LOCUS       sequence-386601-        6155 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  ""pEF1s(low)"" reporter plasmid.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6155)
  AUTHORS   Ma Y, Budde MW, Zhu J, Elowitz MB
  TITLE     Tuning Methylation-Dependent Silencing Dynamics by Synthetic 
            Modulation of CpG Density.
  JOURNAL   ACS Synth Biol. 2023 Aug 12. doi: 10.1021/acssynbio.3c00078.
  PUBMED    37572041
REFERENCE   2  (bases 1 to 6155)
  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: "ACS Synth 
            Biol. 2023 Aug 12. doi: 10.1021/acssynbio.3c00078."
COMMENT     Sequence Label: vYM011_phiC31-nTRE-pEF1s(low)-H2b-Citrine
FEATURES             Location/Qualifiers
     source          1..6155
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      77..665
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     566..585
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     polyA_signal    849..983
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     polyA_signal    1086..1207
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     protein_bind    1244..1313
                     /label=attB
                     /bound_moiety="phage phi-C31 integrase"
                     /note="attB site for the phi-C31 integrase (Groth et al., 
                     2000)"
     CDS             1579..2382
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MGSAIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQ
                     GRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQD
                     LLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDE
                     EHQGLAPAELFARLKARMPDGDDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQ
                     DIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(1642..1661)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     2252..2271
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     primer_bind     complement(2414..2431)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    2420..2644
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     protein_bind    2717..2735
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2753..2771
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2789..2807
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2825..2843
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     protein_bind    2861..2879
                     /gene="tetO"
                     /label=tet operator
                     /bound_moiety="tetracycline repressor TetR"
                     /note="bacterial operator O2 for the tetR and tetA genes"
     LTR             3174..3442
                     /label=5' LTR (truncated)
                     /note="truncated 5' long terminal repeat (LTR) from human 
                     T-cell leukemia virus (HTLV) type 1"
     CDS             3528..3905
                     /codon_start=1
                     /gene="HIST1H2BJ"
                     /product="human histone H2B"
                     /label=H2B
                     /translation="MPEPAKSAPAPKKGSKKAVTKAQKKGGKKRKRSRKESYSIYVYKV
                     LKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLP
                     GELAKHAVSEGTKAITKYTSAK"
     regulatory      3924..3933
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             join(3930..3932,3933..3935,3936..4646)
                     /codon_start=1
                     /product="enhanced variant of YFP (Heikal et al., 2001)"
                     /label=Citrine
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTL
                     KFICTTGKLPVPWPTLVTTFGYGLMCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
                     GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIK
                     VNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLL
                     EFVTAAGITLGMDELYK"
     primer_bind     complement(3975..3996)
                     /label=EGFP-N
                     /note="EGFP, reverse primer"
     primer_bind     complement(4236..4255)
                     /label=EXFP-R
                     /note="For distinguishing EGFP variants, reverse primer"
     primer_bind     4583..4604
                     /label=EGFP-C
                     /note="EGFP, forward primer"
     primer_bind     complement(4697..4716)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(4698..4716)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     polyA_signal    4990..5111
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     promoter        5137..5200
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5201..5269,5270..6061)
                     /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     complement(5419..5438)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
ORIGIN
        1 tcatgaccaa aatcccttaa cgtgagtttt cgttccactg agcgtcagac cccgtagaaa
       61 agatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa
      121 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc
      181 cgaaggtaac tggcttcagc agagcgcaga taccaaatac tgttcttcta gtgtagccgt
      241 agttaggcca ccacttcaag aactctgtag caccgcctac atacctcgct ctgctaatcc
      301 tgttaccagt ggctgctgcc agtggcgata agtcgtgtct taccgggttg gactcaagac
      361 gatagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc acacagccca
      421 gcttggagcg aacgacctac accgaactga gatacctaca gcgtgagcta tgagaaagcg
      481 ccacgcttcc cgaagggaga aaggcggaca ggtatccggt aagcggcagg gtcggaacag
      541 gagagcgcac gagggagctt ccagggggaa acgcctggta tctttatagt cctgtcgggt
      601 ttcgccacct ctgacttgag cgtcgatttt tgtgatgctc gtcagggggg cggagcctat
      661 ggaaaaacgc cagcaacgcg gcctttttac ggttcctggc cttttgctgg ccttttgctc
      721 acatgttctt tcctgcggta ccgatcataa tcagccatac cacatttgta gaggttttac
      781 ttgctttaaa aaacctccca cacctccccc tgaacctgaa acataaaatg aatgcaattg
      841 ttgttgttaa cttgtttatt gcagcttata atggttacaa ataaagcaat agcatcacaa
      901 atttcacaaa taaagcattt ttttcactgc attctagttg tggtttgtcc aaactcatca
      961 atgtatctta tcatgtctgg atcataatca gccataccac atttgtagag gttttacttg
     1021 ctttaaaaaa cctcccacac ctccccctga acctgaaaca taaaatgaat gcaattgttg
     1081 ttgttaactt gtttattgca gcttataatg gttacaaata aagcaatagc atcacaaatt
     1141 tcacaaataa agcatttttt tcactgcatt ctagttgtgg tttgtccaaa ctcatcaatg
     1201 tatcttatca tgtctgctcg aggtcgacga tgtaggtcac ggtctcgaag ccgcggtgcg
     1261 ggtgccaggg cgtgcccttg ggctccccgg gcgcgtactc cacctcaccc atctggtcca
     1321 tcatgatgaa cgggtcgagg tggcggtagt tgatcccggc gaacgcgcgg cgcaccggga
     1381 agccctcgcc ctcgaaaccg ctgggcgcgg tggtcacggt gagcacggga cgtgcgacgg
     1441 cgtcggcggg tgcggatacg cggggcagcg tcagcgggtt ctcgacggtc acggcgggca
     1501 tgtcgacggt atcgataagc ttacgcgtgc tagcgcatgc agatctacta gtcggccgga
     1561 taaagatatc aactcgagat gggatcggcc attgaacaag atggattgca cgcaggttct
     1621 ccggccgctt gggtggagag gctattcggc tatgactggg cacaacagac aatcggctgc
     1681 tctgatgccg ccgtgttccg gctgtcagcg caggggcgcc cggttctttt tgtcaagacc
     1741 gacctgtccg gtgccctgaa tgaactgcag gacgaggcag cgcggctatc gtggctggcc
     1801 acgacgggcg ttccttgcgc agctgtgctc gacgttgtca ctgaagcggg aagggactgg
     1861 ctgctattgg gcgaagtgcc ggggcaggat ctcctgtcat ctcaccttgc tcctgccgag
     1921 aaagtatcca tcatggctga tgcaatgcgg cggctgcata cgcttgatcc ggctacctgc
     1981 ccattcgacc accaagcgaa acatcgcatc gagcgagcac gtactcggat ggaagccggt
     2041 cttgtcgatc aggatgatct ggacgaagag catcaggggc tcgcgccagc cgaactgttc
     2101 gccaggctca aggcgcgcat gcccgacggc gatgatctcg tcgtgaccca tggcgatgcc
     2161 tgcttgccga atatcatggt ggaaaatggc cgcttttctg gattcatcga ctgtggccgg
     2221 ctgggtgtgg cggaccgcta tcaggacata gcgttggcta cccgtgatat tgctgaagag
     2281 cttggcggcg aatgggctga ccgcttcctc gtgctttacg gtatcgccgc tcccgattcg
     2341 cagcgcatcg ccttctatcg ccttcttgac gagttcttct gaggggatca attctctaga
     2401 gctcgctgat cagcctcgac tgtgccttct agttgccagc catctgttgt ttgcccctcc
     2461 cccgtgcctt ccttgaccct ggaaggtgcc actcccactg tcctttccta ataaaatgag
     2521 gaaattgcat cgcattgtct gagtaggtgt cattctattc tggggggtgg ggtggggcag
     2581 gacagcaagg gggaggattg ggaagagaat agcaggcatg ctggggatgc ggtgggctct
     2641 atggcttctg aggcggaaag aaccagctgg gggctagcaa agcctaggaa cagctgcata
     2701 tagcactgca gtttactccc tatcagtgat agagagtcaa aaggccatgc cctccctatc
     2761 agtgatagag agagcagact caaggtggtc cctatcagtg atagagagat tgagcaagag
     2821 ggcctcccta tcagtgatag agattgatcc agtcagggcc tccctatcag tgatagagaa
     2881 gctatgtgca ggtagggctg tacagtggga atgcacgtag gatctgccat tgctccagtg
     2941 cccttcagtg ggcagagagc acatcaccca cagtccccaa gaagttgggg ggaggggtgg
     3001 gcaattgaac tggtgcctag agaaggtggc gcagggtaaa ctgggaaagt gatgtcgtgt
     3061 actggctccg cctttttccc gagggtgggg gagaaccata tataagtgca gtagtccccc
     3121 tgaacgttct tttttgcaac gggtttgccg ccagaacaca gctgaagctt tgaggggcta
     3181 gcatctctcc ttcacgcgcc cgccgcccta cctgaggccg ccatccacac cggttgagtt
     3241 gcgttctgcc gcctcccgcc tgtggtgcct cctgaactgt gtccgccgtc taggtaagtt
     3301 taaagctcag gttgagaccg ggcctttgtc cggtgctccc ttggagccta cctagactca
     3361 gccggctctc cacgctttgc ctgaccctgc ttgctcaact ctacgtcttt gtttcgtttt
     3421 ctgttctgcg ccgttacaga tccaagctgt gacctgggcc tacacctggc cgctctagcc
     3481 cgggcggatc ccccgggctg caggaattcg atatcaagct tgccaccatg ccagagccag
     3541 cgaagtctgc tcccgccccg aaaaagggct ccaagaaggc ggtgactaag gcgcagaaga
     3601 aaggcggcaa gaagcgcaag cgcagccgca aggagagcta ttccatctat gtgtacaagg
     3661 ttctgaagca ggtccaccct gacaccggca tttcgtccaa ggccatgggc atcatgaatt
     3721 cgtttgtgaa cgacattttc gagcgcatcg caggtgaggc ttcccgcctg gcgcattaca
     3781 acaagcgctc gaccatcacc tccagggaga tccagacggc cgtgcgcctg ctgctgcctg
     3841 gggagttggc caagcacgcc gtgtccgagg gtactaaggc catcaccaag tacaccagcg
     3901 ctaaggatcc ccgggtaccg gtcgccacca tggtgagcaa gggcgaggag ctgttcaccg
     3961 gggtggtgcc catcctggtc gagctggacg gcgacgtaaa cggccacaag ttcagcgtgt
     4021 ccggcgaggg cgagggcgat gccacctacg gcaagctgac cctgaagttc atctgcacca
     4081 ccggcaagct gcccgtgccc tggcccaccc tcgtgaccac cttcggctac ggcctgatgt
     4141 gcttcgcccg ctaccccgac cacatgaagc agcacgactt cttcaagtcc gccatgcccg
     4201 aaggctacgt ccaggagcgc accatcttct tcaaggacga cggcaactac aagacccgcg
     4261 ccgaggtgaa gttcgagggc gacaccctgg tgaaccgcat cgagctgaag ggcatcgact
     4321 tcaaggagga cggcaacatc ctggggcaca agctggagta caactacaac agccacaacg
     4381 tctatatcat ggccgacaag cagaagaacg gcatcaaggt gaacttcaag atccgccaca
     4441 acatcgagga cggcagcgtg cagctcgccg accactacca gcagaacacc cccatcggcg
     4501 acggccccgt gctgctgccc gacaaccact acctgagcta ccagtccgcc ctgagcaaag
     4561 accccaacga gaagcgcgat cacatggtcc tgctggagtt cgtgaccgcc gccgggatca
     4621 ctctcggcat ggacgagctg tacaagtagg tcgacctcga gggggggccc ggtaccaggt
     4681 aagtgtaccc aattcgccct atagtgagtc gtattacaat tcactcgatc gcccttccca
     4741 acagttgcgc agcctgaatg gcgaatggag atccaatttt taagtgtata atgtgttaaa
     4801 ctactgattc taattgtttg tgtattttag attcacagtc ccaaggctca tttcaggccc
     4861 ctcagtcctc acagtctgtt catgatcata atcagccata ccacatttgt agaggtttta
     4921 cttgctttaa aaaacctccc acacctcccc ctgaacctga aacataaaat gaatgcaatt
     4981 gttgttgtta acttgtttat tgcagcttat aatggttaca aataaagcaa tagcatcaca
     5041 aatttcacaa ataaagcatt tttttcactg cattctagtt gtggtttgtc caaactcatc
     5101 aatgtatctt aacgcgtaaa ttgtaagcgt ctcaaatatg tatccgctca tgagacaata
     5161 accctgataa atgcttcaat aatattgaaa aaggaagagt atgagtattc aacatttccg
     5221 tgtcgccctt attccctttt ttgcggcatt ttgccttcct gtttttgctc acccagaaac
     5281 gctggtgaaa gtaaaagatg ctgaagatca gttgggtgca cgagtgggtt acatcgaact
     5341 ggatctcaac agcggtaaga tccttgagag ttttcgcccc gaagaacgtt ttccaatgat
     5401 gagcactttt aaagttctgc tatgtggcgc ggtattatcc cgtattgacg ccgggcaaga
     5461 gcaactcggt cgccgcatac actattctca gaatgacttg gttgagtact caccagtcac
     5521 agaaaagcat cttacggatg gcatgacagt aagagaatta tgcagtgctg ccataaccat
     5581 gagtgataac actgcggcca acttacttct gacaacgatc ggaggaccga aggagctaac
     5641 cgcttttttg cacaacatgg gggatcatgt aactcgcctt gatcgttggg aaccggagct
     5701 gaatgaagcc ataccaaacg acgagcgtga caccacgatg cctgtagcaa tggcaacaac
     5761 gttgcgcaaa ctattaactg gcgaactact tactctagct tcccggcaac aattaataga
     5821 ctggatggag gcggataaag ttgcaggacc acttctgcgc tcggcccttc cggctggctg
     5881 gtttattgct gataaatctg gagccggtga gcgtgggtct cgcggtatca ttgcagcact
     5941 ggggccagat ggtaagccct cccgtatcgt agttatctac acgacgggga gtcaggcaac
     6001 tatggatgaa cgaaatagac agatcgctga gataggtgcc tcactgatta agcattggta
     6061 actgtcagac caagtttact catatatact ttagattgat ttaaaacttc atttttaatt
     6121 taaaaggatc taggtgaaga tcctttttga taatc
//
