LOCUS       sequence-173945-        5794 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Vector to measure enhancer responsiveness of candidates from a 
            genomic library (cloned instead of the core promoter) by determining
            the abundance of transcripts originating from each candidate..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5794)
  AUTHORS   Arnold CD, Zabidi MA, Pagani M, Rath M, Schernhuber K, Kazmar T, 
            Stark A
  TITLE     Genome-wide assessment of sequence-intrinsic enhancer responsiveness
            at single-base-pair resolution.
  JOURNAL   Nat Biotechnol. 2016 Dec 26. doi: 10.1038/nbt.3739.
  PUBMED    28024147
REFERENCE   2  (bases 1 to 5794)
  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"; journalName: "Nat 
            Biotechnol. 2016 Dec 26. doi: 10.1038/nbt.3739."
COMMENT     Sequence Label: pSTAP-seq_fly-ncm
FEATURES             Location/Qualifiers
     source          1..5794
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     promoter        join(295..300,301..318,319..325)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             379..1038
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(445..464)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             1380..1685
                     /codon_start=1
                     /gene="ccdB"
                     /product="CcdB, a bacterial toxin that poisons DNA gyrase"
                     /label=ccdB
                     /note="Plasmids containing the ccdB gene cannot be 
                     propagated in standard E. coli strains."
                     /translation="MQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDK
                     VSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI"
     primer_bind     1564..1583
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     regulatory      1773..1782
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     intron          1788..1854
                     /label=Mhc intron
                     /note="modified Drosophila myosin heavy chain intron 16 
                     (Pfeiffer et al., 2010)"
     primer_bind     complement(1899..1927)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     polyA_signal    2094..2215
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2105..2124)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     2159..2178
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(2479..2496)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2650..3238)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(2730..2749)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(3409..4200,4201..4269))
                     /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     4032..4051
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(4270..4374)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      4401..4856
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(4488..4507)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4698..4719
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     polyA_signal    4987..5035
                     /note="synthetic polyadenylation signal"
     misc_feature    5049..5140
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     5089..5108
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
ORIGIN
        1 aaattaattt tataatatgg cactatcgta aattttatag cacagcgaac ctcaatattt
       61 aagggcaacg atttttttac gactaaaaca gtgtaatata tttgttataa catatttggt
      121 tcattgcact gcagaaattt cgaatatcag ctcgaaaatg gaacaaggat atggaacaag
      181 aacattaaat ttgaaacgaa actttttttt tttagcgatt tttgggctcc aaaacgggca
      241 atcagatctt agagcatgca ccggtgatat ccggccgcat taggcacccc aggctttaca
      301 ctttatgctt ccggctcgta taatgtgtgg attttgagtt aggatccgtc gagattttca
      361 ggagctaagg aagctaaaat ggagaaaaaa atcactggat ataccaccgt tgatatatcc
      421 caatggcatc gtaaagaaca ttttgaggca tttcagtcag ttgctcaatg tacctataac
      481 cagaccgttc agctggatat tacggccttt ttaaagaccg taaagaaaaa taagcacaag
      541 ttttatccgg cctttattca cattcttgcc cgcctgatga atgctcatcc ggaattccgt
      601 atggcaatga aagacggtga gctggtgata tgggatagtg ttcacccttg ttacaccgtt
      661 ttccatgagc aaactgaaac gttttcatcg ctctggagtg aataccacga cgatttccgg
      721 cagtttctac acatatattc gcaagatgtg gcgtgttacg gtgaaaacct ggcctatttc
      781 cctaaagggt ttattgagaa tatgtttttc gtctcagcca atccctgggt gagtttcacc
      841 agttttgatt taaacgtggc caatatggac aacttcttcg cccccgtttt caccatgggc
      901 aaatattata cgcaaggcga caaggtgctg atgccgctgg cgattcaggt tcatcatgcc
      961 gtttgtgatg gcttccatgt cggcagaatg cttaatgaat tacaacagta ctgcgatgag
     1021 tggcagggcg gggcgtaaac gcgtggatcc ggcttactaa aagccagata acagtatgcg
     1081 tatttgcgcg ctgatttttg cggtataaga atatatactg atatgtatac ccgaagtatg
     1141 tcaaaaagag gtatgctatg aagcagcgta ttacagtgac agttgacagc gacagctatc
     1201 agttgctcaa ggcatatatg atgtcaatat ctccggtctg gtaagcacaa ccatgcagaa
     1261 tgaagcccgt cgtctgcgtg ccgaacgctg gaaagcggaa aatcaggaag ggatggctga
     1321 ggtcgcccgg tttattgaaa tgaacggctc ttttgctgac gagaacaggg gctggtgaaa
     1381 tgcagtttaa ggtttacacc tataaaagag agagccgtta tcgtctgttt gtggatgtac
     1441 agagtgatat tattgacacg cccgggcgac ggatggtgat ccccctggcc agtgcacgtc
     1501 tgctgtcaga taaagtctcc cgtgaacttt acccggtggt gcatatcggg gatgaaagct
     1561 ggcgcatgat gaccaccgat atggccagtg tgccggtctc cgttatcggg gaagaagtgg
     1621 ctgatctcag ccaccgcgaa aatgacatca aaaacgccat taacctgatg ttctggggaa
     1681 tataaatgtc aggctccctt atacacagcc agtctgcagg atatcgtcga cgaattcggc
     1741 ccctgcaggg gcattccggt actgttggta aagccaccat ggaaaaggta ggttcaacca
     1801 ctgatgccta ggcacaccga aacgactaac cctaattctt atcctttact tcaggccact
     1861 taagcatggc tagcaaagga gaagaactct tcactggagt tgtcccaatt cttgttgaat
     1921 tagatggtga tgttaacggc cacaagttct ctgtcagtgg agagggtgaa ggtgatgcaa
     1981 catacggaaa acttaccctg aagttcatct gcactactgg caaactgcct gttccctggc
     2041 caacactagt ctgatctaga gtcggggcgg ccggccgctt cgagcagaca tgataagata
     2101 cattgatgag tttggacaaa ccacaactag aatgcagtga aaaaaatgct ttatttgtga
     2161 aatttgtgat gctattgctt tatttgtaac cattataagc tgcaataaac aagttaacaa
     2221 caacaattgc attcatttta tgtttcaggt tcagggggag gtgtgggagg ttttttaaag
     2281 caagtaaaac ctctacaaat gtggtaaaat cgataaggat ccgaccgatg ccctcaagct
     2341 ttgagagggg cccccttcaa cccagtcagc tccgacgtct tggcgccccc gcggggcatg
     2401 actatcgtcg ccgcacttat gactgtcttc tttatcatgc aactcgtagg acaggtgccg
     2461 gcagcgctct tccgcttcct cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg
     2521 agcggtatca gctcactcaa aggcggtaat acggttatcc acagaatcag gggataacgc
     2581 aggaaagaac atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa aggccgcgtt
     2641 gctggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag
     2701 tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc
     2761 cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc
     2821 ttcgggaagc gtggcgcttt ctcatagctc acgctgtagg tatctcagtt cggtgtaggt
     2881 cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt
     2941 atccggtaac tatcgtcttg agtccaaccc ggtaagacac gacttatcgc cactggcagc
     3001 agccactggt aacaggatta gcagagcgag gtatgtaggc ggtgctacag agttcttgaa
     3061 gtggtggcct aactacggct acactagaag aacagtattt ggtatctgcg ctctgctgaa
     3121 gccagttacc ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg
     3181 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga
     3241 agatcctttg atcttttcta cggggtctga cgctcagtgg aacgaaaact cacgttaagg
     3301 gattttggtc atgagattat caaaaaggat cttcacctag atccttttaa attaaaaatg
     3361 aagttttaaa tcaatctaaa gtatatatga gtaaacttgg tctgacagtt accaatgctt
     3421 aatcagtgag gcacctatct cagcgatctg tctatttcgt tcatccatag ttgcctgact
     3481 ccccgtcgtg tagataacta cgatacggga gggcttacca tctggcccca gtgctgcaat
     3541 gataccgcga gacccacgct caccggctcc agatttatca gcaataaacc agccagccgg
     3601 aagggccgag cgcagaagtg gtcctgcaac tttatccgcc tccatccagt ctattaattg
     3661 ttgccgggaa gctagagtaa gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat
     3721 tgctacaggc atcgtggtgt cacgctcgtc gtttggtatg gcttcattca gctccggttc
     3781 ccaacgatca aggcgagtta catgatcccc catgttgtgc aaaaaagcgg ttagctcctt
     3841 cggtcctccg atcgttgtca gaagtaagtt ggccgcagtg ttatcactca tggttatggc
     3901 agcactgcat aattctctta ctgtcatgcc atccgtaaga tgcttttctg tgactggtga
     3961 gtactcaacc aagtcattct gagaatagtg tatgcggcga ccgagttgct cttgcccggc
     4021 gtcaatacgg gataataccg cgccacatag cagaacttta aaagtgctca tcattggaaa
     4081 acgttcttcg gggcgaaaac tctcaaggat cttaccgctg ttgagatcca gttcgatgta
     4141 acccactcgt gcacccaact gatcttcagc atcttttact ttcaccagcg tttctgggtg
     4201 agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata agggcgacac ggaaatgttg
     4261 aatactcata ctcttccttt ttcaatatta ttgaagcatt tatcagggtt attgtctcat
     4321 gagcggatac atatttgaat gtatttagaa aaataaacaa ataggggttc cgcgcacatt
     4381 tccccgaaaa gtgccacctg acgcgccctg tagcggcgca ttaagcgcgg cgggtgtggt
     4441 ggttacgcgc agcgtgaccg ctacacttgc cagcgcccta gcgcccgctc ctttcgcttt
     4501 cttcccttcc tttctcgcca cgttcgccgg ctttccccgt caagctctaa atcgggggct
     4561 ccctttaggg ttccgattta gtgctttacg gcacctcgac cccaaaaaac ttgattaggg
     4621 tgatggttca cgtagtgggc catcgccctg atagacggtt tttcgccctt tgacgttgga
     4681 gtccacgttc tttaatagtg gactcttgtt ccaaactgga acaacactca accctatctc
     4741 ggtctattct tttgatttat aagggatttt gccgatttcg gcctattggt taaaaaatga
     4801 gctgatttaa caaaaattta acgcgaattt taacaaaata ttaacgctta caatttgcca
     4861 ttcgccattc aggctgcgca actgttggga agggcgatcg gtgcgggcct cttcgctatt
     4921 acgccagccc aagctaccat gataagtaag taatattaag gtacgggagg tacttggagc
     4981 ggccgcaata aaatatcttt attttcatta catctgtgtg ttggtttttt gtgtgaatcg
     5041 atagtactaa catacgctct ccatcaaaac aaaacgaaac aaaacaaact agcaaaatag
     5101 gctgtcccca gtgcaagtgc aggtgccaga acatttctct atcgataggt acccgctgga
     5161 caggtgtttc aacttttttc gcttcattta atttctcgct ttccgcctcc gcagctgcta
     5221 ctgcttcttc ttgctgcttt tccacgccag cagaatggga aatgtgctgg cgctccgaac
     5281 gaggctcagc cgcaggagtt ttcttctgct cagtgggctg ctcatcctgt ccagcatccc
     5341 tctccttggc acgcttctcc cccctatccg tatcgtcagt tttcttggca tctttggcgg
     5401 attcctcctg ctttgcttcc tcttcctcgc gcccgctgct ttcggaggac gaggactcgc
     5461 tcctggcgtc gctgtcgctg ccactggaag tgtcgctgct gctggaattg ctgctcgaat
     5521 cgctctcggc atcgctttcc cccatcgcgc gtttatttcg agaaattttc agggaaaaca
     5581 acgatgaaaa ttattgggca gcaaaaaaca caacgcggcg atagaattag agatgggaca
     5641 ccagtggcga cggtatcgat atacacatgt gtttgactgc taaatcgtat cgaaattgta
     5701 gtttcgatag tcagctatag aaatgctaaa tgtgtttttt aaattgaact gaaaatttaa
     5761 attcaagttc cacattagaa aaaatgatat ttta
//
