IGEM:IMPERIAL/2008/Sequence: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
mNo edit summary |
mNo edit summary |
||
| Line 19: | Line 19: | ||
|style="background:#dddddd;" |Promoter || || || || || | |style="background:#dddddd;" |Promoter || || || || || | ||
|- | |- | ||
| 1.Promoter - Light|| Pctc || [http://openwetware.org/wiki/Image:Pctc_corrected.doc Pctc] <br> [http://openwetware.org/wiki/Image:Pctc_biobrick_corrected.doc Biobrick]||[http://www.ncbi.nlm.nih.gov/pubmed/3100810?dopt=Abstract Paper] [http://dbtbs.hgc.jp/ DBTBS] || J,QQ || | | 1.Promoter - Light|| Pctc || [http://openwetware.org/wiki/Image:Pctc_corrected.doc Pctc] <br> [http://openwetware.org/wiki/Image:Pctc_biobrick_corrected.doc Biobrick]||[http://www.ncbi.nlm.nih.gov/pubmed/3100810?dopt=Abstract Paper] [http://dbtbs.hgc.jp/ DBTBS] || J,QQ || 99bp | ||
|- | |- | ||
| 2.Promoter - σB || PgsiB || [http://openwetware.org/wiki/Image:PgsiB.doc PgsiB] <br> [http://openwetware.org/wiki/Image:PgsiB_Biobrick.doc Biobrick] || [http://www.ncbi.nlm.nih.gov/pubmed/16005967?dopt=Abstract Paper] [http://dbtbs.hgc.jp/ DBTBS] || J || | | 2.Promoter - σB || PgsiB || [http://openwetware.org/wiki/Image:PgsiB.doc PgsiB] <br> [http://openwetware.org/wiki/Image:PgsiB_Biobrick.doc Biobrick] || [http://www.ncbi.nlm.nih.gov/pubmed/16005967?dopt=Abstract Paper] [http://dbtbs.hgc.jp/ DBTBS] || J || 81bp | ||
|- | |- | ||
| 3.Promoter - ComK upregulated || PcomC || [http://openwetware.org/wiki/Image:PcomC.doc PcomC] <br> [http://openwetware.org/wiki/Image:PcomC_Biobrick.doc Biobrick] || [http://dbtbs.hgc.jp/ DBTBS] || | | 3.Promoter - ComK upregulated || PcomC || [http://openwetware.org/wiki/Image:PcomC.doc PcomC] <br> [http://openwetware.org/wiki/Image:PcomC_Biobrick.doc Biobrick] || [http://dbtbs.hgc.jp/ DBTBS] || The files for this promoter have been re-uploaded, hope they remain this time... C || 137bp | ||
|- | |- | ||
|4.Promoter - Constitutuive || P43 || [http://openwetware.org/wiki/Image:P43.doc P43] <br> [http://openwetware.org/wiki/Image:P43_Biobrick.doc Biobrick] || [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1169017 Paper] <br> [http://www.jbc.org/cgi/reprint/259/13/8619 Paper2] || C,J || | |4.Promoter - Constitutuive || P43 || [http://openwetware.org/wiki/Image:P43.doc P43] <br> [http://openwetware.org/wiki/Image:P43_Biobrick.doc Biobrick] || [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1169017 Paper] <br> [http://www.jbc.org/cgi/reprint/259/13/8619 Paper2] || C,J || 99bp | ||
|- | |- | ||
|5.Promoter - Inducible || Phyper-spank || [http://openwetware.org/wiki/Image:Phs.doc Ph-s] <br> [http://openwetware.org/wiki/Image:Phs_Biobrick.doc Biobrick] || Dr. Angelika Grundling (Imperial College London), [http://openwetware.org/wiki/User:Jan-willem_Veening Dr. Jan-Willem Veening (Newcastle University)], [http://www.ncbi.nlm.nih.gov/pubmed/12169614 Paper1], [http://www.ncbi.nlm.nih.gov/pubmed/17720779 Paper2], [http://jb.asm.org/cgi/content/full/186/7/2028#T1 Paper3], [http://tools.neb.com/NEBcutter2/index.php NEBcutter2] || C,J <font color=red> Extra T on the end of the sequence I think. Also does this require LacI synthesis? </font> The T can be left or removed, I think i left it just for clearance, feel free to remove it.....as for LacI, yes it's needed, I was unable to locate it on the plasmids however, I can look again or we'll have to make a second part to that construct || 145bp | |5.Promoter - Inducible || Phyper-spank || [http://openwetware.org/wiki/Image:Phs.doc Ph-s] <br> [http://openwetware.org/wiki/Image:Phs_Biobrick.doc Biobrick] || Dr. Angelika Grundling (Imperial College London), [http://openwetware.org/wiki/User:Jan-willem_Veening Dr. Jan-Willem Veening (Newcastle University)], [http://www.ncbi.nlm.nih.gov/pubmed/12169614 Paper1], [http://www.ncbi.nlm.nih.gov/pubmed/17720779 Paper2], [http://jb.asm.org/cgi/content/full/186/7/2028#T1 Paper3], [http://tools.neb.com/NEBcutter2/index.php NEBcutter2] || C,J <font color=red> Extra T on the end of the sequence I think. Also does this require LacI synthesis? </font> The T can be left or removed, I think i left it just for clearance, feel free to remove it.....as for LacI, yes it's needed, I was unable to locate it on the plasmids however, I can look again or we'll have to make a second part to that construct || 145bp | ||
|- | |- | ||
|6.Promoter - Inducible || Pxyl || [http://openwetware.org/wiki/Image:Pxyl.doc Pxyl] <br> [http://openwetware.org/wiki/Image:Pxyl_Biobrick.doc Biobrick] || [http://openwetware.org/wiki/User:Jan-willem_Veening Dr. Jan-Willem Veening (Newcastle University)], [http://dbtbs.hgc.jp/ DBTBS], [http://www.ncbi.nlm.nih.gov/pubmed/8973310 Paper1], [http://www.ncbi.nlm.nih.gov/pubmed/11274134 Paper2] || C, J <font color=red> Had a look on DBTBS and papers and the regulatory region that XylR is downstream of the start codon and I guess we would need to add these binding sequences to the genes we want to express</font> damn, missed that one, well spotted, I'll update it tomorrow || | |6.Promoter - Inducible || Pxyl || [http://openwetware.org/wiki/Image:Pxyl.doc Pxyl] <br> [http://openwetware.org/wiki/Image:Pxyl_Biobrick.doc Biobrick] || [http://openwetware.org/wiki/User:Jan-willem_Veening Dr. Jan-Willem Veening (Newcastle University)], [http://dbtbs.hgc.jp/ DBTBS], [http://www.ncbi.nlm.nih.gov/pubmed/8973310 Paper1], [http://www.ncbi.nlm.nih.gov/pubmed/11274134 Paper2] || C, J <font color=red> Had a look on DBTBS and papers and the regulatory region that XylR is downstream of the start codon and I guess we would need to add these binding sequences to the genes we want to express</font> damn, missed that one, well spotted, I'll update it tomorrow || 83-87bp | ||
|- | |- | ||
|7.Promoter - Contitutive (high) || Pveg || [http://openwetware.org/wiki/Image:Pveg.doc Pveg] <br> [http://openwetware.org/wiki/Image:Pveg_Biobrick.doc Biobrick] || [http://openwetware.org/wiki/User:Jan-willem_Veening Dr. Jan-Willem Veening (Newcastle University)], [http://dbtbs.hgc.jp/ DBTBS] || C | |7.Promoter - Contitutive (high) || Pveg || [http://openwetware.org/wiki/Image:Pveg.doc Pveg] <br> [http://openwetware.org/wiki/Image:Pveg_Biobrick.doc Biobrick] || [http://openwetware.org/wiki/User:Jan-willem_Veening Dr. Jan-Willem Veening (Newcastle University)], [http://dbtbs.hgc.jp/ DBTBS] || C - checked NCBI, sequences do match, image as such included in the new Pveg file, J || 87 | ||
|- | |- | ||
|style="background:#dddddd;" |RBS || || || || || | |style="background:#dddddd;" |RBS || || || || || | ||
|- | |- | ||
|1.RBS - Stong || RBS-gsiB || [http://openwetware.org/wiki/Image:RBS-gsiB.doc RBS-gsiB] <br> [http://openwetware.org/wiki/Image:RBS-gsiB_Biobrick.doc Biobrick] || [http://www.ncbi.nlm.nih.gov/pubmed/16005967?dopt=Abstract Paper] [http://dbtbs.hgc.jp/ DBTBS] || || | |1.RBS - Stong || RBS-gsiB || [http://openwetware.org/wiki/Image:RBS-gsiB.doc RBS-gsiB] <br> [http://openwetware.org/wiki/Image:RBS-gsiB_Biobrick.doc Biobrick] || [http://www.ncbi.nlm.nih.gov/pubmed/16005967?dopt=Abstract Paper] [http://dbtbs.hgc.jp/ DBTBS] || || 54bp (343bp with promoter) | ||
|- | |- | ||
|2.RBS - Strong || RBS-spoVG || [http://openwetware.org/wiki/Image:RBS-spoVG.doc RBS-spoVG] <br> [http://openwetware.org/wiki/Image:RBS-spoVG_Biobrick.doc Biobrick] ||[http://www.ncbi.nlm.nih.gov/pubmed/9846745 Paper (reference only)] [http://dbtbs.hgc.jp/ DBTBS] || C || | |2.RBS - Strong || RBS-spoVG || [http://openwetware.org/wiki/Image:RBS-spoVG.doc RBS-spoVG] <br> [http://openwetware.org/wiki/Image:RBS-spoVG_Biobrick.doc Biobrick] ||[http://www.ncbi.nlm.nih.gov/pubmed/9846745 Paper (reference only)] [http://dbtbs.hgc.jp/ DBTBS] || C || 68bp | ||
|- | |- | ||
|3.RBS - Strong || RBS-PBS || [http://openwetware.org/wiki/Image:RBS-spoVG.doc RBS-PBS] <br> [http://openwetware.org/wiki/Image:RBS-PBS_Biobrick.doc Biobrick] || [http://openwetware.org/wiki/User:Jan-willem_Veening Dr. Jan-Willem Veening (Newcastle University)], [http://www.ncbi.nlm.nih.gov/pubmed/1375309 Paper] || Issues - C || | |3.RBS - Strong || RBS-PBS || [http://openwetware.org/wiki/Image:RBS-spoVG.doc RBS-PBS] <br> [http://openwetware.org/wiki/Image:RBS-PBS_Biobrick.doc Biobrick] || [http://openwetware.org/wiki/User:Jan-willem_Veening Dr. Jan-Willem Veening (Newcastle University)], [http://www.ncbi.nlm.nih.gov/pubmed/1375309 Paper] || Issues - C || | ||
Revision as of 17:02, 29 July 2008
Hello Team Sequence, Thought we could use this page to load up all the information. If we could load up the sequence of the parts here, probably load the pure sequence then one with the restriction sites on the end. Here are some useful websites about the ends:
- http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix
- http://partsregistry.org/Assembly:RBS-CDS_issues
First thing tomorrow we need to get a group together (preferably with Kirsten) and decide about whether to use stand-alone RBSs or use Promoter-RBS or RBS-gene combinations
- Chris D Hirst 23:44, 29 July 2008 (UTC):Ok, it seems a lot of the work I did before leaving the office hasn't been registered. The changes I make now better be there tomorrow or I'm gonna be really hacked off
| Part Class | Part Name | Sequence File | Papers | Checked | Biobrick Length (bp) |
| Promoter | |||||
| 1.Promoter - Light | Pctc | Pctc Biobrick |
Paper DBTBS | J,QQ | 99bp |
| 2.Promoter - σB | PgsiB | PgsiB Biobrick |
Paper DBTBS | J | 81bp |
| 3.Promoter - ComK upregulated | PcomC | PcomC Biobrick |
DBTBS | The files for this promoter have been re-uploaded, hope they remain this time... C | 137bp |
| 4.Promoter - Constitutuive | P43 | P43 Biobrick |
Paper Paper2 |
C,J | 99bp |
| 5.Promoter - Inducible | Phyper-spank | Ph-s Biobrick |
Dr. Angelika Grundling (Imperial College London), Dr. Jan-Willem Veening (Newcastle University), Paper1, Paper2, Paper3, NEBcutter2 | C,J Extra T on the end of the sequence I think. Also does this require LacI synthesis? The T can be left or removed, I think i left it just for clearance, feel free to remove it.....as for LacI, yes it's needed, I was unable to locate it on the plasmids however, I can look again or we'll have to make a second part to that construct | 145bp |
| 6.Promoter - Inducible | Pxyl | Pxyl Biobrick |
Dr. Jan-Willem Veening (Newcastle University), DBTBS, Paper1, Paper2 | C, J Had a look on DBTBS and papers and the regulatory region that XylR is downstream of the start codon and I guess we would need to add these binding sequences to the genes we want to express damn, missed that one, well spotted, I'll update it tomorrow | 83-87bp |
| 7.Promoter - Contitutive (high) | Pveg | Pveg Biobrick |
Dr. Jan-Willem Veening (Newcastle University), DBTBS | C - checked NCBI, sequences do match, image as such included in the new Pveg file, J | 87 |
| RBS | |||||
| 1.RBS - Stong | RBS-gsiB | RBS-gsiB Biobrick |
Paper DBTBS | 54bp (343bp with promoter) | |
| 2.RBS - Strong | RBS-spoVG | RBS-spoVG Biobrick |
Paper (reference only) DBTBS | C | 68bp |
| 3.RBS - Strong | RBS-PBS | RBS-PBS Biobrick |
Dr. Jan-Willem Veening (Newcastle University), Paper | Issues - C | |
| Gene | |||||
| 1.Gene | epsE | Protein Biobrick |
Page 9, Online Supplementary Material for "A Molecular Clutch Disables Flagella in the Bacillus subtilis Biofilm" | QQ, J | 878 |
| 2.Gene | ytvA | Protein Biobrick |
Partial sequence (LOV domain) | QQ, J | 786 |
| 3.Gene | sinR | Protein Biobrick |
- | QQ, J | 377 |
| 4.Biomaterial | EP24-20-20 | Biobrick | Paper | 640 | |
| 5.Biomaterial | EAK16-II | Biobrick | Paper | 92 | |
| 6.Signal Peptide | SacB | Biobrick | Paper | 139 | |
| 7.Signal Peptide | LipA | Biobrick | Paper | 145 | |
| 8.Signal Peptide | Epr | Biobrick | Paper | 133 | |
| Terminator | |||||
| 1.Terminator | TermI-VI Consensus of 6 terminators |
6NSCT Protein Biobrick |
Search for additional replication terminators in the Bacillus subtilis chromosome | 30bp |
