggc aactatggat gaacgaaata
     8101 gacagatcgc tgagataggt gcctcactga ttaagcattg gtaactgtca gaccaagttt
     8161 actcatatat actttagatt gatttaaaac ttcattttta atttaaaagg atctaggtga
     8221 agatcctttt tgataatctc atgaccaaaa tcccttaacg tgagttttcg ttccactgag
     8281 cgtcagaccc cgtagaaaag atcaaaggat cttcttgaga tccttttttt ctgcgcgtaa
     8341 tctgctgctt gcaaacaaaa aaaccaccgc taccagcggt ggtttgtttg ccggatcaag
     8401 agctaccaac tctttttccg aaggtaactg gcttcagcag agcgcagata ccaaatactg
     8461 ttcttctagt gtagccgtag ttaggccacc acttcaagaa ctctgtagca ccgcctacat
     8521 acctcgctct gctaatcctg ttaccagtgg ctgctgccag tggcgataag tcgtgtctta
     8581 ccgggttgga ctcaagacga tagttaccgg ataaggcgca gcggtcgggc tgaacggggg
     8641 gttcgtgcac acagcccagc ttggagcgaa cgacctacac cgaactgaga tacctacagc
     8701 gtgagctatg agaaagcgcc acgcttcccg aagggagaaa ggcggacagg tatccggtaa
     8761 gcggcagggt cggaacagga gagcgcacga gggagcttcc agggggaaac gcctggtatc
     8821 tttatagtcc tgtcgggttt cgccacctct gacttgagcg tcgatttttg tgatgctcgt
     8881 caggggggcg gagcctatgg aaaaacgcca gcaacgcggc ctttttacgg ttcctggcct
     8941 tttgctggcc ttttgctcac atggctcgac agatcttcaa tattggccat tagccatatt
     9001 attcattggt tatatagcat aaatcaatat tggctattgg ccattgcata cgttgtatct
     9061 atatcataat atgtacattt atattggctc atgtccaata tgaccgccat gtt
//
