LOCUS       sequence-205642-        7438 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  EDEN15 RNA motif.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7438)
  AUTHORS   Ramanathan M, Majzoub K, Rao DS, Neela PH, Zarnegar BJ, Mondal S, 
            Roth JG, Gai H, Kovalski JR, Siprashvili Z, Palmer TD, Carette JE, 
            Khavari PA
  TITLE     RNA-protein interaction detection in living cells.
  JOURNAL   Nat Methods. 2018 Feb 5. pii: nmeth.4601. doi: 10.1038/nmeth.4601.
  PUBMED    29400715
REFERENCE   2  (bases 1 to 7438)
  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: "Nat 
            Methods. 2018 Feb 5. pii: nmeth.4601. doi: 10.1038/nmeth.4601."
COMMENT     Sequence Label: RNA motif plasmid EDEN15
FEATURES             Location/Qualifiers
     source          1..7438
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     LTR             38..671
                     /label=3' LTR
                     /note="3' long terminal repeat (LTR) from HIV-1"
     misc_feature    718..843
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1340..1573
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1758..1802
                     /codon_start=1
                     /product="antigenic peptide corresponding to amino acids 
                     655 to 669 of the HIV envelope protein gp41 (Lutje Hulsik 
                     et al., 2013)"
                     /label=gp41 peptide
                     /note="recognized by the 2H10 single-chain llama nanobody"
                     /translation="KNEQELLELDKWASL"
     misc_feature    2100..2217
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     enhancer        2400..2703
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        2704..2907
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     2858..2878
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     CDS             join(2939..2941,2942..2944,2945..3658)
                     /codon_start=1
                     /product="the original enhanced GFP (Yang et al., 1996)"
                     /label=EGFP
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     CDS             join(2939..2941,2942..2944,2945..3655)
                     /codon_start=1
                     /product="enhanced GFP"
                     /label=EGFP
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(2984..3005)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(3245..3264)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     3592..3613
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     misc_feature    3885..4473
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(3938..3958)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4356..4367)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             4680..4913
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     rep_origin      5038..5173
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     5100..5119
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     primer_bind     complement(5231..5248)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(5402..5990)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5482..5501)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(6161..6952,6953..7021))
                     /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     6784..6803
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(7022..7126)
                     /gene="bla"
                     /label=AmpR promoter
     polyA_signal    7174..7308
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(7211..7230)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     7265..7284
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
ORIGIN
        1 attgtatttg ttaaatatgt actacaaact tagtagttgg aagggctaat tcactcccaa
       61 agaagacaag atatccttga tctgtggatc taccacacac aaggctactt ccctgattag
      121 cagaactaca caccagggcc aggggtcaga tatccactga cctttggatg gtgctacaag
      181 ctagtaccag ttgagccaga taaggtagaa gaggccaata aaggagagaa caccagcttg
      241 ttacaccctg tgagcctgca tgggatggat gacccggaga gagaagtgtt agagtggagg
      301 tttgacagcc gcctagcatt tcatcacgtg gcccgagagc tgcatccgga gtacttcaag
      361 aactgctgat atcgagcttg ctacaaggga ctttccgctg gggactttcc agggaggcgt
      421 ggcctgggcg ggactgggga gtggcgagcc ctcagatcct gcatataagc agctgctttt
      481 tgcctgtact gggtctctct ggttagacca gatctgagcc tgggagctct ctggctaact
      541 agggaaccca ctgcttaagc ctcaataaag cttgccttga gtgcttcaag tagtgtgtgc
      601 ccgtctgttg tgtgactctg gtaactagag atccctcaga cccttttagt cagtgtggaa
      661 aatctctagc agtggcgccc gaacagggac ttgaaagcga aagggaaacc agaggagctc
      721 tctcgacgca ggactcggct tgctgaagcg cgcacggcaa gaggcgaggg gcggcgactg
      781 gtgagtacgc caaaaatttt gactagcgga ggctagaagg agagagatgg gtgcgagagc
      841 gtcagtatta agcgggggag aattagatcg cgatgggaaa aaattcggtt aaggccaggg
      901 ggaaagaaaa aatataaatt aaaacatata gtatgggcaa gcagggagct agaacgattc
      961 gcagttaatc ctggcctgtt agaaacatca gaaggctgta gacaaatact gggacagcta
     1021 caaccatccc ttcagacagg atcagaagaa cttagatcat tatataatac agtagcaacc
     1081 ctctattgtg tgcatcaaag gatagagata aaagacacca aggaagcttt agacaagata
     1141 gaggaagagc aaaacaaaag taagaccacc gcacagcaag cggccggccg ctgatcttca
     1201 gacctggagg aggagatatg agggacaatt ggagaagtga attatataaa tataaagtag
     1261 taaaaattga accattagga gtagcaccca ccaaggcaaa gagaagagtg gtgcagagag
     1321 aaaaaagagc agtgggaata ggagctttgt tccttgggtt cttgggagca gcaggaagca
     1381 ctatgggcgc agcgtcaatg acgctgacgg tacaggccag acaattattg tctggtatag
     1441 tgcagcagca gaacaatttg ctgagggcta ttgaggcgca acagcatctg ttgcaactca
     1501 cagtctgggg catcaagcag ctccaggcaa gaatcctggc tgtggaaaga tacctaaagg
     1561 atcaacagct cctggggatt tggggttgct ctggaaaact catttgcacc actgctgtgc
     1621 cttggaatgc tagttggagt aataaatctc tggaacagat ttggaatcac acgacctgga
     1681 tggagtggga cagagaaatt aacaattaca caagcttaat acactcctta attgaagaat
     1741 cgcaaaacca gcaagaaaag aatgaacaag aattattgga attagataaa tgggcaagtt
     1801 tgtggaattg gtttaacata acaaattggc tgtggtatat aaaattattc ataatgatag
     1861 taggaggctt ggtaggttta agaatagttt ttgctgtact ttctatagtg aatagagtta
     1921 ggcagggata ttcaccatta tcgtttcaga cccacctccc aaccccgagg ggacccgaca
     1981 ggcccgaagg aatagaagaa gaaggtggag agagagacag agacagatcc attcgattag
     2041 tgaacggatc ggcactgcgt gcgccaattc tgcagacaaa tggcagtatt catccacaat
     2101 tttaaaagaa aaggggggat tggggggtac agtgcagggg aaagaatagt agacataata
     2161 gcaacagaca tacaaactaa agaattacaa aaacaaatta caaaaattca aaattttcgg
     2221 gtttattaca gggacagcag agatccagtt tggttagtac cgggcccgct ctagagatcc
     2281 gactcgagta ctaggatcca ttaggcggcc gcgtggataa ccgtattacc gccatgcatt
     2341 agttattaat agtaatcaat tacggggtca ttagttcata gcccatatat ggagttccgc
     2401 gttacataac ttacggtaaa tggcccgcct ggctgaccgc ccaacgaccc ccgcccattg
     2461 acgtcaataa tgacgtatgt tcccatagta acgccaatag ggactttcca ttgacgtcaa
     2521 tgggtggagt atttacggta aactgcccac ttggcagtac atcaagtgta tcatatgcca
     2581 agtacgcccc ctattgacgt caatgacggt aaatggcccg cctggcatta tgcccagtac
     2641 atgaccttat gggactttcc tacttggcag tacatctacg tattagtcat cgctattacc
     2701 atggtgatgc ggttttggca gtacatcaat gggcgtggat agcggtttga ctcacgggga
     2761 tttccaagtc tccaccccat tgacgtcaat gggagtttgt tttggcacca aaatcaacgg
     2821 gactttccaa aatgtcgtaa caactccgcc ccattgacgc aaatgggcgg taggcgtgta
     2881 cggtgggagg tctatataag cagagctggt ttagtgaacc gtcagatccg ctagcaccat
     2941 ggtgagcaag ggcgaggagc tgttcaccgg ggtggtgccc atcctggtcg agctggacgg
     3001 cgacgtaaac ggccacaagt tcagcgtgtc cggcgagggc gagggcgatg ccacctacgg
     3061 caagctgacc ctgaagttca tctgcaccac cggcaagctg cccgtgccct ggcccaccct
     3121 cgtgaccacc ctgacctacg gcgtgcagtg cttcagccgc taccccgacc acatgaagca
     3181 gcacgacttc ttcaagtccg ccatgcccga aggctacgtc caggagcgca ccatcttctt
     3241 caaggacgac ggcaactaca agacccgcgc cgaggtgaag ttcgagggcg acaccctggt
     3301 gaaccgcatc gagctgaagg gcatcgactt caaggaggac ggcaacatcc tggggcacaa
     3361 gctggagtac aactacaaca gccacaacgt ctatatcatg gccgacaagc agaagaacgg
     3421 catcaaggtg aacttcaaga tccgccacaa catcgaggac ggcagcgtgc agctcgccga
     3481 ccactaccag cagaacaccc ccatcggcga cggccccgtg ctgctgcccg acaaccacta
     3541 cctgagcacc cagtccgccc tgagcaaaga ccccaacgag aagcgcgatc acatggtcct
     3601 gctggagttc gtgaccgccg ccgggatcac tctcggcatg gacgagctgt acaagtaact
     3661 tccctaagtc caagccctga aaaagggcaa gcttggccct gaaaaagggc aagcttggcc
     3721 ctgaaaaagg gcaagctttg tttgtttgtt tgttgtttgt ttgtttgttg tttgtttgtt
     3781 tgtagctctt gccctgaaaa agggcagctc ttgccctgaa aaagggcagc tcttgccctg
     3841 aaaaagggct atcgaggata ttatctcgag gtgaattcgt taacaatcaa cctctggatt
     3901 acaaaatttg tgaaagattg actggtattc ttaactatgt tgctcctttt acgctatgtg
     3961 gatacgctgc tttaatgcct ttgtatcatg ctattgcttc ccgtatggct ttcattttct
     4021 cctccttgta taaatcctgg ttgctgtctc tttatgagga gttgtggccc gttgtcaggc
     4081 aacgtggcgt ggtgtgcact gtgtttgctg acgcaacccc cactggttgg ggcattgcca
     4141 ccacctgtca gctcctttcc gggactttcg ctttccccct ccctattgcc acggcggaac
     4201 tcatcgccgc ctgccttgcc cgctgctgga caggggctcg gctgttgggc actgacaatt
     4261 ccgtggtgtt gtcggggaag ctgacgtcct ttccatggct gctcgcctgt gttgccacct
     4321 ggattctgcg cgggacgtcc ttctgctacg tcccttcggc cctcaatcca gcggaccttc
     4381 cttcccgcgg cctgctgccg gctctgcggc ctcttccgcg tcttcgcctt cgccctcaga
     4441 cgagtcggat ctccctttgg gccgcctccc cgcctggaat taattctgca gtcgagacct
     4501 agaaaaacat ggagcaatca caagtagcaa tacagcagct accaatgctg attgtgcctg
     4561 gctagaagca caagaggagg aggaggtggg ttttccagtc acacctcagg tacctttaag
     4621 accaatgact tacaaggcag ctgtagatct tagccacttt ttaaaagaaa agaggggact
     4681 ggaagggcta attcactccc aacgaagaca agatctgctt tttgcttgta ctgggtctct
     4741 ctggttagac cagatctgag cctgggagct ctctggctaa ctagggaacc cactgcttaa
     4801 gcctcaataa agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt tgtgtgactc
     4861 tggtaactag agatccctca gaccctttta gtcagtgtgg aaaatctcta gcagtagtag
     4921 ttcatgtcat cttattattc agtatttata acttgcaaag aaatgaatat cagagagtga
     4981 gaggccttga cattgtttaa accgtcagca accatagtcc cgcccctaac tccgcccatc
     5041 ccgcccctaa ctccgcccag ttccgcccat tctccgcccc atggctgact aatttttttt
     5101 atttatgcag aggccgaggc cgcctctgcc tctgagctat tccagaagta gtgaggaggc
     5161 ttttttggag gcctaggctt ttgcaaaaag ctcggagagg cggtttgcgt attgggcgct
     5221 cttccgcttc ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg cgagcggtat
     5281 cagctcactc aaaggcggta atacggttat ccacagaatc aggggataac gcaggaaaga
     5341 acatgtgagc aaaaggccag caaaaggcca ggaaccgtaa aaaggccgcg ttgctggcgt
     5401 ttttccatag gctccgcccc cctgacgagc atcacaaaaa tcgacgctca agtcagaggt
     5461 ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggaagc tccctcgtgc
     5521 gctctcctgt tccgaccctg ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa
     5581 gcgtggcgct ttctcatagc tcacgctgta ggtatctcag ttcggtgtag gtcgttcgct
     5641 ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc ttatccggta
     5701 actatcgtct tgagtccaac ccggtaagac acgacttatc gccactggca gcagccactg
     5761 gtaacaggat tagcagagcg aggtatgtag gcggtgctac agagttcttg aagtggtggc
     5821 ctaactacgg ctacactaga agaacagtat ttggtatctg cgctctgctg aagccagtta
     5881 ccttcggaaa aagagttggt agctcttgat ccggcaaaca aaccaccgct ggtagcggtg
     5941 gtttttttgt ttgcaagcag cagattacgc gcagaaaaaa aggatctcaa gaagatcctt
     6001 tgatcttttc tacggggtct gacgctcagt ggaacgaaaa ctcacgttaa gggattttgg
     6061 tcatgagatt atcaaaaagg atcttcacct agatcctttt aaattaaaaa tgaagtttta
     6121 aatcaatcta aagtatatat gagtaaactt ggtctgacag ttaccaatgc ttaatcagtg
     6181 aggcacctat ctcagcgatc tgtctatttc gttcatccat agttgcctga ctccccgtcg
     6241 tgtagataac tacgatacgg gagggcttac catctggccc cagtgctgca atgataccgc
     6301 gagacccacg ctcaccggct ccagatttat cagcaataaa ccagccagcc ggaagggccg
     6361 agcgcagaag tggtcctgca actttatccg cctccatcca gtctattaat tgttgccggg
     6421 aagctagagt aagtagttcg ccagttaata gtttgcgcaa cgttgttgcc attgctacag
     6481 gcatcgtggt gtcacgctcg tcgtttggta tggcttcatt cagctccggt tcccaacgat
     6541 caaggcgagt tacatgatcc cccatgttgt gcaaaaaagc ggttagctcc ttcggtcctc
     6601 cgatcgttgt cagaagtaag ttggccgcag tgttatcact catggttatg gcagcactgc
     6661 ataattctct tactgtcatg ccatccgtaa gatgcttttc tgtgactggt gagtactcaa
     6721 ccaagtcatt ctgagaatag tgtatgcggc gaccgagttg ctcttgcccg gcgtcaatac
     6781 gggataatac cgcgccacat agcagaactt taaaagtgct catcattgga aaacgttctt
     6841 cggggcgaaa actctcaagg atcttaccgc tgttgagatc cagttcgatg taacccactc
     6901 gtgcacccaa ctgatcttca gcatctttta ctttcaccag cgtttctggg tgagcaaaaa
     6961 caggaaggca aaatgccgca aaaaagggaa taagggcgac acggaaatgt tgaatactca
     7021 tactcttcct ttttcaatat tattgaagca tttatcaggg ttattgtctc atgagcggat
     7081 acatatttga atgtatttag aaaaataaac aaataggggt tccgcgcaca tttccccgaa
     7141 aagtgccacc tgacgtcgac ggatcgggag atcaacttgt ttattgcagc ttataatggt
     7201 tacaaataaa gcaatagcat cacaaatttc acaaataaag catttttttc actgcattct
     7261 agttgtggtt tgtccaaact catcaatgta tcttatcatg tctggatcaa ctggataact
     7321 caagctaacc aaaatcatcc caaacttccc accccatacc ctattaccac tgccaattac
     7381 ctgtggtttc atttactcta aacctgtgat tcctctgaat tattttcatt ttaaagaa
//
