LOCUS       sequence-173941-        4939 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Vector to measure the basal activity of CP 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 4939)
  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 4939)
  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-ctrl
FEATURES             Location/Qualifiers
     source          1..4939
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(57..76)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     267..288
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     polyA_signal    556..604
                     /note="synthetic polyadenylation signal"
     misc_feature    618..709
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     658..677
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
     promoter        join(803..808,809..826,827..833)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             887..1546
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(953..972)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             1888..2193
                     /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     2072..2091
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     regulatory      2281..2290
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     intron          2296..2362
                     /label=Mhc intron
                     /note="modified Drosophila myosin heavy chain intron 16 
                     (Pfeiffer et al., 2010)"
     primer_bind     complement(2407..2435)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     polyA_signal    2602..2723
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2613..2632)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     2667..2686
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(2987..3004)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(3158..3746)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3238..3257)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(3917..4708,4709..4777))
                     /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     4540..4559
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(4778..4882)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      join(4909..4939,1..425)
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
ORIGIN
        1 gggtgtggtg gttacgcgca gcgtgaccgc tacacttgcc agcgccctag cgcccgctcc
       61 tttcgctttc ttcccttcct ttctcgccac gttcgccggc tttccccgtc aagctctaaa
      121 tcgggggctc cctttagggt tccgatttag tgctttacgg cacctcgacc ccaaaaaact
      181 tgattagggt gatggttcac gtagtgggcc atcgccctga tagacggttt ttcgcccttt
      241 gacgttggag tccacgttct ttaatagtgg actcttgttc caaactggaa caacactcaa
      301 ccctatctcg gtctattctt ttgatttata agggattttg ccgatttcgg cctattggtt
      361 aaaaaatgag ctgatttaac aaaaatttaa cgcgaatttt aacaaaatat taacgcttac
      421 aatttgccat tcgccattca ggctgcgcaa ctgttgggaa gggcgatcgg tgcgggcctc
      481 ttcgctatta cgccagccca agctaccatg ataagtaagt aatattaagg tacgggaggt
      541 acttggagcg gccgcaataa aatatcttta ttttcattac atctgtgtgt tggttttttg
      601 tgtgaatcga tagtactaac atacgctctc catcaaaaca aaacgaaaca aaacaaacta
      661 gcaaaatagg ctgtccccag tgcaagtgca ggtgccagaa catttctcta tcgataggta
      721 ccgagctctt acgcgtgcta gcccgggctc gagatcttag agcatgcacc ggtgatatcc
      781 ggccgcatta ggcaccccag gctttacact ttatgcttcc ggctcgtata atgtgtggat
      841 tttgagttag gatccgtcga gattttcagg agctaaggaa gctaaaatgg agaaaaaaat
      901 cactggatat accaccgttg atatatccca atggcatcgt aaagaacatt ttgaggcatt
      961 tcagtcagtt gctcaatgta cctataacca gaccgttcag ctggatatta cggccttttt
     1021 aaagaccgta aagaaaaata agcacaagtt ttatccggcc tttattcaca ttcttgcccg
     1081 cctgatgaat gctcatccgg aattccgtat ggcaatgaaa gacggtgagc tggtgatatg
     1141 ggatagtgtt cacccttgtt acaccgtttt ccatgagcaa actgaaacgt tttcatcgct
     1201 ctggagtgaa taccacgacg atttccggca gtttctacac atatattcgc aagatgtggc
     1261 gtgttacggt gaaaacctgg cctatttccc taaagggttt attgagaata tgtttttcgt
     1321 ctcagccaat ccctgggtga gtttcaccag ttttgattta aacgtggcca atatggacaa
     1381 cttcttcgcc cccgttttca ccatgggcaa atattatacg caaggcgaca aggtgctgat
     1441 gccgctggcg attcaggttc atcatgccgt ttgtgatggc ttccatgtcg gcagaatgct
     1501 taatgaatta caacagtact gcgatgagtg gcagggcggg gcgtaaacgc gtggatccgg
     1561 cttactaaaa gccagataac agtatgcgta tttgcgcgct gatttttgcg gtataagaat
     1621 atatactgat atgtataccc gaagtatgtc aaaaagaggt atgctatgaa gcagcgtatt
     1681 acagtgacag ttgacagcga cagctatcag ttgctcaagg catatatgat gtcaatatct
     1741 ccggtctggt aagcacaacc atgcagaatg aagcccgtcg tctgcgtgcc gaacgctgga
     1801 aagcggaaaa tcaggaaggg atggctgagg tcgcccggtt tattgaaatg aacggctctt
     1861 ttgctgacga gaacaggggc tggtgaaatg cagtttaagg tttacaccta taaaagagag
     1921 agccgttatc gtctgtttgt ggatgtacag agtgatatta ttgacacgcc cgggcgacgg
     1981 atggtgatcc ccctggccag tgcacgtctg ctgtcagata aagtctcccg tgaactttac
     2041 ccggtggtgc atatcgggga tgaaagctgg cgcatgatga ccaccgatat ggccagtgtg
     2101 ccggtctccg ttatcgggga agaagtggct gatctcagcc accgcgaaaa tgacatcaaa
     2161 aacgccatta acctgatgtt ctggggaata taaatgtcag gctcccttat acacagccag
     2221 tctgcaggat atcgtcgacg aattcggccc ctgcaggggc attccggtac tgttggtaaa
     2281 gccaccatgg aaaaggtagg ttcaaccact gatgcctagg cacaccgaaa cgactaaccc
     2341 taattcttat cctttacttc aggccactta agcatggcta gcaaaggaga agaactcttc
     2401 actggagttg tcccaattct tgttgaatta gatggtgatg ttaacggcca caagttctct
     2461 gtcagtggag agggtgaagg tgatgcaaca tacggaaaac ttaccctgaa gttcatctgc
     2521 actactggca aactgcctgt tccctggcca acactagtct gatctagagt cggggcggcc
     2581 ggccgcttcg agcagacatg ataagataca ttgatgagtt tggacaaacc acaactagaa
     2641 tgcagtgaaa aaaatgcttt atttgtgaaa tttgtgatgc tattgcttta tttgtaacca
     2701 ttataagctg caataaacaa gttaacaaca acaattgcat tcattttatg tttcaggttc
     2761 agggggaggt gtgggaggtt ttttaaagca agtaaaacct ctacaaatgt ggtaaaatcg
     2821 ataaggatcc gaccgatgcc ctcaagcttt gagaggggcc cccttcaacc cagtcagctc
     2881 cgacgtcttg gcgcccccgc ggggcatgac tatcgtcgcc gcacttatga ctgtcttctt
     2941 tatcatgcaa ctcgtaggac aggtgccggc agcgctcttc cgcttcctcg ctcactgact
     3001 cgctgcgctc ggtcgttcgg ctgcggcgag cggtatcagc tcactcaaag gcggtaatac
     3061 ggttatccac agaatcaggg gataacgcag gaaagaacat gtgagcaaaa ggccagcaaa
     3121 aggccaggaa ccgtaaaaag gccgcgttgc tggcgttttt ccataggctc cgcccccctg
     3181 acgagcatca caaaaatcga cgctcaagtc agaggtggcg aaacccgaca ggactataaa
     3241 gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc
     3301 ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac
     3361 gctgtaggta tctcagttcg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac
     3421 cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg
     3481 taagacacga cttatcgcca ctggcagcag ccactggtaa caggattagc agagcgaggt
     3541 atgtaggcgg tgctacagag ttcttgaagt ggtggcctaa ctacggctac actagaagaa
     3601 cagtatttgg tatctgcgct ctgctgaagc cagttacctt cggaaaaaga gttggtagct
     3661 cttgatccgg caaacaaacc accgctggta gcggtggttt ttttgtttgc aagcagcaga
     3721 ttacgcgcag aaaaaaagga tctcaagaag atcctttgat cttttctacg gggtctgacg
     3781 ctcagtggaa cgaaaactca cgttaaggga ttttggtcat gagattatca aaaaggatct
     3841 tcacctagat ccttttaaat taaaaatgaa gttttaaatc aatctaaagt atatatgagt
     3901 aaacttggtc tgacagttac caatgcttaa tcagtgaggc acctatctca gcgatctgtc
     3961 tatttcgttc atccatagtt gcctgactcc ccgtcgtgta gataactacg atacgggagg
     4021 gcttaccatc tggccccagt gctgcaatga taccgcgaga cccacgctca ccggctccag
     4081 atttatcagc aataaaccag ccagccggaa gggccgagcg cagaagtggt cctgcaactt
     4141 tatccgcctc catccagtct attaattgtt gccgggaagc tagagtaagt agttcgccag
     4201 ttaatagttt gcgcaacgtt gttgccattg ctacaggcat cgtggtgtca cgctcgtcgt
     4261 ttggtatggc ttcattcagc tccggttccc aacgatcaag gcgagttaca tgatccccca
     4321 tgttgtgcaa aaaagcggtt agctccttcg gtcctccgat cgttgtcaga agtaagttgg
     4381 ccgcagtgtt atcactcatg gttatggcag cactgcataa ttctcttact gtcatgccat
     4441 ccgtaagatg cttttctgtg actggtgagt actcaaccaa gtcattctga gaatagtgta
     4501 tgcggcgacc gagttgctct tgcccggcgt caatacggga taataccgcg ccacatagca
     4561 gaactttaaa agtgctcatc attggaaaac gttcttcggg gcgaaaactc tcaaggatct
     4621 taccgctgtt gagatccagt tcgatgtaac ccactcgtgc acccaactga tcttcagcat
     4681 cttttacttt caccagcgtt tctgggtgag caaaaacagg aaggcaaaat gccgcaaaaa
     4741 agggaataag ggcgacacgg aaatgttgaa tactcatact cttccttttt caatattatt
     4801 gaagcattta tcagggttat tgtctcatga gcggatacat atttgaatgt atttagaaaa
     4861 ataaacaaat aggggttccg cgcacatttc cccgaaaagt gccacctgac gcgccctgta
     4921 gcggcgcatt aagcgcggc
//
