LOCUS       sequence-190064-        5461 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 5461)
  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 5461)
  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 PP1
FEATURES             Location/Qualifiers
     source          1..5461
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(39..58)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        230..609
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        610..813
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     764..784
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     858..877
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        858..876
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     promoter        complement(1009..1027)
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     complement(1010..1027)
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     primer_bind     complement(1047..1064)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    1053..1277
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      1323..1751
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1410..1429)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1620..1641
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(1760..1780)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        1765..2094
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      1945..2080
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     2007..2026
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             2161..2955
                     /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(2215..2234)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     2825..2844
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    3129..3250
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3166..3185)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     3220..3239
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(3299..3315)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(3299..3315)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(3312..3334)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    3323..3339
                     /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(3347..3353,3354..3371,3372..3377))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    3392..3413
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(3530..3547)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(3701..4289)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3781..3800)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4460..5251,5252..5320))
                     /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     5083..5102
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5321..5425)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 atcgggagat ctcccgatcc cctatggtgc actctcagta caatctgctc tgatgccgca
       61 tagttaagcc agtatctgct ccctgcttgt gtgttggagg tcgctgagta gtgcgcgagc
      121 aaaatttaag ctacaacaag gcaaggcttg accgacaatt gcatgaagaa tctgcttagg
      181 gttaggcgtt ttgcgctgct tcgcgatgta cgggccagat atacgcgttg acattgatta
      241 ttgactagtt attaatagta atcaattacg gggtcattag ttcatagccc atatatggag
      301 ttccgcgtta cataacttac ggtaaatggc ccgcctggct gaccgcccaa cgacccccgc
      361 ccattgacgt caataatgac gtatgttccc atagtaacgc caatagggac tttccattga
      421 cgtcaatggg tggagtattt acggtaaact gcccacttgg cagtacatca agtgtatcat
      481 atgccaagta cgccccctat tgacgtcaat gacggtaaat ggcccgcctg gcattatgcc
      541 cagtacatga ccttatggga ctttcctact tggcagtaca tctacgtatt agtcatcgct
      601 attaccatgg tgatgcggtt ttggcagtac atcaatgggc gtggatagcg gtttgactca
      661 cggggatttc caagtctcca ccccattgac gtcaatggga gtttgttttg gcaccaaaat
      721 caacgggact ttccaaaatg tcgtaacaac tccgccccat tgacgcaaat gggcggtagg
      781 cgtgtacggt gggaggtcta tataagcaga gctctctggc taactagaga acccactgct
      841 tactggctta tcgaaattaa tacgactcac tatagggaga cccaagcttg gtaccggaat
      901 tctacgaatt tttcttttgt ttatttcctt tcgctttgct tctcttccct tcggttctgt
      961 tccgttttac cttgtcttgc cttatcttac tttactagag ggccctattc tatagtgtca
     1021 cctaaatgct agagctcgct gatcagcctc gactgtgcct tctagttgcc agccatctgt
     1081 tgtttgcccc tcccccgtgc cttccttgac cctggaaggt gccactccca ctgtcctttc
     1141 ctaataaaat gaggaaattg catcgcattg tctgagtagg tgtcattcta ttctgggggg
     1201 tggggtgggg caggacagca agggggagga ttgggaagac aatagcaggc atgctgggga
     1261 tgcggtgggc tctatggctt ctgaggcgga aagaaccagc tggggctcta gggggtatcc
     1321 ccacgcgccc tgtagcggcg cattaagcgc ggcgggtgtg gtggttacgc gcagcgtgac
     1381 cgctacactt gccagcgccc tagcgcccgc tcctttcgct ttcttccctt cctttctcgc
     1441 cacgttcgcc ggctttcccc gtcaagctct aaatcggggg ctccctttag ggttccgatt
     1501 tagtgcttta cggcacctcg accccaaaaa acttgattag ggtgatggtt cacgtagtgg
     1561 gccatcgccc tgatagacgg tttttcgccc tttgacgttg gagtccacgt tctttaatag
     1621 tggactcttg ttccaaactg gaacaacact caaccctatc tcggtctatt cttttgattt
     1681 ataagggatt ttgccgattt cggcctattg gttaaaaaat gagctgattt aacaaaaatt
     1741 taacgcgaat taattctgtg gaatgtgtgt cagttagggt gtggaaagtc cccaggctcc
     1801 ccagcaggca gaagtatgca aagcatgcat ctcaattagt cagcaaccag gtgtggaaag
     1861 tccccaggct ccccagcagg cagaagtatg caaagcatgc atctcaatta gtcagcaacc
     1921 atagtcccgc ccctaactcc gcccatcccg cccctaactc cgcccagttc cgcccattct
     1981 ccgccccatg gctgactaat tttttttatt tatgcagagg ccgaggccgc ctctgcctct
     2041 gagctattcc agaagtagtg aggaggcttt tttggaggcc taggcttttg caaaaagctc
     2101 ccgggagctt gtatatccat tttcggatct gatcaagaga caggatgagg atcgtttcgc
     2161 atgattgaac aagatggatt gcacgcaggt tctccggccg cttgggtgga gaggctattc
     2221 ggctatgact gggcacaaca gacaatcggc tgctctgatg ccgccgtgtt ccggctgtca
     2281 gcgcaggggc gcccggttct ttttgtcaag accgacctgt ccggtgccct gaatgaactg
     2341 caggacgagg cagcgcggct atcgtggctg gccacgacgg gcgttccttg cgcagctgtg
     2401 ctcgacgttg tcactgaagc gggaagggac tggctgctat tgggcgaagt gccggggcag
     2461 gatctcctgt catctcacct tgctcctgcc gagaaagtat ccatcatggc tgatgcaatg
     2521 cggcggctgc atacgcttga tccggctacc tgcccattcg accaccaagc gaaacatcgc
     2581 atcgagcgag cacgtactcg gatggaagcc ggtcttgtcg atcaggatga tctggacgaa
     2641 gagcatcagg ggctcgcgcc agccgaactg ttcgccaggc tcaaggcgcg catgcccgac
     2701 ggcgaggatc tcgtcgtgac ccatggcgat gcctgcttgc cgaatatcat ggtggaaaat
     2761 ggccgctttt ctggattcat cgactgtggc cggctgggtg tggcggaccg ctatcaggac
     2821 atagcgttgg ctacccgtga tattgctgaa gagcttggcg gcgaatgggc tgaccgcttc
     2881 ctcgtgcttt acggtatcgc cgctcccgat tcgcagcgca tcgccttcta tcgccttctt
     2941 gacgagttct tctgagcggg actctggggt tcgaaatgac cgaccaagcg acgcccaacc
     3001 tgccatcacg agatttcgat tccaccgccg ccttctatga aaggttgggc ttcggaatcg
     3061 ttttccggga cgccggctgg atgatcctcc agcgcgggga tctcatgctg gagttcttcg
     3121 cccaccccaa cttgtttatt gcagcttata atggttacaa ataaagcaat agcatcacaa
     3181 atttcacaaa taaagcattt ttttcactgc attctagttg tggtttgtcc aaactcatca
     3241 atgtatctta tcatgtctgt ataccgtcga cctctagcta gagcttggcg taatcatggt
     3301 catagctgtt tcctgtgtga aattgttatc cgctcacaat tccacacaac atacgagccg
     3361 gaagcataaa gtgtaaagcc tggggtgcct aatgagtgag ctaactcaca ttaattgcgt
     3421 tgcgctcact gcccgctttc cagtcgggaa acctgtcgtg ccagctgcat taatgaatcg
     3481 gccaacgcgc ggggagaggc ggtttgcgta ttgggcgctc ttccgcttcc tcgctcactg
     3541 actcgctgcg ctcggtcgtt cggctgcggc gagcggtatc agctcactca aaggcggtaa
     3601 tacggttatc cacagaatca ggggataacg caggaaagaa catgtgagca aaaggccagc
     3661 aaaaggccag gaaccgtaaa aaggccgcgt tgctggcgtt tttccatagg ctccgccccc
     3721 ctgacgagca tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactat
     3781 aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc
     3841 cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct
     3901 cacgctgtag gtatctcagt tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg
     3961 aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc
     4021 cggtaagaca cgacttatcg ccactggcag cagccactgg taacaggatt agcagagcga
     4081 ggtatgtagg cggtgctaca gagttcttga agtggtggcc taactacggc tacactagaa
     4141 gaacagtatt tggtatctgc gctctgctga agccagttac cttcggaaaa agagttggta
     4201 gctcttgatc cggcaaacaa accaccgctg gtagcggtgg tttttttgtt tgcaagcagc
     4261 agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct acggggtctg
     4321 acgctcagtg gaacgaaaac tcacgttaag ggattttggt catgagatta tcaaaaagga
     4381 tcttcaccta gatcctttta aattaaaaat gaagttttaa atcaatctaa agtatatatg
     4441 agtaaacttg gtctgacagt taccaatgct taatcagtga ggcacctatc tcagcgatct
     4501 gtctatttcg ttcatccata gttgcctgac tccccgtcgt gtagataact acgatacggg
     4561 agggcttacc atctggcccc agtgctgcaa tgataccgcg agacccacgc tcaccggctc
     4621 cagatttatc agcaataaac cagccagccg gaagggccga gcgcagaagt ggtcctgcaa
     4681 ctttatccgc ctccatccag tctattaatt gttgccggga agctagagta agtagttcgc
     4741 cagttaatag tttgcgcaac gttgttgcca ttgctacagg catcgtggtg tcacgctcgt
     4801 cgtttggtat ggcttcattc agctccggtt cccaacgatc aaggcgagtt acatgatccc
     4861 ccatgttgtg caaaaaagcg gttagctcct tcggtcctcc gatcgttgtc agaagtaagt
     4921 tggccgcagt gttatcactc atggttatgg cagcactgca taattctctt actgtcatgc
     4981 catccgtaag atgcttttct gtgactggtg agtactcaac caagtcattc tgagaatagt
     5041 gtatgcggcg accgagttgc tcttgcccgg cgtcaatacg ggataatacc gcgccacata
     5101 gcagaacttt aaaagtgctc atcattggaa aacgttcttc ggggcgaaaa ctctcaagga
     5161 tcttaccgct gttgagatcc agttcgatgt aacccactcg tgcacccaac tgatcttcag
     5221 catcttttac tttcaccagc gtttctgggt gagcaaaaac aggaaggcaa aatgccgcaa
     5281 aaaagggaat aagggcgaca cggaaatgtt gaatactcat actcttcctt tttcaatatt
     5341 attgaagcat ttatcagggt tattgtctca tgagcggata catatttgaa tgtatttaga
     5401 aaaataaaca aataggggtt ccgcgcacat ttccccgaaa agtgccacct gacgtcgacg
     5461 g
//
