LOCUS       sequence-437903-        6277 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  For overexpression of Gal4-DBD HOXD4 AroPERFECT.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6277)
  AUTHORS   Naderi J, Magalhaes AP, Kibar G, Stik G, Zhang Y, Mackowiak SD, 
            Wieler HM, Rossi F, Buschow R, Christou-Kent M, Alcoverro-Bertran M,
            Graf T, Vingron M, Hnisz D
  TITLE     An activity-specificity trade-off encoded in human transcription 
            factors.
  JOURNAL   Nat Cell Biol. 2024 Aug;26(8):1309-1321. doi: 
            10.1038/s41556-024-01411-0. Epub 2024 Jul 5.
  PUBMED    38969762
REFERENCE   2  (bases 1 to 6277)
  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: 
            "10.1038/s41556-024-01411-0"; journalName: "Nat Cell Biol"; date: 
            "2024-08"; volume: "26"; issue: "8"; pages: "1309-1321"
COMMENT     Sequence Label: pGAL4-DBD-HOXD4-AroPERFECT
FEATURES             Location/Qualifiers
     source          1..6277
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     320..339
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(558..662)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(737..756)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        928..1307
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        1308..1511
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     1462..1482
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     1556..1575
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        1556..1574
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     CDS             1637..2077
                     /codon_start=1
                     /gene="Saccharomyces cerevisiae GAL4 (truncated)"
                     /product="DNA binding domain of the GAL4 transcriptional 
                     activator"
                     /label=GAL4 DNA binding domain
                     /translation="MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTK
                     RSPLTRAHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGLFVQDNVNK
                     DAVTDRLASVETDMPLTLRQHRISATSSSEESSNKGQRQLTVS"
     promoter        complement(2523..2541)
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     complement(2524..2541)
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     primer_bind     complement(2561..2578)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    2567..2791
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      2837..3265
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2924..2943)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3134..3155
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(3274..3294)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        3279..3608
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      3459..3594
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     3521..3540
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             3675..4469
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(3729..3748)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     4339..4358
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    4643..4764
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4680..4699)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4734..4753
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(4813..4829)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4813..4829)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(4826..4848)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    4837..4853
                     /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(4861..4867,4868..4885,4886..4891))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4906..4927
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(5044..5061)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(5215..5803)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5295..5314)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5974..6277,1..488,489..557))
                     /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"
ORIGIN
        1 gttgccattg ctacaggcat cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc
       61 tccggttccc aacgatcaag gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt
      121 agctccttcg gtcctccgat cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg
      181 gttatggcag cactgcataa ttctcttact gtcatgccat ccgtaagatg cttttctgtg
      241 actggtgagt actcaaccaa gtcattctga gaatagtgta tgcggcgacc gagttgctct
      301 tgcccggcgt caatacggga taataccgcg ccacatagca gaactttaaa agtgctcatc
      361 attggaaaac gttcttcggg gcgaaaactc tcaaggatct taccgctgtt gagatccagt
      421 tcgatgtaac ccactcgtgc acccaactga tcttcagcat cttttacttt caccagcgtt
      481 tctgggtgag caaaaacagg aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg
      541 aaatgttgaa tactcatact cttccttttt caatattatt gaagcattta tcagggttat
      601 tgtctcatga gcggatacat atttgaatgt atttagaaaa ataaacaaat aggggttccg
      661 cgcacatttc cccgaaaagt gccacctgac gtcgacggat cgggagatct cccgatcccc
      721 tatggtgcac tctcagtaca atctgctctg atgccgcata gttaagccag tatctgctcc
      781 ctgcttgtgt gttggaggtc gctgagtagt gcgcgagcaa aatttaagct acaacaaggc
      841 aaggcttgac cgacaattgc atgaagaatc tgcttagggt taggcgtttt gcgctgcttc
      901 gcgatgtacg ggccagatat acgcgttgac attgattatt gactagttat taatagtaat
      961 caattacggg gtcattagtt catagcccat atatggagtt ccgcgttaca taacttacgg
     1021 taaatggccc gcctggctga ccgcccaacg acccccgccc attgacgtca ataatgacgt
     1081 atgttcccat agtaacgcca atagggactt tccattgacg tcaatgggtg gagtatttac
     1141 ggtaaactgc ccacttggca gtacatcaag tgtatcatat gccaagtacg ccccctattg
     1201 acgtcaatga cggtaaatgg cccgcctggc attatgccca gtacatgacc ttatgggact
     1261 ttcctacttg gcagtacatc tacgtattag tcatcgctat taccatggtg atgcggtttt
     1321 ggcagtacat caatgggcgt ggatagcggt ttgactcacg gggatttcca agtctccacc
     1381 ccattgacgt caatgggagt ttgttttggc accaaaatca acgggacttt ccaaaatgtc
     1441 gtaacaactc cgccccattg acgcaaatgg gcggtaggcg tgtacggtgg gaggtctata
     1501 taagcagagc tctctggcta actagagaac ccactgctta ctggcttatc gaaattaata
     1561 cgactcacta tagggagacc caagcttggt accgagctcg gatccactag taacggccgc
     1621 cagtgtgctg gaattcatga agctactgtc ttctatcgaa caagcatgcg atatttgccg
     1681 acttaaaaag ctcaagtgct ccaaagaaaa accgaagtgc gccaagtgtc tgaagaacaa
     1741 ctgggagtgt cgctactctc ccaaaaccaa aaggtctccg ctgactaggg cacatctgac
     1801 agaagtggaa tcaaggctag aaagactgga acagctattt ctactgattt ttcctcgaga
     1861 agaccttgac atgattttga aaatggattc tttacaggat ataaaagcat tgttaacagg
     1921 attatttgta caagataatg tgaataaaga tgccgtcaca gatagattgg cttcagtgga
     1981 gactgatatg cctctaacat tgagacagca tagaataagt gcgacatcat catcggaaga
     2041 gagtagtaac aaaggtcaaa gacagttgac tgtatcggcg ataatggtga tgtcatcaat
     2101 ggttaattac tctaaagttg atcctaaacc accattttgt gaagaacttc aaggtgggct
     2161 ttatggggaa caaggagctg atggtggata tggggcacaa ggggcggatc aaccatttcc
     2221 tggcctgccc aggccagatg gctttgaaca accaggcggg agtggtcctt ttggcccagg
     2281 atcagccctt ccagcataca ggggacatgg tcaggaaccc ggatacggtc ctggcggaca
     2341 tgctgcgcct tatggggaac catgtccggc gccaccctat gcacccccac ctgcacctct
     2401 cccatatgga gcaagggcaa gccaaagcga ttatcctaaa caaccccctt caggcacata
     2461 tgccctgaaa caacctgcgg ttgtatggcc aatgaagaaa gtctgagtct agagggccct
     2521 attctatagt gtcacctaaa tgctagagct cgctgatcag cctcgactgt gccttctagt
     2581 tgccagccat ctgttgtttg cccctccccc gtgccttcct tgaccctgga aggtgccact
     2641 cccactgtcc tttcctaata aaatgaggaa attgcatcgc attgtctgag taggtgtcat
     2701 tctattctgg ggggtggggt ggggcaggac agcaaggggg aggattggga agacaatagc
     2761 aggcatgctg gggatgcggt gggctctatg gcttctgagg cggaaagaac cagctggggc
     2821 tctagggggt atccccacgc gccctgtagc ggcgcattaa gcgcggcggg tgtggtggtt
     2881 acgcgcagcg tgaccgctac acttgccagc gccctagcgc ccgctccttt cgctttcttc
     2941 ccttcctttc tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg ggggctccct
     3001 ttagggttcc gatttagtgc tttacggcac ctcgacccca aaaaacttga ttagggtgat
     3061 ggttcacgta gtgggccatc gccctgatag acggtttttc gccctttgac gttggagtcc
     3121 acgttcttta atagtggact cttgttccaa actggaacaa cactcaaccc tatctcggtc
     3181 tattcttttg atttataagg gattttgccg atttcggcct attggttaaa aaatgagctg
     3241 atttaacaaa aatttaacgc gaattaattc tgtggaatgt gtgtcagtta gggtgtggaa
     3301 agtccccagg ctccccagca ggcagaagta tgcaaagcat gcatctcaat tagtcagcaa
     3361 ccaggtgtgg aaagtcccca ggctccccag caggcagaag tatgcaaagc atgcatctca
     3421 attagtcagc aaccatagtc ccgcccctaa ctccgcccat cccgccccta actccgccca
     3481 gttccgccca ttctccgccc catggctgac taattttttt tatttatgca gaggccgagg
     3541 ccgcctctgc ctctgagcta ttccagaagt agtgaggagg cttttttgga ggcctaggct
     3601 tttgcaaaaa gctcccggga gcttgtatat ccattttcgg atctgatcaa gagacaggat
     3661 gaggatcgtt tcgcatgatt gaacaagatg gattgcacgc aggttctccg gccgcttggg
     3721 tggagaggct attcggctat gactgggcac aacagacaat cggctgctct gatgccgccg
     3781 tgttccggct gtcagcgcag gggcgcccgg ttctttttgt caagaccgac ctgtccggtg
     3841 ccctgaatga actgcaggac gaggcagcgc ggctatcgtg gctggccacg acgggcgttc
     3901 cttgcgcagc tgtgctcgac gttgtcactg aagcgggaag ggactggctg ctattgggcg
     3961 aagtgccggg gcaggatctc ctgtcatctc accttgctcc tgccgagaaa gtatccatca
     4021 tggctgatgc aatgcggcgg ctgcatacgc ttgatccggc tacctgccca ttcgaccacc
     4081 aagcgaaaca tcgcatcgag cgagcacgta ctcggatgga agccggtctt gtcgatcagg
     4141 atgatctgga cgaagagcat caggggctcg cgccagccga actgttcgcc aggctcaagg
     4201 cgcgcatgcc cgacggcgag gatctcgtcg tgacccatgg cgatgcctgc ttgccgaata
     4261 tcatggtgga aaatggccgc ttttctggat tcatcgactg tggccggctg ggtgtggcgg
     4321 accgctatca ggacatagcg ttggctaccc gtgatattgc tgaagagctt ggcggcgaat
     4381 gggctgaccg cttcctcgtg ctttacggta tcgccgctcc cgattcgcag cgcatcgcct
     4441 tctatcgcct tcttgacgag ttcttctgag cgggactctg gggttcgaaa tgaccgacca
     4501 agcgacgccc aacctgccat cacgagattt cgattccacc gccgccttct atgaaaggtt
     4561 gggcttcgga atcgttttcc gggacgccgg ctggatgatc ctccagcgcg gggatctcat
     4621 gctggagttc ttcgcccacc ccaacttgtt tattgcagct tataatggtt acaaataaag
     4681 caatagcatc acaaatttca caaataaagc atttttttca ctgcattcta gttgtggttt
     4741 gtccaaactc atcaatgtat cttatcatgt ctgtataccg tcgacctcta gctagagctt
     4801 ggcgtaatca tggtcatagc tgtttcctgt gtgaaattgt tatccgctca caattccaca
     4861 caacatacga gccggaagca taaagtgtaa agcctggggt gcctaatgag tgagctaact
     4921 cacattaatt gcgttgcgct cactgcccgc tttccagtcg ggaaacctgt cgtgccagct
     4981 gcattaatga atcggccaac gcgcggggag aggcggtttg cgtattgggc gctcttccgc
     5041 ttcctcgctc actgactcgc tgcgctcggt cgttcggctg cggcgagcgg tatcagctca
     5101 ctcaaaggcg gtaatacggt tatccacaga atcaggggat aacgcaggaa agaacatgtg
     5161 agcaaaaggc cagcaaaagg ccaggaaccg taaaaaggcc gcgttgctgg cgtttttcca
     5221 taggctccgc ccccctgacg agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa
     5281 cccgacagga ctataaagat accaggcgtt tccccctgga agctccctcg tgcgctctcc
     5341 tgttccgacc ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc
     5401 gctttctcat agctcacgct gtaggtatct cagttcggtg taggtcgttc gctccaagct
     5461 gggctgtgtg cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg
     5521 tcttgagtcc aacccggtaa gacacgactt atcgccactg gcagcagcca ctggtaacag
     5581 gattagcaga gcgaggtatg taggcggtgc tacagagttc ttgaagtggt ggcctaacta
     5641 cggctacact agaagaacag tatttggtat ctgcgctctg ctgaagccag ttaccttcgg
     5701 aaaaagagtt ggtagctctt gatccggcaa acaaaccacc gctggtagcg gtggtttttt
     5761 tgtttgcaag cagcagatta cgcgcagaaa aaaaggatct caagaagatc ctttgatctt
     5821 ttctacgggg tctgacgctc agtggaacga aaactcacgt taagggattt tggtcatgag
     5881 attatcaaaa aggatcttca cctagatcct tttaaattaa aaatgaagtt ttaaatcaat
     5941 ctaaagtata tatgagtaaa cttggtctga cagttaccaa tgcttaatca gtgaggcacc
     6001 tatctcagcg atctgtctat ttcgttcatc catagttgcc tgacttcccg tcgtgtagat
     6061 aactacgata cgggagggct taccatctgg ccccagtgct gcaatgatac cgcgagaccc
     6121 acgctcaccg gctccagatt tatcagcaat aaaccagcca gccggaaggg ccgagcgcag
     6181 aagtggtcct gcaactttat ccgcctccat ccagtctatt aattgttgcc gggaagctag
     6241 agtaagtagt tcgccagtta atagtttgcg caacgtt
//
