LOCUS       sequence-173933-        5765 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 5765)
  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 5765)
  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-tj
FEATURES             Location/Qualifiers
     source          1..5765
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      101..556
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(188..207)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     398..419
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     polyA_signal    687..735
                     /note="synthetic polyadenylation signal"
     misc_feature    749..840
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     789..808
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
     promoter        join(1760..1765,1766..1783,1784..1790)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             1844..2503
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(1910..1929)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             2845..3150
                     /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     3029..3048
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     regulatory      3238..3247
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     intron          3253..3319
                     /label=Mhc intron
                     /note="modified Drosophila myosin heavy chain intron 16 
                     (Pfeiffer et al., 2010)"
     primer_bind     complement(3364..3392)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     polyA_signal    3559..3680
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3570..3589)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3624..3643
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(3944..3961)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4115..4703)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4195..4214)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4874..5665,5666..5734))
                     /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     5497..5516
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(join(5735..5765,1..74))
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 tatcagggtt attgtctcat gagcggatac atatttgaat gtatttagaa aaataaacaa
       61 ataggggttc cgcgcacatt tccccgaaaa gtgccacctg acgcgccctg tagcggcgca
      121 ttaagcgcgg cgggtgtggt ggttacgcgc agcgtgaccg ctacacttgc cagcgcccta
      181 gcgcccgctc ctttcgcttt cttcccttcc tttctcgcca cgttcgccgg ctttccccgt
      241 caagctctaa atcgggggct ccctttaggg ttccgattta gtgctttacg gcacctcgac
      301 cccaaaaaac ttgattaggg tgatggttca cgtagtgggc catcgccctg atagacggtt
      361 tttcgccctt tgacgttgga gtccacgttc tttaatagtg gactcttgtt ccaaactgga
      421 acaacactca accctatctc ggtctattct tttgatttat aagggatttt gccgatttcg
      481 gcctattggt taaaaaatga gctgatttaa caaaaattta acgcgaattt taacaaaata
      541 ttaacgctta caatttgcca ttcgccattc aggctgcgca actgttggga agggcgatcg
      601 gtgcgggcct cttcgctatt acgccagccc aagctaccat gataagtaag taatattaag
      661 gtacgggagg tacttggagc ggccgcaata aaatatcttt attttcatta catctgtgtg
      721 ttggtttttt gtgtgaatcg atagtactaa catacgctct ccatcaaaac aaaacgaaac
      781 aaaacaaact agcaaaatag gctgtcccca gtgcaagtgc aggtgccaga acatttctct
      841 atcgataggt acctcagtgc aactgtaaac attgatacgg attaaaagat tcattgaatg
      901 ctcatgaact gagagttacg ttcgtttctt tggatgcttg atagtttaaa cattgaagat
      961 cgtaaaaata tagaatgctc agtttttcat agtattcaaa ttgtattcta ttttgtcccc
     1021 atgccacatt catattcata tctgggtttt agaaaccacc gagtgggtct cagcttgcat
     1081 catagatttt gggtttcatc tcgccgtttt ccgagaagtg gcatcttctg tgtggtctgt
     1141 cggcatggat aaatgggctt ccagcgacga cgacccccgc gggcaacagt ttaagaatca
     1201 aaataaacac ttcgatcccg atccctctgg acttcgataa gttatgtcaa caaacttcgg
     1261 tcgcgtaacg gcgcatgcag gagctctgga gtagtaggag ctccagctga agtgcagcat
     1321 tgggttacaa tcgtccacat ggaggagatc agcatcagcc cctaggaggg ggagggggcg
     1381 gtgttggaac tttggagcag tccagcattc agttggggcg gcgtaattcg gcaataatca
     1441 gagggccgta tctacatatc tgcattttca aaccgtaata aatccctaat aaaaatcgtt
     1501 tcctttggcc tgtttatttt catttcaatt tcgattcact tttgcggtgt cgcctcgcta
     1561 cgcttttttc agaatctgaa tttgttattt ttattttgat tatatgagtt tcctgcccta
     1621 ccaagaaccc aaatctctta ggagcttatg taaccagacg aaaccactcg atcgaagagt
     1681 tgcgcaagta tttttgatga aattcgggag atcttagagc atgcaccggt gatatccggc
     1741 cgcattaggc accccaggct ttacacttta tgcttccggc tcgtataatg tgtggatttt
     1801 gagttaggat ccgtcgagat tttcaggagc taaggaagct aaaatggaga aaaaaatcac
     1861 tggatatacc accgttgata tatcccaatg gcatcgtaaa gaacattttg aggcatttca
     1921 gtcagttgct caatgtacct ataaccagac cgttcagctg gatattacgg cctttttaaa
     1981 gaccgtaaag aaaaataagc acaagtttta tccggccttt attcacattc ttgcccgcct
     2041 gatgaatgct catccggaat tccgtatggc aatgaaagac ggtgagctgg tgatatggga
     2101 tagtgttcac ccttgttaca ccgttttcca tgagcaaact gaaacgtttt catcgctctg
     2161 gagtgaatac cacgacgatt tccggcagtt tctacacata tattcgcaag atgtggcgtg
     2221 ttacggtgaa aacctggcct atttccctaa agggtttatt gagaatatgt ttttcgtctc
     2281 agccaatccc tgggtgagtt tcaccagttt tgatttaaac gtggccaata tggacaactt
     2341 cttcgccccc gttttcacca tgggcaaata ttatacgcaa ggcgacaagg tgctgatgcc
     2401 gctggcgatt caggttcatc atgccgtttg tgatggcttc catgtcggca gaatgcttaa
     2461 tgaattacaa cagtactgcg atgagtggca gggcggggcg taaacgcgtg gatccggctt
     2521 actaaaagcc agataacagt atgcgtattt gcgcgctgat ttttgcggta taagaatata
     2581 tactgatatg tatacccgaa gtatgtcaaa aagaggtatg ctatgaagca gcgtattaca
     2641 gtgacagttg acagcgacag ctatcagttg ctcaaggcat atatgatgtc aatatctccg
     2701 gtctggtaag cacaaccatg cagaatgaag cccgtcgtct gcgtgccgaa cgctggaaag
     2761 cggaaaatca ggaagggatg gctgaggtcg cccggtttat tgaaatgaac ggctcttttg
     2821 ctgacgagaa caggggctgg tgaaatgcag tttaaggttt acacctataa aagagagagc
     2881 cgttatcgtc tgtttgtgga tgtacagagt gatattattg acacgcccgg gcgacggatg
     2941 gtgatccccc tggccagtgc acgtctgctg tcagataaag tctcccgtga actttacccg
     3001 gtggtgcata tcggggatga aagctggcgc atgatgacca ccgatatggc cagtgtgccg
     3061 gtctccgtta tcggggaaga agtggctgat ctcagccacc gcgaaaatga catcaaaaac
     3121 gccattaacc tgatgttctg gggaatataa atgtcaggct cccttataca cagccagtct
     3181 gcaggatatc gtcgacgaat tcggcccctg caggggcatt ccggtactgt tggtaaagcc
     3241 accatggaaa aggtaggttc aaccactgat gcctaggcac accgaaacga ctaaccctaa
     3301 ttcttatcct ttacttcagg ccacttaagc atggctagca aaggagaaga actcttcact
     3361 ggagttgtcc caattcttgt tgaattagat ggtgatgtta acggccacaa gttctctgtc
     3421 agtggagagg gtgaaggtga tgcaacatac ggaaaactta ccctgaagtt catctgcact
     3481 actggcaaac tgcctgttcc ctggccaaca ctagtctgat ctagagtcgg ggcggccggc
     3541 cgcttcgagc agacatgata agatacattg atgagtttgg acaaaccaca actagaatgc
     3601 agtgaaaaaa atgctttatt tgtgaaattt gtgatgctat tgctttattt gtaaccatta
     3661 taagctgcaa taaacaagtt aacaacaaca attgcattca ttttatgttt caggttcagg
     3721 gggaggtgtg ggaggttttt taaagcaagt aaaacctcta caaatgtggt aaaatcgata
     3781 aggatccgac cgatgccctc aagctttgag aggggccccc ttcaacccag tcagctccga
     3841 cgtcttggcg cccccgcggg gcatgactat cgtcgccgca cttatgactg tcttctttat
     3901 catgcaactc gtaggacagg tgccggcagc gctcttccgc ttcctcgctc actgactcgc
     3961 tgcgctcggt cgttcggctg cggcgagcgg tatcagctca ctcaaaggcg gtaatacggt
     4021 tatccacaga atcaggggat aacgcaggaa agaacatgtg agcaaaaggc cagcaaaagg
     4081 ccaggaaccg taaaaaggcc gcgttgctgg cgtttttcca taggctccgc ccccctgacg
     4141 agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga ctataaagat
     4201 accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc ctgccgctta
     4261 ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat agctcacgct
     4321 gtaggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc
     4381 ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa
     4441 gacacgactt atcgccactg gcagcagcca ctggtaacag gattagcaga gcgaggtatg
     4501 taggcggtgc tacagagttc ttgaagtggt ggcctaacta cggctacact agaagaacag
     4561 tatttggtat ctgcgctctg ctgaagccag ttaccttcgg aaaaagagtt ggtagctctt
     4621 gatccggcaa acaaaccacc gctggtagcg gtggtttttt tgtttgcaag cagcagatta
     4681 cgcgcagaaa aaaaggatct caagaagatc ctttgatctt ttctacgggg tctgacgctc
     4741 agtggaacga aaactcacgt taagggattt tggtcatgag attatcaaaa aggatcttca
     4801 cctagatcct tttaaattaa aaatgaagtt ttaaatcaat ctaaagtata tatgagtaaa
     4861 cttggtctga cagttaccaa tgcttaatca gtgaggcacc tatctcagcg atctgtctat
     4921 ttcgttcatc catagttgcc tgactccccg tcgtgtagat aactacgata cgggagggct
     4981 taccatctgg ccccagtgct gcaatgatac cgcgagaccc acgctcaccg gctccagatt
     5041 tatcagcaat aaaccagcca gccggaaggg ccgagcgcag aagtggtcct gcaactttat
     5101 ccgcctccat ccagtctatt aattgttgcc gggaagctag agtaagtagt tcgccagtta
     5161 atagtttgcg caacgttgtt gccattgcta caggcatcgt ggtgtcacgc tcgtcgtttg
     5221 gtatggcttc attcagctcc ggttcccaac gatcaaggcg agttacatga tcccccatgt
     5281 tgtgcaaaaa agcggttagc tccttcggtc ctccgatcgt tgtcagaagt aagttggccg
     5341 cagtgttatc actcatggtt atggcagcac tgcataattc tcttactgtc atgccatccg
     5401 taagatgctt ttctgtgact ggtgagtact caaccaagtc attctgagaa tagtgtatgc
     5461 ggcgaccgag ttgctcttgc ccggcgtcaa tacgggataa taccgcgcca catagcagaa
     5521 ctttaaaagt gctcatcatt ggaaaacgtt cttcggggcg aaaactctca aggatcttac
     5581 cgctgttgag atccagttcg atgtaaccca ctcgtgcacc caactgatct tcagcatctt
     5641 ttactttcac cagcgtttct gggtgagcaa aaacaggaag gcaaaatgcc gcaaaaaagg
     5701 gaataagggc gacacggaaa tgttgaatac tcatactctt cctttttcaa tattattgaa
     5761 gcatt
//
