LOCUS       sequence-408148-        8775 bp    DNA     circular SYN 14-APR-2025
DEFINITION  Express mEGFP-tagged fusion protein, NUP98_HOXD13 from 
            patient-derived sequence.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8775)
  AUTHORS   Tripathi S, Shirnekhi HK, Gorman SD, Chandra B, Baggett DW, Park CG,
            Somjee R, Lang B, Hosseini SMH, Pioso BJ, Li Y, Iacobucci I, Gao Q, 
            Edmonson MN, Rice SV, Zhou X, Bollinger J, Mitrea DM, White MR, 
            McGrail DJ, Jarosz DF, Yi SS, Babu MM, Mullighan CG, Zhang J, Sahni 
            N, Kriwacki RW
  TITLE     Defining the condensate landscape of fusion oncoproteins.
  JOURNAL   Nat Commun. 2023 Sep 28;14(1):6008. doi: 10.1038/s41467-023-41655-2.
  PUBMED    37770423
REFERENCE   2  (bases 1 to 8775)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Apr 14, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "Nat 
            Commun."; date: "2023-09-28"; volume: "14(1):6008. doi"; pages: " 
            10.1038/s41467-023-41655-2"
COMMENT     Sequence Label: CL20_mEGFP_NUP98_HOXD13
FEATURES             Location/Qualifiers
     source          1..8775
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     220..239
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     473..490
                     /label=L4440
                     /note="L4440 vector, forward primer"
     polyA_signal    558..692
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(582..601)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     636..655
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     promoter        complement(698..893)
                     /label=SV40 promoter
                     /note="SV40 early promoter"
     rep_origin      712..847
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     protein_bind    952..973
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(988..993,994..1011,1012..1018)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1026..1042
                     /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)."
     primer_bind     1031..1053
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     1050..1066
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     1050..1066
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     1409..1428
                     /label=rbglobpA-R
                     /note="Rabbit beta-globin polyA, reverse primer. Also 
                     called rb-glob-pA-term-R"
     polyA_signal    1427..1482
                     /label=beta-globin poly(A) signal
                     /note="rabbit beta-globin polyadenylation signal (Gil and 
                     Proudfoot, 1987)"
     primer_bind     1528..1547
                     /label=Bglob-pA-R
                     /note="Rabbit beta-globin polyA region, reverse primer"
     CDS             complement(join(3536..4246,4247..4249,4250..4252))
                     /codon_start=1
                     /product="enhanced GFP with monomerizing A206K mutation 
                     (Zacharias et al., 2002)"
                     /label=mEGFP
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(3578..3599)
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     primer_bind     3927..3946
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     4186..4207
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     regulatory      4249..4258
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     promoter        complement(4334..4537)
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     complement(4363..4383)
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     enhancer        4538..4841
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     CDS             complement(5098..5142)
                     /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    5327..5560
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     misc_feature    5920..6037
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     misc_feature    6529..6654
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     LTR             6701..6958
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     enhancer        6960..7339
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        7370..7474
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(7475..7543,7544..8335)
                     /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     complement(7693..7712)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      join(8506..8775,1..319)
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
ORIGIN
        1 gttggactca agacgatagt taccggataa ggcgcagcgg tcgggctgaa cggggggttc
       61 gtgcacacag cccagcttgg agcgaacgac ctacaccgaa ctgagatacc tacagcgtga
      121 gctatgagaa agcgccacgc ttcccgaagg gagaaaggcg gacaggtatc cggtaagcgg
      181 cagggtcgga acaggagagc gcacgaggga gcttccaggg ggaaacgcct ggtatcttta
      241 tagtcctgtc gggtttcgcc acctctgact tgagcgtcga tttttgtgat gctcgtcagg
      301 ggggcggagc ctatggaaaa acgccagcaa cgcggccttt ttacggttcc tggccttttg
      361 ctggcctttt gctcacatgt tctttcctgc gttatcccct gattctgtgg ataaccgtat
      421 taccgccttt gagtgagctg ataccgctcg ccgcagccga acgaccgagc gcagcgagtc
      481 agtgagcgag gaagcggaag agcgcccaat acgcaaaccg cctctccccg cgcgttggcc
      541 gattcattaa tgcagcggat ccagacatga taagatacat tgatgagttt ggacaaacca
      601 caactagaat gcagtgaaaa aaatgcttta tttgtgaaat ttgtgatgct attgctttat
      661 ttgtaaccat tataagctgc aataaacaag ttagcttttt gcaaaagcct aggcctccaa
      721 aaaagcctcc tcactacttc tggaatagct cagaggccga ggcggcctcg gcctctgcat
      781 aaataaaaaa aattagtcag ccatggggcg gagaatgggc ggaactgggc ggagttaggg
      841 gcgggatggg cggagttagg ggcgggacta tggttgctga ctaattgaga tgcggatccg
      901 ctggcacgac aggtttcccg actggaaagc gggcagtgag cgcaacgcaa ttaatgtgag
      961 ttagctcact cattaggcac cccaggcttt acactttatg cttccggctc gtatgttgtg
     1021 tggaattgtg agcggataac aatttcacac aggaaacagc tatgaccatg attacgccaa
     1081 gcttgggctg caggtcgagg gatctccata agagaagagg gacagctatg actgggagta
     1141 gtcaggagag gaggaaaaat ctggctagta aaacatgtaa ggaaaatttt agggatgtta
     1201 aagaaaaaaa taacacaaaa caaaatataa aaaaaatcta acctcaagtc aaggcttttc
     1261 tatggaataa ggaatggaca gcagggggct gtttcatata ctgatgacct ctttatagcc
     1321 aacctttgtt catggcagcc agcatatggg catatgttgc caaactctaa accaaatact
     1381 cattctgatg ttttaaatga tttgccctcc catatgtcct tccgagtgag agacacaaaa
     1441 aattccaaca cactattgca atgaaaataa atttccttta ttagccagaa gtcagatgct
     1501 caaggggctt catgatgtcc ccataatttt tggcagaggg aaaaagatct gctagctcga
     1561 gcagctgaag ctttattgag gcttaagcag tgggttccct agttagccag agagctccca
     1621 ggctcagatc tggtctaacc agagagaccc agtacaggca aaaagcagat cttgtcttct
     1681 ttgggagtga attagccctt ccagtccccc cttttctttt aaaaagtggc taagatctac
     1741 agctgccttg taagtcattg gtcttaaagg taccgtaatc ttatctagac tatgagacag
     1801 tgtctttcag cttactcaca atcttcttgt ccttgacgcg acgattctga aaccagatcg
     1861 tgacctggcg ctccgacaaa ttagtcgcag cagaaatacg acgacgttta tctttattga
     1921 taaacttatt aatagcgtat tcattctcca gctctttcaa ctgtaattta gtatagggca
     1981 cacgcttttt gcgaccacga cggtagacac acatatcggg ctgattcagt gcgacgtcgc
     2041 ctactggggc ctgcggcgcc ccaaaaccca gtgtagccgt cgtggtattg aagcccggag
     2101 ccccaaatgc gccggtgcct aatggacccc caatcttggg ctggttgttt ccgaataaac
     2161 tggcttgccc cgcgccaagg gccgttccga acccagcgcc aagacccgtt ccaagagttc
     2221 cgggcgctgg ttttgagccg aagatagagt tccctgaggt gtttgtaccg aaaccaaaat
     2281 tagaggtatt tgtgttagtt cccaatgtca gtgtaggttt attcccaaaa agtcctcccg
     2341 atgttgttcc aaaggacggt gcggacgtcg tacttgaacc gaaggtagtt aatttattat
     2401 taccaaacaa cgtcgatcca actgcgccaa atccggtatt cgtttgcccg aacaggccgg
     2461 ttccggtgcc gaaggcggtg ccagtcgagg tgttcgttgc cgttccgaaa agacctcccg
     2521 gctgcgaagc ctgtgttact ccgaataaac ccattgtatt cgttgacggc tgaccgattg
     2581 tggaagtatt gccgaatgaa aagccggtgt tctgagtggt ggttgcttgg ccaaacggtt
     2641 tggaaaacag gctcgtggtt tgttgatttt gttggccaaa caaacctccc ggattagtcc
     2701 caaaaccagt agtactggtg ccgaacgcgg tcttattttg cccataggca aagccgctgt
     2761 tggtggtaga agaactgaaa aggcctgttg cggaagaagt tgccggtgaa cttccaaata
     2821 atccggtagt cgtacccgcc cccacttggt tctgcggtcc tttgcggttt gcctgatagt
     2881 cttccaaacg caattcttca agacttttgc tctcgtattc cttcattgcc gtaatgcact
     2941 ggtgttttgt actaatgttt gtactcacgc ccgctttcac catggtatct gtgcctgtag
     3001 ggggattaaa tttgatagta gttcctgttg gggcagccgt aaatgaactc ggtccgaaca
     3061 gacttccgct cgtacttcca aaggggttac tcgttgtgtt cgttgtgccg aaaaggccgc
     3121 cacttgaggt tgaagtcccg aaattaccaa acccggtggg tttattttgt gcaaaggcgt
     3181 tattctggga gctaaacagg gacgtcccag tggaagcagt cccaaataac gtattggctg
     3241 tcccggtgga ggttccaaac ccaaatcctg tagaagtaga tgtagcgggt tgactaaagc
     3301 tggaagttcc aaacaatcct ccgggtttag tttgtgaatt gccaaacaac cccccagtgt
     3361 tgttagagct tccgaaggca ctcgttccaa acgcgccacc gctggttgtt ccgaaccccg
     3421 tattctgccc gaacgtactg gtcgtgccga aacccccagt accgcccccg aaaggtgttc
     3481 cgaacgactt gttaaacata gcggccgcac ttcccccgga gcctccgctt ccgcccttgt
     3541 acagctcgtc catgccgaga gtgatcccgg cggcggtcac gaactccagc aggaccatgt
     3601 gatcgcgctt ctcgttgggg tctttgctca gcttggactg ggtgctcagg tagtggttgt
     3661 cgggcagcag cacggggccg tcgccgatgg gggtgttctg ctggtagtgg tcggcgagct
     3721 gcacgctgcc gtcctcgatg ttgtggcgga tcttgaagtt caccttgatg ccgttcttct
     3781 gcttgtcggc catgatatag acgttgtggc tgttgtagtt gtactccagc ttgtgcccca
     3841 ggatgttgcc gtcctccttg aagtcgatgc ccttcagctc gatgcggttc accagggtgt
     3901 cgccctcgaa cttcacctcg gcgcgggtct tgtagttgcc gtcgtccttg aagaagatgg
     3961 tgcgctcctg gacgtagcct tcgggcatgg cggacttgaa gaagtcgtgc tgcttcatgt
     4021 ggtcggggta gcggctgaag cactgcacgc cgtaggtcag ggtggtcacg agggtgggcc
     4081 agggcacggg cagcttgccg gtggtgcaga tgaacttcag ggtcagcttg ccgtaggtgg
     4141 catcgccctc gccctcgccg gacacgctga acttgtggcc gtttacgtcg ccgtccagct
     4201 cgaccaggat gggcaccacc ccggtgaaca gctcctcgcc cttgctcacc atggtggcga
     4261 ccggtggatc ccgggcccgc ggtaccgtcg actgcagaat tcggttcact aaacgagccc
     4321 ggttcactaa acgagctctg cttatataga cctcccaccg tacacgccta ccgcccattt
     4381 gcgtcaatgg ggcggagttg ttacgacatt ttggaaagtc ccgttgattt tggtgccaaa
     4441 acaaactccc attgacgtca atggggtgga gacttggaaa tccccgtgag tcaaaccgct
     4501 atccacgccc attgatgtac tgccaaaacc gcatcaccat ggtaatagcg atgactaata
     4561 cgtagatgta ctgccaagta ggaaagtccc ataaggtcat gtactgggca taatgccagg
     4621 cgggccattt accgtcattg acgtcaatag ggggcgtact tggcatatga tacacttgat
     4681 gtactgccaa gtgggcagtt taccgtaaat actccaccca ttgacgtcaa tggaaagtcc
     4741 ctattggcgt tactatggga acatacgtca ttattgacgt caatgggcgg gggtcgttgg
     4801 gcggtcagcc aggcgggcca tttaccgtaa gttatgtaac gcggaactcc atatatgggc
     4861 tatgaactaa tgaccccgta attgattact attaataact agcacgcgtt cgaagcttga
     4921 gctcggtccc ctcggggttg ggaggtgggt ctgaaacgat aatggtgaat atccctgcct
     4981 aactctattc actatagaaa gtacagcaaa aactattctt aaacctacca agcctcctac
     5041 tatcattatg aataatttta tataccacag ccaatttgtt atgttaaacc aattccacaa
     5101 acttgcccat ttatctaatt ccaataattc ttgttcattc ttttcttgct ggttttgcga
     5161 ttcttcaatt aaggagtgta ttaagcttgt gtaattgtta atttctctgt cccactccat
     5221 ccaggtcgtg tgattccaaa tctgttccag agatttatta ctccaactag cattccaagg
     5281 cacagcagtg gtgcaaatga gttttccaga gcaaccccaa atccccagga gctgttgatc
     5341 ctttaggtat ctttccacag ccaggattct tgcctggagc tgcttgatgc cccagactgt
     5401 gagttgcaac agatgctgtt gcgcctcaat agccctcagc aaattgttct gctgctgcac
     5461 tataccagac aataattgtc tggcctgtac cgtcagcgtc attgacgctg cgcccatagt
     5521 gcttcctgct gctcccaaga acccaaggaa caaagctcct attcccactg ctcttttttc
     5581 tctctgcacc actcttctct ttgccttggt gggtgctact cctaatggtt caatttttac
     5641 tactttatat ttatataatt cacttctcca attgtccctc atatctcctc cttatggtgt
     5701 tttactaaac ttttccatgt tctaatcctc atcctgtcta cttgccacac aatcatcacc
     5761 tgccatctgt tttccataat ccctaatgat ctttgctttt cttcttggca ctacttttat
     5821 gtcactatta tcttgtatta ctactgcccc ttcacctttc cagaggagct ttgctggtcc
     5881 tttccaaagt ggatttctgc tgtccctgta ataaacccga aaattttgaa tttttgtaat
     5941 ttgtttttgt aattctttag tttgtatgtc tgttgctatt atgtctacta ttctttcccc
     6001 tgcactgtac cccccaatcc ccccttttct tttaaaattg tggatgaata ctgccatttg
     6061 tactgctgtc ttaagatgtt cagcctgatc tcttacctgt cctataattt tctttaattc
     6121 tttattcata gattctacta ctccttgact ttggggattg tagggaattt ccaggtctga
     6181 agatcctgct gcttgctgtg cttttttctt acttttgttt tgctcttcct ctatcttgtc
     6241 taaagcttcc ttggtgtctt ttatctctat cctttgatgc acacaataga gggttgctac
     6301 tgtattatat aatgatctaa gttcttctga tcctgtctga agggatggtt gtagctgtcc
     6361 cagtatttgt ctacagcctt ctgatgtttc taacaggcca gtattaactg cgaatcgttc
     6421 tagctccctg cttgcccata ctatatgttt taatttatat tttttctttc cccctggcct
     6481 taaccgaatt ttttcccatc gcgatctaat tctcccccgc ttaatactga cgctctcgca
     6541 cccatctctc tccttctagc ctccgctagt caaaattttt ggcgtactca ccagtcgccg
     6601 cccctcgcct cttgccgtgc gcgcttcagc aagccgagtc ctgcgtcgag agagctcctc
     6661 tggtttccct ttcgctttca agtccctgtt cgggcgccac tgctagagat tttccacact
     6721 gactaaaagg gtctgaggga tctctagtta ccagagtcac acaacagacg ggcacacact
     6781 acttgaagca ctcaaggcaa gctttattga ggcttaagca gtgggttccc tagttagcca
     6841 gagagctccc aggctcagat ctggtctaac cagagagacc cagtacaggc aaaaagcagc
     6901 tgcttatatg caggatctga gggctcgcca ctccccagtc ccgcccaggc cacgcctccc
     6961 atggtaatag cgatgactaa tacgtagatg tactgccaag taggaaagtc ccataaggtc
     7021 atgtactggg cataatgcca ggcgggccat ttaccgtcat tgacgtcaat agggggcgta
     7081 cttggcatat gatacacttg atgtactgcc aagtgggcag tttaccgtaa atactccacc
     7141 cattgacgtc aatggaaagt ccctattggc gttactatgg gaacatacgt cattattgac
     7201 gtcaatgggc gggggtcgtt gggcggtcag ccaggcgggc catttaccgt aagttatgta
     7261 acgcggaact ccatatatgg gctatgaact aatgaccccg taattgatta ctattaataa
     7321 ctagtcaata atcaatgtcg acccaggtgg cacttttcgg ggaaatgtgc gcggaacccc
     7381 tatttgttta tttttctaaa tacattcaaa tatgtatccg ctcatgagac aataaccctg
     7441 ataaatgctt caataatatt gaaaaaggaa gagtatgagt attcaacatt tccgtgtcgc
     7501 ccttattccc ttttttgcgg cattttgcct tcctgttttt gctcacccag aaacgctggt
     7561 gaaagtaaaa gatgctgaag atcagttggg tgcacgagtg ggttacatcg aactggatct
     7621 caacagcggt aagatccttg agagttttcg ccccgaagaa cgttttccaa tgatgagcac
     7681 ttttaaagtt ctgctatgtg gcgcggtatt atcccgtatt gacgccgggc aagagcaact
     7741 cggtcgccgc atacactatt ctcagaatga cttggttgag tactcaccag tcacagaaaa
     7801 gcatcttacg gatggcatga cagtaagaga attatgcagt gctgccataa ccatgagtga
     7861 taacactgcg gccaacttac ttctgacaac gatcggagga ccgaaggagc taaccgcttt
     7921 tttgcacaac atgggggatc atgtaactcg ccttgatcgt tgggaaccgg agctgaatga
     7981 agccatacca aacgacgagc gtgacaccac gatgcctgta gcaatggcaa caacgttgcg
     8041 caaactatta actggcgaac tacttactct agcttcccgg caacaattaa tagactggat
     8101 ggaggcggat aaagttgcag gaccacttct gcgctcggcc cttccggctg gctggtttat
     8161 tgctgataaa tctggagccg gtgagcgtgg gtctcgcggt atcattgcag cactggggcc
     8221 agatggtaag ccctcccgta tcgtagttat ctacacgacg gggagtcagg caactatgga
     8281 tgaacgaaat agacagatcg ctgagatagg tgcctcactg attaagcatt ggtaactgtc
     8341 agaccaagtt tactcatata tactttagat tgatttaaaa cttcattttt aatttaaaag
     8401 gatctaggtg aagatccttt ttgataatct catgaccaaa atcccttaac gtgagttttc
     8461 gttccactga gcgtcagacc ccgtagaaaa gatcaaagga tcttcttgag atcctttttt
     8521 tctgcgcgta atctgctgct tgcaaacaaa aaaaccaccg ctaccagcgg tggtttgttt
     8581 gccggatcaa gagctaccaa ctctttttcc gaaggtaact ggcttcagca gagcgcagat
     8641 accaaatact gttcttctag tgtagccgta gttaggccac cacttcaaga actctgtagc
     8701 accgcctaca tacctcgctc tgctaatcct gttaccagtg gctgctgcca gtggcgataa
     8761 gtcgtgtctt accgg
//
