LOCUS       sequence-173939-        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-ham
FEATURES             Location/Qualifiers
     source          1..5510
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(56..75)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     266..287
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     polyA_signal    555..603
                     /note="synthetic polyadenylation signal"
     misc_feature    617..708
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     657..676
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
     promoter        join(1373..1378,1379..1396,1397..1403)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             1457..2116
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(1523..1542)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             2458..2763
                     /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     2642..2661
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     regulatory      2851..2860
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     intron          2866..2932
                     /label=Mhc intron
                     /note="modified Drosophila myosin heavy chain intron 16 
                     (Pfeiffer et al., 2010)"
     primer_bind     complement(2977..3005)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     polyA_signal    3172..3293
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3183..3202)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3237..3256
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(3557..3574)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(3728..4316)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3808..3827)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4487..5278,5279..5347))
                     /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     5110..5129
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5348..5452)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      join(5479..5510,1..424)
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
ORIGIN
        1 ggtgtggtgg ttacgcgcag cgtgaccgct acacttgcca gcgccctagc gcccgctcct
       61 ttcgctttct tcccttcctt tctcgccacg ttcgccggct ttccccgtca agctctaaat
      121 cgggggctcc ctttagggtt ccgatttagt gctttacggc acctcgaccc caaaaaactt
      181 gattagggtg atggttcacg tagtgggcca tcgccctgat agacggtttt tcgccctttg
      241 acgttggagt ccacgttctt taatagtgga ctcttgttcc aaactggaac aacactcaac
      301 cctatctcgg tctattcttt tgatttataa gggattttgc cgatttcggc ctattggtta
      361 aaaaatgagc tgatttaaca aaaatttaac gcgaatttta acaaaatatt aacgcttaca
      421 atttgccatt cgccattcag gctgcgcaac tgttgggaag ggcgatcggt gcgggcctct
      481 tcgctattac gccagcccaa gctaccatga taagtaagta atattaaggt acgggaggta
      541 cttggagcgg ccgcaataaa atatctttat tttcattaca tctgtgtgtt ggttttttgt
      601 gtgaatcgat agtactaaca tacgctctcc atcaaaacaa aacgaaacaa aacaaactag
      661 caaaataggc tgtccccagt gcaagtgcag gtgccagaac atttctctat cgataggtac
      721 cttgcgcact gtgctgcgac ttgcagatcg attttcagac gctatcctaa agatccatgc
      781 gggtgcataa gaaaagatac aaatacagat acaactacaa atacagggaa tcggactgat
      841 ctgaatggca gggcagacaa accgcagttt gagatgttaa gttgtttgtt tgttgtgggc
      901 acttcggaat cgaccctgtt tggattgctg ataaatgtct aaaaatacgc aaggcaacca
      961 caacatgaaa gatacaatgt gtgccgagtt ggaagggttc cacggagtct gctcttcgtc
     1021 tggctttatc tcgttcggaa ttttctgaat tttatcgaca acataaagca attgaattgc
     1081 aacataaatc agagaccaca acatgtgttg agcactcgat gatagcggta tgatgtattt
     1141 atattcaaag taatatatct gagtccgcca ttttccccac aatttcccca tccccttgct
     1201 ttcaaccggc tttttaatcc ccagccccca tttggcggcc atagccaagc gtaaagagat
     1261 gtaaagacat gctcgagagt gccactcaat gtggcaagcc atggagaatg ggaaatgggg
     1321 agatcttaga gcatgcaccg gtgatatcgc ggccgcatta ggcaccccag gctttacact
     1381 ttatgcttcc ggctcgtata atgtgtggat tttgagttag gatccgtcga gattttcagg
     1441 agctaaggaa gctaaaatgg agaaaaaaat cactggatat accaccgttg atatatccca
     1501 atggcatcgt aaagaacatt ttgaggcatt tcagtcagtt gctcaatgta cctataacca
     1561 gaccgttcag ctggatatta cggccttttt aaagaccgta aagaaaaata agcacaagtt
     1621 ttatccggcc tttattcaca ttcttgcccg cctgatgaat gctcatccgg aattccgtat
     1681 ggcaatgaaa gacggtgagc tggtgatatg ggatagtgtt cacccttgtt acaccgtttt
     1741 ccatgagcaa actgaaacgt tttcatcgct ctggagtgaa taccacgacg atttccggca
     1801 gtttctacac atatattcgc aagatgtggc gtgttacggt gaaaacctgg cctatttccc
     1861 taaagggttt attgagaata tgtttttcgt ctcagccaat ccctgggtga gtttcaccag
     1921 ttttgattta aacgtggcca atatggacaa cttcttcgcc cccgttttca ccatgggcaa
     1981 atattatacg caaggcgaca aggtgctgat gccgctggcg attcaggttc atcatgccgt
     2041 ttgtgatggc ttccatgtcg gcagaatgct taatgaatta caacagtact gcgatgagtg
     2101 gcagggcggg gcgtaaacgc gtggatccgg cttactaaaa gccagataac agtatgcgta
     2161 tttgcgcgct gatttttgcg gtataagaat atatactgat atgtataccc gaagtatgtc
     2221 aaaaagaggt atgctatgaa gcagcgtatt acagtgacag ttgacagcga cagctatcag
     2281 ttgctcaagg catatatgat gtcaatatct ccggtctggt aagcacaacc atgcagaatg
     2341 aagcccgtcg tctgcgtgcc gaacgctgga aagcggaaaa tcaggaaggg atggctgagg
     2401 tcgcccggtt tattgaaatg aacggctctt ttgctgacga gaacaggggc tggtgaaatg
     2461 cagtttaagg tttacaccta taaaagagag agccgttatc gtctgtttgt ggatgtacag
     2521 agtgatatta ttgacacgcc cgggcgacgg atggtgatcc ccctggccag tgcacgtctg
     2581 ctgtcagata aagtctcccg tgaactttac ccggtggtgc atatcgggga tgaaagctgg
     2641 cgcatgatga ccaccgatat ggccagtgtg ccggtctccg ttatcgggga agaagtggct
     2701 gatctcagcc accgcgaaaa tgacatcaaa aacgccatta acctgatgtt ctggggaata
     2761 taaatgtcag gctcccttat acacagccag tctgcaggat atcgtcgacg aattcggccc
     2821 ctgcaggggc attccggtac tgttggtaaa gccaccatgg aaaaggtagg ttcaaccact
     2881 gatgcctagg cacaccgaaa cgactaaccc taattcttat cctttacttc aggccactta
     2941 agcatggcta gcaaaggaga agaactcttc actggagttg tcccaattct tgttgaatta
     3001 gatggtgatg ttaacggcca caagttctct gtcagtggag agggtgaagg tgatgcaaca
     3061 tacggaaaac ttaccctgaa gttcatctgc actactggca aactgcctgt tccctggcca
     3121 acactagtct gatctagagt cggggcggcc ggccgcttcg agcagacatg ataagataca
     3181 ttgatgagtt tggacaaacc acaactagaa tgcagtgaaa aaaatgcttt atttgtgaaa
     3241 tttgtgatgc tattgcttta tttgtaacca ttataagctg caataaacaa gttaacaaca
     3301 acaattgcat tcattttatg tttcaggttc agggggaggt gtgggaggtt ttttaaagca
     3361 agtaaaacct ctacaaatgt ggtaaaatcg ataaggatcc gaccgatgcc ctcaagcttt
     3421 gagaggggcc cccttcaacc cagtcagctc cgacgtcttg gcgcccccgc ggggcatgac
     3481 tatcgtcgcc gcacttatga ctgtcttctt tatcatgcaa ctcgtaggac aggtgccggc
     3541 agcgctcttc cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag
     3601 cggtatcagc tcactcaaag gcggtaatac ggttatccac agaatcaggg gataacgcag
     3661 gaaagaacat gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc
     3721 tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaatcga cgctcaagtc
     3781 agaggtggcg aaacccgaca ggactataaa gataccaggc gtttccccct ggaagctccc
     3841 tcgtgcgctc tcctgttccg accctgccgc ttaccggata cctgtccgcc tttctccctt
     3901 cgggaagcgt ggcgctttct catagctcac gctgtaggta tctcagttcg gtgtaggtcg
     3961 ttcgctccaa gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat
     4021 ccggtaacta tcgtcttgag tccaacccgg taagacacga cttatcgcca ctggcagcag
     4081 ccactggtaa caggattagc agagcgaggt atgtaggcgg tgctacagag ttcttgaagt
     4141 ggtggcctaa ctacggctac actagaagaa cagtatttgg tatctgcgct ctgctgaagc
     4201 cagttacctt cggaaaaaga gttggtagct cttgatccgg caaacaaacc accgctggta
     4261 gcggtggttt ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag
     4321 atcctttgat cttttctacg gggtctgacg ctcagtggaa cgaaaactca cgttaaggga
     4381 ttttggtcat gagattatca aaaaggatct tcacctagat ccttttaaat taaaaatgaa
     4441 gttttaaatc aatctaaagt atatatgagt aaacttggtc tgacagttac caatgcttaa
     4501 tcagtgaggc acctatctca gcgatctgtc tatttcgttc atccatagtt gcctgactcc
     4561 ccgtcgtgta gataactacg atacgggagg gcttaccatc tggccccagt gctgcaatga
     4621 taccgcgaga cccacgctca ccggctccag atttatcagc aataaaccag ccagccggaa
     4681 gggccgagcg cagaagtggt cctgcaactt tatccgcctc catccagtct attaattgtt
     4741 gccgggaagc tagagtaagt agttcgccag ttaatagttt gcgcaacgtt gttgccattg
     4801 ctacaggcat cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc tccggttccc
     4861 aacgatcaag gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt agctccttcg
     4921 gtcctccgat cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg gttatggcag
     4981 cactgcataa ttctcttact gtcatgccat ccgtaagatg cttttctgtg actggtgagt
     5041 actcaaccaa gtcattctga gaatagtgta tgcggcgacc gagttgctct tgcccggcgt
     5101 caatacggga taataccgcg ccacatagca gaactttaaa agtgctcatc attggaaaac
     5161 gttcttcggg gcgaaaactc tcaaggatct taccgctgtt gagatccagt tcgatgtaac
     5221 ccactcgtgc acccaactga tcttcagcat cttttacttt caccagcgtt tctgggtgag
     5281 caaaaacagg aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa
     5341 tactcatact cttccttttt caatattatt gaagcattta tcagggttat tgtctcatga
     5401 gcggatacat atttgaatgt atttagaaaa ataaacaaat aggggttccg cgcacatttc
     5461 cccgaaaagt gccacctgac gcgccctgta gcggcgcatt aagcgcggcg
//
