LOCUS       sequence-437900-        6277 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  For overexpression of Gal4-DBD HOXD4 WT.
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-WT
FEATURES             Location/Qualifiers
     source          1..6277
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      475..1063
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     964..983
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     1217..1234
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    1351..1372
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(1387..1392,1393..1410,1411..1417)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1425..1441
                     /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     1430..1452
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     1449..1465
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     1449..1465
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     polyA_signal    1514..1635
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(1525..1544)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     1579..1598
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     CDS             complement(1809..2603)
                     /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(1920..1939)
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     primer_bind     2530..2549
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     promoter        complement(2670..2999)
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      2684..2819
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(2738..2757)
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     primer_bind     2984..3004
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     rep_origin      complement(3013..3441)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3123..3144)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     3335..3354
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     polyA_signal    3487..3711
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     primer_bind     3700..3717
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     promoter        3737..3755
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     3737..3754
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     CDS             complement(4201..4641)
                     /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"
     primer_bind     complement(4703..4722)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(4704..4722)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     promoter        complement(4767..4970)
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     complement(4796..4816)
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     enhancer        4971..5350
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     primer_bind     5522..5541
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     promoter        5616..5720
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5721..5789,5790..6277,1..304)
                     /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(5939..5958)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
ORIGIN
        1 aacgttgcgc aaactattaa ctggcgaact acttactcta gcttcccggc aacaattaat
       61 agactggatg gaggcggata aagttgcagg accacttctg cgctcggccc ttccggctgg
      121 ctggtttatt gctgataaat ctggagccgg tgagcgtggg tctcgcggta tcattgcagc
      181 actggggcca gatggtaagc cctcccgtat cgtagttatc tacacgacgg gaagtcaggc
      241 aactatggat gaacgaaata gacagatcgc tgagataggt gcctcactga ttaagcattg
      301 gtaactgtca gaccaagttt actcatatat actttagatt gatttaaaac ttcattttta
      361 atttaaaagg atctaggtga agatcctttt tgataatctc atgaccaaaa tcccttaacg
      421 tgagttttcg ttccactgag cgtcagaccc cgtagaaaag atcaaaggat cttcttgaga
      481 tccttttttt ctgcgcgtaa tctgctgctt gcaaacaaaa aaaccaccgc taccagcggt
      541 ggtttgtttg ccggatcaag agctaccaac tctttttccg aaggtaactg gcttcagcag
      601 agcgcagata ccaaatactg ttcttctagt gtagccgtag ttaggccacc acttcaagaa
      661 ctctgtagca ccgcctacat acctcgctct gctaatcctg ttaccagtgg ctgctgccag
      721 tggcgataag tcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca
      781 gcggtcgggc tgaacggggg gttcgtgcac acagcccagc ttggagcgaa cgacctacac
      841 cgaactgaga tacctacagc gtgagctatg agaaagcgcc acgcttcccg aagggagaaa
      901 ggcggacagg tatccggtaa gcggcagggt cggaacagga gagcgcacga gggagcttcc
      961 agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccacctct gacttgagcg
     1021 tcgatttttg tgatgctcgt caggggggcg gagcctatgg aaaaacgcca gcaacgcggc
     1081 ctttttacgg ttcctggcct tttgctggcc ttttgctcac atgttctttc ctgcgttatc
     1141 ccctgattct gtggataacc gtattaccgc ctttgagtga gctgataccg ctcgccgcag
     1201 ccgaacgacc gagcgcagcg agtcagtgag cgaggaagcg gaagagcgcc caatacgcaa
     1261 accgcctctc cccgcgcgtt ggccgattca ttaatgcagc tggcacgaca ggtttcccga
     1321 ctggaaagcg ggcagtgagc gcaacgcaat taatgtgagt tagctcactc attaggcacc
     1381 ccaggcttta cactttatgc ttccggctcg tatgttgtgt ggaattgtga gcggataaca
     1441 atttcacaca ggaaacagct atgaccatga ttacgccaag ctctagctag aggtcgacgg
     1501 tatacagaca tgataagata cattgatgag tttggacaaa ccacaactag aatgcagtga
     1561 aaaaaatgct ttatttgtga aatttgtgat gctattgctt tatttgtaac cattataagc
     1621 tgcaataaac aagttggggt gggcgaagaa ctccagcatg agatccccgc gctggaggat
     1681 catccagccg gcgtcccgga aaacgattcc gaagcccaac ctttcataga aggcggcggt
     1741 ggaatcgaaa tctcgtgatg gcaggttggg cgtcgcttgg tcggtcattt cgaaccccag
     1801 agtcccgctc agaagaactc gtcaagaagg cgatagaagg cgatgcgctg cgaatcggga
     1861 gcggcgatac cgtaaagcac gaggaagcgg tcagcccatt cgccgccaag ctcttcagca
     1921 atatcacggg tagccaacgc tatgtcctga tagcggtccg ccacacccag ccggccacag
     1981 tcgatgaatc cagaaaagcg gccattttcc accatgatat tcggcaagca ggcatcgcca
     2041 tgggtcacga cgagatcctc gccgtcgggc atgcgcgcct tgagcctggc gaacagttcg
     2101 gctggcgcga gcccctgatg ctcttcgtcc agatcatcct gatcgacaag accggcttcc
     2161 atccgagtac gtgctcgctc gatgcgatgt ttcgcttggt ggtcgaatgg gcaggtagcc
     2221 ggatcaagcg tatgcagccg ccgcattgca tcagccatga tggatacttt ctcggcagga
     2281 gcaaggtgag atgacaggag atcctgcccc ggcacttcgc ccaatagcag ccagtccctt
     2341 cccgcttcag tgacaacgtc gagcacagct gcgcaaggaa cgcccgtcgt ggccagccac
     2401 gatagccgcg ctgcctcgtc ctgcagttca ttcagggcac cggacaggtc ggtcttgaca
     2461 aaaagaaccg ggcgcccctg cgctgacagc cggaacacgg cggcatcaga gcagccgatt
     2521 gtctgttgtg cccagtcata gccgaatagc ctctccaccc aagcggccgg agaacctgcg
     2581 tgcaatccat cttgttcaat catgcgaaac gatcctcatc ctgtctcttg atcagatccg
     2641 aaaatggata tacaagctcc cgggagcttt ttgcaaaagc ctaggcctcc aaaaaagcct
     2701 cctcactact tctggaatag ctcagaggca gaggcggcct cggcctctgc ataaataaaa
     2761 aaaattagtc agccatgggg cggagaatgg gcggaactgg gcggagttag gggcgggatg
     2821 ggcggagtta ggggcgggac tatggttgct gactaattga gatgcatgct ttgcatactt
     2881 ctgcctgctg gggagcctgg ggactttcca cacctggttg ctgactaatt gagatgcatg
     2941 ctttgcatac ttctgcctgc tggggagcct ggggactttc cacaccctaa ctgacacaca
     3001 ttccacagaa ttaattcgcg ttaaattttt gttaaatcag ctcatttttt aaccaatagg
     3061 ccgaaatcgg caaaatccct tataaatcaa aagaatagac cgagataggg ttgagtgttg
     3121 ttccagtttg gaacaagagt ccactattaa agaacgtgga ctccaacgtc aaagggcgaa
     3181 aaaccgtcta tcagggcgat ggcccactac gtgaaccatc accctaatca agttttttgg
     3241 ggtcgaggtg ccgtaaagca ctaaatcgga accctaaagg gagcccccga tttagagctt
     3301 gacggggaaa gccggcgaac gtggcgagaa aggaagggaa gaaagcgaaa ggagcgggcg
     3361 ctagggcgct ggcaagtgta gcggtcacgc tgcgcgtaac caccacaccc gccgcgctta
     3421 atgcgccgct acagggcgcg tggggatacc ccctagagcc ccagctggtt ctttccgcct
     3481 cagaagccat agagcccacc gcatccccag catgcctgct attgtcttcc caatcctccc
     3541 ccttgctgtc ctgccccacc ccacccccca gaatagaatg acacctactc agacaatgcg
     3601 atgcaatttc ctcattttat taggaaagga cagtgggagt ggcaccttcc agggtcaagg
     3661 aaggcacggg ggaggggcaa acaacagatg gctggcaact agaaggcaca gtcgaggctg
     3721 atcagcgagc tctagcattt aggtgacact atagaatagg gccctctaga cctagacttt
     3781 cttcatccac ggataaacaa ccgctggttg tttcaacgct gtgcctgaag ggggttgttt
     3841 tggatcgctt tgggaataag ctcgcgcccc tggaagaggg gctggtggtg gtgcaggtgg
     3901 ggcgggacat ggttccccag gtgctgcata atgtccgcct ggcccacctg gttcctggcc
     3961 atgtcctctt gcgggcaagg cacttccggg tcctggccca cttccgccaa acggttgttc
     4021 tccaaaatct ggacggggat acaatcctgg tggttgaaaa tcagctcctt gagccccgcc
     4081 gccataataa tccgctcctt gttctccaag ataaccacct tgcaggtatt cttcacatgg
     4141 gggaaattta ggatctacgt atttgctatt gaccatgtaa gatgacatca ccattatcgc
     4201 cgatacagtc aactgtcttt gacctttgtt actactctct tccgatgatg atgtcgcact
     4261 tattctatgc tgtctcaatg ttagaggcat atcagtctcc actgaagcca atctatctgt
     4321 gacggcatct ttattcacat tatcttgtac aaataatcct gttaacaatg cttttatatc
     4381 ctgtaaagaa tccattttca aaatcatgtc aaggtcttct cgaggaaaaa tcagtagaaa
     4441 tagctgttcc agtctttcta gccttgattc cacttctgtc agatgtgccc tagtcagcgg
     4501 agaccttttg gttttgggag agtagcgaca ctcccagttg ttcttcagac acttggcgca
     4561 cttcggtttt tctttggagc acttgagctt tttaagtcgg caaatatcgc atgcttgttc
     4621 gatagaagac agtagcttca tgaattccag cacactggcg gccgttacta gtggatccga
     4681 gctcggtacc aagcttgggt ctccctatag tgagtcgtat taatttcgat aagccagtaa
     4741 gcagtgggtt ctctagttag ccagagagct ctgcttatat agacctccca ccgtacacgc
     4801 ctaccgccca tttgcgtcaa tggggcggag ttgttacgac attttggaaa gtcccgttga
     4861 ttttggtgcc aaaacaaact cccattgacg tcaatggggt ggagacttgg aaatccccgt
     4921 gagtcaaacc gctatccacg cccattgatg tactgccaaa accgcatcac catggtaata
     4981 gcgatgacta atacgtagat gtactgccaa gtaggaaagt cccataaggt catgtactgg
     5041 gcataatgcc aggcgggcca tttaccgtca ttgacgtcaa tagggggcgt acttggcata
     5101 tgatacactt gatgtactgc caagtgggca gtttaccgta aatactccac ccattgacgt
     5161 caatggaaag tccctattgg cgttactatg ggaacatacg tcattattga cgtcaatggg
     5221 cgggggtcgt tgggcggtca gccaggcggg ccatttaccg taagttatgt aacgcggaac
     5281 tccatatatg ggctatgaac taatgacccc gtaattgatt actattaata actagtcaat
     5341 aatcaatgtc aacgcgtata tctggcccgt acatcgcgaa gcagcgcaaa acgcctaacc
     5401 ctaagcagat tcttcatgca attgtcggtc aagccttgcc ttgttgtagc ttaaattttg
     5461 ctcgcgcact actcagcgac ctccaacaca caagcaggga gcagatactg gcttaactat
     5521 gcggcatcag agcagattgt actgagagtg caccataggg gatcgggaga tctcccgatc
     5581 cgtcgacgtc aggtggcact tttcggggaa atgtgcgcgg aacccctatt tgtttatttt
     5641 tctaaataca ttcaaatatg tatccgctca tgagacaata accctgataa atgcttcaat
     5701 aatattgaaa aaggaagagt atgagtattc aacatttccg tgtcgccctt attccctttt
     5761 ttgcggcatt ttgccttcct gtttttgctc acccagaaac gctggtgaaa gtaaaagatg
     5821 ctgaagatca gttgggtgca cgagtgggtt acatcgaact ggatctcaac agcggtaaga
     5881 tccttgagag ttttcgcccc gaagaacgtt ttccaatgat gagcactttt aaagttctgc
     5941 tatgtggcgc ggtattatcc cgtattgacg ccgggcaaga gcaactcggt cgccgcatac
     6001 actattctca gaatgacttg gttgagtact caccagtcac agaaaagcat cttacggatg
     6061 gcatgacagt aagagaatta tgcagtgctg ccataaccat gagtgataac actgcggcca
     6121 acttacttct gacaacgatc ggaggaccga aggagctaac cgcttttttg cacaacatgg
     6181 gggatcatgt aactcgcctt gatcgttggg aaccggagct gaatgaagcc ataccaaacg
     6241 acgagcgtga caccacgatg cctgtagcaa tggcaac
//
