LOCUS       sequence-148761-        9471 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Output plasmid: contains 5-state register that regulates expression 
            of GFP. Doesn't behave as expected..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 9471)
  AUTHORS   Roquet N, Soleimany AP, Ferris AC, Aaronson S, Lu TK
  TITLE     Synthetic recombinase-based state machines in living cells.
  JOURNAL   Science. 2016 Jul 22;353(6297):aad8559. doi: 
            10.1126/science.aad8559. Epub 2016 Jul 21.
  PUBMED    27463678
REFERENCE   2  (bases 1 to 9471)
  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: "Science."; 
            date: "2016-07-22"; volume: "353(6297):aad8559. doi"; pages: " 
            10.1126/science.aad8559. Epub 2016 Jul 21"
COMMENT     Sequence Label: pNR186
FEATURES             Location/Qualifiers
     source          1..9471
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     protein_bind    742..790
                     /label=Bxb1 attB
                     /bound_moiety="Mycobacteriophage Bxb1 integrase"
                     /note="attB site for the Mycopbacteriophage Bxb1 integrase 
                     (Xu et al., 2013)"
     protein_bind    1126..1183
                     /label=Bxb1 attP
                     /bound_moiety="Mycobacteriophage Bxb1 integrase"
                     /note="attP site for the Mycopbacteriophage Bxb1 integrase 
                     (Xu et al., 2013)"
     misc_RNA        1552..1601
                     /label=sTRSV HHRz
                     /note="hammerhead ribozyme from the tobacco ringspot virus 
                     satellite RNA (Khvorova et al., 2003)"
     RBS             1644..1652
                     /label=Shine-Dalgarno sequence
                     /note="full consensus sequence for ribosome-binding sites 
                     upstream of start codons in E. coli; complementary to a 
                     region in the 3' end of the 16S rRNA (Chen et al., 1994)"
     primer_bind     complement(1688..1716)
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     primer_bind     2311..2331
                     /label=GFP-F
                     /note="GFP, forward primer. Does NOT anneal to EGFP"
     misc_feature    2815..3288
                     /gene="sopC"
                     /label=sopC
                     /note="centromere-like partitioning region of the bacterial
                     F plasmid"
     CDS             complement(3361..4332)
                     /codon_start=1
                     /gene="sopB"
                     /product="partitioning protein for the bacterial F plasmid"
                     /label=sopB
                     /translation="MKRAPVIPKHTLNTQPVEDTSLSTPAAPMVDSLIARVGVMARGNA
                     ITLPVCGRDVKFTLEVLRGDSVEKTSRVWSGNERDQELLTEDALDDLIPSFLLTGQQTP
                     AFGRRVSGVIEIADGSRRRKAAALTESDYRVLVGELDDEQMAALSRLGNDYRPTSAYER
                     GQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGD
                     ALQKAFTDKEELLKQQASNLHEQKKAGVIFEAEEVITLLTSVLKTSSASRTSLSSRHQF
                     APGATVLYKGDKMVLNLDRSRVPTECIEKIEAILKELEKPAP"
     CDS             complement(4332..5507)
                     /codon_start=1
                     /gene="sopA"
                     /product="partitioning protein for the bacterial F plasmid"
                     /label=sopA
                     /translation="MFRMKLMETLNQCINAGHEMTKAIAIAQFNDDSPEARKITRRWRI
                     GEAADLVGVSSQAIRDAEKAGRLPHPDMEIRGRVEQRVGYTIEQINHMRDVFGTRLRRA
                     EDVFPPVIGVAAHKGGVYKTSVSVHLAQDLALKGLRVLLVEGNDPQGTASMYHGWVPDL
                     HIHAEDTLLPFYLGEKDDVTYAIKPTCWPGLDIIPSCLALHRIETELMGKFDEGKLPTD
                     PHLMLRLAIETVAHDYDVIVIDSAPNLGIGTINVVCAADVLIVPTPAELFDYTSALQFF
                     DMLRDLLKNVDLKGFEPDVRILLTKYSNSNGSQSPWMEEQIRDAWGSMVLKNVVRETDE
                     VGKGQIRMRTVFEQAIDQRSSTGAWRNALSIWEPVCNEIFDRLIKPRWEIR"
     misc_feature    5833..6083
                     /gene="incC"
                     /label=incC
                     /note="incompatibility region of the bacterial F plasmid"
     CDS             complement(6086..6841)
                     /codon_start=1
                     /gene="repE"
                     /product="replication initiation protein for the bacterial 
                     F plasmid"
                     /label=repE
                     /translation="MAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQ
                     IRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAG
                     DEKGYESFPWFIKRAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAM
                     RLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPM
                     RLSYIEKKKGRQTTHIVFSFRDITSMTTG"
     rep_origin      6932..7151
                     /label=ori2
                     /note="secondary origin of replication for the bacterial F 
                     plasmid; also known as oriS"
     rep_origin      7219..7750
                     /label=oriV
                     /note="incP origin of replication"
     rep_origin      7227..7841
                     /label=oriV
                     /note="origin of replication for the bacterial F plasmid"
     promoter        8699..8801
                     /label=cat promoter
                     /note="promoter of the E. coli cat gene encoding 
                     chloramphenicol acetyltransferase"
     CDS             8802..9461
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(8868..8887)
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
ORIGIN
        1 taagtgccca ttcagccagt ataaccagat aaaaaaaatc cttagctttc gctaaggatg
       61 atttctgtca gccaggaagg tataacagga aaaattaaag gggagataaa atcccccctt
      121 tttggttaac tcgaggattc gaaaaggtga aatctccttt cacggcccat tcctcatgga
      181 tgggccgttt atttccccga gccagacgtc caccatacct tcgatattcg cgcccactct
      241 cccattagtc ggagtggatg tgttgcgatt gcccgctaga tcaatgtgca cgtcgagtgc
      301 ggtattcctc tgggcatgcc aacacaatta acatctcaat caaggtaaat gctttttgct
      361 ttttttgccg tggtgcggat ctagctaccc gcacttgagt ccacggctga tgccaacaca
      421 attaacatca gaatcaaggt aaatgctttt tgcttttttt gcgggctcac tagggaatgg
      481 cgtcggcgtt aatccttgtt cactatatgc aaccattatc accgccagag gtaaaatagt
      541 caaacgcacg gtgttagcca cagctaacac cacgtcgtcc ctatctgctg ccctaggtct
      601 atgagtggtt gctggataac tttacgggca tgcataaggc tcgtataata tattcaggga
      661 gaccacaacg gtttccctct acaaataatt ttgtttaact ttctgaatca atcggcggcg
      721 tcgtccgtga cattctgtgc gcggccggct tgtcgacgac ggcggtctcc gtcgtcagga
      781 tcatccgggc cagcggctgt ctatgccaga agtcggtcag gtcggagtcc tagaaaggag
      841 ttttttagtt accttaattc taataaacga aataaaaact cgccgttcgc gcgacatgac
      901 atggcatcca cctgtgcgga caagaacgag taaaaggtcg gtttaaccgg cctttttatt
      961 ttgtgatttg aagtttaggg gatagtaaga cccccgcacc gaaaggtccg ggggtttttt
     1021 ttattagttg aaatcacctg gcacctgtaa aaaaggcagc catctggctg ccttagtctc
     1081 cccacgtggg gcgctatgtt ctaccgacac aatctccctg ctcaggtcgt ggtttgtctg
     1141 gtcaaccacc gcggtctcag tggtgtacgg tacaaacccc gacgcaatag cgccaaccat
     1201 gcacttgctg gtggtttagg cgtactccgg caattaaaaa agcggctaac cacgccgctt
     1261 tttttacgtc tgcactagaa ttacctaccg gcgttaaggt tgaaaaataa aaacggcgct
     1321 aaaaagcgcc gttttttttg acggtggtac gattgcccgc taagatatta caattttcga
     1381 aaaaacccgc ttcggcgggt ttttttatag ctaaaagttg aacgcttcac ggacgatcat
     1441 agccagcctg acagtagcca aaggagtttt ttagttacct taattgaaat aaacgaaata
     1501 aaaactcgcg cagctgagag cgacacagtg tgaggacgag ggatggcaca gctgtcaccg
     1561 gatgtgcttt ccggtctgat gagtccgtga ggacgaaaca gcctctacaa ataattttgt
     1621 ttaaggtcga agccgaccta tattaaggag gtcactaatg agtaaaggag aagaactttt
     1681 cactggagtt gtcccaattc ttgttgaatt agatggtgat gttaatgggc acaaattttc
     1741 tgtcagtgga gagggtgaag gtgatgcaac atacggaaaa cttaccctta aatttatttg
     1801 cactactgga aaactacctg ttccatggcc aacacttgtc actactttcg gttatggtgt
     1861 tcaatgcttt gcgagatacc cagatcatat gaaacagcat gactttttca agagtgccat
     1921 gcccgaaggt tatgtacagg aaagaactat atttttcaaa gatgacggga actacaagac
     1981 acgtgctgaa gtcaagtttg aaggtgatac ccttgttaat agaatcgagt taaaaggtat
     2041 tgattttaaa gaagatggaa acattcttgg acacaaattg gaatacaact ataactcaca
     2101 caatgtatac atcatggcag acaaacaaaa gaatggaatc aaagttaact tcaaaattag
     2161 acacaacatt gaagatggaa gcgttcaact agcagaccat tatcaacaaa atactccaat
     2221 tggcgatggc cctgtccttt taccagacaa ccattacctg tccacacaat ctgccctttc
     2281 gaaagatccc aacgaaaaga gagaccacat ggtccttctt gagtttgtaa cagctgctgg
     2341 gattacacat ggcatggatg atctctacaa ataaggaaac acagaaaaaa gcccgcacct
     2401 gacagtgcgg gctttttttt tcgaccaaag ggtgctttat caaggggaag gtgcctcact
     2461 cctagggtgt aataggcact aaaagagtga tatggcacgc gcatgtggaa cgccgttaga
     2521 gggttgctga gccatcgtgg tccttagact cgggaaaaac aaaaacccgc cgaagcgggt
     2581 taagtgcggg gcggctagcc cgccacctaa gttatgagtc aggaaaaaag gcgacagagt
     2641 aatctgtcgc cttttttctt tgcttgcttt gtaatcactc gatgaccaaa agtaaaaacc
     2701 cgccgaagcg ggtttttacg taaaacaggt gaaactgacg ctagccggtc acatgtcaat
     2761 acttgccctt gacaggcatt gatggaatcg tagtctcacg ctgatagtct gatcgacaat
     2821 acaagtggga ccgtggtccc agaccgataa tcagaccgac aacacgagtg ggatcgtggt
     2881 cccagactaa taatcagacc gacgatacga gtgggaccgt ggtcccagac taataatcag
     2941 accgacgata cgagtgggac cgtggttcca gactaataat cagaccgacg atacgagtgg
     3001 gaccgtggtc ccagactaat aatcagaccg acgatacgag tgggaccatg gtcccagact
     3061 aataatcaga ccgacgatac gagtgggacc gtggtcccag tctgattatc agaccgacga
     3121 tacgagtggg accgtggtcc cagactaata atcagaccga cgatacgagt gggaccgtgg
     3181 tcccagacta ataatcagac cgacgatacg agtgggaccg tggtcccagt ctgattatca
     3241 gaccgacgat acaagtggaa cagtgggccc agagagaata ttcaggccag ttatgctttc
     3301 tggcctgtaa caaaggacat taagtaaaga cagataaacg tagactaaaa cgtggtcgca
     3361 tcagggtgct ggcttttcaa gttccttaag aatggcctca attttctcta tacactcagt
     3421 tggaacacgg gacctgtcca ggttaagcac cattttatcg cccttataca atactgtcgc
     3481 tccaggagca aactgatgtc gtgagcttaa actagttctt gatgcagatg acgttttaag
     3541 cacagaagtt aaaagagtga taacttcttc agcttcaaat atcaccccag cttttttctg
     3601 ctcatgaagg ttagatgcct gctgcttaag taattcctct ttatctgtaa aggctttttg
     3661 aagtgcatca cctgaccggg cagatagttc accggggtga gaaaaaagag caacaactga
     3721 tttaggcaat ttggcggtgt tgatacagcg ggtaataatc ttacgtgaaa tattttccgc
     3781 atcagccagc gcagaaatat ttccagcaaa ttcattctgc aatcggcttg cataacgctg
     3841 accacgttca taagcacttg ttgggcgata atcgttaccc aatctggata atgcagccat
     3901 ctgctcatca tccagctcgc caaccagaac acgataatca ctttcggtaa gtgcagcagc
     3961 tttacgacgg cgactcccat cggcaatttc tatgacacca gatactcttc gaccgaacgc
     4021 cggtgtctgt tgaccagtca gtagaaaaga agggatgaga tcatccagtg cgtcctcagt
     4081 aagcagctcc tggtcacgtt cattacctga ccatacccga gaggtcttct caacactatc
     4141 accccggagc acttcaagag taaacttcac atcccgacca catacaggca aagtaatggc
     4201 attaccgcga gccattactc ctacgcgcgc aattaacgaa tccaccatcg gggcagctgg
     4261 tgtcgataac gaagtatctt caaccggttg agtattgagc gtatgttttg gaataacagg
     4321 cgcacgcttc attatctaat ctcccagcgt ggtttaatca gacgatcgaa aatttcattg
     4381 cagacaggtt cccaaataga aagagcattt ctccaggcac cagttgaaga gcgttgatca
     4441 atggcctgtt caaaaacagt tctcatccgg atctgacctt taccaacttc atccgtttca
     4501 cgtacaacat tttttagaac catgcttccc caggcatccc gaatttgctc ctccatccac
     4561 ggggactgag agccattact attgctgtat ttggtaagca aaatacgtac atcaggctcg
     4621 aaccctttaa gatcaacgtt cttgagcaga tcacgaagca tatcgaaaaa ctgcagtgcg
     4681 gaggtgtagt caaacaactc agcaggcgtg ggaacaatca gcacatcagc agcacatacg
     4741 acattaatcg tgccgatacc caggttaggc gcgctgtcaa taactatgac atcatagtca
     4801 tgagcaacag tttcaatggc cagtcggagc atcaggtgtg gatcggtggg cagtttacct
     4861 tcatcaaatt tgcccattaa ctcagtttca atacggtgca gagccagaca ggaaggaata
     4921 atgtcaagcc ccggccagca agtgggcttt attgcataag tgacatcgtc cttttcccca
     4981 agatagaaag gcaggagagt gtcttctgca tgaatatgaa gatctggtac ccatccgtga
     5041 tacattgagg ctgttccctg ggggtcgtta ccttccacga gcaaaacacg tagccccttc
     5101 agagccagat cctgagcaag atgaacagaa actgaggttt tgtaaacgcc acctttatgg
     5161 gcagcaaccc cgatcaccgg tggaaatacg tcttcagcac gtcgcaatcg cgtaccaaac
     5221 acatcacgca tatgattaat ttgttcaatt gtataaccaa cacgttgctc aacccgtcct
     5281 cgaatttcca tatccgggtg cggtagtcgc cctgctttct cggcatctct gatagcctga
     5341 gaagaaaccc caactaaatc cgctgcttca cctattctcc agcgccgggt tattttcctc
     5401 gcttccgggc tgtcatcatt aaactgtgca atggcgatag ccttcgtcat ttcatgacca
     5461 gcgtttatgc actggttaag tgtttccatg agtttcattc tgaacatcct ttaatcattg
     5521 ctttgcgttt ttttattaaa tcttgcaatt tactgcaaag caacaacaaa atcgcaaagt
     5581 catcaaaaaa ccgcaaagtt gtttaaaata agagcaacac tacaaaagga gataagaaga
     5641 gcacatacct cagtcactta ttatcactag cgctcgccgc agccgtgtaa ccgagcatag
     5701 cgagcgaact ggcgaggaag caaagaagaa ctgttctgtc agatagctct tacgctcagc
     5761 gcaagaagaa atatccaccg tgggaaaaac tccaggtaga ggtacacacg cggatagcca
     5821 attcagagta ataaactgtg ataatcaacc ctcatcaatg atgacgaact aacccccgat
     5881 atcaggtcac atgacgaagg gaaagagaag gaaatcaact gtgacaaact gccctcaaat
     5941 ttggcttcct taaaaattac agttcaaaaa gtatgagaaa atccatgcag gctgaaggaa
     6001 acagcaaaac tgtgacaaat taccctcagt aggtcagaac aaatgtgacg aaccaccctc
     6061 aaatctgtga cagataaccc tcagactatc ctgtcgtcat ggaagtgata tcgcggaagg
     6121 aaaatacgat atgagtcgtc tggcggcctt tctttttctc aatgtatgag aggcgcattg
     6181 gagttctgct gttgatctca ttaacacaga cctgcaggaa gcggcggcgg aagtcaggca
     6241 tacgctggta actttgaggc agctggtaac gctctatgat ccagtcgatt ttcagagaga
     6301 cgatgcctga gccatccggc ttacgatact gacacaggga ttcgtataaa cgcatggcat
     6361 acggattggt gatttctttt gtttcactaa gccgaaactg cgtaaaccgg ttctgtaacc
     6421 cgataaagaa gggaatgaga tatgggttga tatgtacact gtaaagccct ctggatggac
     6481 tgtgcgcacg tttgataaac caaggaaaag attcatagcc tttttcatcg ccggcatcct
     6541 cttcagggcg ataaaaaacc acttccttcc ccgcgaaact cttcaatgcc tgccgtatat
     6601 ccttactggc ttccgcagag gtcaatccga atatttcagc atatttagca acatggatct
     6661 cgcagatacc gtcatgttcc tgtagggtgc catcagattt tctgatctgg tcaacgaaca
     6721 gatacagcat acgtttttga tcccgggaga gactatatgc cgcctcagtg aggtcgtttg
     6781 actggacgat tcgcgggcta tttttacgtt tcttgtgatt gataaccgct gtttccgcca
     6841 tgacagatcc atgtgaagtg tgacaagttt ttagattgtc acactaaata aaaaagagtc
     6901 aataagcagg gataactttg tgaaaaaaca gcttcttctg agggcaattt gtcacagggt
     6961 taagggcaat ttgtcacaga caggactgtc atttgagggt gatttgtcac actgaaaggg
     7021 caatttgtca caacaccttc tctagaacca gcatggataa aggcctacaa ggcgctctaa
     7081 aaaagaagat ctaaaaacta taaaaaaaat aattataaaa atatccccgt ggataagtgg
     7141 ataaccccaa gggaagtttt ttcaggcatc gtgtgtaagc agaatatata agtgctgttc
     7201 cctggtgctt cctcgctcac tcgaccggga gggttcgaga agggggggca ccccccttcg
     7261 gcgtgcgcgg tcacgcgcac agggcgcagc cctggttaaa aacaaggttt ataaatattg
     7321 gtttaaaagc aggttaaaag acaggttagc ggtggccgaa aaacgggcgg aaacccttgc
     7381 aaatgctgga ttttctgcct gtggacagcc cctcaaatgt caataggtgc gcccctcatc
     7441 tgtcagcact ctgcccctca agtgtcaagg atcgcgcccc tcatctgtca gtagtcgcgc
     7501 ccctcaagtg tcaataccgc agggcactta tccccaggct tgtccacatc atctgtggga
     7561 aactcgcgta aaatcaggcg ttttcgccga tttgcgaggc tggccagctc cacgtcgccg
     7621 gccgaaatcg agcctgcccc tcatctgtca acgccgcgcc gggtgagtcg gcccctcaag
     7681 tgtcaacgtc cgcccctcat ctgtcagtga gggccaagtt ttccgcgagg tatccacaac
     7741 gccggcggcc ggccgcggtg tctcgcacac ggcttcgacg gcgtttctgg cgcgtttgca
     7801 gggccataga cggccgccag cccagcggcg agggcaacca gccgagggct tcgccctgtc
     7861 gctcgactgc ggcgagcact actggctgta aaaggacaga ccacatcatg gttctgtgtt
     7921 cattaggttg ttctgtccat tgctgacata atccgctcca cttcaacgta acaccgcacg
     7981 aagatttcta ttgttcctga aggcatattc aaatcgtttt cgttaccgct tgcaggcatc
     8041 atgacagaac actacttcct ataaacgcta cacaggctcc tgagattaat aatgcggatc
     8101 tctacgataa tgggagattt tcccgactgt ttcgttcgct tctcagtgga taacagccag
     8161 cttctctgtt taacagacaa aaacagcata tccactcagt tccacatttc catataaagg
     8221 ccaaggcatt tattctcagg ataattgttt cagcatcgca accgcatcag actccggcat
     8281 cgcaaactgc acccggtgcc gggcagccac atccagcgca aaaaccttcg tgtagacttc
     8341 cgttgaactg atggacttat gtcccatcag gctttgcaga actttcagcg gtataccggc
     8401 atacagcatg tgcatcgcat aggaatggcg gaacgtatgt ggtgtgaccg gaacagagaa
     8461 cgtcacaccg tcagcagcag cggcggcaac cgcctcccca atccaggtcc tgaccgttct
     8521 gtccgtcact tcccagatcc gcgctttctc tgtccttcct gtgcgacggt tacgccgctc
     8581 catgagctta tcgcgaataa atacctgtga cggaagatca cttcgcagaa taaataaatc
     8641 ctggtgtccc tgttgatacc gggaagccct gggccaactt ttggcgaaaa tgagacgttg
     8701 atcggcacgt aagaggttcc aactttcacc ataatgaaat aagatcacta ccgggcgtat
     8761 tttttgagtt atcgagattt tcaggagcta aggaagctaa aatggagaaa aaaatcactg
     8821 gatataccac cgttgatata tcccaatggc atcgtaaaga acattttgag gcatttcagt
     8881 cagttgctca atgtacctat aaccagaccg ttcagctgga tattacggcc tttttaaaga
     8941 ccgtaaagaa aaataagcac aagttttatc cggcctttat tcacattctt gcccgcctga
     9001 tgaatgctca tccggaattt cgtatggcaa tgaaagacgg tgagctggtg atatgggata
     9061 gtgttcaccc ttgttacacc gttttccatg agcaaactga aacgttttca tcgctctgga
     9121 gtgaatacca cgacgatttc cggcagtttc tacacatata ttcgcaagat gtggcgtgtt
     9181 acggtgaaaa cctggcctat ttccctaaag ggtttattga gaatatgttt ttcgtctcag
     9241 ccaatccctg ggtgagtttc accagttttg atttaaacgt ggccaatatg gacaacttct
     9301 tcgcccccgt tttcaccatg ggcaaatatt atacgcaagg cgacaaggtg ctgatgccgc
     9361 tggcgattca ggttcatcat gccgtttgtg atggcttcca tgtcggcaga atgcttaatg
     9421 aattacaaca gtactgcgat gagtggcagg gcggggcgta agacgtctaa g
//
