BBa_K093002 1 PmeIR PmeI endonuclease 2008-10-25T11:00:00Z 2015-05-08T01:08:40Z Synthetic from GENEART This is the PmeI ORF, coding for the PmeI restriction endonuclease gene with the recognition sequence: GTTTAAAC false false _247_ 0 3630 9 It's complicated false The stop codon was changed to TAA. false John Heil BBa_K093008 1 BBa_K093008 reverse BBa_R0011 2008-10-27T12:00:00Z 2015-05-08T01:08:40Z synthetic reverse compliments of BBa_R0011 false false _247_ 0 3630 9 Not in stock false for downstream application false John Heil annotation1992540 1 -10 range1992540 1 8 14 annotation1992542 1 lacO1 range1992542 1 36 52 annotation1992541 1 -35 range1992541 1 30 35 annotation1992543 1 lacO1 range1992543 1 15 29 BBa_C0051 1 cI lam cI repressor from E. coli phage lambda (+LVA) 2003-01-31T12:00:00Z 2015-08-31T04:07:23Z Elowitz, M. B. Transport, Assembly, and Dynamics in Systems of Interacting Proteins. Thesis, Princeton Univ., Princeton (1999). Released HQ 2013 Coding region for the cI repressor based on cI repressor from bacteriophage lambda modified with an LVA tail for rapid degradation of the protein. cI repressor binds to the cI regulator (BBa_R0051).</P> false false _1_ 0 24 7 In stock false References (unparsed) here: <p><a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/abs/403335a0_fs.html&dynoptions=doi1043774228">A synthetic oscillatory network of transcriptional regulators</a> , Elowitz M.B. , Leibler S., Nature(403),335-38: 2000</P> <P><a href="http://www.genesdev.org/cgi/content/full/15/22/3013">Octamerization of CI repressor is needed for effective repression of PRM and efficient switching from lysogeny. </a>Ian B. Dodd,1 Alison J. Perkins, Daniel Tsemitsidis, and J. Barry Egan , Genes and Development (Vol 15, No. 22) 3013-3022: 2001</P> <p></p> <P> References (unparsed) here: <p><a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/abs/403335a0_fs.html&dynoptions=doi1043774228">A synthetic oscillatory network of transcriptional regulators</a> , Elowitz M.B. , Leibler S., Nature(403),335-38: 2000</P> <P><a href="http://www.genesdev.org/cgi/content/full/15/22/3013">Octamerization of CI repressor is needed for effective repression of PRM and efficient switching from lysogeny. </a>Ian B. Dodd,1 Alison J. Perkins, Daniel Tsemitsidis, and J. Barry Egan , Genes and Development (Vol 15, No. 22) 3013-3022: 2001</P> <p></p> <P>BBa_C0051 cI repressor is based on the cI repressor from the Elowitz's repressilator. It has been modified to include a rapid degradation LAA tail, and includes the BioBrick standard assembly head and tail restriction sites. The RBS has been removed. The stop codon has been changed from TAA to a double stop codon TAATAA.<P> true Vinay S Mahajan, Brian Chow, Peter Carr, Voichita Marinescu and Alexander D. Wissner-Gross annotation23334 1 cI lambda range23334 1 4 711 annotation23335 1 LVA range23335 1 712 744 annotation2213991 1 Help:Barcodes range2213991 1 751 775 BBa_K241000 1 BBa_K241000 Nuclease construct, no sense promoter. 2009-10-19T11:00:00Z 2015-05-08T01:11:37Z Synthetic, Phage T7, Phage Lambda, Pseudomonas mendocina. To tightly repress the nuclease genes (T7 gene 6, PmeI) an antisense promoter and the cI repressor are used. The promoter for expression of the integrase plasmid (the sense promoter) is not on this part. However, the design calls for the Lambda Pr promoter. The part is designed to selectively degrade DNA in vivo. false false _334_ 0 3630 9 It's complicated false The main design consideration was to have maximal repression of the toxic nuclease genes. false John Heil component2297596 1 BBa_K093004 component2297608 1 BBa_K093006 component2297584 1 BBa_K093013 component2297597 1 BBa_R0011 component2297580 1 BBa_K093001 component2297579 1 BBa_B0034 component2297615 1 BBa_B0015 annotation2297584 1 BBa_K093013 range2297584 1 930 1640 annotation2297580 1 BBa_K093001 range2297580 1 19 921 annotation2297579 1 BBa_B0034 range2297579 1 1 12 annotation2297608 1 BBa_K093006 range2297608 1 1912 2704 annotation2297615 1 BBa_B0015 range2297615 1 2713 2841 annotation2297596 1 BBa_K093004 range2297596 1 1649 1840 annotation2297597 1 BBa_R0011 range2297597 1 1849 1902 BBa_R0011 1 lacI+pL Promoter (lacI regulated, lambda pL hybrid) 2003-01-31T12:00:00Z 2015-05-08T01:14:14Z represillator of Elowitz and Leibler (2000) Released HQ 2013 Inverting regulatory region controlled by LacI (<bb_part>BBa_C0010</bb_part>, <bb_part>BBa_C0011</bb_part>, etc.) <p> The PLlac 0-1 promoter is a hybrid regulatory region consisting of the promoter P(L) of phage lambda with the cI binding sites replaced with lacO1. The hybrid design allows for strong promotion that can nevertheless be tightly repressed by LacI, the Lac inhibitor (i.e. repressor) (<bb_part>BBa_C0010</bb_part>) ([LUTZ97]). The activity of the promoter can be regulated over a >600-fold range by IPTG in E.Coli DH5-alpha-Z1 (same paper reference). false true _1_ 0 24 7 In stock false <P> <P>hybrid promoter design to create strong promoter that is, at the same time, highly repressible. note that the upstream operator installed in this hybrid is slightly different than the one in the original source (Lutz and Bujard, 1997). the most upstream operator region is slightly truncated in the represillator version, so that both operators in the hybrid are the same sequence. see references for details. also, the sequence has been truncated after the transcriptional start site.<P>LacI binds to this regulator. This part is incompatible with species containing active LacI coding regions. Lactose and IPTG disable the operation of LacI and increase transcription. This part is incompatible with environments containing lactose or lactose analogs. true Neelaksh Varshney, Grace Kenney, Daniel Shen, Samantha Sutton annotation2000 1 -35 range2000 1 20 25 annotation2001 1 lac O1 range2001 1 26 42 annotation7064 1 BBa_R0011 range7064 1 1 54 annotation2002 1 -10 range2002 1 43 48 annotation1999 1 lac O1 range1999 1 3 19 BBa_B0034 1 BBa_B0034 RBS (Elowitz 1999) -- defines RBS efficiency 2003-01-31T12:00:00Z 2015-08-31T04:07:20Z Released HQ 2013 RBS based on Elowitz repressilator. false true _1_ 0 24 7 In stock false Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix. <p>No secondary structures are formed in the given RBS region. Users should check for secondary structures induced in the RBS by upstream and downstream elements in the +50 to -50 region, as such structures will greatly affect the strength of the RBS. Contact info for this part: <a href="mailto:(bchow@media.mit.edu)">Brian Chow</a> true Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003. annotation23325 1 conserved range23325 1 5 8 BBa_K093004 1 rPlac+TT Convergent Promoter System: Reverse Module: rPlac+TT 2008-10-27T12:00:00Z 2015-05-08T01:08:40Z Synthetic This part contains a reverse BBa_R0011 followed by a forward TT, BBa_B0015. false false _247_ 0 3630 9 It's complicated false The forward and reverse efficiencies of TTs in the registry had to be considered, especially for this part's convergent partner, BBa_K093003. R0011 was used instead of R0010 to avoid catabolite repression. The idea is to place BBa_K093003 upstream of the gene of interest, that requires tight repression, and to place BBa_K093004 downstream. If the cells are grown in the presence of IPTG POlacI is induced and anti-sense mRNA is produced. Anti-sense mRNA will repress expression of the gene of interest through RNAi. This system also requires cI repressor (BBa_C0051) under control of POlacI (BBa_R0011). This system would be functional in a laqIq strain such as E. coli. TG1. O'Connor,C.D., & Timmins, K.N. (1987). Highly repressible expression system for cloning genes that specify potentialy toxic proteins. Journal of Bacteriology. 169, 4457-4462. false John Heil, Danielle Nash, Shira Davis component1996701 1 BBa_B0010 component1996703 1 BBa_B0012 component1996700 1 BBa_K093008 annotation1996703 1 BBa_B0012 range1996703 1 152 192 annotation1996701 1 BBa_B0010 range1996701 1 64 143 annotation1996700 1 BBa_K093008 range1996700 1 1 55 BBa_B0010 1 BBa_B0010 T1 from E. coli rrnB 2003-11-19T12:00:00Z 2015-08-31T04:07:20Z Transcriptional terminator consisting of a 64 bp stem-loop. false false _1_ 0 24 7 In stock false true Randy Rettberg annotation4184 1 stem_loop range4184 1 12 55 annotation7018 1 BBa_B0010 range7018 1 1 80 BBa_B0015 1 BBa_B0015 double terminator (B0010-B0012) 2003-07-16T11:00:00Z 2015-08-31T04:07:20Z Released HQ 2013 Double terminator consisting of BBa_B0010 and BBa_B0012 false true _1_ 0 24 7 In stock false true Reshma Shetty component1916612 1 BBa_B0012 component1916610 1 BBa_B0010 annotation1916612 1 BBa_B0012 range1916612 1 89 129 annotation1916610 1 BBa_B0010 range1916610 1 1 80 BBa_K093013 1 RBS-PmeIR PmeI endonuclease with RBS 2008-10-29T12:00:00Z 2015-05-08T01:08:40Z composite part PmeI with RBS false false _247_ 0 3630 9 It's complicated false We wanted to express PmeI. That requires a RBS. false John Heil, Danielle Nash component1996874 1 BBa_B0034 component1996875 1 BBa_K093002 annotation1996874 1 BBa_B0034 range1996874 1 1 12 annotation1996875 1 BBa_K093002 range1996875 1 19 711 BBa_B0012 1 BBa_B0012 TE from coliphageT7 2003-01-31T12:00:00Z 2015-08-31T04:07:20Z Derived from the TE terminator of T7 bacteriophage between Genes 1.3 and 1.4 <genbank>V01146</genbank>. Released HQ 2013 Transcription terminator for the <i>E.coli</i> RNA polymerase. false false _1_ 0 24 7 In stock false <P> <P>Suggested by Sri Kosuri and Drew Endy as a high efficiency terminator. The 5' end cutoff was placed immediately after the TAA stop codon and the 3' end cutoff was placed just prior to the RBS of Gene 1.4 (before AAGGAG).<P> Use anywhere transcription should be stopped when the gene of interest is upstream of this terminator. false Reshma Shetty annotation1690 1 polya range1690 1 28 41 annotation7020 1 BBa_B0012 range7020 1 1 41 annotation1686 1 T7 TE range1686 1 8 27 annotation1687 1 stop range1687 1 34 34 BBa_K093006 1 RBS-cI cI repressor with RBS 2008-10-27T12:00:00Z 2015-05-08T01:08:40Z registry plasmids Released HQ 2013 cI repressor, BBa_C0051, with Elowitz RBS, BBa_B0034. false false _247_ 0 3630 9 In stock false Needed for downstream applications. false John Heil component2244027 1 BBa_B0034 component2244031 1 BBa_C0051 annotation2244027 1 BBa_B0034 range2244027 1 1 12 annotation2244031 1 BBa_C0051 range2244031 1 19 793 BBa_K093001 1 T7Gene6 T7 Gene 6 exonuclease 2008-10-25T11:00:00Z 2015-05-08T01:08:40Z T7 genomic DNA This is the T7 gene 6 ORF, that codes for the T7 gene 6 5'-3' exonuclease. For properties of T7 gene 6 exonuclease see: Kerr and Sadowski "Gene 6 Exonuclease of Bacteriophage T7" The Journal of Biological Chemistry Vol. 247 No. 1 January 10, pp 311-318, 1972. false false _247_ 0 3630 9 It's complicated false We needed to change the stop codon to the standard stop codon TAA. We later realized that we should have added tandem TAA. The Tandem TAA stop codon is present in the composite parts containing this ORF. The ORF alone has the single TAA stop codon. false John Heil, Shira Davis, Danielle Nash BBa_K241000_sequence 1 aaagaggagaaatactagatggcacttcttgaccttaaacaattctatgagttacgtgaaggctgcgacgacaagggtatccttgtgatggacggcgactggctggtcttccaagctatgagtgctgctgagtttgatgcctcttgggaggaagagatttggcaccgatgctgtgaccacgctaaggcccgtcagattcttgaggattccattaagtcctacgagacccgtaagaaggcttgggcaggtgctccaattgtccttgcgttcaccgatagtgttaactggcgtaaagaactggttgacccgaactataaggctaaccgtaaggccgtgaagaaacctgtagggtactttgagttccttgatgctctctttgagcgcgaagagttctattgcatccgtgagcctatgcttgagggtgatgacgttatgggagttattgcttccaatccgtctgccttcggtgctcgtaaggctgtaatcatctcttgcgataaggactttaagaccatccctaactgtgacttcctgtggtgtaccactggtaacatcctgactcagaccgaagagtccgctgactggtggcacctcttccagaccatcaagggtgacatcactgatggttactcagggattgctggatggggtgataccgccgaggacttcttgaataacccgttcataaccgagcctaaaacgtctgtgcttaagtccggtaagaacaaaggccaagaggttactaaatgggttaaacgcgaccctgagcctcatgagacgctttgggactgcattaagtccattggcgcgaaggctggtatgaccgaagaggatattatcaagcagggccaaatggctcgaatcctacggttcaacgagtacaactttattgacaaggagatttacctgtggagaccgtaatactagagaaagaggagaaatactagatgacaacaaactccccctcagacgtcggcatgatcgacgagtgtctgtccatcgtccgaacgtcgcttgcacgatgtttccaacagcaggccccaagcattcaagcctcatggccactttcaggacgcgccgtatctgagattggaggccgcctagtcgagagtttcgttttagcacgactcccgcatgaactgagcaccacgccttttgacggccagattctatgtgaaatacctgaatccggcagagcgatggaagacattgcggtgaccttcatcggcccacatggaagggctcgactactcatcgacgtcaagggtcataacgaataccgcacgggatcgagacccaatttggcttcgatccgaaaatgtctggaactctatcgcagctcctcacataccgttgatgagctcgttgtcttcttctgccgttaccgcccatccgtccacccggatcatcacgcacaagcggtcgaatatcacgttctgcccgagtcgttaatgagcagggattttcctgcttcgtgccctgagcgaaagcaacctggatccagccaatatcggagtggcggccagttgctgcttgccagggaaaacaacatacggttagtgaatcgttcaaggtcggagttcgttcaacttctggagggtctccagtcacgccttcaacgggggcgaagtacggtttaatactagagtgtgctcagtatcttgttatccgctcacaatgtcaattgttatccgctcacaatttactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttatatactagagaattgtgagcggataacaattgacattgtgagcggataacaagatactgagcacatactagagaaagaggagaaatactagatgagcacaaaaaagaaaccattaacacaagagcagcttgaggacgcacgtcgccttaaagcaatttatgaaaaaaagaaaaatgaacttggcttatcccaggaatctgtcgcagacaagatggggatggggcagtcaggcgttggtgctttatttaatggcatcaatgcattaaatgcttataacgccgcattgcttgcaaaaattctcaaagttagcgttgaagaatttagcccttcaatcgccagagaaatctacgagatgtatgaagcggttagtatgcagccgtcacttagaagtgagtatgagtaccctgttttttctcatgttcaggcagggatgttctcacctgagcttagaacctttaccaaaggtgatgcggagagatgggtaagcacaaccaaaaaagccagtgattctgcattctggcttgaggttgaaggtaattccatgaccgcaccaacaggctccaagccaagctttcctgacggaatgttaattctcgttgaccctgagcaggctgttgagccaggtgatttctgcatagccagacttgggggtgatgagtttaccttcaagaaactgatcagggatagcggtcaggtgtttttacaaccactaaacccacagtacccaatgatcccatgcaatgagagttgttccgttgtggggaaagttatcgctagtcagtggcctgaagagacgtttggcgctgcaaacgacgaaaactacgctttagtagcttaataacgctgatagtgctagtgtagatcgctactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata BBa_K093001_sequence 1 atggcacttcttgaccttaaacaattctatgagttacgtgaaggctgcgacgacaagggtatccttgtgatggacggcgactggctggtcttccaagctatgagtgctgctgagtttgatgcctcttgggaggaagagatttggcaccgatgctgtgaccacgctaaggcccgtcagattcttgaggattccattaagtcctacgagacccgtaagaaggcttgggcaggtgctccaattgtccttgcgttcaccgatagtgttaactggcgtaaagaactggttgacccgaactataaggctaaccgtaaggccgtgaagaaacctgtagggtactttgagttccttgatgctctctttgagcgcgaagagttctattgcatccgtgagcctatgcttgagggtgatgacgttatgggagttattgcttccaatccgtctgccttcggtgctcgtaaggctgtaatcatctcttgcgataaggactttaagaccatccctaactgtgacttcctgtggtgtaccactggtaacatcctgactcagaccgaagagtccgctgactggtggcacctcttccagaccatcaagggtgacatcactgatggttactcagggattgctggatggggtgataccgccgaggacttcttgaataacccgttcataaccgagcctaaaacgtctgtgcttaagtccggtaagaacaaaggccaagaggttactaaatgggttaaacgcgaccctgagcctcatgagacgctttgggactgcattaagtccattggcgcgaaggctggtatgaccgaagaggatattatcaagcagggccaaatggctcgaatcctacggttcaacgagtacaactttattgacaaggagatttacctgtggagaccgtaa BBa_B0034_sequence 1 aaagaggagaaa BBa_B0010_sequence 1 ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc BBa_C0051_sequence 1 atgagcacaaaaaagaaaccattaacacaagagcagcttgaggacgcacgtcgccttaaagcaatttatgaaaaaaagaaaaatgaacttggcttatcccaggaatctgtcgcagacaagatggggatggggcagtcaggcgttggtgctttatttaatggcatcaatgcattaaatgcttataacgccgcattgcttgcaaaaattctcaaagttagcgttgaagaatttagcccttcaatcgccagagaaatctacgagatgtatgaagcggttagtatgcagccgtcacttagaagtgagtatgagtaccctgttttttctcatgttcaggcagggatgttctcacctgagcttagaacctttaccaaaggtgatgcggagagatgggtaagcacaaccaaaaaagccagtgattctgcattctggcttgaggttgaaggtaattccatgaccgcaccaacaggctccaagccaagctttcctgacggaatgttaattctcgttgaccctgagcaggctgttgagccaggtgatttctgcatagccagacttgggggtgatgagtttaccttcaagaaactgatcagggatagcggtcaggtgtttttacaaccactaaacccacagtacccaatgatcccatgcaatgagagttgttccgttgtggggaaagttatcgctagtcagtggcctgaagagacgtttggcgctgcaaacgacgaaaactacgctttagtagcttaataacgctgatagtgctagtgtagatcgc BBa_K093006_sequence 1 aaagaggagaaatactagatgagcacaaaaaagaaaccattaacacaagagcagcttgaggacgcacgtcgccttaaagcaatttatgaaaaaaagaaaaatgaacttggcttatcccaggaatctgtcgcagacaagatggggatggggcagtcaggcgttggtgctttatttaatggcatcaatgcattaaatgcttataacgccgcattgcttgcaaaaattctcaaagttagcgttgaagaatttagcccttcaatcgccagagaaatctacgagatgtatgaagcggttagtatgcagccgtcacttagaagtgagtatgagtaccctgttttttctcatgttcaggcagggatgttctcacctgagcttagaacctttaccaaaggtgatgcggagagatgggtaagcacaaccaaaaaagccagtgattctgcattctggcttgaggttgaaggtaattccatgaccgcaccaacaggctccaagccaagctttcctgacggaatgttaattctcgttgaccctgagcaggctgttgagccaggtgatttctgcatagccagacttgggggtgatgagtttaccttcaagaaactgatcagggatagcggtcaggtgtttttacaaccactaaacccacagtacccaatgatcccatgcaatgagagttgttccgttgtggggaaagttatcgctagtcagtggcctgaagagacgtttggcgctgcaaacgacgaaaactacgctttagtagcttaataacgctgatagtgctagtgtagatcgc BBa_K093008_sequence 1 tgtgctcagtatcttgttatccgctcacaatgtcaattgttatccgctcacaatt BBa_K093004_sequence 1 tgtgctcagtatcttgttatccgctcacaatgtcaattgttatccgctcacaatttactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata BBa_B0012_sequence 1 tcacactggctcaccttcgggtgggcctttctgcgtttata BBa_K093013_sequence 1 aaagaggagaaatactagatgacaacaaactccccctcagacgtcggcatgatcgacgagtgtctgtccatcgtccgaacgtcgcttgcacgatgtttccaacagcaggccccaagcattcaagcctcatggccactttcaggacgcgccgtatctgagattggaggccgcctagtcgagagtttcgttttagcacgactcccgcatgaactgagcaccacgccttttgacggccagattctatgtgaaatacctgaatccggcagagcgatggaagacattgcggtgaccttcatcggcccacatggaagggctcgactactcatcgacgtcaagggtcataacgaataccgcacgggatcgagacccaatttggcttcgatccgaaaatgtctggaactctatcgcagctcctcacataccgttgatgagctcgttgtcttcttctgccgttaccgcccatccgtccacccggatcatcacgcacaagcggtcgaatatcacgttctgcccgagtcgttaatgagcagggattttcctgcttcgtgccctgagcgaaagcaacctggatccagccaatatcggagtggcggccagttgctgcttgccagggaaaacaacatacggttagtgaatcgttcaaggtcggagttcgttcaacttctggagggtctccagtcacgccttcaacgggggcgaagtacggtttaa BBa_R0011_sequence 1 aattgtgagcggataacaattgacattgtgagcggataacaagatactgagcaca BBa_K093002_sequence 1 atgacaacaaactccccctcagacgtcggcatgatcgacgagtgtctgtccatcgtccgaacgtcgcttgcacgatgtttccaacagcaggccccaagcattcaagcctcatggccactttcaggacgcgccgtatctgagattggaggccgcctagtcgagagtttcgttttagcacgactcccgcatgaactgagcaccacgccttttgacggccagattctatgtgaaatacctgaatccggcagagcgatggaagacattgcggtgaccttcatcggcccacatggaagggctcgactactcatcgacgtcaagggtcataacgaataccgcacgggatcgagacccaatttggcttcgatccgaaaatgtctggaactctatcgcagctcctcacataccgttgatgagctcgttgtcttcttctgccgttaccgcccatccgtccacccggatcatcacgcacaagcggtcgaatatcacgttctgcccgagtcgttaatgagcagggattttcctgcttcgtgccctgagcgaaagcaacctggatccagccaatatcggagtggcggccagttgctgcttgccagggaaaacaacatacggttagtgaatcgttcaaggtcggagttcgttcaacttctggagggtctccagtcacgccttcaacgggggcgaagtacggtttaa BBa_B0015_sequence 1 ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata igem2sbol 1 iGEM to SBOL conversion Conversion of the iGEM parts registry to SBOL2.1 James Alastair McLaughlin Chris J. Myers 2017-03-06T15:00:00.000Z