LOCUS       sequence-129004-        5542 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  flySTARR-seq screening vector with NipB core promoter.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5542)
  AUTHORS   Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, 
            Stark A
  TITLE     Enhancer-core-promoter specificity separates developmental and 
            housekeeping gene regulation.
  JOURNAL   Nature. 2015 Feb 26;518(7540):556-9. doi: 10.1038/nature13994. Epub 
            2014 Dec 15.
  PUBMED    25517091
REFERENCE   2  (bases 1 to 5542)
  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/nature13994"; journalName: "Nature"; date: "2015-02-26- 
            26"; volume: "518"; issue: "7540"; pages: "556-9"
COMMENT     Sequence Label: pSTARR-seq_fly-NipB
FEATURES             Location/Qualifiers
     source          1..5542
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     polyA_signal    1..49
                     /note="synthetic polyadenylation signal"
     misc_feature    63..154
                     /label=pause site
                     /note="RNA polymerase II transcriptional pause signal from 
                     the human alpha-2 globin gene"
     primer_bind     103..122
                     /label=RVprimer3
                     /note="pGL3 vector, forward primer"
     regulatory      340..349
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     intron          355..421
                     /label=Mhc intron
                     /note="modified Drosophila myosin heavy chain intron 16 
                     (Pfeiffer et al., 2010)"
     primer_bind     complement(466..494)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     primer_bind     1089..1109
                     /label=GFP-F
                     /note="GFP, forward primer. Does NOT anneal to EGFP"
     promoter        join(1201..1206,1207..1224,1225..1231)
                     /label=lac UV5 promoter
                     /note="E. coli lac promoter with an ""up"" mutation"
     CDS             1285..1944
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(1351..1370)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     CDS             2286..2591
                     /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     2470..2489
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     polyA_signal    2669..2790
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(2680..2699)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     2734..2753
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     complement(3035..3052)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(3206..3794)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3286..3305)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(3965..4756,4757..4825))
                     /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     4588..4607
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(4826..4930)
                     /gene="bla"
                     /label=AmpR promoter
     rep_origin      4957..5412
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(5044..5063)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     5254..5275
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
ORIGIN
        1 aataaaatat ctttattttc attacatctg tgtgttggtt ttttgtgtga atcgatagta
       61 ctaacatacg ctctccatca aaacaaaacg aaacaaaaca aactagcaaa ataggctgtc
      121 cccagtgcaa gtgcaggtgc cagaacattt ctctatcgat aggtaccgag ctcttacgcg
      181 tgctagcccg ggctcgagat ctgcgatcaa aggagtatta tatatgaagt attaacgttt
      241 cggtctgaaa aggtattttt ttattaagtt tagcgcggcc acactatcct acaggtcggc
      301 catattctcc tgcaggggca ttccggtact gttggtaaag ccaccatgga aaaggtaggt
      361 tcaaccactg atgcctaggc acaccgaaac gactaaccct aattcttatc ctttacttca
      421 ggccacttaa gcatggctag caaaggagaa gaactcttca ctggagttgt cccaattctt
      481 gttgaattag atggtgatgt taacggccac aagttctctg tcagtggaga gggtgaaggt
      541 gatgcaacat acggaaaact taccctgaag ttcatctgca ctactggcaa actgcctgtt
      601 ccctggccaa cactagtcac tactctgtgc tatggtgttc aatgcttttc aagatacccg
      661 gatcatatga aacggcatga ctttttcaag agtgccatgc ccgaaggtta tgtacaggaa
      721 aggaccatct tcttcaaaga tgacggcaac tacaagacac gtgctgaagt caagtttgaa
      781 ggtgataccc ttgttaatag aatcgagtta aaaggtattg acttcaagga agatggcaac
      841 attctgggac acaaattgga atacaactat aactcacaca atgtatacat catggcagac
      901 aaacaaaaga atggaatcaa agcgaacttc aagacccgcc acaacattga agatggaagc
      961 gttcaactag cagaccatta tcaacaaaat actccaattg gcgatggccc tgtcctttta
     1021 ccagacaacc attacctgtc cacacaatct gccctttcga aagatcccaa cgaaaagaga
     1081 gaccacatgg tccttcttga gtttgtaaca gctgctggga ttacacatgg catggatgaa
     1141 ctgtacaact gatctagagc atgcaccggt gatatcgcgg ccgcattagg caccccaggc
     1201 tttacacttt atgcttccgg ctcgtataat gtgtggattt tgagttagga tccgtcgaga
     1261 ttttcaggag ctaaggaagc taaaatggag aaaaaaatca ctggatatac caccgttgat
     1321 atatcccaat ggcatcgtaa agaacatttt gaggcatttc agtcagttgc tcaatgtacc
     1381 tataaccaga ccgttcagct ggatattacg gcctttttaa agaccgtaaa gaaaaataag
     1441 cacaagtttt atccggcctt tattcacatt cttgcccgcc tgatgaatgc tcatccggaa
     1501 ttccgtatgg caatgaaaga cggtgagctg gtgatatggg atagtgttca cccttgttac
     1561 accgttttcc atgagcaaac tgaaacgttt tcatcgctct ggagtgaata ccacgacgat
     1621 ttccggcagt ttctacacat atattcgcaa gatgtggcgt gttacggtga aaacctggcc
     1681 tatttcccta aagggtttat tgagaatatg tttttcgtct cagccaatcc ctgggtgagt
     1741 ttcaccagtt ttgatttaaa cgtggccaat atggacaact tcttcgcccc cgttttcacc
     1801 atgggcaaat attatacgca aggcgacaag gtgctgatgc cgctggcgat tcaggttcat
     1861 catgccgttt gtgatggctt ccatgtcggc agaatgctta atgaattaca acagtactgc
     1921 gatgagtggc agggcggggc gtaaacgcgt ggatccggct tactaaaagc cagataacag
     1981 tatgcgtatt tgcgcgctga tttttgcggt ataagaatat atactgatat gtatacccga
     2041 agtatgtcaa aaagaggtat gctatgaagc agcgtattac agtgacagtt gacagcgaca
     2101 gctatcagtt gctcaaggca tatatgatgt caatatctcc ggtctggtaa gcacaaccat
     2161 gcagaatgaa gcccgtcgtc tgcgtgccga acgctggaaa gcggaaaatc aggaagggat
     2221 ggctgaggtc gcccggttta ttgaaatgaa cggctctttt gctgacgaga acaggggctg
     2281 gtgaaatgca gtttaaggtt tacacctata aaagagagag ccgttatcgt ctgtttgtgg
     2341 atgtacagag tgatattatt gacacgcccg ggcgacggat ggtgatcccc ctggccagtg
     2401 cacgtctgct gtcagataaa gtctcccgtg aactttaccc ggtggtgcat atcggggatg
     2461 aaagctggcg catgatgacc accgatatgg ccagtgtgcc ggtctccgtt atcggggaag
     2521 aagtggctga tctcagccac cgcgaaaatg acatcaaaaa cgccattaac ctgatgttct
     2581 ggggaatata aatgtcaggc tcccttatac acagccagtc tgcaggatat cgtcgacgaa
     2641 ttcggccggc cgcttcgagc agacatgata agatacattg atgagtttgg acaaaccaca
     2701 actagaatgc agtgaaaaaa atgctttatt tgtgaaattt gtgatgctat tgctttattt
     2761 gtaaccatta taagctgcaa taaacaagtt aacaacaaca attgcattca ttttatgttt
     2821 caggttcagg gggaggtgtg ggaggttttt taaagcaagt aaaacctcta caaatgtggt
     2881 aaaatcgata aggatccgac cgatgccctt gagagccttc aacccagtca gctccttccg
     2941 gtgggcgcgg ggcatgacta tcgtcgccgc acttatgact gtcttcttta tcatgcaact
     3001 cgtaggacag gtgccggcag cgctcttccg cttcctcgct cactgactcg ctgcgctcgg
     3061 tcgttcggct gcggcgagcg gtatcagctc actcaaaggc ggtaatacgg ttatccacag
     3121 aatcagggga taacgcagga aagaacatgt gagcaaaagg ccagcaaaag gccaggaacc
     3181 gtaaaaaggc cgcgttgctg gcgtttttcc ataggctccg cccccctgac gagcatcaca
     3241 aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg actataaaga taccaggcgt
     3301 ttccccctgg aagctccctc gtgcgctctc ctgttccgac cctgccgctt accggatacc
     3361 tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca tagctcacgc tgtaggtatc
     3421 tcagttcggt gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc
     3481 ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc caacccggta agacacgact
     3541 tatcgccact ggcagcagcc actggtaaca ggattagcag agcgaggtat gtaggcggtg
     3601 ctacagagtt cttgaagtgg tggcctaact acggctacac tagaagaaca gtatttggta
     3661 tctgcgctct gctgaagcca gttaccttcg gaaaaagagt tggtagctct tgatccggca
     3721 aacaaaccac cgctggtagc ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa
     3781 aaaaaggatc tcaagaagat cctttgatct tttctacggg gtctgacgct cagtggaacg
     3841 aaaactcacg ttaagggatt ttggtcatga gattatcaaa aaggatcttc acctagatcc
     3901 ttttaaatta aaaatgaagt tttaaatcaa tctaaagtat atatgagtaa acttggtctg
     3961 acagttacca atgcttaatc agtgaggcac ctatctcagc gatctgtcta tttcgttcat
     4021 ccatagttgc ctgactcccc gtcgtgtaga taactacgat acgggagggc ttaccatctg
     4081 gccccagtgc tgcaatgata ccgcgagacc cacgctcacc ggctccagat ttatcagcaa
     4141 taaaccagcc agccggaagg gccgagcgca gaagtggtcc tgcaacttta tccgcctcca
     4201 tccagtctat taattgttgc cgggaagcta gagtaagtag ttcgccagtt aatagtttgc
     4261 gcaacgttgt tgccattgct acaggcatcg tggtgtcacg ctcgtcgttt ggtatggctt
     4321 cattcagctc cggttcccaa cgatcaaggc gagttacatg atcccccatg ttgtgcaaaa
     4381 aagcggttag ctccttcggt cctccgatcg ttgtcagaag taagttggcc gcagtgttat
     4441 cactcatggt tatggcagca ctgcataatt ctcttactgt catgccatcc gtaagatgct
     4501 tttctgtgac tggtgagtac tcaaccaagt cattctgaga atagtgtatg cggcgaccga
     4561 gttgctcttg cccggcgtca atacgggata ataccgcgcc acatagcaga actttaaaag
     4621 tgctcatcat tggaaaacgt tcttcggggc gaaaactctc aaggatctta ccgctgttga
     4681 gatccagttc gatgtaaccc actcgtgcac ccaactgatc ttcagcatct tttactttca
     4741 ccagcgtttc tgggtgagca aaaacaggaa ggcaaaatgc cgcaaaaaag ggaataaggg
     4801 cgacacggaa atgttgaata ctcatactct tcctttttca atattattga agcatttatc
     4861 agggttattg tctcatgagc ggatacatat ttgaatgtat ttagaaaaat aaacaaatag
     4921 gggttccgcg cacatttccc cgaaaagtgc cacctgacgc gccctgtagc ggcgcattaa
     4981 gcgcggcggg tgtggtggtt acgcgcagcg tgaccgctac acttgccagc gccctagcgc
     5041 ccgctccttt cgctttcttc ccttcctttc tcgccacgtt cgccggcttt ccccgtcaag
     5101 ctctaaatcg ggggctccct ttagggttcc gatttagtgc tttacggcac ctcgacccca
     5161 aaaaacttga ttagggtgat ggttcacgta gtgggccatc gccctgatag acggtttttc
     5221 gccctttgac gttggagtcc acgttcttta atagtggact cttgttccaa actggaacaa
     5281 cactcaaccc tatctcggtc tattcttttg atttataagg gattttgccg atttcggcct
     5341 attggttaaa aaatgagctg atttaacaaa aatttaacgc gaattttaac aaaatattaa
     5401 cgcttacaat ttgccattcg ccattcaggc tgcgcaactg ttgggaaggg cgatcggtgc
     5461 gggcctcttc gctattacgc cagcccaagc taccatgata agtaagtaat attaaggtac
     5521 gggaggtact tggagcggcc gc
//
