LOCUS       sequence-437906-        6277 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  For overexpression of Gal4-DBD HOXD4 AroPLUS.
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-AroPLUS
FEATURES             Location/Qualifiers
     source          1..6277
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     480..499
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    784..905
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(821..840)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     875..894
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(954..970)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(954..970)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(967..989)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    978..994
                     /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(1002..1008,1009..1026,1027..1032))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1047..1068
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(1185..1202)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(1356..1944)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(1436..1455)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2115..2906,2907..2975))
                     /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     2738..2757
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(2976..3080)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(3155..3174)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        3346..3725
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        3726..3929
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     3880..3900
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     3974..3993
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        3974..3992
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     CDS             4055..4495
                     /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(4941..4959)
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     complement(4942..4959)
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     primer_bind     complement(4979..4996)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    4985..5209
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      5255..5683
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5342..5361)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5552..5573
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(5692..5712)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        5697..6026
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      5877..6012
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     5939..5958
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             join(6093..6277,1..610)
                     /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(6147..6166)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
ORIGIN
        1 cgaggcagcg cggctatcgt ggctggccac gacgggcgtt ccttgcgcag ctgtgctcga
       61 cgttgtcact gaagcgggaa gggactggct gctattgggc gaagtgccgg ggcaggatct
      121 cctgtcatct caccttgctc ctgccgagaa agtatccatc atggctgatg caatgcggcg
      181 gctgcatacg cttgatccgg ctacctgccc attcgaccac caagcgaaac atcgcatcga
      241 gcgagcacgt actcggatgg aagccggtct tgtcgatcag gatgatctgg acgaagagca
      301 tcaggggctc gcgccagccg aactgttcgc caggctcaag gcgcgcatgc ccgacggcga
      361 ggatctcgtc gtgacccatg gcgatgcctg cttgccgaat atcatggtgg aaaatggccg
      421 cttttctgga ttcatcgact gtggccggct gggtgtggcg gaccgctatc aggacatagc
      481 gttggctacc cgtgatattg ctgaagagct tggcggcgaa tgggctgacc gcttcctcgt
      541 gctttacggt atcgccgctc ccgattcgca gcgcatcgcc ttctatcgcc ttcttgacga
      601 gttcttctga gcgggactct ggggttcgaa atgaccgacc aagcgacgcc caacctgcca
      661 tcacgagatt tcgattccac cgccgccttc tatgaaaggt tgggcttcgg aatcgttttc
      721 cgggacgccg gctggatgat cctccagcgc ggggatctca tgctggagtt cttcgcccac
      781 cccaacttgt ttattgcagc ttataatggt tacaaataaa gcaatagcat cacaaatttc
      841 acaaataaag catttttttc actgcattct agttgtggtt tgtccaaact catcaatgta
      901 tcttatcatg tctgtatacc gtcgacctct agctagagct tggcgtaatc atggtcatag
      961 ctgtttcctg tgtgaaattg ttatccgctc acaattccac acaacatacg agccggaagc
     1021 ataaagtgta aagcctgggg tgcctaatga gtgagctaac tcacattaat tgcgttgcgc
     1081 tcactgcccg ctttccagtc gggaaacctg tcgtgccagc tgcattaatg aatcggccaa
     1141 cgcgcgggga gaggcggttt gcgtattggg cgctcttccg cttcctcgct cactgactcg
     1201 ctgcgctcgg tcgttcggct gcggcgagcg gtatcagctc actcaaaggc ggtaatacgg
     1261 ttatccacag aatcagggga taacgcagga aagaacatgt gagcaaaagg ccagcaaaag
     1321 gccaggaacc gtaaaaaggc cgcgttgctg gcgtttttcc ataggctccg cccccctgac
     1381 gagcatcaca aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg actataaaga
     1441 taccaggcgt ttccccctgg aagctccctc gtgcgctctc ctgttccgac cctgccgctt
     1501 accggatacc tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca tagctcacgc
     1561 tgtaggtatc tcagttcggt gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc
     1621 cccgttcagc ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc caacccggta
     1681 agacacgact tatcgccact ggcagcagcc actggtaaca ggattagcag agcgaggtat
     1741 gtaggcggtg ctacagagtt cttgaagtgg tggcctaact acggctacac tagaagaaca
     1801 gtatttggta tctgcgctct gctgaagcca gttaccttcg gaaaaagagt tggtagctct
     1861 tgatccggca aacaaaccac cgctggtagc ggtggttttt ttgtttgcaa gcagcagatt
     1921 acgcgcagaa aaaaaggatc tcaagaagat cctttgatct tttctacggg gtctgacgct
     1981 cagtggaacg aaaactcacg ttaagggatt ttggtcatga gattatcaaa aaggatcttc
     2041 acctagatcc ttttaaatta aaaatgaagt tttaaatcaa tctaaagtat atatgagtaa
     2101 acttggtctg acagttacca atgcttaatc agtgaggcac ctatctcagc gatctgtcta
     2161 tttcgttcat ccatagttgc ctgacttccc gtcgtgtaga taactacgat acgggagggc
     2221 ttaccatctg gccccagtgc tgcaatgata ccgcgagacc cacgctcacc ggctccagat
     2281 ttatcagcaa taaaccagcc agccggaagg gccgagcgca gaagtggtcc tgcaacttta
     2341 tccgcctcca tccagtctat taattgttgc cgggaagcta gagtaagtag ttcgccagtt
     2401 aatagtttgc gcaacgttgt tgccattgct acaggcatcg tggtgtcacg ctcgtcgttt
     2461 ggtatggctt cattcagctc cggttcccaa cgatcaaggc gagttacatg atcccccatg
     2521 ttgtgcaaaa aagcggttag ctccttcggt cctccgatcg ttgtcagaag taagttggcc
     2581 gcagtgttat cactcatggt tatggcagca ctgcataatt ctcttactgt catgccatcc
     2641 gtaagatgct tttctgtgac tggtgagtac tcaaccaagt cattctgaga atagtgtatg
     2701 cggcgaccga gttgctcttg cccggcgtca atacgggata ataccgcgcc acatagcaga
     2761 actttaaaag tgctcatcat tggaaaacgt tcttcggggc gaaaactctc aaggatctta
     2821 ccgctgttga gatccagttc gatgtaaccc actcgtgcac ccaactgatc ttcagcatct
     2881 tttactttca ccagcgtttc tgggtgagca aaaacaggaa ggcaaaatgc cgcaaaaaag
     2941 ggaataaggg cgacacggaa atgttgaata ctcatactct tcctttttca atattattga
     3001 agcatttatc agggttattg tctcatgagc ggatacatat ttgaatgtat ttagaaaaat
     3061 aaacaaatag gggttccgcg cacatttccc cgaaaagtgc cacctgacgt cgacggatcg
     3121 ggagatctcc cgatccccta tggtgcactc tcagtacaat ctgctctgat gccgcatagt
     3181 taagccagta tctgctccct gcttgtgtgt tggaggtcgc tgagtagtgc gcgagcaaaa
     3241 tttaagctac aacaaggcaa ggcttgaccg acaattgcat gaagaatctg cttagggtta
     3301 ggcgttttgc gctgcttcgc gatgtacggg ccagatatac gcgttgacat tgattattga
     3361 ctagttatta atagtaatca attacggggt cattagttca tagcccatat atggagttcc
     3421 gcgttacata acttacggta aatggcccgc ctggctgacc gcccaacgac ccccgcccat
     3481 tgacgtcaat aatgacgtat gttcccatag taacgccaat agggactttc cattgacgtc
     3541 aatgggtgga gtatttacgg taaactgccc acttggcagt acatcaagtg tatcatatgc
     3601 caagtacgcc ccctattgac gtcaatgacg gtaaatggcc cgcctggcat tatgcccagt
     3661 acatgacctt atgggacttt cctacttggc agtacatcta cgtattagtc atcgctatta
     3721 ccatggtgat gcggttttgg cagtacatca atgggcgtgg atagcggttt gactcacggg
     3781 gatttccaag tctccacccc attgacgtca atgggagttt gttttggcac caaaatcaac
     3841 gggactttcc aaaatgtcgt aacaactccg ccccattgac gcaaatgggc ggtaggcgtg
     3901 tacggtggga ggtctatata agcagagctc tctggctaac tagagaaccc actgcttact
     3961 ggcttatcga aattaatacg actcactata gggagaccca agcttggtac cgagctcgga
     4021 tccactagta acggccgcca gtgtgctgga attcatgaag ctactgtctt ctatcgaaca
     4081 agcatgcgat atttgccgac ttaaaaagct caagtgctcc aaagaaaaac cgaagtgcgc
     4141 caagtgtctg aagaacaact gggagtgtcg ctactctccc aaaaccaaaa ggtctccgct
     4201 gactagggca catctgacag aagtggaatc aaggctagaa agactggaac agctatttct
     4261 actgattttt cctcgagaag accttgacat gattttgaaa atggattctt tacaggatat
     4321 aaaagcattg ttaacaggat tatttgtaca agataatgtg aataaagatg ccgtcacaga
     4381 tagattggct tcagtggaga ctgatatgcc tctaacattg agacagcata gaataagtgc
     4441 gacatcatca tcggaagaga gtagtaacaa aggtcaaaga cagttgactg tatcggcgat
     4501 catggttatg agcagttaca tggtcaatag caaatacgtc gatcctaaat ttccaccttg
     4561 tgaagaatat ctccaaggcg gatatcttgg agaacaagga gcagattatt atggtggcgg
     4621 agcccaagga gcggattttc aaccacccgg actgtatcct cgaccagatt ttggcgaaca
     4681 accatttggt gggtccggtc ctggctacgg tagcgctctc cccgctaggt atcatgggca
     4741 ggaaccttac gggccaggcg gacattatgc tgcccctggt gaaccttgtc cttacccgcc
     4801 cgccccacca ccatatcctc ttccaggggc tagggcatat tcacaatcag atccgaaata
     4861 tcccccatct ggcaccgcct acaaacaacc agcggtagtg tatccttgga tgaagaaagt
     4921 atgagtctag agggccctat tctatagtgt cacctaaatg ctagagctcg ctgatcagcc
     4981 tcgactgtgc cttctagttg ccagccatct gttgtttgcc cctcccccgt gccttccttg
     5041 accctggaag gtgccactcc cactgtcctt tcctaataaa atgaggaaat tgcatcgcat
     5101 tgtctgagta ggtgtcattc tattctgggg ggtggggtgg ggcaggacag caagggggag
     5161 gattgggaag acaatagcag gcatgctggg gatgcggtgg gctctatggc ttctgaggcg
     5221 gaaagaacca gctggggctc tagggggtat ccccacgcgc cctgtagcgg cgcattaagc
     5281 gcggcgggtg tggtggttac gcgcagcgtg accgctacac ttgccagcgc cctagcgccc
     5341 gctcctttcg ctttcttccc ttcctttctc gccacgttcg ccggctttcc ccgtcaagct
     5401 ctaaatcggg ggctcccttt agggttccga tttagtgctt tacggcacct cgaccccaaa
     5461 aaacttgatt agggtgatgg ttcacgtagt gggccatcgc cctgatagac ggtttttcgc
     5521 cctttgacgt tggagtccac gttctttaat agtggactct tgttccaaac tggaacaaca
     5581 ctcaacccta tctcggtcta ttcttttgat ttataaggga ttttgccgat ttcggcctat
     5641 tggttaaaaa atgagctgat ttaacaaaaa tttaacgcga attaattctg tggaatgtgt
     5701 gtcagttagg gtgtggaaag tccccaggct ccccagcagg cagaagtatg caaagcatgc
     5761 atctcaatta gtcagcaacc aggtgtggaa agtccccagg ctccccagca ggcagaagta
     5821 tgcaaagcat gcatctcaat tagtcagcaa ccatagtccc gcccctaact ccgcccatcc
     5881 cgcccctaac tccgcccagt tccgcccatt ctccgcccca tggctgacta atttttttta
     5941 tttatgcaga ggccgaggcc gcctctgcct ctgagctatt ccagaagtag tgaggaggct
     6001 tttttggagg cctaggcttt tgcaaaaagc tcccgggagc ttgtatatcc attttcggat
     6061 ctgatcaaga gacaggatga ggatcgtttc gcatgattga acaagatgga ttgcacgcag
     6121 gttctccggc cgcttgggtg gagaggctat tcggctatga ctgggcacaa cagacaatcg
     6181 gctgctctga tgccgccgtg ttccggctgt cagcgcaggg gcgcccggtt ctttttgtca
     6241 agaccgacct gtccggtgcc ctgaatgaac tgcagga
//
