LOCUS       sequence-162259-        5454 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Pentaprobe for assesing the RNA binding potential of a protein.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5454)
  AUTHORS   Bendak K, Loughlin FE, Cheung V, O'Connell MR, Crossley M, Mackay JP
  TITLE     A rapid method for assessing the RNA-binding potential of a protein.
  JOURNAL   Nucleic Acids Res. 2012 Aug;40(14):e105. doi: 10.1093/nar/gks285. 
            Epub 2012 Apr 3.
  PUBMED    22492509
REFERENCE   2  (bases 1 to 5454)
  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: "2012-08"; volume: "40(14):e105. doi"; pages: " 
            10.1093/nar/gks285. Epub 2012 Apr 3"
COMMENT     Sequence Label: Pentaprobe PP12
FEATURES             Location/Qualifiers
     source          1..5454
                     /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(1006..1024)
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     complement(1007..1024)
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     primer_bind     complement(1044..1061)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    1050..1274
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      1320..1748
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1407..1426)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1617..1638
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(1757..1777)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        1762..2092
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      1943..2078
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     2005..2024
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             2159..2953
                     /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(2213..2232)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     2823..2842
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    3127..3248
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3164..3183)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     3218..3237
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(3297..3313)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3297..3313)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(3310..3332)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    3321..3337
                     /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(3345..3351,3352..3369,3370..3375))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    3390..3411
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(3528..3545)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(3699..4287)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3779..3798)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4458..5249,5250..5318))
                     /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     5081..5100
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5319..5423)
                     /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 atgggtggag 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 gggatcccgt accatactat accgtggcgc ggcgtgacat cgcaccgcat ggcacgtcag
      961 gctgagattc caggtcggac tccaacctca cctagagggc cctattctat agtgtcacct
     1021 aaatgctaga gctcgctgat cagcctcgac tgtgccttct agttgccagc catctgttgt
     1081 ttgcccctcc cccgtgcctt ccttgaccct ggaaggtgcc actcccactg tcctttccta
     1141 ataaaatgag gaaattgcat cgcattgtct gagtaggtgt cattctattc tggggggtgg
     1201 ggtggggcag gacagcaagg gggaggattg ggaagacaat agcaggcatg ctggggatgc
     1261 ggtgggctct atggcttctg aggcggaaag aaccagctgg ggctctaggg ggtatcccca
     1321 cgcgccctgt agcggcgcat taagcgcggc gggtgtggtg gttacgcgca gcgtgaccgc
     1381 tacacttgcc agcgccctag cgcccgctcc tttcgctttc ttcccttcct ttctcgccac
     1441 gttcgccggc tttccccgtc aagctctaaa tcgggggctc cctttagggt tccgatttag
     1501 tgctttacgg cacctcgacc ccaaaaaact tgattagggt gatggttcac gtagtgggcc
     1561 atcgccctga tagacggttt ttcgcccttt gacgttggag tccacgttct ttaatagtgg
     1621 actcttgttc caaactggaa caacactcaa ccctatctcg gtctattctt ttgatttata
     1681 agggattttg ccgatttcgg cctattggtt aaaaaatgag ctgatttaac aaaaatttaa
     1741 cgcgaattaa ttctgtggaa tgtgtgtcag ttagggtgtg gaaagtcccc aggctcccca
     1801 ggcaggcaga agtatgcaaa gcatgcatct caattagtca gcaaccaggt gtggaaagtc
     1861 cccaggctcc ccagcaggca gaagtatgca aagcatgcat ctcaattagt cagcaaccat
     1921 agtcccgccc ctaactccgc ccatcccgcc cctaactccg cccagttccg cccattctcc
     1981 gccccatggc tgactaattt tttttattta tgcagaggcc gaggccgcct ctgcctctga
     2041 gctattccag aagtagtgag gaggcttttt tggaggccta ggcttttgca aaaagctccc
     2101 gggagcttgt atatccattt tcggatctga tcaagagaca ggatgaggat cgtttcgcat
     2161 gattgaacaa gatggattgc acgcaggttc tccggccgct tgggtggaga ggctattcgg
     2221 ctatgactgg gcacaacaga caatcggctg ctctgatgcc gccgtgttcc ggctgtcagc
     2281 gcaggggcgc ccggttcttt ttgtcaagac cgacctgtcc ggtgccctga atgaactgca
     2341 ggacgaggca gcgcggctat cgtggctggc cacgacgggc gttccttgcg cagctgtgct
     2401 cgacgttgtc actgaagcgg gaagggactg gctgctattg ggcgaagtgc cggggcagga
     2461 tctcctgtca tctcaccttg ctcctgccga gaaagtatcc atcatggctg atgcaatgcg
     2521 gcggctgcat acgcttgatc cggctacctg cccattcgac caccaagcga aacatcgcat
     2581 cgagcgagca cgtactcgga tggaagccgg tcttgtcgat caggatgatc tggacgaaga
     2641 gcatcagggg ctcgcgccag ccgaactgtt cgccaggctc aaggcgcgca tgcccgacgg
     2701 cgaggatctc gtcgtgaccc atggcgatgc ctgcttgccg aatatcatgg tggaaaatgg
     2761 ccgcttttct ggattcatcg actgtggccg gctgggtgtg gcggaccgct atcaggacat
     2821 agcgttggct acccgtgata ttgctgaaga gcttggcggc gaatgggctg accgcttcct
     2881 cgtgctttac ggtatcgccg ctcccgattc gcagcgcatc gccttctatc gccttcttga
     2941 cgagttcttc tgagcgggac tctggggttc gaaatgaccg accaagcgac gcccaacctg
     3001 ccatcacgag atttcgattc caccgccgcc ttctatgaaa ggttgggctt cggaatcgtt
     3061 ttccgggacg ccggctggat gatcctccag cgcggggatc tcatgctgga gttcttcgcc
     3121 caccccaact tgtttattgc agcttataat ggttacaaat aaagcaatag catcacaaat
     3181 ttcacaaata aagcattttt ttcactgcat tctagttgtg gtttgtccaa actcatcaat
     3241 gtatcttatc atgtctgtat accgtcgacc tctagctaga gcttggcgta atcatggtca
     3301 tagctgtttc ctgtgtgaaa ttgttatccg ctcacaattc cacacaacat acgagccgga
     3361 agcataaagt gtaaagcctg gggtgcctaa tgagtgagct aactcacatt aattgcgttg
     3421 cgctcactgc ccgctttcca gtcgggaaac ctgtcgtgcc agctgcatta atgaatcggc
     3481 caacgcgcgg ggagaggcgg tttgcgtatt gggcgctctt ccgcttcctc gctcactgac
     3541 tcgctgcgct cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa ggcggtaata
     3601 cggttatcca cagaatcagg ggataacgca ggaaagaaca tgtgagcaaa aggccagcaa
     3661 aaggccagga accgtaaaaa ggccgcgttg ctggcgtttt tccataggct ccgcccccct
     3721 gacgagcatc acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggactataa
     3781 agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg
     3841 cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcaatgctca
     3901 cgctgtaggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa
     3961 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg
     4021 gtaagacacg acttatcgcc actggcagca gccactggta acaggattag cagagcgagg
     4081 tatgtaggcg gtgctacaga gttcttgaag tggtggccta actacggcta cactagaagg
     4141 acagtatttg gtatctgcgc tctgctgaag ccagttacct tcggaaaaag agttggtagc
     4201 tcttgatccg gcaaacaaac caccgctggt agcggtggtt tttttgtttg caagcagcag
     4261 attacgcgca gaaaaaaagg atctcaagaa gatcctttga tcttttctac ggggtctgac
     4321 gctcagtgga acgaaaactc acgttaaggg attttggtca tgagattatc aaaaaggatc
     4381 ttcacctaga tccttttaaa ttaaaaatga agttttaaat caatctaaag tatatatgag
     4441 taaacttggt ctgacagtta ccaatgctta atcagtgagg cacctatctc agcgatctgt
     4501 ctatttcgtt catccatagt tgcctgactc cccgtcgtgt agataactac gatacgggag
     4561 ggcttaccat ctggccccag tgctgcaatg ataccgcgag acccacgctc accggctcca
     4621 gatttatcag caataaacca gccagccgga agggccgagc gcagaagtgg tcctgcaact
     4681 ttatccgcct ccatccagtc tattaattgt tgccgggaag ctagagtaag tagttcgcca
     4741 gttaatagtt tgcgcaacgt tgttgccatt gctacaggca tcgtggtgtc acgctcgtcg
     4801 tttggtatgg cttcattcag ctccggttcc caacgatcaa ggcgagttac atgatccccc
     4861 atgttgtgca aaaaagcggt tagctccttc ggtcctccga tcgttgtcag aagtaagttg
     4921 gccgcagtgt tatcactcat ggttatggca gcactgcata attctcttac tgtcatgcca
     4981 tccgtaagat gcttttctgt gactggtgag tactcaacca agtcattctg agaatagtgt
     5041 atgcggcgac cgagttgctc ttgcccggcg tcaatacggg ataataccgc gccacatagc
     5101 agaactttaa aagtgctcat cattggaaaa cgttcttcgg ggcgaaaact ctcaaggatc
     5161 ttaccgctgt tgagatccag ttcgatgtaa cccactcgtg cacccaactg atcttcagca
     5221 tcttttactt tcaccagcgt ttctgggtga gcaaaaacag gaaggcaaaa tgccgcaaaa
     5281 aagggaataa gggcgacacg gaaatgttga atactcatac tcttcctttt tcaatattat
     5341 tgaagcattt atcagggtta ttgtctcatg agcggataca tatttgaatg tatttagaaa
     5401 aataaacaaa taggggttcc gcgcacattt ccccgaaaag tgccacctga cgtc
//
