LOCUS       sequence-421018-        7314 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  LR vector for integration of Kdm1a-exon into N2a FRT rtTA3 
            expression cells.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7314)
  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 7314)
  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'-3xFLAG Kdm1a-exon minimal CMV pCDNA5
FEATURES             Location/Qualifiers
     source          1..7314
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     polyA_signal    933..1054
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(970..989)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     1024..1043
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(1103..1119)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1103..1119)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(1116..1138)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    1127..1143
                     /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(1151..1157,1158..1175,1176..1181))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1196..1217
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(1334..1351)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(1505..2093)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(1585..1604)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2264..3055,3056..3124))
                     /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     2887..2906
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(3125..3229)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(3304..3323)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     protein_bind    3522..3540
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    3559..3577
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    3596..3614
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    3633..3651
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     primer_bind     3673..3697
                     /label=LNCX
                     /note="Human CMV promoter, forward primer"
     CDS             3849..3872
                     /codon_start=1
                     /product="FLAG(R) epitope tag, followed by an enterokinase 
                     cleavage site"
                     /label=FLAG
                     /translation="DYKDDDDK"
     protein_bind    3873..3897
                     /gene="mutant version of attB"
                     /label=attB1
                     /bound_moiety="BP Clonase(TM)"
                     /note="recombination site for the Gateway(R) BP reaction"
     protein_bind    complement(6460..6484)
                     /gene="mutant version of attB"
                     /label=attB2
                     /bound_moiety="BP Clonase(TM)"
                     /note="recombination site for the Gateway(R) BP reaction"
     primer_bind     complement(6526..6543)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    6532..6756
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     primer_bind     complement(6889..6908)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     protein_bind    7040..7087
                     /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(7095..7314,1..803)
                     /codon_start=1
                     /product="hygromycin B phosphotransferase"
                     /label=HygR
                     /note="confers resistance to hygromycin"
                     /translation="KKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRGY
                     VLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLPE
                     TELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQT
                     VMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMFG
                     DSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDGN
                     FDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAKE
                     "
ORIGIN
        1 cggaagtgct tgacattggg gagttcagcg agagcctgac ctattgcatc tcccgccgtg
       61 cacagggtgt cacgttgcaa gacctgcctg aaaccgaact gcccgctgtt ctgcagccgg
      121 tcgcggaggc catggatgcg atcgctgcgg ccgatcttag ccagacgagc gggttcggcc
      181 cattcggacc gcaaggaatc ggtcaataca ctacatggcg tgatttcata tgcgcgattg
      241 ctgatcccca tgtgtatcac tggcaaactg tgatggacga caccgtcagt gcgtccgtcg
      301 cgcaggctct cgatgagctg atgctttggg ccgaggactg ccccgaagtc cggcacctcg
      361 tgcacgcgga tttcggctcc aacaatgtcc tgacggacaa tggccgcata acagcggtca
      421 ttgactggag cgaggcgatg ttcggggatt cccaatacga ggtcgccaac atcttcttct
      481 ggaggccgtg gttggcttgt atggagcagc agacgcgcta cttcgagcgg aggcatccgg
      541 agcttgcagg atcgccgcgg ctccgggcgt atatgctccg cattggtctt gaccaactct
      601 atcagagctt ggttgacggc aatttcgatg atgcagcttg ggcgcagggt cgatgcgacg
      661 caatcgtccg atccggagcc gggactgtcg ggcgtacaca aatcgcccgc agaagcgcgg
      721 ccgtctggac cgatggctgt gtagaagtac tcgccgatag tggaaaccga cgccccagca
      781 ctcgtccgag ggcaaaggaa tagcacgtac tacgagattt cgattccacc gccgccttct
      841 atgaaaggtt gggcttcgga atcgttttcc gggacgccgg ctggatgatc ctccagcgcg
      901 gggatctcat gctggagttc ttcgcccacc ccaacttgtt tattgcagct tataatggtt
      961 acaaataaag caatagcatc acaaatttca caaataaagc atttttttca ctgcattcta
     1021 gttgtggttt gtccaaactc atcaatgtat cttatcatgt ctgtataccg tcgacctcta
     1081 gctagagctt ggcgtaatca tggtcatagc tgtttcctgt gtgaaattgt tatccgctca
     1141 caattccaca caacatacga gccggaagca taaagtgtaa agcctggggt gcctaatgag
     1201 tgagctaact cacattaatt gcgttgcgct cactgcccgc tttccagtcg ggaaacctgt
     1261 cgtgccagct gcattaatga atcggccaac gcgcggggag aggcggtttg cgtattgggc
     1321 gctcttccgc ttcctcgctc actgactcgc tgcgctcggt cgttcggctg cggcgagcgg
     1381 tatcagctca ctcaaaggcg gtaatacggt tatccacaga atcaggggat aacgcaggaa
     1441 agaacatgtg agcaaaaggc cagcaaaagg ccaggaaccg taaaaaggcc gcgttgctgg
     1501 cgtttttcca taggctccgc ccccctgacg agcatcacaa aaatcgacgc tcaagtcaga
     1561 ggtggcgaaa cccgacagga ctataaagat accaggcgtt tccccctgga agctccctcg
     1621 tgcgctctcc tgttccgacc ctgccgctta ccggatacct gtccgccttt ctcccttcgg
     1681 gaagcgtggc gctttctcat agctcacgct gtaggtatct cagttcggtg taggtcgttc
     1741 gctccaagct gggctgtgtg cacgaacccc ccgttcagcc cgaccgctgc gccttatccg
     1801 gtaactatcg tcttgagtcc aacccggtaa gacacgactt atcgccactg gcagcagcca
     1861 ctggtaacag gattagcaga gcgaggtatg taggcggtgc tacagagttc ttgaagtggt
     1921 ggcctaacta cggctacact agaagaacag tatttggtat ctgcgctctg ctgaagccag
     1981 ttaccttcgg aaaaagagtt ggtagctctt gatccggcaa acaaaccacc gctggtagcg
     2041 gtggtttttt tgtttgcaag cagcagatta cgcgcagaaa aaaaggatct caagaagatc
     2101 ctttgatctt ttctacgggg tctgacgctc agtggaacga aaactcacgt taagggattt
     2161 tggtcatgag attatcaaaa aggatcttca cctagatcct tttaaattaa aaatgaagtt
     2221 ttaaatcaat ctaaagtata tatgagtaaa cttggtctga cagttaccaa tgcttaatca
     2281 gtgaggcacc tatctcagcg atctgtctat ttcgttcatc catagttgcc tgactccccg
     2341 tcgtgtagat aactacgata cgggagggct taccatctgg ccccagtgct gcaatgatac
     2401 cgcgagaccc acgctcaccg gctccagatt tatcagcaat aaaccagcca gccggaaggg
     2461 ccgagcgcag aagtggtcct gcaactttat ccgcctccat ccagtctatt aattgttgcc
     2521 gggaagctag agtaagtagt tcgccagtta atagtttgcg caacgttgtt gccattgcta
     2581 caggcatcgt ggtgtcacgc tcgtcgtttg gtatggcttc attcagctcc ggttcccaac
     2641 gatcaaggcg agttacatga tcccccatgt tgtgcaaaaa agcggttagc tccttcggtc
     2701 ctccgatcgt tgtcagaagt aagttggccg cagtgttatc actcatggtt atggcagcac
     2761 tgcataattc tcttactgtc atgccatccg taagatgctt ttctgtgact ggtgagtact
     2821 caaccaagtc attctgagaa tagtgtatgc ggcgaccgag ttgctcttgc ccggcgtcaa
     2881 tacgggataa taccgcgcca catagcagaa ctttaaaagt gctcatcatt ggaaaacgtt
     2941 cttcggggcg aaaactctca aggatcttac cgctgttgag atccagttcg atgtaaccca
     3001 ctcgtgcacc caactgatct tcagcatctt ttactttcac cagcgtttct gggtgagcaa
     3061 aaacaggaag gcaaaatgcc gcaaaaaagg gaataagggc gacacggaaa tgttgaatac
     3121 tcatactctt cctttttcaa tattattgaa gcatttatca gggttattgt ctcatgagcg
     3181 gatacatatt tgaatgtatt tagaaaaata aacaaatagg ggttccgcgc acatttcccc
     3241 gaaaagtgcc acctgacgtc gacggatcgg gagatctccc gatcccctat ggtgcactct
     3301 cagtacaatc tgctctgatg ccgcatagtt aagccagtat ctgctccctg cttgtgtgtt
     3361 ggaggtcgct gagtagtgcg cgagcaaaat ttaagctaca acaaggcaag gcttgaccga
     3421 caattgcatg aagaatctgc ttagggttag gcgttttgcg ctgcttcgcg atgtacgggc
     3481 cagatatacg cgtctcgagg gatccaagct ggccgcacgt ctccctatca gtgatagaga
     3541 agtcgacacg tctcgagctc cctatcagtg atagagaagg tacgtctaga acgtctccct
     3601 atcagtgata gagaagtcga cacgtctcga gctccctatc agtgatagag aaggtacccc
     3661 ctatataagc agagctcgtt tagtgaaccg tcagatcgcc tggagacgcc atccacgctg
     3721 ttttgacctc catagaagac accgggaccg atccagcctc cgcggaggct ggatcctcta
     3781 gcgtttaaac ttaagcttcc accatggact acaaagacca tgacggtgat acatatgatc
     3841 atgacatcga ttacaaggat gacgatgaca agacaagttt gtacaaaaaa gttggcacct
     3901 tgtctgggaa gaaggcggcg gcggcggcag cggcagcggc ggcggcggcg gctgctggga
     3961 ccgaggccgg gtccggggcg gcgggcggtg ccgagaacgg ctctgaggtg gccgcgccgc
     4021 ccgcgggcct gacgggcccc accgacatgg ctacgggggc ggcgggcgag cgcactcccc
     4081 gaaagaagga gcctccgcgg gcctcgccgc ccgggggcct agccgagccg ccggggtctg
     4141 ctgggcccca ggcggggccc acagccgggc ccggctccgc gacgcccatg gagaccggaa
     4201 tagccgagac cccggagggc cgacggacca gccggcgcaa gcgggccaag gtagaataca
     4261 gagaaatgga tgaaagcttg gccaacctct cagaagatga atattattcg gaagaagaaa
     4321 gaaatgctaa agcagagaag gaaaagaagc ttcccccacc acctcctcaa gccccacctg
     4381 aggaagaaaa tgaaagtgag ccggaagagc cgtctggtgt ggagggtgca gcttttcaaa
     4441 gccgacttcc ccatgaccga atgacctctc aggaagcagc ctgtttccca gacatcatca
     4501 gtgggcctca gcagacacag aaggtttttc tgttcatcag gaatcgcaca ttgcagttat
     4561 ggctggacaa cccaaagatc cagctgacgt ttgaagccac tctccagcag ctggaagcgc
     4621 cttacaacag cgatactgtg cttgtccacc gagttcacag ttacttagag cgccatggtc
     4681 ttatcaactt cggcatctac aagaggataa aacccttacc aattaaaaag acaggaaagg
     4741 tgattattat aggttcaggt gtttctggct tggcagcagc tcgacagcta cagagttttg
     4801 ggatggatgt cacacttctg gaagccaggg atcgagtagg tggacgagtt gctacatttc
     4861 gaaaaggaaa ctatgtagct gatcttggcg ccatggttgt aacaggtctt ggagggaatc
     4921 ccatggctgt cgtcagcaaa caagtaaata tggaactggc caagatcaag caaaaatgcc
     4981 cactttatga agccaatgga caagctgttc caaaagaaaa agatgaaatg gtagaacaag
     5041 aatttaaccg gttgctagaa gccacttctt accttagtca ccagttagac ttcaacgtcc
     5101 tcaataataa acctgtatcc cttggccagg cattggaggt tgtcattcag ctgcaagaaa
     5161 agcatgtcaa agatgagcag attgaacatt ggaagaagat agtgaaaact caggaggagt
     5221 tgaaagagct tcttaataag atggtaaatt tgaaggagaa aattaaagag ctccatcagc
     5281 aatacaaaga agcttcagaa gtgaagccgc ccagagatat cacagccgag ttcctggtga
     5341 agagcaagca cagggacctg actgccctct gcaaggaata tgatgaatta gctgaaacac
     5401 aaggaaagct agaagaaaaa cttcaagaat tggaagccaa tcccccaagt gatgtatacc
     5461 tctcatcaag agacagacaa atacttgact ggcattttgc aaatcttgaa tttgccaacg
     5521 ccacacctct ctctaccctc tctcttaaac attgggatca ggatgatgac tttgagttta
     5581 ctggaagcca cctgacagta aggaatggct actcatgtgt gcctgtggct ttagctgaag
     5641 gcttggacat taaactgaac acagcagtgc ggcaggttcg ctacacagcc tcaggatgtg
     5701 aagtgattgc tgtgaacaca cgttccacaa gtcaaacctt tatttataag tgtgatgcag
     5761 ttctctgtac acttcctttg ggagtgttga agcagcagcc accagctgtt cagtttgtgc
     5821 cacctcttcc tgagtggaaa acatctgcag tccaaaggat gggatttggc aaccttaaca
     5881 aggtggtgtt atgctttgac cgtgtgttct gggacccaag tgtcaatttg tttgggcacg
     5941 ttggcagtac aactgctagc aggggtgagc tcttcctctt ctggaaccta tataaagctc
     6001 caatactatt ggccctggta gcaggagaag ctgctggcat tatggagaac attagtgatg
     6061 atgtgattgt cggccggtgc ctggccattc tcaaagggat ttttggcagc agtgcagtcc
     6121 cacagcccaa ggaaactgtg gtatctcgtt ggcgtgctga tccgtgggcc cggggctcct
     6181 attcttatgt ggctgcagga tcctctggaa atgactatga tttaatggct cagccgatca
     6241 ctcctggccc ctcaattcca ggtgccccac agccaatccc aagactcttc tttgctggag
     6301 aacacacaat ccggaactac ccagctacag tccatggtgc tctgttgagt gggcttcgag
     6361 aagcaggaag gattgccgac cagtttttgg gagccatgta cactttgcct cgtcaggcca
     6421 caccaggtgt ccctgcacag cagtccccaa gtatgtgata cccaactttc ttgtacaaag
     6481 tggtctgact cgagtctaga gggcccgttt aaacccgctg atcagcctcg actgtgcctt
     6541 ctagttgcca gccatctgtt gtttgcccct cccccgtgcc ttccttgacc ctggaaggtg
     6601 ccactcccac tgtcctttcc taataaaatg aggaaattgc atcgcattgt ctgagtaggt
     6661 gtcattctat tctggggggt ggggtggggc aggacagcaa gggggaggat tgggaagaca
     6721 atagcaggca tgctggggat gcggtgggct ctatggcttc tgaggcggaa agaaccagct
     6781 ggggctctag ggggtatccc cacgcgccct gtagcggcgc attaagcgcg gcgggtgtgg
     6841 tggttacgcg cagcgtgacc gctacacttg ccagcgccct agcgcccgct cctttcgctt
     6901 tcttcccttc ctttctcgcc acgttcgccg gctttccccg tcaagctcta aatcgggggc
     6961 tccctttagg gttccgattt agtgctttac ggcacctcga ccccaaaaaa cttgattagg
     7021 gtgatggttc acgtacctag aagttcctat tccgaagttc ctattctcta gaaagtatag
     7081 gaacttcctt ggccaaaaag cctgaactca ccgcgacgtc tgtcgagaag tttctgatcg
     7141 aaaagttcga cagcgtctcc gacctgatgc agctctcgga gggcgaagaa tctcgtgctt
     7201 tcagcttcga tgtaggaggg cgtggatatg tcctgcgggt aaatagctgc gccgatggtt
     7261 tctacaaaga tcgttatgtt tatcggcact ttgcatcggc cgcgctcccg attc
//
