LOCUS       pPK076_PCymR-U64_Ribo-t 5119 bp ds-DNA     circular     04-FEB-2025
DEFINITION  .
COMMENT     Note: 7/Aug/24 - I removed these 5 bases now (14/Aug/24) //  Kiara
            inserted 5 bp at 332 (CTCGT) that seem inadvertent? This is absent
            in the actual sequencing data -- Kiara said this was a mistake
            Issue with cloning variants from this plasmid August (pAOS107):
            Seen recombination product of ~1200 bp. : tVoigtS4 and S5 (ConL2)
            have 25 bp in common :( Matt Dysart might have a stabler version of
            this. Start cloning from that instead. Lavanya Karinje  Prashant,
            August, Matthew discussion - Oct'2023 EFM calculator : Score = 85.1
            (E. coli) ; 70 (RecA-) Need to change or remove the terminator to
            be different from tVoigtS5 in the insulator? - AOS MSD : changing
            this will make it hard to compare with old data in RAM paper right?
            Summary EFM Aignments
FEATURES             Location/Qualifiers
     CDS             complement(1..666)
                     /label="rep"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    complement(1..1524)
                     /label="pBBR1 rep region"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    1..2662
                     /label="pBBR1-mob origin"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     promoter        complement(742..776)
                     /label="repp"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    complement(748..756)
                     /label=-10
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    complement(771..776)
                     /label=-35
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    complement(853..865)
                     /label="IHF binding site"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    1525..2662
                     /label="pBBR1 mob region"
                     /ApEinfo_revcolor="#d6b295"
                     /ApEinfo_fwdcolor="#d6b295"
     misc_feature    1542..1593
                     /label="oriT region"
                     /ApEinfo_revcolor="#d6b295"
                     /ApEinfo_fwdcolor="#d6b295"
     misc_feature    1552..1557
                     /label=-35
                     /ApEinfo_revcolor="#d6b295"
                     /ApEinfo_fwdcolor="#d6b295"
     promoter        1552..1585
                     /label="mobp"
                     /ApEinfo_revcolor="#d6b295"
                     /ApEinfo_fwdcolor="#d6b295"
     misc_feature    1560..1582
                     /label="recombination site A (RSA)"
                     /ApEinfo_revcolor="#d6b295"
                     /ApEinfo_fwdcolor="#d6b295"
     misc_feature    complement(1574..1574)
                     /label="nicking site"
                     /ApEinfo_revcolor="#d6b295"
                     /ApEinfo_fwdcolor="#d6b295"
     misc_feature    1574..1579
                     /label=-10
                     /ApEinfo_revcolor="#d6b295"
                     /ApEinfo_fwdcolor="#d6b295"
     CDS             1661..2662
                     /label="mob"
                     /ApEinfo_revcolor="#d6b295"
                     /ApEinfo_fwdcolor="#d6b295"
     misc_feature    2624..2653
                     /label="AmpR promoter homology"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     terminator      2667..2705
                     /label="bidir. modified thrLt BBa_B1006 "
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    2667..2816
                     /label="ConL2"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     terminator      2706..2754
                     /label="tVoigtS5, L3S3P22 47C>G"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    2730..2754
                     /label="homology tVoigtS4"
                     /ApEinfo_revcolor="#f58a5e"
                     /ApEinfo_fwdcolor="#f58a5e"
     misc_feature    2755..2769
                     /label="6-frame STOP a"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    complement(2770..2791)
                     /label="BioBrick Prefix BBa_G00000"
                     /ApEinfo_revcolor="#d59687"
                     /ApEinfo_fwdcolor="#d59687"
     misc_feature    2821..2852
                     /label="CymR operator"
                     /ApEinfo_revcolor="#ffef86"
                     /ApEinfo_fwdcolor="#ffef86"
     promoter        2821..2910
                     /label="P.CymRC (Marionette)"
                     /ApEinfo_revcolor="#ffef86"
                     /ApEinfo_fwdcolor="#ffef86"
     misc_feature    2844..2849
                     /label=-35
                     /ApEinfo_revcolor="#ffef86"
                     /ApEinfo_fwdcolor="#ffef86"
     misc_feature    2867..2872
                     /label=-10
                     /ApEinfo_revcolor="#ffef86"
                     /ApEinfo_fwdcolor="#ffef86"
     misc_feature    2879..2879
                     /label="TSS"
                     /ApEinfo_revcolor="#ffef86"
                     /ApEinfo_fwdcolor="#ffef86"
     misc_feature    2879..2910
                     /label="CymR operator"
                     /ApEinfo_revcolor="#ffef86"
                     /ApEinfo_fwdcolor="#ffef86"
     misc_feature    2915..2970
                     /label="U64 RNA Guide"
                     /ApEinfo_revcolor="#faac61"
                     /ApEinfo_fwdcolor="#faac61"
     misc_feature    2915..3875
                     /label="U64 Ribozyme transcript"
                     /ApEinfo_revcolor="#d59687"
                     /ApEinfo_fwdcolor="#d59687"
                     /note="https://rnacentral.org/rna/URS0002349E27/5911"
     misc_feature    2965..2970
                     /label="IGS"
                     /ApEinfo_revcolor="#c7b0e3"
                     /ApEinfo_fwdcolor="#c7b0e3"
     misc_feature    2971..3357
                     /label="Group I Intron Ribozyme (from p-OiRS3GG)"
                     /ApEinfo_revcolor="#b4abac"
                     /ApEinfo_fwdcolor="#b4abac"
     misc_feature    3358..3378
                     /label="Probe binding site"
                     /ApEinfo_revcolor="#ff9ccd"
                     /ApEinfo_fwdcolor="#ff9ccd"
     misc_feature    3358..3875
                     /label="Barcode (sfGFP_2)"
                     /ApEinfo_revcolor="#84b0dc"
                     /ApEinfo_fwdcolor="#84b0dc"
     terminator      3880..3932
                     /label="tVoigtS4 L3S3P21 51C>G"
                     /ApEinfo_revcolor="#f58a5e"
                     /ApEinfo_fwdcolor="#f58a5e"
     misc_feature    3908..3932
                     /label="homology tVoigtS5"
                     /ApEinfo_revcolor="#f58a5e"
                     /ApEinfo_fwdcolor="#f58a5e"
     misc_feature    complement(3937..4097)
                     /label="ConR2"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     misc_feature    complement(3948..3968)
                     /label="BioBrick Suffix BBa_G00001"
                     /ApEinfo_revcolor="#d59687"
                     /ApEinfo_fwdcolor="#d59687"
     misc_feature    3969..3983
                     /label="6-frame STOP b"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     terminator      3984..4044
                     /label="tVoigtS1, L3S2P21"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     terminator      complement(4045..4097)
                     /label="tVoigtS19, L3S1P00"
                     /ApEinfo_revcolor="#c6c9d1"
                     /ApEinfo_fwdcolor="#c6c9d1"
     gene            complement(4102..5056)
                     /label="Kanᴿ.II, kanamycin resistance"
                     /ApEinfo_revcolor="#f6989d"
                     /ApEinfo_fwdcolor="#f6989d"
     CDS             complement(4103..4900)
                     /label="aph(3′)-II / nptII / neo, aminoglycoside 3′-phosphotransferase type II (KanR)"
                     /ApEinfo_revcolor="#f6989d"
                     /ApEinfo_fwdcolor="#f6989d"
     misc_feature    complement(4901..5056)
                     /label="aphIIp, KanR promoter/UTR"
                     /ApEinfo_revcolor="#f6989d"
                     /ApEinfo_fwdcolor="#f6989d"
     misc_feature    complement(5004..5012)
                     /label="aphIIp -10"
                     /ApEinfo_revcolor="#f6989d"
                     /ApEinfo_fwdcolor="#f6989d"
     misc_feature    complement(5027..5032)
                     /label="aphIIp -35"
                     /ApEinfo_revcolor="#f6989d"
                     /ApEinfo_fwdcolor="#f6989d"
     terminator      5061..5115
                     /label="tVoigtN17, tonBt (bidir), BBa_B0054"
                     /ApEinfo_revcolor="#f58a5e"
                     /ApEinfo_fwdcolor="#f58a5e"
ORIGIN
        1 ttactaccgg cgcggcagcg tgacccgtgt cggcggctcc aacggctcgc catcgtccag
       61 aaaacacggc tcatcgggca tcggcaggcg ctgctgcccg cgccgttccc attcctccgt
      121 ttcggtcaag gctggcaggt ctggttccat gcccggaatg ccgggctggc tgggcggctc
      181 ctcgccgggg ccggtcggta gttgctgctc gcccggatac agggtcggga tgcggcgcag
      241 gtcgccatgc cccaacagcg attcgtcctg gtcgtcgtga tcaaccacca cggcggcact
      301 gaacaccgac aggcgcaact ggtcgcgggg ctggccccac gccacgcggt cattgaccac
      361 gtaggccgac acggtgccgg ggccgttgag cttcacgacg gagatccagc gctcggccac
      421 caagtccttg actgcgtatt ggaccgtccg caaagaacgt ccgatgagct tggaaagtgt
      481 tttctggctg accaccacgg cgttctggtg gcccatctgc gccacgaggt gatgcagcag
      541 cattgccgcc gtgggtttcc tcgcaataag cccggcccac gcctcatgcg ctttgcgttc
      601 cgtttgcacc cagtgaccgg gcttgttctt ggcttgaatg ccgatttctc tggactgcgt
      661 ggccatgctt atctccatgc ggtaggggtg ccgcacggtt gcggcaccat gcgcaatcag
      721 ctgcaacttt tcggcagcgc gacaacaatt atgcgttgcg taaaagtggc agtcaattac
      781 agattttctt taacctacgc aatgagctat tgcggggggt gccgcaatga gctgttgcgt
      841 accccccttt tttaagttgt tgatttttaa gtctttcgca tttcgcccta tatctagttc
      901 tttggtgccc aaagaagggc acccctgcgg ggttccccca cgccttcggc gcggctcccc
      961 ctccggcaaa aagtggcccc tccggggctt gttgatcgac tgcgcggcct tcggccttgc
     1021 ccaaggtggc gctgccccct tggaaccccc gcactcgccg ccgtgaggct cggggggcag
     1081 gcgggcgggc ttcgccttcg actgccccca ctcgcatagg cttgggtcgt tccaggcgcg
     1141 tcaaggccaa gccgctgcgc ggtcgctgcg cgagccttga cccgccttcc acttggtgtc
     1201 caaccggcaa gcgaagcgcg caggccgcag gccggaggct tttccccaga gaaaattaaa
     1261 aaaattgatg gggcaaggcc gcaggccgcg cagttggagc cggtgggtat gtggtcgaag
     1321 gctgggtagc cggtgggcaa tccctgtggt caagctcgtg ggcaggcgca gcctgtccat
     1381 cagcttgtcc agcagggttg tccacgggcc gagcgaagcg agccagccgg tggccgctcg
     1441 cggccatcgt ccacatatcc acgggctggc aagggagcgc agcgaccgcg cagggcgaag
     1501 cccggagagc aagcccgtag ggcgccgcag ccgccgtagg cggtcacgac tttgcgaagc
     1561 aaagtctagt gagtatactc aagcattgag tggcccgccg gaggcaccgc cttgcgctgc
     1621 ccccgtcgag ccggttggac accaaaaggg aggggcaggc atggcggcat acgcgatcat
     1681 gcgatgcaag aagctggcga aaatgggcaa cgtggcggcc agtctcaagc acgcctaccg
     1741 cgagcgcgag actcccaacg ctgacgccag caggacgcca gagaacgagc actgggcggc
     1801 cagcagcacc gatgaagcga tgggccgact gcgcgagttg ctgccagaga agcggcgcaa
     1861 ggacgctgtg ttggcggtcg agtacgtcat gacggccagc ccggaatggt ggaagtcggc
     1921 cagccaagaa cagcaggcgg cgttcttcga gaaggcgcac aagtggctgg cggacaagta
     1981 cggggcggat cgcatcgtga cggccagcat ccaccgtgac gaaaccagcc cgcacatgac
     2041 cgcgttcgtg gtgccgctga cgcaggacgg caggctgtcg gccaaggagt tcatcggcaa
     2101 caaagcgcag atgacccgcg accagaccac gtttgcggcA gctgtggccg atctagggct
     2161 gcaacggggc atcgagggca gcaaggcacg tcacacgcgc attcaggcgt tctacgaggc
     2221 cctggagcgg ccaccagtgg gccacgtcac catcagcccg caagcggtcg agccacgcgc
     2281 ctatgcaccg cagggattgg ccgaaaagct gggaatctca aagcgcgttg aAacgccgga
     2341 agccgtggcc gaccggctga caaaagcggt tcggcagggg tatgagcctg ccctacaggc
     2401 cgccgcagga gcgcgtgaga tgcgcaagaa ggccgatcaa gcccaagaga cagcccgaga
     2461 Tcttcgggag cgcctgaagc ccgttctgga cgccctgggg ccgttgaatc gggatatgca
     2521 ggccaaggcc gccgcgatca tcaaggccgt gggcgaaaag ctgctgacgg aacagcggga
     2581 agtccagcgc cagaaacagg cccagcgcca gcaggaacgc gggcgcgcac atttccccga
     2641 aaagtgccac ctgggctgat aaACGGaaaa aaaaaccccg cccctgacag ggcggggttt
     2701 tttttccaat tattgaaggc cgctaacgcg gccttttttt gtttctggtc tgccttaatc
     2761 aatgactaag aattcgcggc cgcttctaga gCGTCTCaCG TTgctagccc tgcaggCTTC
     2821 aacaaacaga caatctggtc tgtttgtatt atggaaaatt tttctgtata atagattcaa
     2881 caaacagaca atctggtctg tttgtattat cgacCAACCC ACTCCCATGG TGTGACGGGC
     2941 GGTGTGTACA AGGCCCGGGA ACGTgTTCAC AAAAGTTATC AGGCATGCAC CTGGTAGCTA
     3001 GTCTTTAAAC CAATAGATTG CATCGGTTTA AAAGGCAAGA CCGTCAAATT GCGGGAAAGG
     3061 GGTCAACAGC CGTTCAGTAC CAAGTCTCAG GGGAAACTTT GAGATGGCCT TGCAAAGGGT
     3121 ATGGTAATAA GCTGACGGAC ATGGTCCTAA CCACGCAGCC AAGTCCTAAG TCAACAGATC
     3181 TTCTGTTGAT ATGGATGCAG TTCACAGACT AAATGTCGGT CGGGGAAGAT GTATTCTTCT
     3241 CATAAGATAT AGTCGGACCT CTCCTTAATG GGAGCTAGCG GATGAAGTGA TGCAACACTG
     3301 GAGCCGCTGG GAACTAATTT GTATGCGAAA GTATATTGAT TAGTTTTGGA GTACTCGATG
     3361 GTGTTCAATG CTTTTCCCGT TATCCGGATC ACATGAAACG GCATGACTTT TTCAAGAGTG
     3421 CCATGCCCGA AGGTTATGTA CAGGAACGCA CTATATCTTT CAAAGATGAC GGGACCTACA
     3481 AGACGCGTGC TGAAGTCAAG TTTGAAGGTG ATACCCTTGT TAATCGTATC GAGTTAAAGG
     3541 GTATTGATTT TAAAGAAGAT GGAAACATTC TTGGACACAA ACTCGAGTAC AACTTTAACT
     3601 CACACAATGT ATACATCACG GCAGACAAAC AAAAGAATGG AATCAAAGCT AACTTCAAAA
     3661 TTCGCCACAA CGTTGAAGAT GGTTCCGTTC AACTAGCAGA CCATTATCAA CAAAATACTC
     3721 CAATTGGCGA TGGCCCTGTC CTTTTACCAG ACAACCATTA CCTGTCGACA CAATCTGTCC
     3781 TTTCGAAAGA TCCCAACGAA AAGCGTGACC ACATGGTCCT TCTTGAGTTT GTAACTGCTG
     3841 CTGGGATTAC ACATGGCATG GATGAGCTCT ACAAATGGCc caattattga aggcctccct
     3901 aacggggggc ctttttttgt ttctggtctG ccGCTGCGTT tGAGACGtac tagtagcggc
     3961 cgctgcagtt aatcactgat taactcggta ccaaattcca gaaaagaggc ctcccgaaag
     4021 gggggccttt tttcgttttg gtccttttgt tatcaataaa aaaggggagc ggtttcccgc
     4081 tccccttatt gttcgtcTAC Aattattaga agaactcgtc aagaaggcga tagaaggcga
     4141 tgcgctgcga atcgggagcg gcgataccgt aaagcacgag gaagcggtca gcccattcgc
     4201 cgccaagctc ttcagcaata tcacgggtag ccaacgctat gtcctgatag cggtccgcca
     4261 cacccagccg gccacagtcg atgaatccag aaaagcggcc attttccacc atgatattcg
     4321 gcaagcaggc atcgccatgg gtcacgacga gatcctcgcc gtcgggcatg cgcgccttga
     4381 gcctggcgaa cagttcggct ggcgcgagcc cctgatgctc ttcgtccaga tcatcctgat
     4441 cgacaagacc ggcttccatc cgagtacgtg ctcgctcgat gcgatgtttc gcttggtggt
     4501 cgaatgggca ggtagccgga tcaagcgtat gcagccgccg cattgcatca gccatgatgg
     4561 atactttctc ggcaggagca aggtgagatg acaggagatc ctgccccggc acttcgccca
     4621 atagcagcca gtcccttccc gcttcagtga caacgtcgag cacagctgcg caaggaacgc
     4681 ccgtcgtggc cagccacgat agccgcgctg cctcgtcctg cagttcattc agggcaccgg
     4741 acaggtcggt cttgacaaaa agaaccgggc gcccctgcgc tgacagccgg aacacggcgg
     4801 catcagagca gccgattgtc tgttgtgccc agtcatagcc gaatagcctc tccacccaag
     4861 cggccggaga acctgcgtgc aatccatctt gttcaatcat gcgaaacgat cctcatcctg
     4921 tctcttgatc agatcttgat cccctgcgcc atcagatcct tggcggcaag aaagccatcc
     4981 agtttacttt gcagggcttc ccaaccttac cagagggcgc cccagctggc aattccggtt
     5041 cgcttgctgt ccataaGAGT cctgttgagt aatagtcaaa agcctccggt cggaggcttt
     5101 tgactttctg cttacCCAA
//