LOCUS       sequence-422664-        8172 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  expression of mutant U2AF1 in mammalian cells.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8172)
  AUTHORS   Ilagan JO, Ramakrishnan A, Hayes B, Murphy ME, Zebari AS, Bradley P,
            Bradley RK
  TITLE     U2AF1 mutations alter splice site recognition in hematological 
            malignancies.
  JOURNAL   Genome Res. 2015 Jan;25(1):14-26. doi: 10.1101/gr.181016.114. Epub 
            2014 Sep 29.
  PUBMED    25267526
REFERENCE   2  (bases 1 to 8172)
  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"; doi: 
            "10.1101/gr.181016.114"; journalName: "Genome Res"; date: "2015-01";
            volume: "25"; issue: "1"; pages: "14-26"
COMMENT     Sequence Label: pRRL_U2AF1_S34F_mCherry
FEATURES             Location/Qualifiers
     source          1..8172
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     LTR             224..404
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from HIV-1"
     misc_feature    451..576
                     /label=HIV-1 Psi
                     /note="packaging signal of human immunodeficiency virus 
                     type 1"
     misc_feature    1069..1302
                     /label=RRE
                     /note="The Rev response element (RRE) of HIV-1 allows for 
                     Rev-dependent mRNA export from the nucleus to the 
                     cytoplasm."
     CDS             1487..1531
                     /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    1798..1915
                     /label=cPPT/CTS
                     /note="central polypurine tract and central termination 
                     sequence of HIV-1"
     promoter        1961..2471
                     /label=hPGK promoter
                     /note="human phosphoglycerate kinase 1 promoter"
     primer_bind     2390..2408
                     /label=hPGK-F
                     /note="Human PGK promoter, forward primer"
     CDS             3209..3232
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     CDS             3233..3286
                     /codon_start=1
                     /product="2A peptide from Thosea asigna virus capsid 
                     protein"
                     /label=T2A
                     /note="Eukaryotic ribosomes fail to insert a peptide bond 
                     between the Gly and Pro residues, yielding separate 
                     polypeptides."
                     /translation="EGRGSLLTCGDVEENPGP"
     CDS             3287..3997
                     /codon_start=1
                     /product="monomeric derivative of DsRed fluorescent protein
                     (Shaner et al., 2004)"
                     /label=mCherry
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEG
                     TQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNF
                     EDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALK
                     GEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERA
                     EGRHSTGGMDELYK"
     primer_bind     complement(3432..3450)
                     /label=mCherry-R
                     /note="mCherry, reverse primer"
     primer_bind     3700..3719
                     /label=mCherry-F
                     /note="mCherry, forward primer"
     misc_feature    4012..4600
                     /label=WPRE
                     /note="woodchuck hepatitis virus posttranscriptional 
                     regulatory element"
     primer_bind     complement(4065..4085)
                     /label=WPRE-R
                     /note="WPRE, reverse primer"
     CDS             complement(4483..4494)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     LTR             4687..4920
                     /label=3' LTR (Delta-U3)
                     /note="self-inactivating 3' long terminal repeat (LTR) from
                     HIV-1"
     polyA_signal    4992..5113
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(5029..5048)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     5083..5102
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     rep_origin      5153..5288
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(5308..5327)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(5309..5327)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(5337..5354)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(5337..5353)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(5346..5368)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      5495..5950
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5582..5601)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5792..5813
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     promoter        5976..6080
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(6081..6149,6150..6941)
                     /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(6299..6318)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      7112..7700
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     7601..7620
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     7854..7871
                     /label=L4440
                     /note="L4440 vector, forward primer"
     promoter        join(8024..8029,8030..8047,8048..8054)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    8062..8078
                     /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     8067..8089
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     8086..8102
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     8086..8102
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     8121..8141
                     /label=T3
                     /note="T3 promoter, forward primer"
     promoter        8123..8141
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     promoter        join(8169..8172,1..223)
                     /label=RSV promoter
                     /note="Rous sarcoma virus enhancer/promoter"
ORIGIN
        1 gtcttatgca atactcttgt agtcttgcaa catggtaacg atgagttagc aacatgcctt
       61 acaaggagag aaaaagcacc gtgcatgccg attggtggaa gtaaggtggt acgatcgtgc
      121 cttattagga aggcaacaga cgggtctgac atggattgga cgaaccactg aattgccgca
      181 ttgcagagat attgtattta agtgcctagc tcgatacata aacgggtctc tctggttaga
      241 ccagatctga gcctgggagc tctctggcta actagggaac ccactgctta agcctcaata
      301 aagcttgcct tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta
      361 gagatccctc agaccctttt agtcagtgtg gaaaatctct agcagtggcg cccgaacagg
      421 gacttgaaag cgaaagggaa accagaggag ctctctcgac gcaggactcg gcttgctgaa
      481 gcgcgcacgg caagaggcga ggggcggcga ctggtgagta cgccaaaaat tttgactagc
      541 ggaggctaga aggagagaga tgggtgcgag agcgtcagta ttaagcgggg gagaattaga
      601 tcgcgatggg aaaaaattcg gttaaggcca gggggaaaga aaaaatataa attaaaacat
      661 atagtatggg caagcaggga gctagaacga ttcgcagtta atcctggcct gttagaaaca
      721 tcagaaggct gtagacaaat actgggacag ctacaaccat cccttcagac aggatcagaa
      781 gaacttagat cattatataa tacagtagca accctctatt gtgtgcatca aaggatagag
      841 ataaaagaca ccaaggaagc tttagacaag atagaggaag agcaaaacaa aagtaagacc
      901 accgcacagc aagcggccgc tgatcttcag acctggagga ggagatatga gggacaattg
      961 gagaagtgaa ttatataaat ataaagtagt aaaaattgaa ccattaggag tagcacccac
     1021 caaggcaaag agaagagtgg tgcagagaga aaaaagagca gtgggaatag gagctttgtt
     1081 ccttgggttc ttgggagcag caggaagcac tatgggcgca gcgtcaatga cgctgacggt
     1141 acaggccaga caattattgt ctggtatagt gcagcagcag aacaatttgc tgagggctat
     1201 tgaggcgcaa cagcatctgt tgcaactcac agtctggggc atcaagcagc tccaggcaag
     1261 aatcctggct gtggaaagat acctaaagga tcaacagctc ctggggattt ggggttgctc
     1321 tggaaaactc atttgcacca ctgctgtgcc ttggaatgct agttggagta ataaatctct
     1381 ggaacagatt tggaatcaca cgacctggat ggagtgggac agagaaatta acaattacac
     1441 aagcttaata cactccttaa ttgaagaatc gcaaaaccag caagaaaaga atgaacaaga
     1501 attattggaa ttagataaat gggcaagttt gtggaattgg tttaacataa caaattggct
     1561 gtggtatata aaattattca taatgatagt aggaggcttg gtaggtttaa gaatagtttt
     1621 tgctgtactt tctatagtga atagagttag gcagggatat tcaccattat cgtttcagac
     1681 ccacctccca accccgaggg gacccgacag gcccgaagga atagaagaag aaggtggaga
     1741 gagagacaga gacagatcca ttcgattagt gaacggatct cgacggtatc ggttaacttt
     1801 taaaagaaaa ggggggattg gggggtacag tgcaggggaa agaatagtag acataatagc
     1861 aacagacata caaactaaag aattacaaaa acaaattaca aaaattcaaa attttatcga
     1921 tcacgagact agcctcgaga agcttgatat cgaattccac ggggttgggg ttgcgccttt
     1981 tccaaggcag ccctgggttt gcgcagggac gcggctgctc tgggcgtggt tccgggaaac
     2041 gcagcggcgc cgaccctggg tctcgcacat tcttcacgtc cgttcgcagc gtcacccgga
     2101 tcttcgccgc tacccttgtg ggccccccgg cgacgcttcc tgctccgccc ctaagtcggg
     2161 aaggttcctt gcggttcgcg gcgtgccgga cgtgacaaac ggaagccgca cgtctcacta
     2221 gtaccctcgc agacggacag cgccagggag caatggcagc gcgccgaccg cgatgggctg
     2281 tggccaatag cggctgctca gcagggcgcg ccgagagcag cggccgggaa ggggcggtgc
     2341 gggaggcggg gtgtggggcg gtagtgtggg ccctgttcct gcccgcgcgg tgttccgcat
     2401 tctgcaagcc tccggagcgc acgtcggcag tcggctccct cgttgaccga atcaccgacc
     2461 tctctcccca gggggatccg aaatggcgga gtatctggcc tccatcttcg gcaccgagaa
     2521 agacaaagtc aactgttcat tttatttcaa aattggagca tgtcgtcatg gagacaggtg
     2581 ctttcggttg cacaataaac cgacgtttag ccagaccatt gccctcttga acatttaccg
     2641 taaccctcaa aactcttccc agtctgctga cggtttgcgc tgtgccgtga gcgatgtgga
     2701 gatgcaggaa cactatgatg agttttttga ggaggttttt acagaaatgg aggagaagta
     2761 tggggaagta gaggagatga acgtctgtga caacctggga gaccacctgg tggggaacgt
     2821 gtacgtcaag tttcgccgtg aggaagatgc ggaaaaggct gtgattgact tgaataaccg
     2881 ttggtttaat ggacagccga tccacgccga gctgtcaccc gtgacggact tcagagaagc
     2941 ctgctgccgt cagtatgaga tgggagaatg cacacgaggc ggcttctgca acttcatgca
     3001 tttgaagccc atttccagag agctgcggcg ggagctgtat ggccgccgtc gcaagaagca
     3061 tagatcaaga tcccgatccc gggagcgtcg ttctcggtct agagaccgtg gtcgtggcgg
     3121 tggcggtggc ggtggtggag gtggcggcgg acgggagcgt gacaggaggc ggtcgagaga
     3181 tcgtgaaaga tctgggcgat tcggcggcga ctacaaagac gatgacgaca aggagggcag
     3241 aggaagtctt ctaacatgcg gtgacgtgga ggagaatccc ggccctatgg tgagcaaggg
     3301 cgaggaggat aacatggcca tcatcaagga gttcatgcgc ttcaaggtgc acatggaggg
     3361 ctccgtgaac ggccacgagt tcgagatcga gggcgagggc gagggccgcc cctacgaggg
     3421 cacccagacc gccaagctga aggtgaccaa gggtggcccc ctgcccttcg cctgggacat
     3481 cctgtcccct cagttcatgt acggctccaa ggcctacgtg aagcaccccg ccgacatccc
     3541 cgactacttg aagctgtcct tccccgaggg cttcaagtgg gagcgcgtga tgaacttcga
     3601 ggacggcggc gtggtgaccg tgacccagga ctcctccctg caggacggcg agttcatcta
     3661 caaggtgaag ctgcgcggca ccaacttccc ctccgacggc cccgtaatgc agaagaagac
     3721 catgggctgg gaggcctcct ccgagcggat gtaccccgag gacggcgccc tgaagggcga
     3781 gatcaagcag aggctgaagc tgaaggacgg cggccactac gacgctgagg tcaagaccac
     3841 ctacaaggcc aagaagcccg tgcagctgcc cggcgcctac aacgtcaaca tcaagttgga
     3901 catcacctcc cacaacgagg actacaccat cgtggaacag tacgaacgcg ccgagggccg
     3961 ccactccacc ggcggcatgg acgagctgta caagtaagcg gccgcctcga caatcaacct
     4021 ctggattaca aaatttgtga aagattgact ggtattctta actatgttgc tccttttacg
     4081 ctatgtggat acgctgcttt aatgcctttg tatcatgcta ttgcttcccg tatggctttc
     4141 attttctcct ccttgtataa atcctggttg ctgtctcttt atgaggagtt gtggcccgtt
     4201 gtcaggcaac gtggcgtggt gtgcactgtg tttgctgacg caacccccac tggttggggc
     4261 attgccacca cctgtcagct cctttccggg actttcgctt tccccctccc tattgccacg
     4321 gcggaactca tcgccgcctg ccttgcccgc tgctggacag gggctcggct gttgggcact
     4381 gacaattccg tggtgttgtc ggggaagctg acgtcctttc catggctgct cgcctgtgtt
     4441 gccacctgga ttctgcgcgg gacgtccttc tgctacgtcc cttcggccct caatccagcg
     4501 gaccttcctt cccgcggcct gctgccggct ctgcggcctc ttccgcgtct tcgccttcgc
     4561 cctcagacga gtcggatctc cctttgggcc gcctccccgc ctggaattcg agctcggtac
     4621 ctttaagacc aatgacttac aaggcagctg tagatcttag ccacttttta aaagaaaagg
     4681 ggggactgga agggctaatt cactcccaac gaagacaaga tctgcttttt gcttgtactg
     4741 ggtctctctg gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac
     4801 tgcttaagcc tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt
     4861 gtgactctgg taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca
     4921 gtagtagttc atgtcatctt attattcagt atttataact tgcaaagaaa tgaatatcag
     4981 agagtgagag gaacttgttt attgcagctt ataatggtta caaataaagc aatagcatca
     5041 caaatttcac aaataaagca tttttttcac tgcattctag ttgtggtttg tccaaactca
     5101 tcaatgtatc ttatcatgtc tggctctagc tatcccgccc ctaactccgc ccatcccgcc
     5161 cctaactccg cccagttccg cccattctcc gccccatggc tgactaattt tttttattta
     5221 tgcagaggcc gaggccgcct cggcctctga gctattccag aagtagtgag gaggcttttt
     5281 tggaggccta gggacgtacc caattcgccc tatagtgagt cgtattacgc gcgctcactg
     5341 gccgtcgttt tacaacgtcg tgactgggaa aaccctggcg ttacccaact taatcgcctt
     5401 gcagcacatc cccctttcgc cagctggcgt aatagcgaag aggcccgcac cgatcgccct
     5461 tcccaacagt tgcgcagcct gaatggcgaa tgggacgcgc cctgtagcgg cgcattaagc
     5521 gcggcgggtg tggtggttac gcgcagcgtg accgctacac ttgccagcgc cctagcgccc
     5581 gctcctttcg ctttcttccc ttcctttctc gccacgttcg ccggctttcc ccgtcaagct
     5641 ctaaatcggg ggctcccttt agggttccga tttagtgctt tacggcacct cgaccccaaa
     5701 aaacttgatt agggtgatgg ttcacgtagt gggccatcgc cctgatagac ggtttttcgc
     5761 cctttgacgt tggagtccac gttctttaat agtggactct tgttccaaac tggaacaaca
     5821 ctcaacccta tctcggtcta ttcttttgat ttataaggga ttttgccgat ttcggcctat
     5881 tggttaaaaa atgagctgat ttaacaaaaa tttaacgcga attttaacaa aatattaacg
     5941 cttacaattt aggtggcact tttcggggaa atgtgcgcgg aacccctatt tgtttatttt
     6001 tctaaataca ttcaaatatg tatccgctca tgagacaata accctgataa atgcttcaat
     6061 aatattgaaa aaggaagagt atgagtattc aacatttccg tgtcgccctt attccctttt
     6121 ttgcggcatt ttgccttcct gtttttgctc acccagaaac gctggtgaaa gtaaaagatg
     6181 ctgaagatca gttgggtgca cgagtgggtt acatcgaact ggatctcaac agcggtaaga
     6241 tccttgagag ttttcgcccc gaagaacgtt ttccaatgat gagcactttt aaagttctgc
     6301 tatgtggcgc ggtattatcc cgtattgacg ccgggcaaga gcaactcggt cgccgcatac
     6361 actattctca gaatgacttg gttgagtact caccagtcac agaaaagcat cttacggatg
     6421 gcatgacagt aagagaatta tgcagtgctg ccataaccat gagtgataac actgcggcca
     6481 acttacttct gacaacgatc ggaggaccga aggagctaac cgcttttttg cacaacatgg
     6541 gggatcatgt aactcgcctt gatcgttggg aaccggagct gaatgaagcc ataccaaacg
     6601 acgagcgtga caccacgatg cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg
     6661 gcgaactact tactctagct tcccggcaac aattaataga ctggatggag gcggataaag
     6721 ttgcaggacc acttctgcgc tcggcccttc cggctggctg gtttattgct gataaatctg
     6781 gagccggtga gcgtgggtct cgcggtatca ttgcagcact ggggccagat ggtaagccct
     6841 cccgtatcgt agttatctac acgacgggga gtcaggcaac tatggatgaa cgaaatagac
     6901 agatcgctga gataggtgcc tcactgatta agcattggta actgtcagac caagtttact
     6961 catatatact ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga
     7021 tcctttttga taatctcatg accaaaatcc cttaacgtga gttttcgttc cactgagcgt
     7081 cagaccccgt agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct
     7141 gctgcttgca aacaaaaaaa ccaccgctac cagcggtggt ttgtttgccg gatcaagagc
     7201 taccaactct ttttccgaag gtaactggct tcagcagagc gcagatacca aatactgttc
     7261 ttctagtgta gccgtagtta ggccaccact tcaagaactc tgtagcaccg cctacatacc
     7321 tcgctctgct aatcctgtta ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg
     7381 ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt
     7441 cgtgcacaca gcccagcttg gagcgaacga cctacaccga actgagatac ctacagcgtg
     7501 agctatgaga aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg
     7561 gcagggtcgg aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt
     7621 atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag
     7681 gggggcggag cctatggaaa aacgccagca acgcggcctt tttacggttc ctggcctttt
     7741 gctggccttt tgctcacatg ttctttcctg cgttatcccc tgattctgtg gataaccgta
     7801 ttaccgcctt tgagtgagct gataccgctc gccgcagccg aacgaccgag cgcagcgagt
     7861 cagtgagcga ggaagcggaa gagcgcccaa tacgcaaacc gcctctcccc gcgcgttggc
     7921 cgattcatta atgcagctgg cacgacaggt ttcccgactg gaaagcgggc agtgagcgca
     7981 acgcaattaa ggtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc
     8041 cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga aacagctatg
     8101 accatgatta cgccaagcgc gcaattaacc ctcactaaag ggaacaaaag ctggagctgc
     8161 aagcttaatg ta
//
