LOCUS       sequence-64908-e        5593 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  synthetic circular DNA
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5593)
  AUTHORS   Iioka H, Loiselle D, Haystead TA, Macara IG
  TITLE     Efficient detection of RNA-protein interactions using tethered RNAs.
  JOURNAL   Nucleic Acids Res. 2011 Apr;39(8):e53. Epub 2011 Feb 7.
  PUBMED    21300640
REFERENCE   2  (bases 1 to 5593)
  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: "Nucleic 
            Acids Res."; date: "2011-04"; volume: "39(8)"; pages: "e53. Epub 
            2011 Feb 7"
COMMENT     Sequence Label: pcDNA3-tRNA scaffolded SA (tRSA)
FEATURES             Location/Qualifiers
     source          1..5593
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(44..63)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        235..614
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        615..818
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     769..789
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     863..882
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        863..881
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     promoter        complement(1145..1163)
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     complement(1146..1163)
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     primer_bind     complement(1183..1200)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    1189..1413
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      1459..1887
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1546..1565)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1756..1777
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(1896..1916)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        1901..2231
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      2082..2217
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     2144..2163
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             2298..3092
                     /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(2352..2371)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     2962..2981
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    3266..3387
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3303..3322)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     3357..3376
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(3436..3452)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3436..3452)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(3449..3471)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    3460..3476
                     /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(3484..3490,3491..3508,3509..3514))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    3529..3550
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(3667..3684)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(3838..4426)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3918..3937)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4597..5388,5389..5457))
                     /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     5220..5239
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5458..5562)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 gacggatcgg gagatctccc gatcccctat ggtcgactct cagtacaatc tgctctgatg
       61 ccgcatagtt aagccagtat ctgctccctg cttgtgtgtt ggaggtcgct gagtagtgcg
      121 cgagcaaaat ttaagctaca acaaggcaag gcttgaccga caattgcatg aagaatctgc
      181 ttagggttag gcgttttgcg ctgcttcgcg atgtacgggc cagatatacg cgttgacatt
      241 gattattgac tagttattaa tagtaatcaa ttacggggtc attagttcat agcccatata
      301 tggagttccg cgttacataa cttacggtaa atggcccgcc tggctgaccg cccaacgacc
      361 cccgcccatt gacgtcaata atgacgtatg ttcccatagt aacgccaata gggactttcc
      421 attgacgtca atgggtggac tatttacggt aaactgccca cttggcagta catcaagtgt
      481 atcatatgcc aagtacgccc cctattgacg tcaatgacgg taaatggccc gcctggcatt
      541 atgcccagta catgacctta tgggactttc ctacttggca gtacatctac gtattagtca
      601 tcgctattac catggtgatg cggttttggc agtacatcaa tgggcgtgga tagcggtttg
      661 actcacgggg atttccaagt ctccacccca ttgacgtcaa tgggagtttg ttttggcacc
      721 aaaatcaacg ggactttcca aaatgtcgta acaactccgc cccattgacg caaatgggcg
      781 gtaggcgtgt acggtgggag gtctatataa gcagagctct ctggctaact agagaaccca
      841 ctgcttactg gcttatcgaa attaatacga ctcactatag ggagacccaa gcttggtacc
      901 gagctcggat ccactagtaa cggccgccag tgtgctggaa ttgaaaaaaa aaaaagcccg
      961 gatagctcag tcggtagagc agcggcctcg accagaatca tgcaagtgcg taagatagtc
     1021 gcgggtcgag gccgcgtcca gggttcaagt ccctgttcgg gcgccactgc agaaaaaaaa
     1081 aaaagaattc tgcagatatc catcacactg gcggccgctc gagcatgcat ctagagggcc
     1141 ctattctata gtgtcaccta aatgctagag ctcgctgatc agcctcgact gtgccttcta
     1201 gttgccagcc atctgttgtt tgcccctccc ccgtgccttc cttgaccctg gaaggtgcca
     1261 ctcccactgt cctttcctaa taaaatgagg aaattgcatc gcattgtctg agtaggtgtc
     1321 attctattct ggggggtggg gtggggcagg acagcaaggg ggaggattgg gaagacaata
     1381 gcaggcatgc tggggatgcg gtgggctcta tggcttctga ggcggaaaga accagctggg
     1441 gctctagggg gtatccccac gcgccctgta gcggcgcatt aagcgcggcg ggtgtggtgg
     1501 ttacgcgcag cgtgaccgct acacttgcca gcgccctagc gcccgctcct ttcgctttct
     1561 tcccttcctt tctcgccacg ttcgccggct ttccccgtca agctctaaat cggggcatcc
     1621 ctttagggtt ccgatttagt gctttacggc acctcgaccc caaaaaactt gattagggtg
     1681 atggttcacg tagtgggcca tcgccctgat agacggtttt tcgccctttg acgttggagt
     1741 ccacgttctt taatagtgga ctcttgttcc aaactggaac aacactcaac cctatctcgg
     1801 tctattcttt tgatttataa gggattttgg ggatttcggc ctattggtta aaaaatgagc
     1861 tgatttaaca aaaatttaac gcgaattaat tctgtggaat gtgtgtcagt tagggtgtgg
     1921 aaagtcccca ggctccccag gcaggcagaa gtatgcaaag catgcatctc aattagtcag
     1981 caaccaggtg tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa agcatgcatc
     2041 tcaattagtc agcaaccata gtcccgcccc taactccgcc catcccgccc ctaactccgc
     2101 ccagttccgc ccattctccg ccccatggct gactaatttt ttttatttat gcagaggccg
     2161 aggccgcctc tgcctctgag ctattccaga agtagtgagg aggctttttt ggaggcctag
     2221 gcttttgcaa aaagctcccg ggagcttgta tatccatttt cggatctgat caagagacag
     2281 gatgaggatc gtttcgcatg attgaacaag atggattgca cgcaggttct ccggccgctt
     2341 gggtggagag gctattcggc tatgactggg cacaacagac aatcggctgc tctgatgccg
     2401 ccgtgttccg gctgtcagcg caggggcgcc cggttctttt tgtcaagacc gacctgtccg
     2461 gtgccctgaa tgaactgcag gacgaggcag cgcggctatc gtggctggcc acgacgggcg
     2521 ttccttgcgc agctgtgctc gacgttgtca ctgaagcggg aagggactgg ctgctattgg
     2581 gcgaagtgcc ggggcaggat ctcctgtcat ctcaccttgc tcctgccgag aaagtatcca
     2641 tcatggctga tgcaatgcgg cggctgcata cgcttgatcc ggctacctgc ccattcgacc
     2701 accaagcgaa acatcgcatc gagcgagcac gtactcggat ggaagccggt cttgtcgatc
     2761 aggatgatct ggacgaagag catcaggggc tcgcgccagc cgaactgttc gccaggctca
     2821 aggcgcgcat gcccgacggc gaggatctcg tcgtgaccca tggcgatgcc tgcttgccga
     2881 atatcatggt ggaaaatggc cgcttttctg gattcatcga ctgtggccgg ctgggtgtgg
     2941 cggaccgcta tcaggacata gcgttggcta cccgtgatat tgctgaagag cttggcggcg
     3001 aatgggctga ccgcttcctc gtgctttacg gtatcgccgc tcccgattcg cagcgcatcg
     3061 ccttctatcg ccttcttgac gagttcttct gagcgggact ctggggttcg aaatgaccga
     3121 ccaagcgacg cccaacctgc catcacgaga tttcgattcc accgccgcct tctatgaaag
     3181 gttgggcttc ggaatcgttt tccgggacgc cggctggatg atcctccagc gcggggatct
     3241 catgctggag ttcttcgccc accccaactt gtttattgca gcttataatg gttacaaata
     3301 aagcaatagc atcacaaatt tcacaaataa agcatttttt tcactgcatt ctagttgtgg
     3361 tttgtccaaa ctcatcaatg tatcttatca tgtctgtata ccgtcgacct ctagctagag
     3421 cttggcgtaa tcatggtcat agctgtttcc tgtgtgaaat tgttatccgc tcacaattcc
     3481 acacaacata cgagccggaa gcataaagtg taaagcctgg ggtgcctaat gagtgagcta
     3541 actcacatta attgcgttgc gctcactgcc cgctttccag tcgggaaacc tgtcgtgcca
     3601 gctgcattaa tgaatcggcc aacgcgcggg gagaggcggt ttgcgtattg ggcgctcttc
     3661 cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag cggtatcagc
     3721 tcactcaaag gcggtaatac ggttatccac agaatcaggg gataacgcag gaaagaacat
     3781 gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc tggcgttttt
     3841 ccataggctc cgcccccctg acgagcatca caaaaatcga cgctcaagtc agaggtggcg
     3901 aaacccgaca ggactataaa gataccaggc gtttccccct ggaagctccc tcgtgcgctc
     3961 tcctgttccg accctgccgc ttaccggata cctgtccgcc tttctccctt cgggaagcgt
     4021 ggcgctttct caatgctcac gctgtaggta tctcagttcg gtgtaggtcg ttcgctccaa
     4081 gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta
     4141 tcgtcttgag tccaacccgg taagacacga cttatcgcca ctggcagcag ccactggtaa
     4201 caggattagc agagcgaggt atgtaggcgg tgctacagag ttcttgaagt ggtggcctaa
     4261 ctacggctac actagaagga cagtatttgg tatctgcgct ctgctgaagc cagttacctt
     4321 cggaaaaaga gttggtagct cttgatccgg caaacaaacc accgctggta gcggtggttt
     4381 ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag atcctttgat
     4441 cttttctacg gggtctgacg ctcagtggaa cgaaaactca cgttaaggga ttttggtcat
     4501 gagattatca aaaaggatct tcacctagat ccttttaaat taaaaatgaa gttttaaatc
     4561 aatctaaagt atatatgagt aaacttggtc tgacagttac caatgcttaa tcagtgaggc
     4621 acctatctca gcgatctgtc tatttcgttc atccatagtt gcctgactcc ccgtcgtgta
     4681 gataactacg atacgggagg gcttaccatc tggccccagt gctgcaatga taccgcgaga
     4741 cccacgctca ccggctccag atttatcagc aataaaccag ccagccggaa gggccgagcg
     4801 cagaagtggt cctgcaactt tatccgcctc catccagtct attaattgtt gccgggaagc
     4861 tagagtaagt agttcgccag ttaatagttt gcgcaacgtt gttgccattg ctacaggcat
     4921 cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc tccggttccc aacgatcaag
     4981 gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt agctccttcg gtcctccgat
     5041 cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg gttatggcag cactgcataa
     5101 ttctcttact gtcatgccat ccgtaagatg cttttctgtg actggtgagt actcaaccaa
     5161 gtcattctga gaatagtgta tgcggcgacc gagttgctct tgcccggcgt caatacggga
     5221 taataccgcg ccacatagca gaactttaaa agtgctcatc attggaaaac gttcttcggg
     5281 gcgaaaactc tcaaggatct taccgctgtt gagatccagt tcgatgtaac ccactcgtgc
     5341 acccaactga tcttcagcat cttttacttt caccagcgtt tctgggtgag caaaaacagg
     5401 aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa tactcatact
     5461 cttccttttt caatattatt gaagcattta tcagggttat tgtctcatga gcggatacat
     5521 atttgaatgt atttagaaaa ataaacaaat aggggttccg cgcacatttc cccgaaaagt
     5581 gccacctgac gtc
//
