LOCUS       sequence-245943-        5857 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Vector to measure CP candidates (spike-in) expression by determining
            the abundance of transcripts originating from the candidate by a 
            D.pse enhancer in fly cells.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5857)
  AUTHORS   Haberle V, Arnold CD, Pagani M, Rath M, Schernhuber K, Stark A
  TITLE     Transcriptional cofactors display specificity for distinct types of 
            core promoters.
  JOURNAL   Nature. 2019 Jun;570(7759):122-126. doi: 10.1038/s41586-019-1210-7. 
            Epub 2019 May 15.
  PUBMED    31092928
REFERENCE   2  (bases 1 to 5857)
  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"; doi: 
            "10.1038/s41586-019-1210-7"; journalName: "Nature"; date: "2019-06";
            volume: "570"; issue: "7759"; pages: "122-126"
COMMENT     Sequence Label: pSTAP-seq_fly_spike-in
FEATURES             Location/Qualifiers
     source          1..5857
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      13..468
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(100..119)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     310..331
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     polyA_signal    599..647
                     /note="synthetic polyadenylation signal"
     misc_feature    661..752
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     701..720
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
     promoter        join(1764..1769,1770..1787,1788..1794)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             1848..2507
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(1914..1933)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             2849..3154
                     /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     3033..3052
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     regulatory      3242..3251
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     intron          3257..3323
                     /label=Mhc intron
                     /note="modified Drosophila myosin heavy chain intron 16 
                     (Pfeiffer et al., 2010)"
     primer_bind     complement(3368..3396)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     polyA_signal    3563..3684
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(3574..3593)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     3628..3647
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(3948..3965)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4119..4707)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4199..4218)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(4878..5669,5670..5738))
                     /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     5501..5520
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(5739..5843)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 aagtgccacc tgacgcgccc tgtagcggcg cattaagcgc ggcgggtgtg gtggttacgc
       61 gcagcgtgac cgctacactt gccagcgccc tagcgcccgc tcctttcgct ttcttccctt
      121 cctttctcgc cacgttcgcc ggctttcccc gtcaagctct aaatcggggg ctccctttag
      181 ggttccgatt tagtgcttta cggcacctcg accccaaaaa acttgattag ggtgatggtt
      241 cacgtagtgg gccatcgccc tgatagacgg tttttcgccc tttgacgttg gagtccacgt
      301 tctttaatag tggactcttg ttccaaactg gaacaacact caaccctatc tcggtctatt
      361 cttttgattt ataagggatt ttgccgattt cggcctattg gttaaaaaat gagctgattt
      421 aacaaaaatt taacgcgaat tttaacaaaa tattaacgct tacaatttgc cattcgccat
      481 tcaggctgcg caactgttgg gaagggcgat cggtgcgggc ctcttcgcta ttacgccagc
      541 ccaagctacc atgataagta agtaatatta aggtacggga ggtacttgga gcggccgcaa
      601 taaaatatct ttattttcat tacatctgtg tgttggtttt ttgtgtgaat cgatagtact
      661 aacatacgct ctccatcaaa acaaaacgaa acaaaacaaa ctagcaaaat aggctgtccc
      721 cagtgcaagt gcaggtgcca gaacatttct ctatcgatag gtaccctact ggtgtgacaa
      781 tttaaggtga gtgcagtgcg cgttggggtg gggaaaagtg cctagtcatc ggaaatctat
      841 ctaggcgaga acagcagcag ttcttaaccc aatggcctct ccccgtttgt tcattgtttg
      901 cgagccataa gtgttccttt ccccaacgat aagacaatca atctgcaatc accgcaatag
      961 tattcgacgc gactgtcgtc gccattcccg ataacctttg tggcgactgc tctagttcct
     1021 ccgtcctatt cttgttttgc agttatgcct ccctctctct ctctctctct gtgttctcca
     1081 gtgcgctttg ttttcgacgc tcttgccgtt aatcgaatta acaatccgac gcctgcagct
     1141 gaacaaagtt aatcagtctc tgcttcatca accgccccac tatttgcatg actaagccag
     1201 agttcatgcg atctggggag catttgacag ccgatctgtt ctgctctgct cgttatcggc
     1261 ataactatgt atatgactga acctgactaa ttccaaatgc atgtgtcaca tacggtacgg
     1321 gtgtagtttt tacaaacggg gttccttatc gttggactta tcgctaggtt taccatatag
     1381 taccataacc gattcctttg ttctttgatt gatttatttt taaacacctc tcgaggaaaa
     1441 tccagcattt ctcttaaccg ttctttgttt gacaaaaaaa cgtcgccatt gctgaaaata
     1501 ttaaaaacaa tatcacatac accacaaatg aacaaccata taatatttgt gtagatgtac
     1561 ccagatatac aacccataca tacatagcca cacacatatg tattcaagac gtttccgtgc
     1621 ttatcttttg ttgtttttcc tccccccccg gtcccactct ccctagacgt acgtgtattt
     1681 ctgtctgaat tcccatcaga cgtctggctc gagatcttag agcatgcacc ggtgatatcg
     1741 cggccgcatt aggcacccca ggctttacac tttatgcttc cggctcgtat aatgtgtgga
     1801 ttttgagtta ggatccgtcg agattttcag gagctaagga agctaaaatg gagaaaaaaa
     1861 tcactggata taccaccgtt gatatatccc aatggcatcg taaagaacat tttgaggcat
     1921 ttcagtcagt tgctcaatgt acctataacc agaccgttca gctggatatt acggcctttt
     1981 taaagaccgt aaagaaaaat aagcacaagt tttatccggc ctttattcac attcttgccc
     2041 gcctgatgaa tgctcatccg gaattccgta tggcaatgaa agacggtgag ctggtgatat
     2101 gggatagtgt tcacccttgt tacaccgttt tccatgagca aactgaaacg ttttcatcgc
     2161 tctggagtga ataccacgac gatttccggc agtttctaca catatattcg caagatgtgg
     2221 cgtgttacgg tgaaaacctg gcctatttcc ctaaagggtt tattgagaat atgtttttcg
     2281 tctcagccaa tccctgggtg agtttcacca gttttgattt aaacgtggcc aatatggaca
     2341 acttcttcgc ccccgttttc accatgggca aatattatac gcaaggcgac aaggtgctga
     2401 tgccgctggc gattcaggtt catcatgccg tttgtgatgg cttccatgtc ggcagaatgc
     2461 ttaatgaatt acaacagtac tgcgatgagt ggcagggcgg ggcgtaaacg cgtggatccg
     2521 gcttactaaa agccagataa cagtatgcgt atttgcgcgc tgatttttgc ggtataagaa
     2581 tatatactga tatgtatacc cgaagtatgt caaaaagagg tatgctatga agcagcgtat
     2641 tacagtgaca gttgacagcg acagctatca gttgctcaag gcatatatga tgtcaatatc
     2701 tccggtctgg taagcacaac catgcagaat gaagcccgtc gtctgcgtgc cgaacgctgg
     2761 aaagcggaaa atcaggaagg gatggctgag gtcgcccggt ttattgaaat gaacggctct
     2821 tttgctgacg agaacagggg ctggtgaaat gcagtttaag gtttacacct ataaaagaga
     2881 gagccgttat cgtctgtttg tggatgtaca gagtgatatt attgacacgc ccgggcgacg
     2941 gatggtgatc cccctggcca gtgcacgtct gctgtcagat aaagtctccc gtgaacttta
     3001 cccggtggtg catatcgggg atgaaagctg gcgcatgatg accaccgata tggccagtgt
     3061 gccggtctcc gttatcgggg aagaagtggc tgatctcagc caccgcgaaa atgacatcaa
     3121 aaacgccatt aacctgatgt tctggggaat ataaatgtca ggctccctta tacacagcca
     3181 gtctgcagga tatcgtcgac gaattcggcc cctgcagggg cattccggta ctgttggtaa
     3241 agccaccatg gaaaaggtag gttcaaccac tgatgcctag gcacaccgaa acgactaacc
     3301 ctaattctta tcctttactt caggccactt aagcatggct agcaaaggag aagaactctt
     3361 cactggagtt gtcccaattc ttgttgaatt agatggtgat gttaacggcc acaagttctc
     3421 tgtcagtgga gagggtgaag gtgatgcaac atacggaaaa cttaccctga agttcatctg
     3481 cactactggc aaactgcctg ttccctggcc aacactagtc tgatctagag tcggggcggc
     3541 cggccgcttc gagcagacat gataagatac attgatgagt ttggacaaac cacaactaga
     3601 atgcagtgaa aaaaatgctt tatttgtgaa atttgtgatg ctattgcttt atttgtaacc
     3661 attataagct gcaataaaca agttaacaac aacaattgca ttcattttat gtttcaggtt
     3721 cagggggagg tgtgggaggt tttttaaagc aagtaaaacc tctacaaatg tggtaaaatc
     3781 gataaggatc cgaccgatgc cctcaagctt tgagaggggc ccccttcaac ccagtcagct
     3841 ccgacgtctt ggcgcccccg cggggcatga ctatcgtcgc cgcacttatg actgtcttct
     3901 ttatcatgca actcgtagga caggtgccgg cagcgctctt ccgcttcctc gctcactgac
     3961 tcgctgcgct cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa ggcggtaata
     4021 cggttatcca cagaatcagg ggataacgca ggaaagaaca tgtgagcaaa aggccagcaa
     4081 aaggccagga accgtaaaaa ggccgcgttg ctggcgtttt tccataggct ccgcccccct
     4141 gacgagcatc acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggactataa
     4201 agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg
     4261 cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca
     4321 cgctgtaggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa
     4381 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg
     4441 gtaagacacg acttatcgcc actggcagca gccactggta acaggattag cagagcgagg
     4501 tatgtaggcg gtgctacaga gttcttgaag tggtggccta actacggcta cactagaaga
     4561 acagtatttg gtatctgcgc tctgctgaag ccagttacct tcggaaaaag agttggtagc
     4621 tcttgatccg gcaaacaaac caccgctggt agcggtggtt tttttgtttg caagcagcag
     4681 attacgcgca gaaaaaaagg atctcaagaa gatcctttga tcttttctac ggggtctgac
     4741 gctcagtgga acgaaaactc acgttaaggg attttggtca tgagattatc aaaaaggatc
     4801 ttcacctaga tccttttaaa ttaaaaatga agttttaaat caatctaaag tatatatgag
     4861 taaacttggt ctgacagtta ccaatgctta atcagtgagg cacctatctc agcgatctgt
     4921 ctatttcgtt catccatagt tgcctgactc cccgtcgtgt agataactac gatacgggag
     4981 ggcttaccat ctggccccag tgctgcaatg ataccgcgag acccacgctc accggctcca
     5041 gatttatcag caataaacca gccagccgga agggccgagc gcagaagtgg tcctgcaact
     5101 ttatccgcct ccatccagtc tattaattgt tgccgggaag ctagagtaag tagttcgcca
     5161 gttaatagtt tgcgcaacgt tgttgccatt gctacaggca tcgtggtgtc acgctcgtcg
     5221 tttggtatgg cttcattcag ctccggttcc caacgatcaa ggcgagttac atgatccccc
     5281 atgttgtgca aaaaagcggt tagctccttc ggtcctccga tcgttgtcag aagtaagttg
     5341 gccgcagtgt tatcactcat ggttatggca gcactgcata attctcttac tgtcatgcca
     5401 tccgtaagat gcttttctgt gactggtgag tactcaacca agtcattctg agaatagtgt
     5461 atgcggcgac cgagttgctc ttgcccggcg tcaatacggg ataataccgc gccacatagc
     5521 agaactttaa aagtgctcat cattggaaaa cgttcttcgg ggcgaaaact ctcaaggatc
     5581 ttaccgctgt tgagatccag ttcgatgtaa cccactcgtg cacccaactg atcttcagca
     5641 tcttttactt tcaccagcgt ttctgggtga gcaaaaacag gaaggcaaaa tgccgcaaaa
     5701 aagggaataa gggcgacacg gaaatgttga atactcatac tcttcctttt tcaatattat
     5761 tgaagcattt atcagggtta ttgtctcatg agcggataca tatttgaatg tatttagaaa
     5821 aataaacaaa taggggttcc gcgcacattt ccccgaa
//
