LOCUS       sequence-392218-        8151 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Control construct of elongation reporter to quantify elongation of 
            YFP.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8151)
  AUTHORS   Hou W, Harjono V, Harvey AT, Subramaniam AR, Zid BM
  TITLE     Quantification of elongation stalls and impact on gene expression in
            yeast.
  JOURNAL   RNA. 2023 Dec;29(12):1928-1938. doi: 10.1261/rna.079663.123. Epub 
            2023 Oct 2.
  PUBMED    37783489
REFERENCE   2  (bases 1 to 8151)
  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"; doi: 
            "10.1261/rna.079663.123"; journalName: "RNA"; date: "2023-12"; 
            volume: "29"; issue: "12"; pages: "1928-1938"
COMMENT     Sequence Label: pAG306-pTet07-nLuc
FEATURES             Location/Qualifiers
     source          1..8151
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(29..51)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     151..170
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     promoter        194..409
                     /gene="S. cerevisiae URA3"
                     /label=URA3 promoter
     CDS             410..1213
                     /codon_start=1
                     /gene="S. cerevisiae URA3"
                     /product="orotidine-5'-phosphate decarboxylase, required 
                     for uracil biosynthesis"
                     /label=URA3
                     /note="yeast auxotrophic marker, counterselectable with 
                     5-fluoroorotic acid (5-FOA)"
                     /translation="MSKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELL
                     ELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQ
                     YSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLSTGE
                     YTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDD
                     VVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQN"
     rep_origin      complement(1344..1799)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1481..1502)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     1693..1712
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1925..1947
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     1939..1956
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     1940..1956
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     1963..1982
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        1963..1981
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     promoter        2034..2430
                     /gene="S. cerevisiae ADH1"
                     /label=ADH1 promoter
                     /note="promoter for alcohol dehydrogenase 1"
     CDS             join(2443..3063,3064..3450)
                     /codon_start=1
                     /product="tetracycline-controlled transactivator, 
                     comprising a fusion of the tetracycline repressor TetR with
                     the C-terminal activation domain of herpes simplex virus 
                     VP16"
                     /label=tTA
                     /note="In the Tet-Off(R) system, tTA binds to the 
                     Tet-responsive element and stimulates transcription only in
                     the absence of tetracycline or doxycycline."
                     /translation="MPRLDKSKVINSALELLNGVGIEGLTTRKLAQKLGVEQPTLYWHV
                     KNKRALLDALPIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTR
                     PTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEEQEHQVAKEERETPTT
                     DSMPPLLRQAIELFDRQGAEPAFLFGLELIICGLEKQLKCESGSAYSRARTKNNYGSTI
                     EGLLDLPDDDAPEEAGLAAPRLSFLPAGHTRRLSTAPPTDVSLGDELHLDGEDVAMAHA
                     DALDDFDLDMLGDGDSPGPGFTPHDSAPYGALDMADFEFEQMFTDALGIDEYGG"
     primer_bind     complement(2516..2535)
                     /label=Tet-R
                     /note="Tetracycline resistance gene, reverse primer"
     terminator      3471..3658
                     /gene="S. cerevisiae ADH1"
                     /label=ADH1 terminator
                     /note="transcription terminator for the S. cerevisiae 
                     alcohol dehydrogenase 1 (ADH1) gene"
     primer_bind     complement(3526..3550)
                     /label=pHybLex-R
                     /note="ADH terminator, reverse primer"
     protein_bind    join(3716..3734,3735..3757,3758..3776,3777..3799,3800..3818,
                     3819..3841,3842..3860,3861..3883,3884..3902,3903..3925,
                     3926..3944,3945..3967,3968..3986)
                     /label=tetracycline response element
                     /bound_moiety="tetracycline repressor TetR"
                     /note="contains seven copies of the tetracycline operator 
                     tetO"
     primer_bind     complement(4713..4731)
                     /label=CYC1
                     /note="CYC1 transcription termination signal, reverse 
                     primer"
     terminator      4743..4932
                     /gene="S. cerevisiae CYC1"
                     /label=CYC1 terminator
                     /note="transcription terminator for CYC1"
     promoter        complement(4981..4999)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(5020..5036)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(5020..5036)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(5033..5055)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    5044..5060
                     /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(5068..5074,5075..5092,5093..5098))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5113..5134
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(5251..5268)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(5422..6010)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5502..5521)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(6181..6972,6973..7041))
                     /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     6804..6823
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(7042..7146)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     8124..8142
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
ORIGIN
        1 tcgcgcgttt cggtgatgac ggtgaaaacc tctgacacat gcagctcccg gagacggtca
       61 cagcttgtct gtaagcggat gccgggagca gacaagcccg tcagggcgcg tcagcgggtg
      121 ttggcgggtg tcggggctgg cttaactatg cggcatcaga gcagattgta ctgagagtgc
      181 accataccac cttttcaatt catcattttt tttttattct tttttttgat ttcggtttcc
      241 ttgaaatttt tttgattcgg taatctccga acagaaggaa gaacgaagga aggagcacag
      301 acttagattg gtatatatac gcatatgtag tgttgaagaa acatgaaatt gcccagtatt
      361 cttaacccaa ctgcacagaa caaaaacctg caggaaacga agataaatca tgtcgaaagc
      421 tacatataag gaacgtgctg ctactcatcc tagtcctgtt gctgccaagc tatttaatat
      481 catgcacgaa aagcaaacaa acttgtgtgc ttcattggat gttcgtacca ccaaggaatt
      541 actggagtta gttgaagcat taggtcccaa aatttgttta ctaaaaacac atgtggatat
      601 cttgactgat ttttccatgg agggcacagt taagccgcta aaggcattat ccgccaagta
      661 caatttttta ctcttcgaag acagaaaatt tgctgacatt ggtaatacag tcaaattgca
      721 gtactctgcg ggtgtataca gaatagcaga atgggcagac attacgaatg cacacggtgt
      781 ggtgggccca ggtattgtta gcggtttgaa gcaggcggca gaagaagtaa caaaggaacc
      841 tagaggcctt ttgatgttag cagaattgtc atgcaagggc tccctatcta ctggagaata
      901 tactaagggt actgttgaca ttgcgaagag cgacaaagat tttgttatcg gctttattgc
      961 tcaaagagac atgggtggaa gagatgaagg ttacgattgg ttgattatga cacccggtgt
     1021 gggtttagat gacaagggag acgcattggg tcaacagtat agaaccgtgg atgatgtggt
     1081 ctctacagga tctgacatta ttattgttgg aagaggacta tttgcaaagg gaagggatgc
     1141 taaggtagag ggtgaacgtt acagaaaagc aggctgggaa gcatatttga gaagatgcgg
     1201 ccagcaaaac taaaaaactg tattataagt aaatgcatgt atactaaact cacaaattag
     1261 agcttcaatt taattatatc agttattacc ctatgcggtg tgaaataccg cacagatgcg
     1321 taaggagaaa ataccgcatc aggaaattgt aagcgttaat attttgttaa aattcgcgtt
     1381 aaatttttgt taaatcagct cattttttaa ccaataggcc gaaatcggca aaatccctta
     1441 taaatcaaaa gaatagaccg agatagggtt gagtgttgtt ccagtttgga acaagagtcc
     1501 actattaaag aacgtggact ccaacgtcaa agggcgaaaa accgtctatc agggcgatgg
     1561 cccactacgt gaaccatcac cctaatcaag ttttttgggg tcgaggtgcc gtaaagcact
     1621 aaatcggaac cctaaaggga gcccccgatt tagagcttga cggggaaagc cggcgaacgt
     1681 ggcgagaaag gaagggaaga aagcgaaagg agcgggcgct agggcgctgg caagtgtagc
     1741 ggtcacgctg cgcgtaacca ccacacccgc cgcgcttaat gcgccgctac agggcgcgtc
     1801 cattcgccat tcaggctgcg caactgttgg gaagggcgat cggtgcgggc ctcttcgcta
     1861 ttacgccagc tggcgaaagg gggatgtgct gcaaggcgat taagttgggt aacgccaggg
     1921 ttttcccagt cacgacgttg taaaacgacg gccagtgaat tgtaatacga ctcactatag
     1981 ggcgaattgg agctcagttt atcattatca atactcgcca tttcaaagaa taccaacttc
     2041 ttttcttttt ttttcttttc tctctccccc gttgttgtct caccatatcc gcaatgacaa
     2101 aaaaatgatg gaagacacta aaggaaaaaa ttaacgacaa agacagcacc aacagatgtc
     2161 gttgttccag agctgatgag gggtatctcg aagcacacga aactttttcc ttccttcatt
     2221 cacgcacact actctctaat gagcaacggt atacggcctt ccttccagtt acttgaattt
     2281 gaaataaaaa aaagtttgct gtcttgctat caagtataaa tagacctgca attattaatc
     2341 ttttgtttcc tcgtcattgt tctcgttccc tttcttcctt gtttcttttt ctgcacaata
     2401 tttcaagcta taccaagcat acaatcaact atctcatcta gaatgcctag attagataaa
     2461 agtaaagtga ttaacagcgc attagagctg cttaatgggg tcggaatcga aggtttaaca
     2521 acccgtaaac tcgcccagaa gctaggtgta gagcagccta cattgtattg gcatgtaaaa
     2581 aataagcggg ctttgctcga cgccttaccc attgagatgt tagataggca ccatactcac
     2641 ttttgccctt tagaagggga aagctggcaa gattttttac gtaataacgc taaaagtttt
     2701 agatgtgctt tactaagtca tcgcgatgga gcaaaagtac atttaggtac acggcctaca
     2761 gaaaaacagt atgaaactct cgaaaatcaa ttagcctttt tatgccaaca aggtttttca
     2821 ctagagaatg cattatatgc actcagcgct gtggggcact ttactttagg ttgcgtattg
     2881 gaagaacaag agcatcaagt cgctaaagaa gaaagggaaa cacctactac tgatagtatg
     2941 ccgccattat tacgacaagc tatcgaatta tttgatcgcc aaggtgcaga gccagccttc
     3001 ttattcggcc ttgaattgat catatgcgga ttagaaaaac aacttaaatg tgaaagtggg
     3061 tccgcgtaca gccgcgcgcg tacgaaaaac aattacgggt ctaccatcga gggcctgctc
     3121 gatctcccgg acgacgacgc ccccgaagag gcggggctgg cggctccgcg cctgtccttt
     3181 ctccccgcgg gacacacgcg cagactgtcg acggcccccc cgaccgatgt cagcctgggg
     3241 gacgagctcc acttagacgg cgaggacgtg gcgatggcgc atgccgacgc gctagacgat
     3301 ttcgatctgg acatgttggg ggacggggat tccccgggtc cgggatttac cccccacgac
     3361 tccgccccct acggcgctct ggatatggcc gacttcgagt ttgagcagat gtttaccgat
     3421 gcccttggaa ttgacgagta cggtgggtag ctcgagccac ttctaaataa gcgaatttct
     3481 tatgatttat gatttttatt attaaataag ttataaaaaa aataagtgta tacaaatttt
     3541 aaagtgactc ttaggtttta aaacgaaaat tcttattctt gagtaactct ttcctgtagg
     3601 tcaggttgct ttctcaggta tagtatgagg tcgctcttat tgaccacacc tctaccggca
     3661 gatccgctag ggataacagg gtaatataga tcaattcctc gatcgagttt accactccct
     3721 atcagtgata gagaaaagtg aaagtcgagt ttaccactcc ctatcagtga tagagaaaag
     3781 tgaaagtcga gtttaccact ccctatcagt gatagagaaa agtgaaagtc gagtttacca
     3841 ctccctatca gtgatagaga aaagtgaaag tcgagtttac cactccctat cagtgataga
     3901 gaaaagtgaa agtcgagttt accactccct atcagtgata gagaaaagtg aaagtcgagt
     3961 ttaccactcc ctatcagtga tagagaaaag tgaaagtcga gctcggtacc ctatggcatg
     4021 catgtgctct gtatgtatat aaaactcttg ttttcttctt ttctctaaat attctttcct
     4081 tatacattag gtcctttgta gcataaatta ctatacttct atagacacgc aaacacaaat
     4141 acacacacta aattaccgga tcaattatgg tttttacttt agaagatttt gttggtgatt
     4201 ggcgtcaaac tgctggttat aatttagatc aagttttaga acaaggtggt gtttcttctt
     4261 tatttcaaaa tttaggtgtt tctgttactc ctattcaacg tattgtttta tctggtgaaa
     4321 atggtttaaa aattgatatt catgttatta ttccttatga aggtttatct ggtgatcaaa
     4381 tgggtcaaat tgaaaaaatt tttaaagttg tttatcctgt tgatgatcat cattttaaag
     4441 ttattttaca ttatggtact ttagttattg atggtgttac tcctaatatg attgattatt
     4501 ttggtcgtcc ttatgaaggt attgctgttt ttgatggtaa aaaaattact gttactggta
     4561 ctttatggaa tggtaataaa attattgatg aacgtttaat taatcctgat ggttctttat
     4621 tatttcgtgt tactattaat ggtgttactg gttggcgttt atgtgaacgt attttagcta
     4681 attctcatgg tttttaaaag cttattagtt atgtcacgct tacattcacg ccctcccccc
     4741 acatccgctc taaccgaaaa ggaaggagtt agacaacctg aagtctaggt ccctatttat
     4801 ttttttatag ttatgttagt attaagaacg ttatttatat ttcaaatttt tctttttttt
     4861 ctgtacagac gcgtgtacgc atgtaacatt atactgaaaa ccttgcttga gaaggttttg
     4921 ggacgctcga aggctttaat ttgcggccgt cgaggggggg cccggtacca gcttttgttc
     4981 cctttagtga gggttaattt cgagcttggc gtaatcatgg tcatagctgt ttcctgtgtg
     5041 aaattgttat ccgctcacaa ttccacacaa catacgagcc ggaagcataa agtgtaaagc
     5101 ctggggtgcc taatgagtga gctaactcac attaattgcg ttgcgctcac tgcccgcttt
     5161 ccagtcggga aacctgtcgt gccagctgca ttaatgaatc ggccaacgcg cggggagagg
     5221 cggtttgcgt attgggcgct cttccgcttc ctcgctcact gactcgctgc gctcggtcgt
     5281 tcggctgcgg cgagcggtat cagctcactc aaaggcggta atacggttat ccacagaatc
     5341 aggggataac gcaggaaaga acatgtgagc aaaaggccag caaaaggcca ggaaccgtaa
     5401 aaaggccgcg ttgctggcgt ttttccatag gctccgcccc cctgacgagc atcacaaaaa
     5461 tcgacgctca agtcagaggt ggcgaaaccc gacaggacta taaagatacc aggcgtttcc
     5521 ccctggaagc tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg gatacctgtc
     5581 cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc tcacgctgta ggtatctcag
     5641 ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga
     5701 ccgctgcgcc ttatccggta actatcgtct tgagtccaac ccggtaagac acgacttatc
     5761 gccactggca gcagccactg gtaacaggat tagcagagcg aggtatgtag gcggtgctac
     5821 agagttcttg aagtggtggc ctaactacgg ctacactaga agaacagtat ttggtatctg
     5881 cgctctgctg aagccagtta ccttcggaaa aagagttggt agctcttgat ccggcaaaca
     5941 aaccaccgct ggtagcggtg gtttttttgt ttgcaagcag cagattacgc gcagaaaaaa
     6001 aggatctcaa gaagatcctt tgatcttttc tacggggtct gacgctcagt ggaacgaaaa
     6061 ctcacgttaa gggattttgg tcatgagatt atcaaaaagg atcttcacct agatcctttt
     6121 aaattaaaaa tgaagtttta aatcaatcta aagtatatat gagtaaactt ggtctgacag
     6181 ttaccaatgc ttaatcagtg aggcacctat ctcagcgatc tgtctatttc gttcatccat
     6241 agttgcctga ctccccgtcg tgtagataac tacgatacgg gagggcttac catctggccc
     6301 cagtgctgca atgataccgc gagacccacg ctcaccggct ccagatttat cagcaataaa
     6361 ccagccagcc ggaagggccg agcgcagaag tggtcctgca actttatccg cctccatcca
     6421 gtctattaat tgttgccggg aagctagagt aagtagttcg ccagttaata gtttgcgcaa
     6481 cgttgttgcc attgctacag gcatcgtggt gtcacgctcg tcgtttggta tggcttcatt
     6541 cagctccggt tcccaacgat caaggcgagt tacatgatcc cccatgttgt gcaaaaaagc
     6601 ggttagctcc ttcggtcctc cgatcgttgt cagaagtaag ttggccgcag tgttatcact
     6661 catggttatg gcagcactgc ataattctct tactgtcatg ccatccgtaa gatgcttttc
     6721 tgtgactggt gagtactcaa ccaagtcatt ctgagaatag tgtatgcggc gaccgagttg
     6781 ctcttgcccg gcgtcaatac gggataatac cgcgccacat agcagaactt taaaagtgct
     6841 catcattgga aaacgttctt cggggcgaaa actctcaagg atcttaccgc tgttgagatc
     6901 cagttcgatg taacccactc gtgcacccaa ctgatcttca gcatctttta ctttcaccag
     6961 cgtttctggg tgagcaaaaa caggaaggca aaatgccgca aaaaagggaa taagggcgac
     7021 acggaaatgt tgaatactca tactcttcct ttttcaatat tattgaagca tttatcaggg
     7081 ttattgtctc atgagcggat acatatttga atgtatttag aaaaataaac aaataggggt
     7141 tccgcgcaca tttccccgaa aagtgccacc tggggggtgc taattatggc attgattggg
     7201 gcggtaaaac attcaaagtc aatgaaaagg atgctaaatt gaatgatact gaagacattt
     7261 cattcgcttc tcagatcaaa aacttaaatc tgtctatatg agctgtccca aagccacttc
     7321 ttacctttca agaaaacatg gaccttgctt tgccacaaaa taattgcctg taagatagtt
     7381 ttttatttgc acattgttat tactaaccta tgctttgcta cggacgactg cttggtaaaa
     7441 atgcaaaagt attaggatgt ctcacaagaa actgctcgtg gtgaaaattt tcagccgcga
     7501 ccatcctccc acgccaacaa gccctctttt gcccatcctt ctggaattcg cggtgaaaat
     7561 caatttgata tataaaattc cctcataata tctaggaacg ggatcacata tctcaatgag
     7621 ctaaagcggc cgcttcttcg aatgggacca gctaaagtga tcaaacttca tgcaggatgt
     7681 tggacacttt ttctttcaag aagctccaaa tatataaatt tttgcaatct aggaattgaa
     7741 atatcgtact tccgattcag aatatctcaa ctctactaca tctatatatg actgtactcg
     7801 cgttcttggt aaacatcaat tagtaggtgt ttttgcgagc atatgttgag ctcagaaaat
     7861 atgagcacaa tcttcgaaac cattgttttt ttgtgcaaaa gtcaccatcg ggtttatagt
     7921 atggactctt gaacgaacca ttctgatctg tatttctctc atatttactc catttatttt
     7981 ttgctgctct ttgctttact tcaacacgat gcttttccta agtaattttt tattttattc
     8041 acaatgctcc ataactcttc aggccttaaa cgaccatcca tggcccctaa gaaaccatta
     8101 ttatcatgac attaacctat aaaaataggc gtatcacgag gccctttcgt c
//
