LOCUS       sequence-173935-        5805 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 5805)
  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 5805)
  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-zfh1
FEATURES             Location/Qualifiers
     source          1..5805
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      1..456
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(88..107)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     298..319
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     polyA_signal    587..635
                     /note="synthetic polyadenylation signal"
     misc_feature    649..740
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     689..708
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
     promoter        join(1700..1705,1706..1723,1724..1730)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             1784..2443
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(1850..1869)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             2785..3090
                     /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     2969..2988
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     regulatory      3178..3187
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     intron          3193..3259
                     /label=Mhc intron
                     /note="modified Drosophila myosin heavy chain intron 16 
                     (Pfeiffer et al., 2010)"
     primer_bind     complement(3304..3332)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     polyA_signal    3499..3620
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3510..3529)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3564..3583
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(3884..3901)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4055..4643)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4135..4154)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4814..5605,5606..5674))
                     /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     5437..5456
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5675..5779)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 acgcgccctg tagcggcgca ttaagcgcgg cgggtgtggt ggttacgcgc agcgtgaccg
       61 ctacacttgc cagcgcccta gcgcccgctc ctttcgcttt cttcccttcc tttctcgcca
      121 cgttcgccgg ctttccccgt caagctctaa atcgggggct ccctttaggg ttccgattta
      181 gtgctttacg gcacctcgac cccaaaaaac ttgattaggg tgatggttca cgtagtgggc
      241 catcgccctg atagacggtt tttcgccctt tgacgttgga gtccacgttc tttaatagtg
      301 gactcttgtt ccaaactgga acaacactca accctatctc ggtctattct tttgatttat
      361 aagggatttt gccgatttcg gcctattggt taaaaaatga gctgatttaa caaaaattta
      421 acgcgaattt taacaaaata ttaacgctta caatttgcca ttcgccattc aggctgcgca
      481 actgttggga agggcgatcg gtgcgggcct cttcgctatt acgccagccc aagctaccat
      541 gataagtaag taatattaag gtacgggagg tacttggagc ggccgcaata aaatatcttt
      601 attttcatta catctgtgtg ttggtttttt gtgtgaatcg atagtactaa catacgctct
      661 ccatcaaaac aaaacgaaac aaaacaaact agcaaaatag gctgtcccca gtgcaagtgc
      721 aggtgccaga acatttctct atcgataggt accttaaaag tgccagtgct tgtggcgtgc
      781 acggagaaaa aaaccttgag gtcatatttg aaaaaaaaaa aaaaaaaact aaattccaag
      841 tgagtagttt actcttagtc actatcgagt gtgtgctgtt tgtttttyga aatatgcata
      901 tcttagctac ttgcgttgct gttttttttt tttttttttt tttgacgatt tgtcaacagg
      961 aaatatgcat aaggttggct cgggatccgg atcggatggc atggggtttg attggatgcc
     1021 gtacttggca ccgcactgcc gttatcggtt ggctcatttc ccgttagccg cgaacaaagc
     1081 ccacgcattg tgctacgacc gccgtgatgt gttcaaagat caagtgcccc cagaaccatc
     1141 tcctgccatc cctgccatcc ctgcccgcct gcatccatcg cgggcattca gattccgact
     1201 gcgcatgagc agcggtctcc aacacgtaag caagtggaag gcgagggata agaacaagta
     1261 acttctctct tatcggacgc ttccaggaat ttcgatcctc gcaccgcatt ccgcaggttt
     1321 agtcactgga ttccacggct tttcgagtcg attgtcccaa gaaacattat tttggacatg
     1381 tgactcactg actcaaagct attatcactt ctcggacata tgcgtgtata taaaatattt
     1441 ttaaacatta ttaggtatac tataaactct gcctcattca tgcctacaga acttcagcct
     1501 tgacattcta tatatagaaa cccttactac gtctttactc tttaaatagt tctttggata
     1561 ttatattagc acattgatgt gctttttttt tggatggttg tgtccaactc acggtaccga
     1621 gctcttacgc gtgctagccc gggctcgaga tcttagagca tgcaccggtg atatcgcggc
     1681 cgcattaggc accccaggct ttacacttta tgcttccggc tcgtataatg tgtggatttt
     1741 gagttaggat ccgtcgagat tttcaggagc taaggaagct aaaatggaga aaaaaatcac
     1801 tggatatacc accgttgata tatcccaatg gcatcgtaaa gaacattttg aggcatttca
     1861 gtcagttgct caatgtacct ataaccagac cgttcagctg gatattacgg cctttttaaa
     1921 gaccgtaaag aaaaataagc acaagtttta tccggccttt attcacattc ttgcccgcct
     1981 gatgaatgct catccggaat tccgtatggc aatgaaagac ggtgagctgg tgatatggga
     2041 tagtgttcac ccttgttaca ccgttttcca tgagcaaact gaaacgtttt catcgctctg
     2101 gagtgaatac cacgacgatt tccggcagtt tctacacata tattcgcaag atgtggcgtg
     2161 ttacggtgaa aacctggcct atttccctaa agggtttatt gagaatatgt ttttcgtctc
     2221 agccaatccc tgggtgagtt tcaccagttt tgatttaaac gtggccaata tggacaactt
     2281 cttcgccccc gttttcacca tgggcaaata ttatacgcaa ggcgacaagg tgctgatgcc
     2341 gctggcgatt caggttcatc atgccgtttg tgatggcttc catgtcggca gaatgcttaa
     2401 tgaattacaa cagtactgcg atgagtggca gggcggggcg taaacgcgtg gatccggctt
     2461 actaaaagcc agataacagt atgcgtattt gcgcgctgat ttttgcggta taagaatata
     2521 tactgatatg tatacccgaa gtatgtcaaa aagaggtatg ctatgaagca gcgtattaca
     2581 gtgacagttg acagcgacag ctatcagttg ctcaaggcat atatgatgtc aatatctccg
     2641 gtctggtaag cacaaccatg cagaatgaag cccgtcgtct gcgtgccgaa cgctggaaag
     2701 cggaaaatca ggaagggatg gctgaggtcg cccggtttat tgaaatgaac ggctcttttg
     2761 ctgacgagaa caggggctgg tgaaatgcag tttaaggttt acacctataa aagagagagc
     2821 cgttatcgtc tgtttgtgga tgtacagagt gatattattg acacgcccgg gcgacggatg
     2881 gtgatccccc tggccagtgc acgtctgctg tcagataaag tctcccgtga actttacccg
     2941 gtggtgcata tcggggatga aagctggcgc atgatgacca ccgatatggc cagtgtgccg
     3001 gtctccgtta tcggggaaga agtggctgat ctcagccacc gcgaaaatga catcaaaaac
     3061 gccattaacc tgatgttctg gggaatataa atgtcaggct cccttataca cagccagtct
     3121 gcaggatatc gtcgacgaat tcggcccctg caggggcatt ccggtactgt tggtaaagcc
     3181 accatggaaa aggtaggttc aaccactgat gcctaggcac accgaaacga ctaaccctaa
     3241 ttcttatcct ttacttcagg ccacttaagc atggctagca aaggagaaga actcttcact
     3301 ggagttgtcc caattcttgt tgaattagat ggtgatgtta acggccacaa gttctctgtc
     3361 agtggagagg gtgaaggtga tgcaacatac ggaaaactta ccctgaagtt catctgcact
     3421 actggcaaac tgcctgttcc ctggccaaca ctagtctgat ctagagtcgg ggcggccggc
     3481 cgcttcgagc agacatgata agatacattg atgagtttgg acaaaccaca actagaatgc
     3541 agtgaaaaaa atgctttatt tgtgaaattt gtgatgctat tgctttattt gtaaccatta
     3601 taagctgcaa taaacaagtt aacaacaaca attgcattca ttttatgttt caggttcagg
     3661 gggaggtgtg ggaggttttt taaagcaagt aaaacctcta caaatgtggt aaaatcgata
     3721 aggatccgac cgatgccctc aagctttgag aggggccccc ttcaacccag tcagctccga
     3781 cgtcttggcg cccccgcggg gcatgactat cgtcgccgca cttatgactg tcttctttat
     3841 catgcaactc gtaggacagg tgccggcagc gctcttccgc ttcctcgctc actgactcgc
     3901 tgcgctcggt cgttcggctg cggcgagcgg tatcagctca ctcaaaggcg gtaatacggt
     3961 tatccacaga atcaggggat aacgcaggaa agaacatgtg agcaaaaggc cagcaaaagg
     4021 ccaggaaccg taaaaaggcc gcgttgctgg cgtttttcca taggctccgc ccccctgacg
     4081 agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga ctataaagat
     4141 accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc ctgccgctta
     4201 ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat agctcacgct
     4261 gtaggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc
     4321 ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa
     4381 gacacgactt atcgccactg gcagcagcca ctggtaacag gattagcaga gcgaggtatg
     4441 taggcggtgc tacagagttc ttgaagtggt ggcctaacta cggctacact agaagaacag
     4501 tatttggtat ctgcgctctg ctgaagccag ttaccttcgg aaaaagagtt ggtagctctt
     4561 gatccggcaa acaaaccacc gctggtagcg gtggtttttt tgtttgcaag cagcagatta
     4621 cgcgcagaaa aaaaggatct caagaagatc ctttgatctt ttctacgggg tctgacgctc
     4681 agtggaacga aaactcacgt taagggattt tggtcatgag attatcaaaa aggatcttca
     4741 cctagatcct tttaaattaa aaatgaagtt ttaaatcaat ctaaagtata tatgagtaaa
     4801 cttggtctga cagttaccaa tgcttaatca gtgaggcacc tatctcagcg atctgtctat
     4861 ttcgttcatc catagttgcc tgactccccg tcgtgtagat aactacgata cgggagggct
     4921 taccatctgg ccccagtgct gcaatgatac cgcgagaccc acgctcaccg gctccagatt
     4981 tatcagcaat aaaccagcca gccggaaggg ccgagcgcag aagtggtcct gcaactttat
     5041 ccgcctccat ccagtctatt aattgttgcc gggaagctag agtaagtagt tcgccagtta
     5101 atagtttgcg caacgttgtt gccattgcta caggcatcgt ggtgtcacgc tcgtcgtttg
     5161 gtatggcttc attcagctcc ggttcccaac gatcaaggcg agttacatga tcccccatgt
     5221 tgtgcaaaaa agcggttagc tccttcggtc ctccgatcgt tgtcagaagt aagttggccg
     5281 cagtgttatc actcatggtt atggcagcac tgcataattc tcttactgtc atgccatccg
     5341 taagatgctt ttctgtgact ggtgagtact caaccaagtc attctgagaa tagtgtatgc
     5401 ggcgaccgag ttgctcttgc ccggcgtcaa tacgggataa taccgcgcca catagcagaa
     5461 ctttaaaagt gctcatcatt ggaaaacgtt cttcggggcg aaaactctca aggatcttac
     5521 cgctgttgag atccagttcg atgtaaccca ctcgtgcacc caactgatct tcagcatctt
     5581 ttactttcac cagcgtttct gggtgagcaa aaacaggaag gcaaaatgcc gcaaaaaagg
     5641 gaataagggc gacacggaaa tgttgaatac tcatactctt cctttttcaa tattattgaa
     5701 gcatttatca gggttattgt ctcatgagcg gatacatatt tgaatgtatt tagaaaaata
     5761 aacaaatagg ggttccgcgc acatttcccc gaaaagtgcc acctg
//
