LOCUS       sequence-420888-        6488 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  LR vector for integration of Chtop+exon(138nt) into N2a FRT rtTA3 
            expression cells (BioID vector).
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6488)
  AUTHORS   Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt 
            RJ, Gingras AC, Blencowe BJ
  TITLE     Systematic analysis of alternative exon-dependent interactome 
            remodeling reveals multitasking functions of gene regulatory 
            factors.
  JOURNAL   Mol Cell. 2023 Dec 7;83(23):4222-4238.e10. doi: 
            10.1016/j.molcel.2023.10.034.
  PUBMED    38065061
REFERENCE   2  (bases 1 to 6488)
  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: 
            "10.1016/j.molcel.2023.10"; journalName: "Mol Cell"; date: 
            "2023-12-7- 7"; volume: "83"; issue: "23"; pages: "4222-4238.e10"
COMMENT     Sequence Label: 5'-BirA-FLAG Chtop+exon minimal CMV pCDNA5
FEATURES             Location/Qualifiers
     source          1..6488
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     polyA_signal    520..641
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(557..576)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     611..630
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(690..706)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(690..706)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(703..725)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    714..730
                     /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(738..744,745..762,763..768))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    783..804
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(921..938)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(1092..1680)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(1172..1191)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(1851..2642,2643..2711))
                     /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     2474..2493
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(2712..2816)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(2891..2910)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     protein_bind    3109..3127
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    3146..3164
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    3183..3201
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    3220..3238
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     primer_bind     3260..3284
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     CDS             join(3417..3767,3768..3770,3771..4379)
                     /codon_start=1
                     /product="promiscuous R118G mutant of the E. coli biotin 
                     protein ligase (Cronan, 2005)"
                     /label=BirA(R118G)
                     /note="also known as BirA* or BioID"
                     /translation="MKDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRD
                     WGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSG
                     DACIAEYQQAGRGGRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRK
                     LGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQG
                     WITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIG
                     DKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLRSAEK"
     CDS             4410..4433
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     protein_bind    4446..4470
                     /gene="mutant version of attB"
                     /label=attB1
                     /bound_moiety="BP Clonase(TM)"
                     /note="recombination site for the Gateway(R) BP reaction"
     protein_bind    complement(5221..5245)
                     /gene="mutant version of attB"
                     /label=attB2
                     /bound_moiety="BP Clonase(TM)"
                     /note="recombination site for the Gateway(R) BP reaction"
     primer_bind     complement(5287..5304)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    5293..5517
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     primer_bind     complement(5650..5669)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     protein_bind    5801..5848
                     /label=FRT
                     /bound_moiety="FLP recombinase from the Saccharomyces 
                     cerevisiae 2u plasmid"
                     /note="FLP-mediated recombination occurs in the 8-bp core 
                     sequence TCTAGAAA (Turan and Bode, 2011)."
     CDS             join(5856..6488,1..390)
                     /codon_start=1
                     /product="hygromycin B phosphotransferase"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="KKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRGY
                     VLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLPE
                     TELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQT
                     VMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMFG
                     DSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDGN
                     FDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAKE
                     "
     CDS             join(5856..6488,1..390)
                     /codon_start=1
                     /gene="aph(4)-Ia"
                     /product="aminoglycoside phosphotransferase from E. coli"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="KKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRGY
                     VLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLPE
                     TELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQT
                     VMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMFG
                     DSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDGN
                     FDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAKE
                     "
ORIGIN
        1 gcggtcattg actggagcga ggcgatgttc ggggattccc aatacgaggt cgccaacatc
       61 ttcttctgga ggccgtggtt ggcttgtatg gagcagcaga cgcgctactt cgagcggagg
      121 catccggagc ttgcaggatc gccgcggctc cgggcgtata tgctccgcat tggtcttgac
      181 caactctatc agagcttggt tgacggcaat ttcgatgatg cagcttgggc gcagggtcga
      241 tgcgacgcaa tcgtccgatc cggagccggg actgtcgggc gtacacaaat cgcccgcaga
      301 agcgcggccg tctggaccga tggctgtgta gaagtactcg ccgatagtgg aaaccgacgc
      361 cccagcactc gtccgagggc aaaggaatag cacgtactac gagatttcga ttccaccgcc
      421 gccttctatg aaaggttggg cttcggaatc gttttccggg acgccggctg gatgatcctc
      481 cagcgcgggg atctcatgct ggagttcttc gcccacccca acttgtttat tgcagcttat
      541 aatggttaca aataaagcaa tagcatcaca aatttcacaa ataaagcatt tttttcactg
      601 cattctagtt gtggtttgtc caaactcatc aatgtatctt atcatgtctg tataccgtcg
      661 acctctagct agagcttggc gtaatcatgg tcatagctgt ttcctgtgtg aaattgttat
      721 ccgctcacaa ttccacacaa catacgagcc ggaagcataa agtgtaaagc ctggggtgcc
      781 taatgagtga gctaactcac attaattgcg ttgcgctcac tgcccgcttt ccagtcggga
      841 aacctgtcgt gccagctgca ttaatgaatc ggccaacgcg cggggagagg cggtttgcgt
      901 attgggcgct cttccgcttc ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg
      961 cgagcggtat cagctcactc aaaggcggta atacggttat ccacagaatc aggggataac
     1021 gcaggaaaga acatgtgagc aaaaggccag caaaaggcca ggaaccgtaa aaaggccgcg
     1081 ttgctggcgt ttttccatag gctccgcccc cctgacgagc atcacaaaaa tcgacgctca
     1141 agtcagaggt ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggaagc
     1201 tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg gatacctgtc cgcctttctc
     1261 ccttcgggaa gcgtggcgct ttctcatagc tcacgctgta ggtatctcag ttcggtgtag
     1321 gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc
     1381 ttatccggta actatcgtct tgagtccaac ccggtaagac acgacttatc gccactggca
     1441 gcagccactg gtaacaggat tagcagagcg aggtatgtag gcggtgctac agagttcttg
     1501 aagtggtggc ctaactacgg ctacactaga agaacagtat ttggtatctg cgctctgctg
     1561 aagccagtta ccttcggaaa aagagttggt agctcttgat ccggcaaaca aaccaccgct
     1621 ggtagcggtg gtttttttgt ttgcaagcag cagattacgc gcagaaaaaa aggatctcaa
     1681 gaagatcctt tgatcttttc tacggggtct gacgctcagt ggaacgaaaa ctcacgttaa
     1741 gggattttgg tcatgagatt atcaaaaagg atcttcacct agatcctttt aaattaaaaa
     1801 tgaagtttta aatcaatcta aagtatatat gagtaaactt ggtctgacag ttaccaatgc
     1861 ttaatcagtg aggcacctat ctcagcgatc tgtctatttc gttcatccat agttgcctga
     1921 ctccccgtcg tgtagataac tacgatacgg gagggcttac catctggccc cagtgctgca
     1981 atgataccgc gagacccacg ctcaccggct ccagatttat cagcaataaa ccagccagcc
     2041 ggaagggccg agcgcagaag tggtcctgca actttatccg cctccatcca gtctattaat
     2101 tgttgccggg aagctagagt aagtagttcg ccagttaata gtttgcgcaa cgttgttgcc
     2161 attgctacag gcatcgtggt gtcacgctcg tcgtttggta tggcttcatt cagctccggt
     2221 tcccaacgat caaggcgagt tacatgatcc cccatgttgt gcaaaaaagc ggttagctcc
     2281 ttcggtcctc cgatcgttgt cagaagtaag ttggccgcag tgttatcact catggttatg
     2341 gcagcactgc ataattctct tactgtcatg ccatccgtaa gatgcttttc tgtgactggt
     2401 gagtactcaa ccaagtcatt ctgagaatag tgtatgcggc gaccgagttg ctcttgcccg
     2461 gcgtcaatac gggataatac cgcgccacat agcagaactt taaaagtgct catcattgga
     2521 aaacgttctt cggggcgaaa actctcaagg atcttaccgc tgttgagatc cagttcgatg
     2581 taacccactc gtgcacccaa ctgatcttca gcatctttta ctttcaccag cgtttctggg
     2641 tgagcaaaaa caggaaggca aaatgccgca aaaaagggaa taagggcgac acggaaatgt
     2701 tgaatactca tactcttcct ttttcaatat tattgaagca tttatcaggg ttattgtctc
     2761 atgagcggat acatatttga atgtatttag aaaaataaac aaataggggt tccgcgcaca
     2821 tttccccgaa aagtgccacc tgacgtcgac ggatcgggag atctcccgat cccctatggt
     2881 gcactctcag tacaatctgc tctgatgccg catagttaag ccagtatctg ctccctgctt
     2941 gtgtgttgga ggtcgctgag tagtgcgcga gcaaaattta agctacaaca aggcaaggct
     3001 tgaccgacaa ttgcatgaag aatctgctta gggttaggcg ttttgcgctg cttcgcgatg
     3061 tacgggccag atatacgcgt ctcgagggat ccaagctggc cgcacgtctc cctatcagtg
     3121 atagagaagt cgacacgtct cgagctccct atcagtgata gagaaggtac gtctagaacg
     3181 tctccctatc agtgatagag aagtcgacac gtctcgagct ccctatcagt gatagagaag
     3241 gtacccccta tataagcaga gctcgtttag tgaaccgtca gatcgcctgg agacgccatc
     3301 cacgctgttt tgacctccat agaagacacc gggaccgatc cagcctccgc ggaggctgga
     3361 tcctctagcg tttaaactta agcttggtac cgagctcgga tccagctagc gccaccatga
     3421 aggacaacac cgtgcccctg aagctgatcg ccctgctggc caacggcgag ttccacagcg
     3481 gcgagcagct gggcgagacc ctgggcatga gccgggccgc catcaacaag cacatccaga
     3541 ccctgcggga ctggggcgtg gacgtgttca ccgtgcccgg caagggctac agcctgcccg
     3601 agcccatcca gctgctgaac gccaagcaga tcctgggcca gctggacggc ggcagcgtgg
     3661 ccgtgctgcc cgtgatcgac agcaccaacc agtacctgct ggaccggatc ggcgagctga
     3721 agagcggcga cgcctgcatc gccgagtacc agcaggccgg ccggggcggc cggggccgga
     3781 agtggttcag ccccttcggc gccaacctgt acctgagcat gttctggcgg ctggagcagg
     3841 gccccgccgc cgccatcggc ctgagcctgg tgatcggcat cgtgatggcc gaggtgctgc
     3901 ggaagctggg cgccgacaag gtgcgggtga agtggcccaa cgacctgtac ctgcaggacc
     3961 ggaagctggc cggcatcctg gtggagctga ccggcaagac cggcgacgcc gcccagatcg
     4021 tgatcggcgc cggcatcaac atggccatgc ggcgggtgga ggagagcgtg gtgaaccagg
     4081 gctggatcac cctgcaggag gccggcatca acctggaccg gaacaccctg gccgccatgc
     4141 tgatccggga gctgcgggcc gccctggagc tgttcgagca ggagggcctg gccccctacc
     4201 tgagccggtg ggagaagctg gacaacttca tcaaccggcc cgtgaagctg atcatcggcg
     4261 acaaggagat cttcggcatc agccggggca tcgacaagca gggcgccctg ctgctggagc
     4321 aggacggcat catcaagccc tggatgggcg gcgagatcag cctgcggagc gccgagaagg
     4381 ggggatctgg ccccggcggc ggcgcgccag actacaaaga cgatgacgat aaactaggcg
     4441 cgcccacaag tttgtacaaa aaagttggca ccgctgcaca gtcagcgccg aaagttgtgc
     4501 taaaaagcac caccaagatg tctctaaatg agcgctttac taatatgctg aagaacaaac
     4561 agccgatgcc agtgaatatt cgggcttcga tgcagcagca gcagcagcta gccagtgcca
     4621 gaaacagaag actggcccag cagatggaga atagaccctc tgtccaggca gcattaaaac
     4681 ttaagcagaa gagcttaaag cagcgcctgg gtaagagtaa tatccaggca cggttaggcc
     4741 gacccatagg tgccctggcc aggggagcaa ttggaggaag aggcctaccc ataatccaga
     4801 gaggcttgcc ccgaggagga ctacgtgggg gacgtgctac cagaaccctg cttaggggtg
     4861 ggatgtcgct ccgaggtcaa aacctgctcc gaggtggacg agccgtagct ccccgaatgg
     4921 gcttaagaag aggtggtgtt cgaggtcgtg gaggtcctgg gagagggggc ctagggcgtg
     4981 gagctatggg tcgtggcgga atcggtggta gaggtcgggg tatgataggt cggggaagag
     5041 ggggctttgg aggcagaggc cgaggtcgtg gccgagggag aggtgccctc actcgccctg
     5101 tattgaccaa ggagcagctg gacaaccaat tggatgcata catgtcgaaa actaaaggac
     5161 acctggatgc tgaattggat gcctacatgg cacagacaga tcctgaaacc aatgattgat
     5221 acccaacttt cttgtacaaa gtggtgtgac tcgagtctag agggcccgtt taaacccgct
     5281 gatcagcctc gactgtgcct tctagttgcc agccatctgt tgtttgcccc tcccccgtgc
     5341 cttccttgac cctggaaggt gccactccca ctgtcctttc ctaataaaat gaggaaattg
     5401 catcgcattg tctgagtagg tgtcattcta ttctgggggg tggggtgggg caggacagca
     5461 agggggagga ttgggaagac aatagcaggc atgctgggga tgcggtgggc tctatggctt
     5521 ctgaggcgga aagaaccagc tggggctcta gggggtatcc ccacgcgccc tgtagcggcg
     5581 cattaagcgc ggcgggtgtg gtggttacgc gcagcgtgac cgctacactt gccagcgccc
     5641 tagcgcccgc tcctttcgct ttcttccctt cctttctcgc cacgttcgcc ggctttcccc
     5701 gtcaagctct aaatcggggg ctccctttag ggttccgatt tagtgcttta cggcacctcg
     5761 accccaaaaa acttgattag ggtgatggtt cacgtaccta gaagttccta ttccgaagtt
     5821 cctattctct agaaagtata ggaacttcct tggccaaaaa gcctgaactc accgcgacgt
     5881 ctgtcgagaa gtttctgatc gaaaagttcg acagcgtctc cgacctgatg cagctctcgg
     5941 agggcgaaga atctcgtgct ttcagcttcg atgtaggagg gcgtggatat gtcctgcggg
     6001 taaatagctg cgccgatggt ttctacaaag atcgttatgt ttatcggcac tttgcatcgg
     6061 ccgcgctccc gattccggaa gtgcttgaca ttggggaatt cagcgagagc ctgacctatt
     6121 gcatctcccg ccgtgcacag ggtgtcacgt tgcaagacct gcctgaaacc gaactgcccg
     6181 ctgttctgca gccggtcgcg gaggccatgg atgcgatcgc tgcggccgat cttagccaga
     6241 cgagcgggtt cggcccattc ggaccgcaag gaatcggtca atacactaca tggcgtgatt
     6301 tcatatgcgc gattgctgat ccccatgtgt atcactggca aactgtgatg gacgacaccg
     6361 tcagtgcgtc cgtcgcgcag gctctcgatg agctgatgct ttgggccgag gactgccccg
     6421 aagtccggca cctcgtgcac gcggatttcg gctccaacaa tgtcctgacg gacaatggcc
     6481 gcataaca
//
