LOCUS       sequence-173940-        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-sgl
FEATURES             Location/Qualifiers
     source          1..5510
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     polyA_signal    52..173
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(63..82)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     117..136
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(437..454)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(608..1196)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(688..707)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(1367..2158,2159..2227))
                     /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     1990..2009
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(2228..2332)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      2359..2814
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2446..2465)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2656..2677
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     polyA_signal    2945..2993
                     /note="synthetic polyadenylation signal"
     misc_feature    3007..3098
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     3047..3066
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
     promoter        join(3763..3768,3769..3786,3787..3793)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             3847..4506
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(3913..3932)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             4848..5153
                     /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     5032..5051
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     regulatory      5241..5250
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     intron          5256..5322
                     /label=Mhc intron
                     /note="modified Drosophila myosin heavy chain intron 16 
                     (Pfeiffer et al., 2010)"
     primer_bind     complement(5367..5395)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
ORIGIN
        1 acactagtct gatctagagt cggggcggcc ggccgcttcg agcagacatg ataagataca
       61 ttgatgagtt tggacaaacc acaactagaa tgcagtgaaa aaaatgcttt atttgtgaaa
      121 tttgtgatgc tattgcttta tttgtaacca ttataagctg caataaacaa gttaacaaca
      181 acaattgcat tcattttatg tttcaggttc agggggaggt gtgggaggtt ttttaaagca
      241 agtaaaacct ctacaaatgt ggtaaaatcg ataaggatcc gaccgatgcc ctcaagcttt
      301 gagaggggcc cccttcaacc cagtcagctc cgacgtcttg gcgcccccgc ggggcatgac
      361 tatcgtcgcc gcacttatga ctgtcttctt tatcatgcaa ctcgtaggac aggtgccggc
      421 agcgctcttc cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag
      481 cggtatcagc tcactcaaag gcggtaatac ggttatccac agaatcaggg gataacgcag
      541 gaaagaacat gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc
      601 tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaatcga cgctcaagtc
      661 agaggtggcg aaacccgaca ggactataaa gataccaggc gtttccccct ggaagctccc
      721 tcgtgcgctc tcctgttccg accctgccgc ttaccggata cctgtccgcc tttctccctt
      781 cgggaagcgt ggcgctttct catagctcac gctgtaggta tctcagttcg gtgtaggtcg
      841 ttcgctccaa gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat
      901 ccggtaacta tcgtcttgag tccaacccgg taagacacga cttatcgcca ctggcagcag
      961 ccactggtaa caggattagc agagcgaggt atgtaggcgg tgctacagag ttcttgaagt
     1021 ggtggcctaa ctacggctac actagaagaa cagtatttgg tatctgcgct ctgctgaagc
     1081 cagttacctt cggaaaaaga gttggtagct cttgatccgg caaacaaacc accgctggta
     1141 gcggtggttt ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag
     1201 atcctttgat cttttctacg gggtctgacg ctcagtggaa cgaaaactca cgttaaggga
     1261 ttttggtcat gagattatca aaaaggatct tcacctagat ccttttaaat taaaaatgaa
     1321 gttttaaatc aatctaaagt atatatgagt aaacttggtc tgacagttac caatgcttaa
     1381 tcagtgaggc acctatctca gcgatctgtc tatttcgttc atccatagtt gcctgactcc
     1441 ccgtcgtgta gataactacg atacgggagg gcttaccatc tggccccagt gctgcaatga
     1501 taccgcgaga cccacgctca ccggctccag atttatcagc aataaaccag ccagccggaa
     1561 gggccgagcg cagaagtggt cctgcaactt tatccgcctc catccagtct attaattgtt
     1621 gccgggaagc tagagtaagt agttcgccag ttaatagttt gcgcaacgtt gttgccattg
     1681 ctacaggcat cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc tccggttccc
     1741 aacgatcaag gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt agctccttcg
     1801 gtcctccgat cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg gttatggcag
     1861 cactgcataa ttctcttact gtcatgccat ccgtaagatg cttttctgtg actggtgagt
     1921 actcaaccaa gtcattctga gaatagtgta tgcggcgacc gagttgctct tgcccggcgt
     1981 caatacggga taataccgcg ccacatagca gaactttaaa agtgctcatc attggaaaac
     2041 gttcttcggg gcgaaaactc tcaaggatct taccgctgtt gagatccagt tcgatgtaac
     2101 ccactcgtgc acccaactga tcttcagcat cttttacttt caccagcgtt tctgggtgag
     2161 caaaaacagg aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa
     2221 tactcatact cttccttttt caatattatt gaagcattta tcagggttat tgtctcatga
     2281 gcggatacat atttgaatgt atttagaaaa ataaacaaat aggggttccg cgcacatttc
     2341 cccgaaaagt gccacctgac gcgccctgta gcggcgcatt aagcgcggcg ggtgtggtgg
     2401 ttacgcgcag cgtgaccgct acacttgcca gcgccctagc gcccgctcct ttcgctttct
     2461 tcccttcctt tctcgccacg ttcgccggct ttccccgtca agctctaaat cgggggctcc
     2521 ctttagggtt ccgatttagt gctttacggc acctcgaccc caaaaaactt gattagggtg
     2581 atggttcacg tagtgggcca tcgccctgat agacggtttt tcgccctttg acgttggagt
     2641 ccacgttctt taatagtgga ctcttgttcc aaactggaac aacactcaac cctatctcgg
     2701 tctattcttt tgatttataa gggattttgc cgatttcggc ctattggtta aaaaatgagc
     2761 tgatttaaca aaaatttaac gcgaatttta acaaaatatt aacgcttaca atttgccatt
     2821 cgccattcag gctgcgcaac tgttgggaag ggcgatcggt gcgggcctct tcgctattac
     2881 gccagcccaa gctaccatga taagtaagta atattaaggt acgggaggta cttggagcgg
     2941 ccgcaataaa atatctttat tttcattaca tctgtgtgtt ggttttttgt gtgaatcgat
     3001 agtactaaca tacgctctcc atcaaaacaa aacgaaacaa aacaaactag caaaataggc
     3061 tgtccccagt gcaagtgcag gtgccagaac atttctctat cgataggtac cgaatgaact
     3121 aaatatatgc cctataccat cttccaaaat gtatgggttt ttaactgata atggttacta
     3181 ctgctatagg atacaaatac caaattattg tctaattgaa aacaaaacat atatactgag
     3241 tgtttggctg attgtacata cttctattcg tgcttttttt caccagagat actggctgtt
     3301 tgtcgggaac gtgggtaatt ggacaatttc caactaatgt gcgctcgcta gaccaaaaaa
     3361 aaaaaatata agaaaagaaa cgccatgccc agcgagctta tctcgacccg agactttgtt
     3421 ttggcgcaga gccgataaga agagtgggta gctcgacata tgtacagtgg gaaatgaggg
     3481 cggacggaag ccaggacgga aatgcgccag tggtgtggtg gatgggaggc aatccgcttg
     3541 caccttatgg cttcgtttgg cgcattttgt agtatctgga attttaggcc taatggagcg
     3601 acgccgatgg tcacgcagtc tggaaagtaa aatcgattcc cacgctactt ttccgttccg
     3661 aatcatattt cagcaatcaa acggctctgc gcgcttttca tggtttattt agatcttaga
     3721 gcatgcaccg gtgatatcgc ggccgcatta ggcaccccag gctttacact ttatgcttcc
     3781 ggctcgtata atgtgtggat tttgagttag gatccgtcga gattttcagg agctaaggaa
     3841 gctaaaatgg agaaaaaaat cactggatat accaccgttg atatatccca atggcatcgt
     3901 aaagaacatt ttgaggcatt tcagtcagtt gctcaatgta cctataacca gaccgttcag
     3961 ctggatatta cggccttttt aaagaccgta aagaaaaata agcacaagtt ttatccggcc
     4021 tttattcaca ttcttgcccg cctgatgaat gctcatccgg aattccgtat ggcaatgaaa
     4081 gacggtgagc tggtgatatg ggatagtgtt cacccttgtt acaccgtttt ccatgagcaa
     4141 actgaaacgt tttcatcgct ctggagtgaa taccacgacg atttccggca gtttctacac
     4201 atatattcgc aagatgtggc gtgttacggt gaaaacctgg cctatttccc taaagggttt
     4261 attgagaata tgtttttcgt ctcagccaat ccctgggtga gtttcaccag ttttgattta
     4321 aacgtggcca atatggacaa cttcttcgcc cccgttttca ccatgggcaa atattatacg
     4381 caaggcgaca aggtgctgat gccgctggcg attcaggttc atcatgccgt ttgtgatggc
     4441 ttccatgtcg gcagaatgct taatgaatta caacagtact gcgatgagtg gcagggcggg
     4501 gcgtaaacgc gtggatccgg cttactaaaa gccagataac agtatgcgta tttgcgcgct
     4561 gatttttgcg gtataagaat atatactgat atgtataccc gaagtatgtc aaaaagaggt
     4621 atgctatgaa gcagcgtatt acagtgacag ttgacagcga cagctatcag ttgctcaagg
     4681 catatatgat gtcaatatct ccggtctggt aagcacaacc atgcagaatg aagcccgtcg
     4741 tctgcgtgcc gaacgctgga aagcggaaaa tcaggaaggg atggctgagg tcgcccggtt
     4801 tattgaaatg aacggctctt ttgctgacga gaacaggggc tggtgaaatg cagtttaagg
     4861 tttacaccta taaaagagag agccgttatc gtctgtttgt ggatgtacag agtgatatta
     4921 ttgacacgcc cgggcgacgg atggtgatcc ccctggccag tgcacgtctg ctgtcagata
     4981 aagtctcccg tgaactttac ccggtggtgc atatcgggga tgaaagctgg cgcatgatga
     5041 ccaccgatat ggccagtgtg ccggtctccg ttatcgggga agaagtggct gatctcagcc
     5101 accgcgaaaa tgacatcaaa aacgccatta acctgatgtt ctggggaata taaatgtcag
     5161 gctcccttat acacagccag tctgcaggat atcgtcgacg aattcggccc ctgcaggggc
     5221 attccggtac tgttggtaaa gccaccatgg aaaaggtagg ttcaaccact gatgcctagg
     5281 cacaccgaaa cgactaaccc taattcttat cctttacttc aggccactta agcatggcta
     5341 gcaaaggaga agaactcttc actggagttg tcccaattct tgttgaatta gatggtgatg
     5401 ttaacggcca caagttctct gtcagtggag agggtgaagg tgatgcaaca tacggaaaac
     5461 ttaccctgaa gttcatctgc actactggca aactgcctgt tccctggcca
//
