LOCUS       sequence-148839-        9038 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Output plasmid: contains 5-state register that regulates expression 
            of GFP..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 9038)
  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 9038)
  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: pNR165
FEATURES             Location/Qualifiers
     source          1..9038
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(415..435)
                     /label=GFP-F
                     /note="GFP, forward primer. Does NOT anneal to EGFP"
     primer_bind     1030..1058
                     /label=GFP-R
                     /note="GFP, reverse primer. Does NOT anneal to EGFP"
     RBS             1094..1102
                     /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_RNA        complement(1145..1194)
                     /label=sTRSV HHRz
                     /note="hammerhead ribozyme from the tobacco ringspot virus 
                     satellite RNA (Khvorova et al., 2003)"
     protein_bind    1502..1550
                     /label=Bxb1 attB
                     /bound_moiety="Mycobacteriophage Bxb1 integrase"
                     /note="attB site for the Mycopbacteriophage Bxb1 integrase 
                     (Xu et al., 2013)"
     protein_bind    1848..1905
                     /label=Bxb1 attP
                     /bound_moiety="Mycobacteriophage Bxb1 integrase"
                     /note="attP site for the Mycopbacteriophage Bxb1 integrase 
                     (Xu et al., 2013)"
     misc_feature    2382..2855
                     /gene="sopC"
                     /label=sopC
                     /note="centromere-like partitioning region of the bacterial
                     F plasmid"
     CDS             complement(2928..3899)
                     /codon_start=1
                     /gene="sopB"
                     /product="partitioning protein for the bacterial F plasmid"
                     /label=sopB
                     /translation="MKRAPVIPKHTLNTQPVEDTSLSTPAAPMVDSLIARVGVMARGNA
                     ITLPVCGRDVKFTLEVLRGDSVEKTSRVWSGNERDQELLTEDALDDLIPSFLLTGQQTP
                     AFGRRVSGVIEIADGSRRRKAAALTESDYRVLVGELDDEQMAALSRLGNDYRPTSAYER
                     GQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGD
                     ALQKAFTDKEELLKQQASNLHEQKKAGVIFEAEEVITLLTSVLKTSSASRTSLSSRHQF
                     APGATVLYKGDKMVLNLDRSRVPTECIEKIEAILKELEKPAP"
     CDS             complement(3899..5074)
                     /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    5400..5650
                     /gene="incC"
                     /label=incC
                     /note="incompatibility region of the bacterial F plasmid"
     CDS             complement(5653..6408)
                     /codon_start=1
                     /gene="repE"
                     /product="replication initiation protein for the bacterial 
                     F plasmid"
                     /label=repE
                     /translation="MAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQ
                     IRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAG
                     DEKGYESFPWFIKRAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAM
                     RLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPM
                     RLSYIEKKKGRQTTHIVFSFRDITSMTTG"
     rep_origin      6499..6718
                     /label=ori2
                     /note="secondary origin of replication for the bacterial F 
                     plasmid; also known as oriS"
     rep_origin      6786..7317
                     /label=oriV
                     /note="incP origin of replication"
     rep_origin      6794..7408
                     /label=oriV
                     /note="origin of replication for the bacterial F plasmid"
     promoter        8266..8368
                     /label=cat promoter
                     /note="promoter of the E. coli cat gene encoding 
                     chloramphenicol acetyltransferase"
     CDS             8369..9028
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     complement(8435..8454)
                     /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 cgtcccttcc
      301 ccttgataaa gcaccctttg gtcgaaaaaa aaagcccgca ctgtcaggtg cgggcttttt
      361 tctgtgtttc cttatttgta gagatcatcc atgccatgtg taatcccagc agctgttaca
      421 aactcaagaa ggaccatgtg gtctctcttt tcgttgggat ctttcgaaag ggcagattgt
      481 gtggacaggt aatggttgtc tggtaaaagg acagggccat cgccaattgg agtattttgt
      541 tgataatggt ctgctagttg aacgcttcca tcttcaatgt tgtgtctaat tttgaagtta
      601 actttgattc cattcttttg tttgtctgcc atgatgtata cattgtgtga gttatagttg
      661 tattccaatt tgtgtccaag aatgtttcca tcttctttaa aatcaatacc ttttaactcg
      721 attctattaa caagggtatc accttcaaac ttgacttcag cacgtgtctt gtagttcccg
      781 tcatctttga aaaatatagt tctttcctgt acataacctt cgggcatggc actcttgaaa
      841 aagtcatgct gtttcatatg atctgggtat ctcgcaaagc attgaacacc ataaccgaaa
      901 gtagtgacaa gtgttggcca tggaacaggt agttttccag tagtgcaaat aaatttaagg
      961 gtaagttttc cgtatgttgc atcaccttca ccctctccac tgacagaaaa tttgtgccca
     1021 ttaacatcac catctaattc aacaagaatt gggacaactc cagtgaaaag ttcttctcct
     1081 ttactcatta gtgacctcct taatataggt cggcttcgac cttaaacaaa attatttgta
     1141 gaggctgttt cgtcctcacg gactcatcag accggaaagc acatccggtg acagctgtgc
     1201 catccctcgt cctcacgagt gcggtattcc tctgggcatg ccaacacaat taacatctca
     1261 atcaaggtaa atgctttttg ctttttttgc cgtggtgcgg atctagctac ctcggcgtta
     1321 atccttgttc actatatgca accattatca ccgccagagg taaaatagtc aaacgcacgg
     1381 tgttagccgc acttgagtcc acggctgatg ccaacacaat taacatcaga atcaaggtaa
     1441 atgctttttg ctttttttgc gggctcacta gggaatggcg tcgtccgtga cattctgtgc
     1501 gcggccggct tgtcgacgac ggcggtctcc gtcgtcagga tcatccgggc cagcggctgt
     1561 ctatgccaga agtcggtcag gtcggagtcc tagaaaggag ttttttagtt accttaattc
     1621 taataaacga aataaaaact cgccgttcgc gcgacatgac atgcgccgcc gattgattca
     1681 gaaagttaaa caaaattatt tgtagaggga aaccgttgtg gtctccctga atatattata
     1741 cgagccttat gcatgcccgt aaagttatcc agcaaccact catagaccta gggcagcaga
     1801 tagggacgac gtggtgttag ctgtgccgac acaatctccc tgctcaggtc gtggtttgtc
     1861 tggtcaacca ccgcggtctc agtggtgtac ggtacaaacc ccgacgcaat agcgccaacc
     1921 atgcaccata gccagcctga cagtagccaa aggagttttt tagttacctt aattgaaata
     1981 aacgaaataa aaactcgcgc agctgagagc gacacagttg cctcactcct agggtgtaat
     2041 aggcactaaa agagtgatat ggcacgcgca tgtggaacgc cgttagaggg ttgctgagcc
     2101 atcgtggtcc ttagactcgg gaaaaacaaa aacccgccga agcgggttaa gtgcggggcg
     2161 gctagcccgc cacctaagtt atgagtcagg aaaaaaggcg acagagtaat ctgtcgcctt
     2221 ttttctttgc ttgctttgta atcactcgat gaccaaaagt aaaaacccgc cgaagcgggt
     2281 ttttacgtaa aacaggtgaa actgacgcta gccggtcaca tgtcaatact tgcccttgac
     2341 aggcattgat ggaatcgtag tctcacgctg atagtctgat cgacaataca agtgggaccg
     2401 tggtcccaga ccgataatca gaccgacaac acgagtggga tcgtggtccc agactaataa
     2461 tcagaccgac gatacgagtg ggaccgtggt cccagactaa taatcagacc gacgatacga
     2521 gtgggaccgt ggttccagac taataatcag accgacgata cgagtgggac cgtggtccca
     2581 gactaataat cagaccgacg atacgagtgg gaccatggtc ccagactaat aatcagaccg
     2641 acgatacgag tgggaccgtg gtcccagtct gattatcaga ccgacgatac gagtgggacc
     2701 gtggtcccag actaataatc agaccgacga tacgagtggg accgtggtcc cagactaata
     2761 atcagaccga cgatacgagt gggaccgtgg tcccagtctg attatcagac cgacgataca
     2821 agtggaacag tgggcccaga gagaatattc aggccagtta tgctttctgg cctgtaacaa
     2881 aggacattaa gtaaagacag ataaacgtag actaaaacgt ggtcgcatca gggtgctggc
     2941 ttttcaagtt ccttaagaat ggcctcaatt ttctctatac actcagttgg aacacgggac
     3001 ctgtccaggt taagcaccat tttatcgccc ttatacaata ctgtcgctcc aggagcaaac
     3061 tgatgtcgtg agcttaaact agttcttgat gcagatgacg ttttaagcac agaagttaaa
     3121 agagtgataa cttcttcagc ttcaaatatc accccagctt ttttctgctc atgaaggtta
     3181 gatgcctgct gcttaagtaa ttcctcttta tctgtaaagg ctttttgaag tgcatcacct
     3241 gaccgggcag atagttcacc ggggtgagaa aaaagagcaa caactgattt aggcaatttg
     3301 gcggtgttga tacagcgggt aataatctta cgtgaaatat tttccgcatc agccagcgca
     3361 gaaatatttc cagcaaattc attctgcaat cggcttgcat aacgctgacc acgttcataa
     3421 gcacttgttg ggcgataatc gttacccaat ctggataatg cagccatctg ctcatcatcc
     3481 agctcgccaa ccagaacacg ataatcactt tcggtaagtg cagcagcttt acgacggcga
     3541 ctcccatcgg caatttctat gacaccagat actcttcgac cgaacgccgg tgtctgttga
     3601 ccagtcagta gaaaagaagg gatgagatca tccagtgcgt cctcagtaag cagctcctgg
     3661 tcacgttcat tacctgacca tacccgagag gtcttctcaa cactatcacc ccggagcact
     3721 tcaagagtaa acttcacatc ccgaccacat acaggcaaag taatggcatt accgcgagcc
     3781 attactccta cgcgcgcaat taacgaatcc accatcgggg cagctggtgt cgataacgaa
     3841 gtatcttcaa ccggttgagt attgagcgta tgttttggaa taacaggcgc acgcttcatt
     3901 atctaatctc ccagcgtggt ttaatcagac gatcgaaaat ttcattgcag acaggttccc
     3961 aaatagaaag agcatttctc caggcaccag ttgaagagcg ttgatcaatg gcctgttcaa
     4021 aaacagttct catccggatc tgacctttac caacttcatc cgtttcacgt acaacatttt
     4081 ttagaaccat gcttccccag gcatcccgaa tttgctcctc catccacggg gactgagagc
     4141 cattactatt gctgtatttg gtaagcaaaa tacgtacatc aggctcgaac cctttaagat
     4201 caacgttctt gagcagatca cgaagcatat cgaaaaactg cagtgcggag gtgtagtcaa
     4261 acaactcagc aggcgtggga acaatcagca catcagcagc acatacgaca ttaatcgtgc
     4321 cgatacccag gttaggcgcg ctgtcaataa ctatgacatc atagtcatga gcaacagttt
     4381 caatggccag tcggagcatc aggtgtggat cggtgggcag tttaccttca tcaaatttgc
     4441 ccattaactc agtttcaata cggtgcagag ccagacagga aggaataatg tcaagccccg
     4501 gccagcaagt gggctttatt gcataagtga catcgtcctt ttccccaaga tagaaaggca
     4561 ggagagtgtc ttctgcatga atatgaagat ctggtaccca tccgtgatac attgaggctg
     4621 ttccctgggg gtcgttacct tccacgagca aaacacgtag ccccttcaga gccagatcct
     4681 gagcaagatg aacagaaact gaggttttgt aaacgccacc tttatgggca gcaaccccga
     4741 tcaccggtgg aaatacgtct tcagcacgtc gcaatcgcgt accaaacaca tcacgcatat
     4801 gattaatttg ttcaattgta taaccaacac gttgctcaac ccgtcctcga atttccatat
     4861 ccgggtgcgg tagtcgccct gctttctcgg catctctgat agcctgagaa gaaaccccaa
     4921 ctaaatccgc tgcttcacct attctccagc gccgggttat tttcctcgct tccgggctgt
     4981 catcattaaa ctgtgcaatg gcgatagcct tcgtcatttc atgaccagcg tttatgcact
     5041 ggttaagtgt ttccatgagt ttcattctga acatccttta atcattgctt tgcgtttttt
     5101 tattaaatct tgcaatttac tgcaaagcaa caacaaaatc gcaaagtcat caaaaaaccg
     5161 caaagttgtt taaaataaga gcaacactac aaaaggagat aagaagagca catacctcag
     5221 tcacttatta tcactagcgc tcgccgcagc cgtgtaaccg agcatagcga gcgaactggc
     5281 gaggaagcaa agaagaactg ttctgtcaga tagctcttac gctcagcgca agaagaaata
     5341 tccaccgtgg gaaaaactcc aggtagaggt acacacgcgg atagccaatt cagagtaata
     5401 aactgtgata atcaaccctc atcaatgatg acgaactaac ccccgatatc aggtcacatg
     5461 acgaagggaa agagaaggaa atcaactgtg acaaactgcc ctcaaatttg gcttccttaa
     5521 aaattacagt tcaaaaagta tgagaaaatc catgcaggct gaaggaaaca gcaaaactgt
     5581 gacaaattac cctcagtagg tcagaacaaa tgtgacgaac caccctcaaa tctgtgacag
     5641 ataaccctca gactatcctg tcgtcatgga agtgatatcg cggaaggaaa atacgatatg
     5701 agtcgtctgg cggcctttct ttttctcaat gtatgagagg cgcattggag ttctgctgtt
     5761 gatctcatta acacagacct gcaggaagcg gcggcggaag tcaggcatac gctggtaact
     5821 ttgaggcagc tggtaacgct ctatgatcca gtcgattttc agagagacga tgcctgagcc
     5881 atccggctta cgatactgac acagggattc gtataaacgc atggcatacg gattggtgat
     5941 ttcttttgtt tcactaagcc gaaactgcgt aaaccggttc tgtaacccga taaagaaggg
     6001 aatgagatat gggttgatat gtacactgta aagccctctg gatggactgt gcgcacgttt
     6061 gataaaccaa ggaaaagatt catagccttt ttcatcgccg gcatcctctt cagggcgata
     6121 aaaaaccact tccttccccg cgaaactctt caatgcctgc cgtatatcct tactggcttc
     6181 cgcagaggtc aatccgaata tttcagcata tttagcaaca tggatctcgc agataccgtc
     6241 atgttcctgt agggtgccat cagattttct gatctggtca acgaacagat acagcatacg
     6301 tttttgatcc cgggagagac tatatgccgc ctcagtgagg tcgtttgact ggacgattcg
     6361 cgggctattt ttacgtttct tgtgattgat aaccgctgtt tccgccatga cagatccatg
     6421 tgaagtgtga caagttttta gattgtcaca ctaaataaaa aagagtcaat aagcagggat
     6481 aactttgtga aaaaacagct tcttctgagg gcaatttgtc acagggttaa gggcaatttg
     6541 tcacagacag gactgtcatt tgagggtgat ttgtcacact gaaagggcaa tttgtcacaa
     6601 caccttctct agaaccagca tggataaagg cctacaaggc gctctaaaaa agaagatcta
     6661 aaaactataa aaaaaataat tataaaaata tccccgtgga taagtggata accccaaggg
     6721 aagttttttc aggcatcgtg tgtaagcaga atatataagt gctgttccct ggtgcttcct
     6781 cgctcactcg accgggaggg ttcgagaagg gggggcaccc cccttcggcg tgcgcggtca
     6841 cgcgcacagg gcgcagccct ggttaaaaac aaggtttata aatattggtt taaaagcagg
     6901 ttaaaagaca ggttagcggt ggccgaaaaa cgggcggaaa cccttgcaaa tgctggattt
     6961 tctgcctgtg gacagcccct caaatgtcaa taggtgcgcc cctcatctgt cagcactctg
     7021 cccctcaagt gtcaaggatc gcgcccctca tctgtcagta gtcgcgcccc tcaagtgtca
     7081 ataccgcagg gcacttatcc ccaggcttgt ccacatcatc tgtgggaaac tcgcgtaaaa
     7141 tcaggcgttt tcgccgattt gcgaggctgg ccagctccac gtcgccggcc gaaatcgagc
     7201 ctgcccctca tctgtcaacg ccgcgccggg tgagtcggcc cctcaagtgt caacgtccgc
     7261 ccctcatctg tcagtgaggg ccaagttttc cgcgaggtat ccacaacgcc ggcggccggc
     7321 cgcggtgtct cgcacacggc ttcgacggcg tttctggcgc gtttgcaggg ccatagacgg
     7381 ccgccagccc agcggcgagg gcaaccagcc gagggcttcg ccctgtcgct cgactgcggc
     7441 gagcactact ggctgtaaaa ggacagacca catcatggtt ctgtgttcat taggttgttc
     7501 tgtccattgc tgacataatc cgctccactt caacgtaaca ccgcacgaag atttctattg
     7561 ttcctgaagg catattcaaa tcgttttcgt taccgcttgc aggcatcatg acagaacact
     7621 acttcctata aacgctacac aggctcctga gattaataat gcggatctct acgataatgg
     7681 gagattttcc cgactgtttc gttcgcttct cagtggataa cagccagctt ctctgtttaa
     7741 cagacaaaaa cagcatatcc actcagttcc acatttccat ataaaggcca aggcatttat
     7801 tctcaggata attgtttcag catcgcaacc gcatcagact ccggcatcgc aaactgcacc
     7861 cggtgccggg cagccacatc cagcgcaaaa accttcgtgt agacttccgt tgaactgatg
     7921 gacttatgtc ccatcaggct ttgcagaact ttcagcggta taccggcata cagcatgtgc
     7981 atcgcatagg aatggcggaa cgtatgtggt gtgaccggaa cagagaacgt cacaccgtca
     8041 gcagcagcgg cggcaaccgc ctccccaatc caggtcctga ccgttctgtc cgtcacttcc
     8101 cagatccgcg ctttctctgt ccttcctgtg cgacggttac gccgctccat gagcttatcg
     8161 cgaataaata cctgtgacgg aagatcactt cgcagaataa ataaatcctg gtgtccctgt
     8221 tgataccggg aagccctggg ccaacttttg gcgaaaatga gacgttgatc ggcacgtaag
     8281 aggttccaac tttcaccata atgaaataag atcactaccg ggcgtatttt ttgagttatc
     8341 gagattttca ggagctaagg aagctaaaat ggagaaaaaa atcactggat ataccaccgt
     8401 tgatatatcc caatggcatc gtaaagaaca ttttgaggca tttcagtcag ttgctcaatg
     8461 tacctataac cagaccgttc agctggatat tacggccttt ttaaagaccg taaagaaaaa
     8521 taagcacaag ttttatccgg cctttattca cattcttgcc cgcctgatga atgctcatcc
     8581 ggaatttcgt atggcaatga aagacggtga gctggtgata tgggatagtg ttcacccttg
     8641 ttacaccgtt ttccatgagc aaactgaaac gttttcatcg ctctggagtg aataccacga
     8701 cgatttccgg cagtttctac acatatattc gcaagatgtg gcgtgttacg gtgaaaacct
     8761 ggcctatttc cctaaagggt ttattgagaa tatgtttttc gtctcagcca atccctgggt
     8821 gagtttcacc agttttgatt taaacgtggc caatatggac aacttcttcg cccccgtttt
     8881 caccatgggc aaatattata cgcaaggcga caaggtgctg atgccgctgg cgattcaggt
     8941 tcatcatgcc gtttgtgatg gcttccatgt cggcagaatg cttaatgaat tacaacagta
     9001 ctgcgatgag tggcagggcg gggcgtaaga cgtctaag
//
