LOCUS       sequence-173943-        5510 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 5510)
  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 5510)
  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-ssp3
FEATURES             Location/Qualifiers
     source          1..5510
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      59..514
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(146..165)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     356..377
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     polyA_signal    645..693
                     /note="synthetic polyadenylation signal"
     misc_feature    707..798
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     747..766
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
     promoter        join(1463..1468,1469..1486,1487..1493)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             1547..2206
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(1613..1632)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             2548..2853
                     /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     2732..2751
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     regulatory      2941..2950
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     intron          2956..3022
                     /label=Mhc intron
                     /note="modified Drosophila myosin heavy chain intron 16 
                     (Pfeiffer et al., 2010)"
     primer_bind     complement(3067..3095)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     polyA_signal    3262..3383
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3273..3292)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3327..3346
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(3647..3664)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(3818..4406)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3898..3917)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4577..5368,5369..5437))
                     /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     5200..5219
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(join(5438..5510,1..32))
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 atttagaaaa ataaacaaat aggggttccg cgcacatttc cccgaaaagt gccacctgac
       61 gcgccctgta gcggcgcatt aagcgcggcg ggtgtggtgg ttacgcgcag cgtgaccgct
      121 acacttgcca gcgccctagc gcccgctcct ttcgctttct tcccttcctt tctcgccacg
      181 ttcgccggct ttccccgtca agctctaaat cgggggctcc ctttagggtt ccgatttagt
      241 gctttacggc acctcgaccc caaaaaactt gattagggtg atggttcacg tagtgggcca
      301 tcgccctgat agacggtttt tcgccctttg acgttggagt ccacgttctt taatagtgga
      361 ctcttgttcc aaactggaac aacactcaac cctatctcgg tctattcttt tgatttataa
      421 gggattttgc cgatttcggc ctattggtta aaaaatgagc tgatttaaca aaaatttaac
      481 gcgaatttta acaaaatatt aacgcttaca atttgccatt cgccattcag gctgcgcaac
      541 tgttgggaag ggcgatcggt gcgggcctct tcgctattac gccagcccaa gctaccatga
      601 taagtaagta atattaaggt acgggaggta cttggagcgg ccgcaataaa atatctttat
      661 tttcattaca tctgtgtgtt ggttttttgt gtgaatcgat agtactaaca tacgctctcc
      721 atcaaaacaa aacgaaacaa aacaaactag caaaataggc tgtccccagt gcaagtgcag
      781 gtgccagaac atttctctat cgataggtac ctttgttgct cctatttcag acgtcgcttc
      841 tttgttgttt ttatcgcaga attttgcaac gccagtggac ttggtagcat tttccaaagg
      901 cgtaacgagt ctaaagaaac cgcgatgtgt tcaatcaatg cctgaaagat tccccttcac
      961 tattccagtt gtctgctgct tgtcttgtgt cggttagaga gaaattagaa tttttgattt
     1021 ctgccaaact cagccgagca gagccagctg atttaagcgt tgggctgcaa ttgtgcaata
     1081 tctgtcattg ggtaatcgat agaagctaaa ctatcgatac gagcgcgcac ttaatcgaca
     1141 ttataagtaa attcaattgt aagagcaact ttttgagtat tcaacaaaaa aaacagaaaa
     1201 aataccaaac acaattattt cacattaacg cttacaaaaa ctttctataa aaatgcacaa
     1261 taattctttt gtttacagga gaaaagtaaa acagcgaaag agaaaaaaag aactcaaatt
     1321 tgaaattttt ggattacaaa attgccttca aaattggccc ttaaccgcaa agctccatcc
     1381 gaaagctcac cgcgggcgag cgagacaacc agatcttaga gcatgcaccg gtgatatcgc
     1441 ggccgcatta ggcaccccag gctttacact ttatgcttcc ggctcgtata atgtgtggat
     1501 tttgagttag gatccgtcga gattttcagg agctaaggaa gctaaaatgg agaaaaaaat
     1561 cactggatat accaccgttg atatatccca atggcatcgt aaagaacatt ttgaggcatt
     1621 tcagtcagtt gctcaatgta cctataacca gaccgttcag ctggatatta cggccttttt
     1681 aaagaccgta aagaaaaata agcacaagtt ttatccggcc tttattcaca ttcttgcccg
     1741 cctgatgaat gctcatccgg aattccgtat ggcaatgaaa gacggtgagc tggtgatatg
     1801 ggatagtgtt cacccttgtt acaccgtttt ccatgagcaa actgaaacgt tttcatcgct
     1861 ctggagtgaa taccacgacg atttccggca gtttctacac atatattcgc aagatgtggc
     1921 gtgttacggt gaaaacctgg cctatttccc taaagggttt attgagaata tgtttttcgt
     1981 ctcagccaat ccctgggtga gtttcaccag ttttgattta aacgtggcca atatggacaa
     2041 cttcttcgcc cccgttttca ccatgggcaa atattatacg caaggcgaca aggtgctgat
     2101 gccgctggcg attcaggttc atcatgccgt ttgtgatggc ttccatgtcg gcagaatgct
     2161 taatgaatta caacagtact gcgatgagtg gcagggcggg gcgtaaacgc gtggatccgg
     2221 cttactaaaa gccagataac agtatgcgta tttgcgcgct gatttttgcg gtataagaat
     2281 atatactgat atgtataccc gaagtatgtc aaaaagaggt atgctatgaa gcagcgtatt
     2341 acagtgacag ttgacagcga cagctatcag ttgctcaagg catatatgat gtcaatatct
     2401 ccggtctggt aagcacaacc atgcagaatg aagcccgtcg tctgcgtgcc gaacgctgga
     2461 aagcggaaaa tcaggaaggg atggctgagg tcgcccggtt tattgaaatg aacggctctt
     2521 ttgctgacga gaacaggggc tggtgaaatg cagtttaagg tttacaccta taaaagagag
     2581 agccgttatc gtctgtttgt ggatgtacag agtgatatta ttgacacgcc cgggcgacgg
     2641 atggtgatcc ccctggccag tgcacgtctg ctgtcagata aagtctcccg tgaactttac
     2701 ccggtggtgc atatcgggga tgaaagctgg cgcatgatga ccaccgatat ggccagtgtg
     2761 ccggtctccg ttatcgggga agaagtggct gatctcagcc accgcgaaaa tgacatcaaa
     2821 aacgccatta acctgatgtt ctggggaata taaatgtcag gctcccttat acacagccag
     2881 tctgcaggat atcgtcgacg aattcggccc ctgcaggggc attccggtac tgttggtaaa
     2941 gccaccatgg aaaaggtagg ttcaaccact gatgcctagg cacaccgaaa cgactaaccc
     3001 taattcttat cctttacttc aggccactta agcatggcta gcaaaggaga agaactcttc
     3061 actggagttg tcccaattct tgttgaatta gatggtgatg ttaacggcca caagttctct
     3121 gtcagtggag agggtgaagg tgatgcaaca tacggaaaac ttaccctgaa gttcatctgc
     3181 actactggca aactgcctgt tccctggcca acactagtct gatctagagt cggggcggcc
     3241 ggccgcttcg agcagacatg ataagataca ttgatgagtt tggacaaacc acaactagaa
     3301 tgcagtgaaa aaaatgcttt atttgtgaaa tttgtgatgc tattgcttta tttgtaacca
     3361 ttataagctg caataaacaa gttaacaaca acaattgcat tcattttatg tttcaggttc
     3421 agggggaggt gtgggaggtt ttttaaagca agtaaaacct ctacaaatgt ggtaaaatcg
     3481 ataaggatcc gaccgatgcc ctcaagcttt gagaggggcc cccttcaacc cagtcagctc
     3541 cgacgtcttg gcgcccccgc ggggcatgac tatcgtcgcc gcacttatga ctgtcttctt
     3601 tatcatgcaa ctcgtaggac aggtgccggc agcgctcttc cgcttcctcg ctcactgact
     3661 cgctgcgctc ggtcgttcgg ctgcggcgag cggtatcagc tcactcaaag gcggtaatac
     3721 ggttatccac agaatcaggg gataacgcag gaaagaacat gtgagcaaaa ggccagcaaa
     3781 aggccaggaa ccgtaaaaag gccgcgttgc tggcgttttt ccataggctc cgcccccctg
     3841 acgagcatca caaaaatcga cgctcaagtc agaggtggcg aaacccgaca ggactataaa
     3901 gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc
     3961 ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac
     4021 gctgtaggta tctcagttcg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac
     4081 cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg
     4141 taagacacga cttatcgcca ctggcagcag ccactggtaa caggattagc agagcgaggt
     4201 atgtaggcgg tgctacagag ttcttgaagt ggtggcctaa ctacggctac actagaagaa
     4261 cagtatttgg tatctgcgct ctgctgaagc cagttacctt cggaaaaaga gttggtagct
     4321 cttgatccgg caaacaaacc accgctggta gcggtggttt ttttgtttgc aagcagcaga
     4381 ttacgcgcag aaaaaaagga tctcaagaag atcctttgat cttttctacg gggtctgacg
     4441 ctcagtggaa cgaaaactca cgttaaggga ttttggtcat gagattatca aaaaggatct
     4501 tcacctagat ccttttaaat taaaaatgaa gttttaaatc aatctaaagt atatatgagt
     4561 aaacttggtc tgacagttac caatgcttaa tcagtgaggc acctatctca gcgatctgtc
     4621 tatttcgttc atccatagtt gcctgactcc ccgtcgtgta gataactacg atacgggagg
     4681 gcttaccatc tggccccagt gctgcaatga taccgcgaga cccacgctca ccggctccag
     4741 atttatcagc aataaaccag ccagccggaa gggccgagcg cagaagtggt cctgcaactt
     4801 tatccgcctc catccagtct attaattgtt gccgggaagc tagagtaagt agttcgccag
     4861 ttaatagttt gcgcaacgtt gttgccattg ctacaggcat cgtggtgtca cgctcgtcgt
     4921 ttggtatggc ttcattcagc tccggttccc aacgatcaag gcgagttaca tgatccccca
     4981 tgttgtgcaa aaaagcggtt agctccttcg gtcctccgat cgttgtcaga agtaagttgg
     5041 ccgcagtgtt atcactcatg gttatggcag cactgcataa ttctcttact gtcatgccat
     5101 ccgtaagatg cttttctgtg actggtgagt actcaaccaa gtcattctga gaatagtgta
     5161 tgcggcgacc gagttgctct tgcccggcgt caatacggga taataccgcg ccacatagca
     5221 gaactttaaa agtgctcatc attggaaaac gttcttcggg gcgaaaactc tcaaggatct
     5281 taccgctgtt gagatccagt tcgatgtaac ccactcgtgc acccaactga tcttcagcat
     5341 cttttacttt caccagcgtt tctgggtgag caaaaacagg aaggcaaaat gccgcaaaaa
     5401 agggaataag ggcgacacgg aaatgttgaa tactcatact cttccttttt caatattatt
     5461 gaagcattta tcagggttat tgtctcatga gcggatacat atttgaatgt
//
