LOCUS       sequence-209438-        9243 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Expresses wild type TPI reporter; contains partial RAB7A control 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 9243)
  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 9243)
  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-RAB7A_3UTR-xrRNA-4H
FEATURES             Location/Qualifiers
     source          1..9243
                     /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    4947..5068
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4958..4977)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     5012..5031
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     rep_origin      5254..5709
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5341..5360)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5551..5572
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        5826..6183
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     enhancer        5826..6017
                     /label=SV40 enhancer
                     /note="enhancer for the SV40 early promoter (Herr, 1993)"
     primer_bind     complement(5849..5869)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     rep_origin      6034..6169
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     CDS             6234..7028
                     /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(6288..6307)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     6898..6917
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    7092..7140
                     /note="synthetic polyadenylation signal"
     primer_bind     complement(7181..7200)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     7300..7322
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(7360..7378)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        7446..7550
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(7551..7619,7620..8411)
                     /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(7769..7788)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      8582..9170
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     9071..9090
                     /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 gcctcggctc cagcaccatg gcgccctcca ggaagttctt cgttggggga
     1141 aactggaaga tgaacgggcg gaagcagagt ctgggggagc tcatcggcac tctgaacgcg
     1201 gccaaggtgc cggccgacac cggtaagccc tcgccgagga ggggtctggc cgggccgggg
     1261 ccggggccgg ggcaggagtg gcagcgccct ctcccgaggc cccgaggccc cgaggccggt
     1321 atccgcgcgg acctgatgca gggctgtggg acgagggccg ctggggtccg ggcaggggcc
     1381 tcgcagccgc agccccgtcg gtgcgtcgag ggggcagggc ggagcacatg atgccccttg
     1441 gactatgggg caggtaagga cgttttcttc ccttcggcaa cctgaacgac tcccgccttc
     1501 cacggaaggg accgagcccg tgccaaacag gctgagcgat ttgggagtga ggagccatcc
     1561 taccgctttc cccaacctgg aaacagcaaa gcgcaaggcc tctgagtcag ttaggtctct
     1621 gccacccacg ggcaaaggat gctctcctcc atcctccttc ctccctccac cgaaatcgga
     1681 gagccgcggg cctgatccaa agaggcatcc ccttctcgtt cattccccag aggcctcaat
     1741 acaaacccca ggagttggcc cctctccttt tgctacaaat ccttgccttg caaaggggag
     1801 gtgaggatgg gctattttag aagggaagca gggttgctcc ctggagaatg ctgagtctgt
     1861 gaggtgccta tgccgagaat aggtcgagga aattggagcc ccagctgtta aaagagcaga
     1921 gggcagggtg agggccgtgg cctctcaggg gtatctggaa ggctcttcga gttgagtgca
     1981 gacccagcct gggctggaaa atggacaaag gtcatcttgc tggggtgaaa agggggagag
     2041 cagaaccaag aagaagaggg tgagggctgg ggggctccag ggcactggtt aggaattgtg
     2101 gggaatgaag gctttcttta gtctcatccc cctgtggtac catcttgtcc tcagaggtgg
     2161 tttgtgctcc ccctactgcc tatatcgact tcgcccggca gaagctagat cccaagattg
     2221 ctgtggctgc gcagaactgc tacaaagtga ctaatggggc ttttactggg gagatcaggt
     2281 gagatcgagg tggagagggg tgtgtgggac ccttccctca ctttcctcgt tgaggggaaa
     2341 gccacagggt gggctccctg ctgaaccttg gcttcatctc ttcctttagc cctggcatga
     2401 tcaaagactg cggagccacg tgggtggtcc tggggcactc agagagaagg catgtctttg
     2461 gggagtcaga tgaggttagt agccaagaga gaagataagg gatgtctttt tccaagaagg
     2521 atgtctcacc aagtctgttt ctcaacagct gattgggcag aaagtggccc atgctctggc
     2581 agagggactc ggagtaatcg cctgcattgg ggagaagcta gatgaaaggg aagctggcat
     2641 cactgagaag gttgttttcg agcagacaaa ggtcatcgca ggtatctctg gagaaaggga
     2701 cctttgagcc tatccagggc cacagagact cagagggtag ggtcaggccc tggagcctgt
     2761 cttggtcccc atgctgatcc agaaaaggaa aaaggggagg gggagtgaca atctttgctt
     2821 ggggcctatg acttctccag ccccaaggta gatgccacct ggaaatcccc caatgtccac
     2881 tagggggcag taggccaccg ttcttcgtac tccggagaac ctggctggag agctctttct
     2941 tgttcaccct tccctccatc tgtatctctg ccctgcagat aacgtgaagg actggagcaa
     3001 ggtcgtcctg gcctatgagc ctgtgtgggc cattggtact ggcaagactg caacacccca
     3061 acaggtaacc gggcccagga gccctgccct catcccagcc tgcctcaata ggtttggaca
     3121 gacacagccc acatggggca accccttatt tcaaagacac agagaccttg aacccagaga
     3181 cagtgacttg tccaagggca tccagtccag ggcctggctt ggatcagagc cctggtactc
     3241 tgactcagtc agaaaccaca ctaagtgtcc actggtgcca gtgatttttc ctcttagaga
     3301 ggcagaaaag gtcttactta ggccagcttc ttgttctagg cccaggaagt acacgagaag
     3361 ctccgaggat ggctgaagtc caacgtctct gatgcggtgg ctcagagcac ccgtatcatt
     3421 tatggaggtg agtggctttg gttcccggct gaggtggagt gggctgagga ctagactgag
     3481 ccctcggaca tggaggtggg gatggggcag actcatccca ttcttgacca agcccttgtt
     3541 ctgctccctt cccaggctct gtgactgggg caacctgcaa ggagctggcc agccagcctg
     3601 atgtggatgg cttccttgtg ggtggtgctt ccctcaagcc cgaattcgtg gacatcatca
     3661 atgccaaaca atgagcccca tccatcttcc ctacccttcc tgccaagcca gggactcgag
     3721 cagtgagagt tgagcacaga gtccttcaca aaccaagaac acacgtaggc cttcaacaca
     3781 attcccctct cctcttccaa acaaaacata cattgatctc tcacatccag ctgccaaaag
     3841 aaaaccccat caaacacagt tacaccccac atatctctca cacacacaca cacacacgca
     3901 cacacacaca cacagatctg acgtaatcaa actccagccc ttgcccgtga tggctccttg
     3961 gggtctgcct gcccacccac atgagcccgc gagtatggca gcaggacaag ccagcggtgg
     4021 aagtcattct gatatggagt tggcattgga agcttattct ttttgttcac tggagagaga
     4081 gagaactgtt tacagttaat ctgtgtctaa ttatctgatt ttttttattg gtcttgtggt
     4141 ctttttaccc cccctttccc ctccctcctt gagtcgaggt gagcaagggc gaggagctgt
     4201 tcaccggggt ggtgcccatc ctggtggact tgatagtcag gccagccggt taggctgcca
     4261 ccgaaggttg gtagacggtg ctgcctgcga ccaaccccag gaggactggg ttaccaaagc
     4321 tgattctcca cggttggaaa gcctcccaga accgtctcgg aagaggagtc cctgccaaca
     4381 atggagatga agcccgtgtc agatcgcgaa agcgccactt cgccgaggag tgcaatctgt
     4441 gaggccccag gaggactggg taaacagtcg agcaccccac cagtgcaggc tgcctatcag
     4501 aaagtggtgg ctggtgtggc taatgccctg gcccacaagt atcactaagc tcgctttctt
     4561 gctgtccaat ttgtcgagca ccccaccagt gcaggctgcc tatcagaaag tggtggctgg
     4621 tgtggctaat gccctggccc acaagtatca ctaagctcgc tttcttgctg tccaatttgt
     4681 cgagcacccc accagtgcag gctgcctatc agaaagtggt ggctggtgtg gctaatgccc
     4741 tggcccacaa gtatcactaa gctcgctttc ttgctgtcca atttgtcgag caccccacca
     4801 gtgcaggctg cctatcagaa agtggtggct ggtgtggcta atgccctggc ccacaagtat
     4861 cactaagctc gctttcttgc tgtccaattt gtcgacccgg gcggccgctt ccctttagtg
     4921 agggttaatg cttcgagcag acatgataag atacattgat gagtttggac aaaccacaac
     4981 tagaatgcag tgaaaaaaat gctttatttg tgaaatttgt gatgctattg ctttatttgt
     5041 aaccattata agctgcaata aacaagttaa caacaacaat tgcattcatt ttatgtttca
     5101 ggttcagggg gagatgtggg aggtttttta aagcaagtaa aacctctaca aatgtggtaa
     5161 aatccgataa ggatcgatcc gggctggcgt aatagcgaag aggcccgcac cgatcgccct
     5221 tcccaacagt tgcgcagcct gaatggcgaa tggacgcgcc ctgtagcggc gcattaagcg
     5281 cggcgggtgt ggtggttacg cgcagcgtga ccgctacact tgccagcgcc ctagcgcccg
     5341 ctcctttcgc tttcttccct tcctttctcg ccacgttcgc cggctttccc cgtcaagctc
     5401 taaatcgggg gctcccttta gggttccgat ttagtgcttt acggcacctc gaccccaaaa
     5461 aacttgatta gggtgatggt tcacgtagtg ggccatcgcc ctgatagacg gtttttcgcc
     5521 ctttgacgtt ggagtccacg ttctttaata gtggactctt gttccaaact ggaacaacac
     5581 tcaaccctat ctcggtctat tcttttgatt tataagggat tttgccgatt tcggcctatt
     5641 ggttaaaaaa tgagctgatt taacaaaaat ttaacgcgaa ttttaacaaa atattaacgc
     5701 ttacaatttc ctgatgcggt attttctcct tacgcatctg tgcggtattt cacaccgcat
     5761 acgcggatct gcgcagcacc atggcctgaa ataacctctg aaagaggaac ttggttaggt
     5821 accttctgag gcggaaagaa ccagctgtgg aatgtgtgtc agttagggtg tggaaagtcc
     5881 ccaggctccc cagcaggcag aagtatgcaa agcatgcatc tcaattagtc agcaaccagg
     5941 tgtggaaagt ccccaggctc cccagcaggc agaagtatgc aaagcatgca tctcaattag
     6001 tcagcaacca tagtcccgcc cctaactccg cccatcccgc ccctaactcc gcccagttcc
     6061 gcccattctc cgccccatgg ctgactaatt ttttttattt atgcagaggc cgaggccgcc
     6121 tcggcctctg agctattcca gaagtagtga ggaggctttt ttggaggcct aggcttttgc
     6181 aaaaagcttg attcttctga cacaacagtc tcgaacttaa ggctagagcc accatgattg
     6241 aacaagatgg attgcacgca ggttctccgg ccgcttgggt ggagaggcta ttcggctatg
     6301 actgggcaca acagacaatc ggctgctctg atgccgccgt gttccggctg tcagcgcagg
     6361 ggcgcccggt tctttttgtc aagaccgacc tgtccggtgc cctgaatgaa ctgcaggacg
     6421 aggcagcgcg gctatcgtgg ctggccacga cgggcgttcc ttgcgcagct gtgctcgacg
     6481 ttgtcactga agcgggaagg gactggctgc tattgggcga agtgccgggg caggatctcc
     6541 tgtcatctca ccttgctcct gccgagaaag tatccatcat ggctgatgca atgcggcggc
     6601 tgcatacgct tgatccggct acctgcccat tcgaccacca agcgaaacat cgcatcgagc
     6661 gagcacgtac tcggatggaa gccggtcttg tcgatcagga tgatctggac gaagagcatc
     6721 aggggctcgc gccagccgaa ctgttcgcca ggctcaaggc gcgcatgccc gacggcgagg
     6781 atctcgtcgt gacccatggc gatgcctgct tgccgaatat catggtggaa aatggccgct
     6841 tttctggatt catcgactgt ggccggctgg gtgtggcgga ccgctatcag gacatagcgt
     6901 tggctacccg tgatattgct gaagagcttg gcggcgaatg ggctgaccgc ttcctcgtgc
     6961 tttacggtat cgccgctccc gattcgcagc gcatcgcctt ctatcgcctt cttgacgagt
     7021 tcttctgagc gggactctgg ggttcgaaat gaccgaccaa gcgacgccca acctgccatc
     7081 acgatggccg caataaaata tctttatttt cattacatct gtgtgttggt tttttgtgtg
     7141 aatcgatagc gataaggatc cgcgtatggt gcactctcag tacaatctgc tctgatgccg
     7201 catagttaag ccagccccga cacccgccaa cacccgctga cgcgccctga cgggcttgtc
     7261 tgctcccggc atccgcttac agacaagctg tgaccgtctc cgggagctgc atgtgtcaga
     7321 ggttttcacc gtcatcaccg aaacgcgcga gacgaaaggg cctcgtgata cgcctatttt
     7381 tataggttaa tgtcatgata ataatggttt cttagacgtc aggtggcact tttcggggaa
     7441 atgtgcgcgg aacccctatt tgtttatttt tctaaataca ttcaaatatg tatccgctca
     7501 tgagacaata accctgataa atgcttcaat aatattgaaa aaggaagagt atgagtattc
     7561 aacatttccg tgtcgccctt attccctttt ttgcggcatt ttgccttcct gtttttgctc
     7621 acccagaaac gctggtgaaa gtaaaagatg ctgaagatca gttgggtgca cgagtgggtt
     7681 acatcgaact ggatctcaac agcggtaaga tccttgagag ttttcgcccc gaagaacgtt
     7741 ttccaatgat gagcactttt aaagttctgc tatgtggcgc ggtattatcc cgtattgacg
     7801 ccgggcaaga gcaactcggt cgccgcatac actattctca gaatgacttg gttgagtact
     7861 caccagtcac agaaaagcat cttacggatg gcatgacagt aagagaatta tgcagtgctg
     7921 ccataaccat gagtgataac actgcggcca acttacttct gacaacgatc ggaggaccga
     7981 aggagctaac cgcttttttg cacaacatgg gggatcatgt aactcgcctt gatcgttggg
     8041 aaccggagct gaatgaagcc ataccaaacg acgagcgtga caccacgatg cctgtagcaa
     8101 tggcaacaac gttgcgcaaa ctattaactg gcgaactact tactctagct tcccggcaac
     8161 aattaataga ctggatggag gcggataaag ttgcaggacc acttctgcgc tcggcccttc
     8221 cggctggctg gtttattgct gataaatctg gagccggtga gcgtgggtct cgcggtatca
     8281 ttgcagcact ggggccagat ggtaagccct cccgtatcgt agttatctac acgacgggga
     8341 gtcaggcaac tatggatgaa cgaaatagac agatcgctga gataggtgcc tcactgatta
     8401 agcattggta actgtcagac caagtttact catatatact ttagattgat ttaaaacttc
     8461 atttttaatt taaaaggatc taggtgaaga tcctttttga taatctcatg accaaaatcc
     8521 cttaacgtga gttttcgttc cactgagcgt cagaccccgt agaaaagatc aaaggatctt
     8581 cttgagatcc tttttttctg cgcgtaatct gctgcttgca aacaaaaaaa ccaccgctac
     8641 cagcggtggt ttgtttgccg gatcaagagc taccaactct ttttccgaag gtaactggct
     8701 tcagcagagc gcagatacca aatactgttc ttctagtgta gccgtagtta ggccaccact
     8761 tcaagaactc tgtagcaccg cctacatacc tcgctctgct aatcctgtta ccagtggctg
     8821 ctgccagtgg cgataagtcg tgtcttaccg ggttggactc aagacgatag ttaccggata
     8881 aggcgcagcg gtcgggctga acggggggtt cgtgcacaca gcccagcttg gagcgaacga
     8941 cctacaccga actgagatac ctacagcgtg agctatgaga aagcgccacg cttcccgaag
     9001 ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg aacaggagag cgcacgaggg
     9061 agcttccagg gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc cacctctgac
     9121 ttgagcgtcg atttttgtga tgctcgtcag gggggcggag cctatggaaa aacgccagca
     9181 acgcggcctt tttacggttc ctggcctttt gctggccttt tgctcacatg gctcgacaga
     9241 tct
//
