LOCUS       sequence-148765-        9520 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Output plasmid: contains 16-state register that regulates expression
            of GFP. Implements RSM with 3-input passcode behavior..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 9520)
  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 9520)
  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: pNR292
FEATURES             Location/Qualifiers
     source          1..9520
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     protein_bind    547..604
                     /label=Bxb1 attP
                     /bound_moiety="Mycobacteriophage Bxb1 integrase"
                     /note="attP site for the Mycopbacteriophage Bxb1 integrase 
                     (Xu et al., 2013)"
     protein_bind    832..880
                     /label=Bxb1 attB
                     /bound_moiety="Mycobacteriophage Bxb1 integrase"
                     /note="attB site for the Mycopbacteriophage Bxb1 integrase 
                     (Xu et al., 2013)"
     protein_bind    1175..1232
                     /label=Bxb1 attP
                     /bound_moiety="Mycobacteriophage Bxb1 integrase"
                     /note="attP site for the Mycopbacteriophage Bxb1 integrase 
                     (Xu et al., 2013)"
     RBS             2194..2202
                     /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)"
     misc_feature    2864..3337
                     /gene="sopC"
                     /label=sopC
                     /note="centromere-like partitioning region of the bacterial
                     F plasmid"
     CDS             complement(3410..4381)
                     /codon_start=1
                     /gene="sopB"
                     /product="partitioning protein for the bacterial F plasmid"
                     /label=sopB
                     /translation="MKRAPVIPKHTLNTQPVEDTSLSTPAAPMVDSLIARVGVMARGNA
                     ITLPVCGRDVKFTLEVLRGDSVEKTSRVWSGNERDQELLTEDALDDLIPSFLLTGQQTP
                     AFGRRVSGVIEIADGSRRRKAAALTESDYRVLVGELDDEQMAALSRLGNDYRPTSAYER
                     GQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGD
                     ALQKAFTDKEELLKQQASNLHEQKKAGVIFEAEEVITLLTSVLKTSSASRTSLSSRHQF
                     APGATVLYKGDKMVLNLDRSRVPTECIEKIEAILKELEKPAP"
     CDS             complement(4381..5556)
                     /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    5882..6132
                     /gene="incC"
                     /label=incC
                     /note="incompatibility region of the bacterial F plasmid"
     CDS             complement(6135..6890)
                     /codon_start=1
                     /gene="repE"
                     /product="replication initiation protein for the bacterial 
                     F plasmid"
                     /label=repE
                     /translation="MAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQ
                     IRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAG
                     DEKGYESFPWFIKRAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAM
                     RLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPM
                     RLSYIEKKKGRQTTHIVFSFRDITSMTTG"
     rep_origin      6981..7200
                     /label=ori2
                     /note="secondary origin of replication for the bacterial F 
                     plasmid; also known as oriS"
     rep_origin      7268..7799
                     /label=oriV
                     /note="incP origin of replication"
     rep_origin      7276..7890
                     /label=oriV
                     /note="origin of replication for the bacterial F plasmid"
     promoter        8748..8850
                     /label=cat promoter
                     /note="promoter of the E. coli cat gene encoding 
                     chloramphenicol acetyltransferase"
     CDS             8851..9510
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(8917..8936)
                     /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 cgacactgct
      301 cgatccgctc gcacattgcc cgctagatca atgtgtacgt cgagtgcggt attcctctgg
      361 gccggccggc ttgtcgacga cggcgcactc cgtcgtcagg atcatccggg ccgtggtgcg
      421 gatctagcta cccgcacttg agtccacggc tgatgccaac acaattaaca tcagaatcaa
      481 ggtaaatgct ttttgctttt tttgcgggct cactagggaa tggcgtcgtc cgtgacattc
      541 tgtgcggtcg gggtttgtac cgtacaccac tgagtgcgcg gtggttgacc agacaaacca
      601 cgaccagcgg ctgtctatgc cagaagtcgg tcaggtcgga gtcctaggcg agtttttatt
      661 tcgtttatta gaattaaggt aactaaaaaa ctcctttcgt tcgcgcgaca tgacatgccg
      721 acacaatctc cctgctcaga acttttcgga tcaagctatg aaaaacgcaa agagggaact
      781 aaacacttgc aatagcgcca accatgcacc atagccagcc tgacagtagc ccggccggct
      841 tgtcgacgac ggcggtctcc gtcgtcagga tcatccgggc gcagctgaga gcgacacagt
      901 cctgtacttg ggatgctggc gtttagtttc tcgtttcttc ttcttttaac gagagaaaac
      961 gaggaactaa cttggggtgc aggtaggcca tcgccgccga ttgattcaga aagttaaaca
     1021 aaattatttg tagagggaaa ccgttgtggt ctccctgaat atattatacg agccttatgc
     1081 atgcccgtaa agttatccag caaccactca tagacctagg gcagcagata gggacgacgt
     1141 ggtgttagct gtgattgtct tcggggcccc actcgtcgtg gtttgtctgg tcaaccaccg
     1201 cggtctcagt ggtgtacggt acaaaccccg acgaggcgat aagctcggca aggctgatta
     1261 cgcctgctcg tgtgatgcca acacaattaa catctcaatc aaggtaaatg ctttttgctt
     1321 tttttgcccg gatctcctta gtgtaggttc cgactcgcgc ttcgtcgaca caacttttcg
     1381 gatcaagcta tgaaggacgc aaagagggaa ctaaacactt cgtccctgag gctgcagttc
     1441 agcaactaca cctagctgag acataaaaaa acccgcttgc gcgggctttt tcacattagt
     1501 gccccagttt gctagggagg tcgcagtatc tggccactgc cacctcgtgc tgctcgacgt
     1561 aggtctcgtt gttggcctcc ttgattcttt ccagtctgta gtccacatag tagacgccag
     1621 gcatcttgag gttcttagcg ggtttcttgg atctatatgt ggtcttgatg tttgcgatca
     1681 gatggctccc gcccacgagc ttcagggcca tgtcgtttct gccttccagg ccgccgtcag
     1741 cggggtacag cgtctcggtg aaggcctccc agccgagtgt tttcttctgc atcacagggc
     1801 cgttggatgt gaagttcacc cctctgatct tgacgttgta gatgaggcag ccgtcctgga
     1861 ggctggtgtc ctgggtagcg gtcagcacgc ccccgtcttc gtatgtggtg actctctccc
     1921 atgtgaagcc ctcagggaag gactgcttga agaagtcggg gatgccctgg gtgtggttga
     1981 tgaaggtctt gctgccgtag aggaagctag tagccaggat gtcgaaggcg aaggggagag
     2041 ggccgccctc gaccaccttg attctcatgg tctgggtgcc ctcgtagggc ttgccttcgc
     2101 cctcggatgt gcacttgaag tgatggttgt ccacggtgcc ctccatgtac agcttcatgt
     2161 gcatgttctc cttaatcagc tcgctcattc gttacctcct tagtatactc ttttgacttt
     2221 aaacaaaatt atttgtagag gcggtttcga catcactgtc tcatcagaac gcaaagcaca
     2281 tgcgttgacc gctgctccgt ttacactatc ctcgcgtacg atcgcacgcc ccatgaaagg
     2341 agttttttag ttaccttaat tgaaataaac gaaataaaaa ctcgccagat cgacaggtag
     2401 accaggtgcg gtgcgaatac gagtcgtagt tagttcctcg ttttctctcg ttggaagaag
     2461 aagaaacgag aaactaaagc aatgctggtc tggctatgac tgcctcactc ctagggtgta
     2521 ataggcacta aaagagtgat atggcacgcg catgtggaac gccgttagag ggttgctgag
     2581 ccatcgtggt ccttagactc gggaaaaaca aaaacccgcc gaagcgggtt aagtgcgggg
     2641 cggctagccc gccacctaag ttatgagtca ggaaaaaagg cgacagagta atctgtcgcc
     2701 ttttttcttt gcttgctttg taatcactcg atgaccaaaa gtaaaaaccc gccgaagcgg
     2761 gtttttacgt aaaacaggtg aaactgacgc tagccggtca catgtcaata cttgcccttg
     2821 acaggcattg atggaatcgt agtctcacgc tgatagtctg atcgacaata caagtgggac
     2881 cgtggtccca gaccgataat cagaccgaca acacgagtgg gatcgtggtc ccagactaat
     2941 aatcagaccg acgatacgag tgggaccgtg gtcccagact aataatcaga ccgacgatac
     3001 gagtgggacc gtggttccag actaataatc agaccgacga tacgagtggg accgtggtcc
     3061 cagactaata atcagaccga cgatacgagt gggaccatgg tcccagacta ataatcagac
     3121 cgacgatacg agtgggaccg tggtcccagt ctgattatca gaccgacgat acgagtggga
     3181 ccgtggtccc agactaataa tcagaccgac gatacgagtg ggaccgtggt cccagactaa
     3241 taatcagacc gacgatacga gtgggaccgt ggtcccagtc tgattatcag accgacgata
     3301 caagtggaac agtgggccca gagagaatat tcaggccagt tatgctttct ggcctgtaac
     3361 aaaggacatt aagtaaagac agataaacgt agactaaaac gtggtcgcat cagggtgctg
     3421 gcttttcaag ttccttaaga atggcctcaa ttttctctat acactcagtt ggaacacggg
     3481 acctgtccag gttaagcacc attttatcgc ccttatacaa tactgtcgct ccaggagcaa
     3541 actgatgtcg tgagcttaaa ctagttcttg atgcagatga cgttttaagc acagaagtta
     3601 aaagagtgat aacttcttca gcttcaaata tcaccccagc ttttttctgc tcatgaaggt
     3661 tagatgcctg ctgcttaagt aattcctctt tatctgtaaa ggctttttga agtgcatcac
     3721 ctgaccgggc agatagttca ccggggtgag aaaaaagagc aacaactgat ttaggcaatt
     3781 tggcggtgtt gatacagcgg gtaataatct tacgtgaaat attttccgca tcagccagcg
     3841 cagaaatatt tccagcaaat tcattctgca atcggcttgc ataacgctga ccacgttcat
     3901 aagcacttgt tgggcgataa tcgttaccca atctggataa tgcagccatc tgctcatcat
     3961 ccagctcgcc aaccagaaca cgataatcac tttcggtaag tgcagcagct ttacgacggc
     4021 gactcccatc ggcaatttct atgacaccag atactcttcg accgaacgcc ggtgtctgtt
     4081 gaccagtcag tagaaaagaa gggatgagat catccagtgc gtcctcagta agcagctcct
     4141 ggtcacgttc attacctgac catacccgag aggtcttctc aacactatca ccccggagca
     4201 cttcaagagt aaacttcaca tcccgaccac atacaggcaa agtaatggca ttaccgcgag
     4261 ccattactcc tacgcgcgca attaacgaat ccaccatcgg ggcagctggt gtcgataacg
     4321 aagtatcttc aaccggttga gtattgagcg tatgttttgg aataacaggc gcacgcttca
     4381 ttatctaatc tcccagcgtg gtttaatcag acgatcgaaa atttcattgc agacaggttc
     4441 ccaaatagaa agagcatttc tccaggcacc agttgaagag cgttgatcaa tggcctgttc
     4501 aaaaacagtt ctcatccgga tctgaccttt accaacttca tccgtttcac gtacaacatt
     4561 ttttagaacc atgcttcccc aggcatcccg aatttgctcc tccatccacg gggactgaga
     4621 gccattacta ttgctgtatt tggtaagcaa aatacgtaca tcaggctcga accctttaag
     4681 atcaacgttc ttgagcagat cacgaagcat atcgaaaaac tgcagtgcgg aggtgtagtc
     4741 aaacaactca gcaggcgtgg gaacaatcag cacatcagca gcacatacga cattaatcgt
     4801 gccgataccc aggttaggcg cgctgtcaat aactatgaca tcatagtcat gagcaacagt
     4861 ttcaatggcc agtcggagca tcaggtgtgg atcggtgggc agtttacctt catcaaattt
     4921 gcccattaac tcagtttcaa tacggtgcag agccagacag gaaggaataa tgtcaagccc
     4981 cggccagcaa gtgggcttta ttgcataagt gacatcgtcc ttttccccaa gatagaaagg
     5041 caggagagtg tcttctgcat gaatatgaag atctggtacc catccgtgat acattgaggc
     5101 tgttccctgg gggtcgttac cttccacgag caaaacacgt agccccttca gagccagatc
     5161 ctgagcaaga tgaacagaaa ctgaggtttt gtaaacgcca cctttatggg cagcaacccc
     5221 gatcaccggt ggaaatacgt cttcagcacg tcgcaatcgc gtaccaaaca catcacgcat
     5281 atgattaatt tgttcaattg tataaccaac acgttgctca acccgtcctc gaatttccat
     5341 atccgggtgc ggtagtcgcc ctgctttctc ggcatctctg atagcctgag aagaaacccc
     5401 aactaaatcc gctgcttcac ctattctcca gcgccgggtt attttcctcg cttccgggct
     5461 gtcatcatta aactgtgcaa tggcgatagc cttcgtcatt tcatgaccag cgtttatgca
     5521 ctggttaagt gtttccatga gtttcattct gaacatcctt taatcattgc tttgcgtttt
     5581 tttattaaat cttgcaattt actgcaaagc aacaacaaaa tcgcaaagtc atcaaaaaac
     5641 cgcaaagttg tttaaaataa gagcaacact acaaaaggag ataagaagag cacatacctc
     5701 agtcacttat tatcactagc gctcgccgca gccgtgtaac cgagcatagc gagcgaactg
     5761 gcgaggaagc aaagaagaac tgttctgtca gatagctctt acgctcagcg caagaagaaa
     5821 tatccaccgt gggaaaaact ccaggtagag gtacacacgc ggatagccaa ttcagagtaa
     5881 taaactgtga taatcaaccc tcatcaatga tgacgaacta acccccgata tcaggtcaca
     5941 tgacgaaggg aaagagaagg aaatcaactg tgacaaactg ccctcaaatt tggcttcctt
     6001 aaaaattaca gttcaaaaag tatgagaaaa tccatgcagg ctgaaggaaa cagcaaaact
     6061 gtgacaaatt accctcagta ggtcagaaca aatgtgacga accaccctca aatctgtgac
     6121 agataaccct cagactatcc tgtcgtcatg gaagtgatat cgcggaagga aaatacgata
     6181 tgagtcgtct ggcggccttt ctttttctca atgtatgaga ggcgcattgg agttctgctg
     6241 ttgatctcat taacacagac ctgcaggaag cggcggcgga agtcaggcat acgctggtaa
     6301 ctttgaggca gctggtaacg ctctatgatc cagtcgattt tcagagagac gatgcctgag
     6361 ccatccggct tacgatactg acacagggat tcgtataaac gcatggcata cggattggtg
     6421 atttcttttg tttcactaag ccgaaactgc gtaaaccggt tctgtaaccc gataaagaag
     6481 ggaatgagat atgggttgat atgtacactg taaagccctc tggatggact gtgcgcacgt
     6541 ttgataaacc aaggaaaaga ttcatagcct ttttcatcgc cggcatcctc ttcagggcga
     6601 taaaaaacca cttccttccc cgcgaaactc ttcaatgcct gccgtatatc cttactggct
     6661 tccgcagagg tcaatccgaa tatttcagca tatttagcaa catggatctc gcagataccg
     6721 tcatgttcct gtagggtgcc atcagatttt ctgatctggt caacgaacag atacagcata
     6781 cgtttttgat cccgggagag actatatgcc gcctcagtga ggtcgtttga ctggacgatt
     6841 cgcgggctat ttttacgttt cttgtgattg ataaccgctg tttccgccat gacagatcca
     6901 tgtgaagtgt gacaagtttt tagattgtca cactaaataa aaaagagtca ataagcaggg
     6961 ataactttgt gaaaaaacag cttcttctga gggcaatttg tcacagggtt aagggcaatt
     7021 tgtcacagac aggactgtca tttgagggtg atttgtcaca ctgaaagggc aatttgtcac
     7081 aacaccttct ctagaaccag catggataaa ggcctacaag gcgctctaaa aaagaagatc
     7141 taaaaactat aaaaaaaata attataaaaa tatccccgtg gataagtgga taaccccaag
     7201 ggaagttttt tcaggcatcg tgtgtaagca gaatatataa gtgctgttcc ctggtgcttc
     7261 ctcgctcact cgaccgggag ggttcgagaa gggggggcac cccccttcgg cgtgcgcggt
     7321 cacgcgcaca gggcgcagcc ctggttaaaa acaaggttta taaatattgg tttaaaagca
     7381 ggttaaaaga caggttagcg gtggccgaaa aacgggcgga aacccttgca aatgctggat
     7441 tttctgcctg tggacagccc ctcaaatgtc aataggtgcg cccctcatct gtcagcactc
     7501 tgcccctcaa gtgtcaagga tcgcgcccct catctgtcag tagtcgcgcc cctcaagtgt
     7561 caataccgca gggcacttat ccccaggctt gtccacatca tctgtgggaa actcgcgtaa
     7621 aatcaggcgt tttcgccgat ttgcgaggct ggccagctcc acgtcgccgg ccgaaatcga
     7681 gcctgcccct catctgtcaa cgccgcgccg ggtgagtcgg cccctcaagt gtcaacgtcc
     7741 gcccctcatc tgtcagtgag ggccaagttt tccgcgaggt atccacaacg ccggcggccg
     7801 gccgcggtgt ctcgcacacg gcttcgacgg cgtttctggc gcgtttgcag ggccatagac
     7861 ggccgccagc ccagcggcga gggcaaccag ccgagggctt cgccctgtcg ctcgactgcg
     7921 gcgagcacta ctggctgtaa aaggacagac cacatcatgg ttctgtgttc attaggttgt
     7981 tctgtccatt gctgacataa tccgctccac ttcaacgtaa caccgcacga agatttctat
     8041 tgttcctgaa ggcatattca aatcgttttc gttaccgctt gcaggcatca tgacagaaca
     8101 ctacttccta taaacgctac acaggctcct gagattaata atgcggatct ctacgataat
     8161 gggagatttt cccgactgtt tcgttcgctt ctcagtggat aacagccagc ttctctgttt
     8221 aacagacaaa aacagcatat ccactcagtt ccacatttcc atataaaggc caaggcattt
     8281 attctcagga taattgtttc agcatcgcaa ccgcatcaga ctccggcatc gcaaactgca
     8341 cccggtgccg ggcagccaca tccagcgcaa aaaccttcgt gtagacttcc gttgaactga
     8401 tggacttatg tcccatcagg ctttgcagaa ctttcagcgg tataccggca tacagcatgt
     8461 gcatcgcata ggaatggcgg aacgtatgtg gtgtgaccgg aacagagaac gtcacaccgt
     8521 cagcagcagc ggcggcaacc gcctccccaa tccaggtcct gaccgttctg tccgtcactt
     8581 cccagatccg cgctttctct gtccttcctg tgcgacggtt acgccgctcc atgagcttat
     8641 cgcgaataaa tacctgtgac ggaagatcac ttcgcagaat aaataaatcc tggtgtccct
     8701 gttgataccg ggaagccctg ggccaacttt tggcgaaaat gagacgttga tcggcacgta
     8761 agaggttcca actttcacca taatgaaata agatcactac cgggcgtatt ttttgagtta
     8821 tcgagatttt caggagctaa ggaagctaaa atggagaaaa aaatcactgg atataccacc
     8881 gttgatatat cccaatggca tcgtaaagaa cattttgagg catttcagtc agttgctcaa
     8941 tgtacctata accagaccgt tcagctggat attacggcct ttttaaagac cgtaaagaaa
     9001 aataagcaca agttttatcc ggcctttatt cacattcttg cccgcctgat gaatgctcat
     9061 ccggaatttc gtatggcaat gaaagacggt gagctggtga tatgggatag tgttcaccct
     9121 tgttacaccg ttttccatga gcaaactgaa acgttttcat cgctctggag tgaataccac
     9181 gacgatttcc ggcagtttct acacatatat tcgcaagatg tggcgtgtta cggtgaaaac
     9241 ctggcctatt tccctaaagg gtttattgag aatatgtttt tcgtctcagc caatccctgg
     9301 gtgagtttca ccagttttga tttaaacgtg gccaatatgg acaacttctt cgcccccgtt
     9361 ttcaccatgg gcaaatatta tacgcaaggc gacaaggtgc tgatgccgct ggcgattcag
     9421 gttcatcatg ccgtttgtga tggcttccat gtcggcagaa tgcttaatga attacaacag
     9481 tactgcgatg agtggcaggg cggggcgtaa gacgtctaag
//
