LOCUS       sequence-436951-        7875 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Base construct used to create the PUF3/PUP2 tagging strain. (aka 
            pCS2/3HA/PUM1_RBD/PUP2/URA3).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7875)
  AUTHORS   Lapointe CP, Wilinski D, Saunders HA, Wickens M
  TITLE     Protein-RNA networks revealed through covalent RNA marks.
  JOURNAL   Nat Methods. 2015 Dec;12(12):1163-70. doi: 10.1038/nmeth.3651. Epub 
            2015 Nov 2.
  PUBMED    26524240
REFERENCE   2  (bases 1 to 7875)
  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: 
            "10.1038/nmeth.3651"; journalName: "Nat Methods"; date: "2015-12"; 
            volume: "12"; issue: "12"; pages: "1163-70"
COMMENT     Sequence Label: RT-3
FEATURES             Location/Qualifiers
     source          1..7875
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             2544..3347
                     /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"
     polyA_signal    3462..3596
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3486..3505)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3540..3559
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(3709..3729)
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        complement(3709..3727)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(3748..3764)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3748..3764)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(3761..3783)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    3772..3788
                     /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(3796..3802,3803..3820,3821..3826))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    3841..3862
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(3979..3996)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4150..4738)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4230..4249)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4909..5700,5701..5769))
                     /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     5532..5551
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5770..5874)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      complement(5900..6355)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(6037..6058)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     6249..6268
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     promoter        6426..7410
                     /label=CMV IE94 promoter
                     /note="enhancer/promoter region of simian cytomegalovirus 
                     major immediate early transcription unit IE94"
     promoter        7445..7463
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     7445..7462
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     CDS             7498..7524
                     /codon_start=1
                     /product="HA (human influenza hemagglutinin) epitope tag"
                     /label=HA
                     /translation="YPYDVPDYA"
     CDS             7534..7560
                     /codon_start=1
                     /product="HA (human influenza hemagglutinin) epitope tag"
                     /label=HA
                     /translation="YPYDVPDYA"
     CDS             7570..7596
                     /codon_start=1
                     /product="HA (human influenza hemagglutinin) epitope tag"
                     /label=HA
                     /translation="YPYDVPDYA"
ORIGIN
        1 gctgaacgga ttcgtgggca cgtactttca ctggcattgc aaatgtacgg atgtcgggtg
       61 atacaaaagg cattggagtt tattccacct gatcagcagg ttattaatga aatggtcaga
      121 gagttggatg gtcatgtctt gaagtgtgta aaggaccaga atgggaatca cgtggttcaa
      181 aaatgcatag agtgtgtaca gccgcagtcc cttcaattca ttattgatgc cttcaagagc
      241 caggtatttg cactgtctac gcatccgtat ggctgtcgag tgatccagcg cattttggag
      301 cattgccttc ctgagcagac actgcctatt ttagaagaat tacaccagca cacggagcaa
      361 cttgttcagg atcagtatgg taactacgtt attcagcatg ttttggagca tggtcggccg
      421 gaggacaaaa gtaaaatcgt tgcggagatt cgtggaaatg ttctagtcct gagtcagcac
      481 aaatttgcca gtaatgtagt tgaaaagtgt gtgacacatg catctcgtac ggaaagggcc
      541 atgctgatag acgaggtgtg cacaatgaat gatgggcctc atagtgcctt atacaccatg
      601 atgaaggacc agtatgctaa ctatgttgta cagaaaatga tcgatgtagc agaaccagct
      661 cagcgcaaga ttgttatgca caagatcaga ccacatattg ccactcttcg taaatacaca
      721 tatggcaagc acatcctggc caagttggaa aagtactaca tgaaaaatgg aatggatctg
      781 ggtccaatgt gtggaccctc aaatggaatc attgcgaggc ctatgacagt tattcagaag
      841 tcgtctccta cagtgaaagg agtgaagaca acaacatcag attgcaccga aagacgtcac
      901 tcatcgagtt caccttgcaa aatgagtcaa aacggaagca gtggatacta tgaaggagat
      961 gttttactgg atgatgatgc tcttgtttcg atgccagaag caacgctcat tgagtgcttt
     1021 ggtaatctgg ctgtcacaaa aagacctgca catctgagac ctccggcagc tttctgtcta
     1081 ccgtttgtat caatgaacaa cgatttgacg agcggacatg ccttgaaaca tatcacattg
     1141 acatcagtat tcgacgcact acatccgtac gttgccatgc cgtacatcaa cagaatggat
     1201 atatgctctg caatgaacgt atattggatc agaaactgtt tggaagctga acaatccgat
     1261 ttatttcatc gattcgctct ggaaatgcaa gtacatttga gtgcatgttt tggatgtcgc
     1321 gttgtcctgg atatctatgg atcaaccaga aacggattcg gtacccgatt ctgtgatgtt
     1381 gatatgtcac tttctttttc accgagtcca ccttcatggg caaccaattc ggatcgagtg
     1441 atgagagctg ttgcgaaggc acttgtcgat tttccgaaag cagttgatga gagatatgtc
     1501 aacgccaaag ttccaattgt cagattcaga agcagtgaca tggatatgga agcagacatc
     1561 agttacaaga atgatttggc tcttcacaat actcagcttt tgcaacaata ctgcaaatgg
     1621 gatcccgaaa gactaccgac tcttggagtt tgggtcaaag cgtgggcgaa acgaagtgga
     1681 gttggagatg catcaaaagg atcgctgtct tcatatgctt ggattgtgat gcttattcat
     1741 tatcttcagc aagtcgaacc aattcctgtg ttgccatgtc ttcaggaaat gaaccatcag
     1801 aaaagtgaaa atgtctacgt ccaaggttac aacacgtatt attggaaatt cgtagacact
     1861 gctcgtacac gacgttgtcg tgcttctgtc gttgatttgt tcgttggatt cttggattac
     1921 tatgccacat actttgacta ctccacaaat gttatccaga tggtgtccaa gaaattggaa
     1981 ttcaaaccgg atcgctggtg caagtatcca atgtgtattg ctgatccgtt cgagacggat
     2041 cataatttgg cacaaggtgt tgatatgcca atgtttgaat acattagatc gtgtatggaa
     2101 cactcgaaga aagtattcac ggatcgccgc atgcgctcgg agtttctttc gggatacggg
     2161 ttcgacgttg acgaatttga tgcaaggcat cgaggcgaaa tgaacatgga aatggcgtca
     2221 caatttgggg aattccttct tcacaagtgc ataatggtga aacaagcccc gaatcgtcaa
     2281 ttccgtgatc gcagtatgag tcaatcgacg agcataagca acacatcgag tatttcctcg
     2341 tcgggatagt gactcgagcc tctagacggt ttctttgaaa tttttttgat tcggtaatct
     2401 ccgaacagaa ggaagaacga aggaaggagc acagacttag attggtatat atacgcatat
     2461 gtagtgttga agaaacatga aattgcccag tattcttaac ccaactgcac agaacaaaaa
     2521 cctgcaggaa acgaagataa atcatgtcga aagctacata taaggaacgt gctgctactc
     2581 atcctagtcc tgttgctgcc aagctattta atatcatgca cgaaaagcaa acaaacttgt
     2641 gtgcttcatt ggatgttcgt accaccaagg aattactgga gttagttgaa gcattaggtc
     2701 ccaaaatttg tttactaaaa acacatgtgg atatcttgac tgatttttcc atggagggca
     2761 cagttaagcc gctaaaggca ttatccgcca agtacaattt tttactcttc gaagacagaa
     2821 aatttgctga cattggtaat acagtcaaat tgcagtactc tgcgggtgta tacagaatag
     2881 cagaatgggc agacattacg aatgcacacg gtgtggtggg cccaggtatt gttagcggtt
     2941 tgaagcaggc ggcagaagaa gtaacaaagg aacctagagg ccttttgatg ttagcagaat
     3001 tgtcatgcaa gggctcccta tctactggag aatatactaa gggtactgtt gacattgcga
     3061 agagcgacaa agattttgtt atcggcttta ttgctcaaag agacatgggt ggaagagatg
     3121 aaggttacga ttggttgatt atgacacccg gtgtgggttt agatgacaag ggagacgcat
     3181 tgggtcaaca gtatagaacc gtggatgatg tggtctctac aggatctgac attattattg
     3241 ttggaagagg actatttgca aagggaaggg atgctaaggt agagggtgaa cgttacagaa
     3301 aagcaggctg ggaagcatat ttgagaagat gcggccagca aaactaaaaa actgtattat
     3361 aagtaaatgc atgtatacta aactcacaaa ttagagcttc aatttaatta tatcagttat
     3421 taccctatgc ggtctagaac tatagtgagt cgtattacgt agatccagac atgataagat
     3481 acattgatga gtttggacaa accacaacta gaatgcagtg aaaaaaatgc tttatttgtg
     3541 aaatttgtga tgctattgct ttatttgtaa ccattataag ctgcaataaa caagttaaca
     3601 acaacaattg cattcatttt atgtttcagg ttcaggggga ggtgtgggag gttttttaat
     3661 tcgcggccgc ggcgccaatg cattgggccc ggtacccagc ttttgttccc tttagtgagg
     3721 gttaattgcg cgcttggcgt aatcatggtc atagctgttt cctgtgtgaa attgttatcc
     3781 gctcacaatt ccacacaaca tacgagccgg gagcataaag tgtaaagcct ggggtgccta
     3841 atgagtgagc taactcacat taattgcgtt gcgctcactg cccgctttcc agtcgggaaa
     3901 cctgtcgtgc cagctgcatt aatgaatcgg ccaacgcgcg gggagaggcg gtttgcgtat
     3961 tgggcgctct tccgcttcct cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg
     4021 agcggtatca gctcactcaa aggcggtaat acggttatcc acagaatcag gggataacgc
     4081 aggaaagaac atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa aggccgcgtt
     4141 gctggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag
     4201 tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc
     4261 cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc
     4321 ttcgggaagc gtggcgcttt ctcatagctc acgctgtagg tatctcagtt cggtgtaggt
     4381 cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt
     4441 atccggtaac tatcgtcttg agtccaaccc ggtaagacac gacttatcgc cactggcagc
     4501 agccactggt aacaggatta gcagagcgag gtatgtaggc ggtgctacag agttcttgaa
     4561 gtggtggcct aactacggct acactagaag aacagtattt ggtatctgcg ctctgctgaa
     4621 gccagttacc ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg
     4681 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga
     4741 agatcctttg atcttttcta cggggtctga cgctcagtgg aacgaaaact cacgttaagg
     4801 gattttggtc atgagattat caaaaaggat cttcacctag atccttttaa attaaaaatg
     4861 aagttttaaa tcaatctaaa gtatatatga gtaaacttgg tctgacagtt accaatgctt
     4921 aatcagtgag gcacctatct cagcgatctg tctatttcgt tcatccatag ttgcctgact
     4981 ccccgtcgtg tagataacta cgatacggga gggcttacca tctggcccca gtgctgcaat
     5041 gataccgcga gacccacgct caccggctcc agatttatca gcaataaacc agccagccgg
     5101 aagggccgag cgcagaagtg gtcctgcaac tttatccgcc tccatccagt ctattaattg
     5161 ttgccgggaa gctagagtaa gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat
     5221 tgctacaggc atcgtggtgt cacgctcgtc gtttggtatg gcttcattca gctccggttc
     5281 ccaacgatca aggcgagtta catgatcccc catgttgtgc aaaaaagcgg ttagctcctt
     5341 cggtcctccg atcgttgtca gaagtaagtt ggccgcagtg ttatcactca tggttatggc
     5401 agcactgcat aattctctta ctgtcatgcc atccgtaaga tgcttttctg tgactggtga
     5461 gtactcaacc aagtcattct gagaatagtg tatgcggcga ccgagttgct cttgcccggc
     5521 gtcaatacgg gataataccg cgccacatag cagaacttta aaagtgctca tcattggaaa
     5581 acgttcttcg gggcgaaaac tctcaaggat cttaccgctg ttgagatcca gttcgatgta
     5641 acccactcgt gcacccaact gatcttcagc atcttttact ttcaccagcg tttctgggtg
     5701 agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata agggcgacac ggaaatgttg
     5761 aatactcata ctcttccttt ttcaatatta ttgaagcatt tatcagggtt attgtctcat
     5821 gagcggatac atatttgaat gtatttagaa aaataaacaa ataggggttc cgcgcacatt
     5881 tccccgaaaa gtgccaccta aattgtaagc gttaatattt tgttaaaatt cgcgttaaat
     5941 ttttgttaaa tcagctcatt ttttaaccaa taggccgaaa tcggcaaaat cccttataaa
     6001 tcaaaagaat agaccgagat agggttgagt gttgttccag tttggaacaa gagtccacta
     6061 ttaaagaacg tggactccaa cgtcaaaggg cgaaaaaccg tctatcaggg cgatggccca
     6121 ctacgtgaac catcacccta atcaagtttt ttggggtcga ggtgccgtaa agcactaaat
     6181 cggaacccta aagggagccc ccgatttaga gcttgacggg gaaagccggc gaacgtggcg
     6241 agaaaggaag ggaagaaagc gaaaggagcg ggcgctaggg cgctggcaag tgtagcggtc
     6301 acgctgcgcg taaccaccac acccgccgcg cttaatgcgc cgctacaggg cgcgtcccat
     6361 tcgccattca ggctgcgcaa ctgttgggaa gggcgatcgg tgcgggcctc ttcgctatta
     6421 cgccagtcga ccgccaattc aatatggcgt atatggactc atgccaattc aatatggtgg
     6481 atctggacct gtgccaattc aatatggcgt atatggactc gtgccaattc aatatggtgg
     6541 atctggaccc cagccaattc aatatggcgg acttggcacc atgccaattc aatatggcgg
     6601 acctggcact gtgccaactg gggaggggtc tacttggcac ggtgccaagt ttgaggaggg
     6661 gtcttggccc tgtgccaagt ccgccatatt gaattggcat ggtgccaata atggcggcca
     6721 tattggctat atgccaggat caatatatag gcaatatcca atatggccct atgccaatat
     6781 ggctattggc caggttcaat actatgtatt ggccctatgc catatagtat tccatatatg
     6841 ggttttccta ttgacgtaga tagcccctcc caatgggcgg tcccatatac catatatggg
     6901 gcttcctaat accgcccata gccactcccc cattgacgtc aatggtctct atatatggtc
     6961 tttcctattg acgtcatatg ggcggtccta ttgacgtata tggcgcctcc cccattgacg
     7021 tcaattacgg taaatggccc gcctggctca atgcccattg acgtcaatag gaccacccac
     7081 cattgacgtc aatgggatgg ctcattgccc attcatatcc gttctcacgc cccctattga
     7141 cgtcaatgac ggtaaatggc ccacttggca gtacatcaat atctattaat agtaacttgg
     7201 caagtacatt actattggaa gtacgccagg gtacattggc agtactccca ttgacgtcaa
     7261 tggcggtaaa tggcccgcga tggctgccaa gtacatcccc attgacgtca atggggaggg
     7321 gcaatgacgc aaatgggcgt tccattgacg taaatgggcg gtaggcgtgc ctaatgggag
     7381 gtctatataa gcaatgctcg tttagggaac cgccattctg cctggggacg tcggagcaag
     7441 cttgatttag gtgacactat agaatacaag ctacttgttc tttttgcagg atccatgtac
     7501 ccatacgatg ttccagatta cgctgctggt gcttacccat acgatgttcc agattacgct
     7561 gctggtgctt acccatacga tgttccagat tacgctccat ggtctggtag aagcagacta
     7621 cttgaagatt tccggaacaa ccgctaccca aatttgcagt tacgagaaat cgctggccac
     7681 atcatggagt tttcccagga ccagcatgga tcaaggttta ttcagttgaa gctggagcga
     7741 gctacacctg cagaaaggca actggtgttc aacgagatcc ttcaagcagc ttaccagctt
     7801 atggtggatg tatttgggaa ttatgtcata cagaaatttt ttgagtttgg cagcctagag
     7861 cagaagcttg cactt
//
