IGEM:IMPERIAL/2008/Sequence
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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
Strategy For Assembly
Construct Sequence (Updated Version)
Parts
Part Class | Part Name | Sequence File | Papers/References | Checked | Biobrick Length (bp) |
Promoter | |||||
1.Promoter - Light | Pctc | Pctc Biobrick |
Paper DBTBS | J, QQ, C | 99 |
2.Promoter - σB | PgsiB | PgsiB Biobrick |
Paper DBTBS | J, C, QQ | 81 |
3.Promoter - Constitutuive | P43 | P43 Biobrick |
Paper Paper2 |
C, J, QQ | 99 |
4.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, QQ | 144 |
5.Promoter - Inducible | Pxyl | Pxyl Biobrick |
Dr. Jan-Willem Veening (Newcastle University), DBTBS, Paper1, Paper2 | C, J | 125 |
6.Promoter - Contitutive (high) | Pveg | Pveg Biobrick |
Dr. Jan-Willem Veening (Newcastle University), DBTBS | C, J, QQ | 87 |
RBS | |||||
1.RBS | RBS-gsiB | Alt RBS Biobrick | Alt paper reference | J, QQ, C | 54 |
2.RBS | RBS-SpoVG | RBS-spoVG Alt Biobrick | Paper | J, C, QQ | 55 |
Gene | |||||
1.Gene | epsE | Protein Biobrick |
Page 9, Online Supplementary Material for "A Molecular Clutch Disables Flagella in the Bacillus subtilis Biofilm" | QQ, J, C | 878 |
2.Gene | ytvA | Protein Biobrick |
Partial sequence (LOV domain) | QQ, J, C | 827 |
3.Gene | XylR | XylR Gene Biobrick | NCBI GENE | C, J | 1094, 1097 with the extra stop codon |
4. Gene | LacI | BBa_C0012 | |||
5.Biomaterial | EP24-20-20 | Biobrick | Paper | QQ, J, C needs codon usage modification for B.subtilis and Need to resolve issue of signal peptide and biomaterial | 638 |
6.Biomaterial | EAK16-II | Biobrick | Paper | QQ, J, C Need to resolve issue of signal peptide and biomaterial | 89 |
7.Signal Peptide | SacB | Biobrick | Paper for signal peptide | QQ, C, J | 137 |
8.Signal Peptide | LipA | Biobrick | Paper for signal peptide | QQ, C ,J | 143 |
Terminator | |||||
1.Terminator | Traditional Double Stop (BBa_B0015) | See main page --> | BBa_B0015 Main Page | Checking | 129 |
Integration Sites | |||||
1. Integration site | AmyE | PCR out of vector pDR111/pDR00 |
vectors pDR111/pDR00 | ||
2. Integration site - 5' and 3' | PyrD - dihydroorotate dehydrogenase 1B | 5'Biobrick and 3'Biobrick | Paper + NCBI | J | 511 + 511 |
The Parts Grave Yard
For those parts that never made, rest in peace!!
Part Class | Part Name | Sequence File | Papers/References | Reason Scrapped | Biobrick Length (bp) |
Promoter | |||||
3.Promoter - ComK upregulated | PcomC | PcomC Biobrick |
DBTBS Paper | C, J, QQ | 137 |
Terminator | |||||
1.Terminator | TermI-VI Consensus of 6 terminators |
6NSCT Protein Biobrick |
Search for additional replication terminators in the Bacillus subtilis chromosome | For rep not scrip - BRB, killing self ~ Tom Adie 09:41, 30 July 2008 (UTC) | 30bp |
2.Terminator | rrnO | rrnO Biobrick | Dr. Jan-Willem Veening (Newcastle University) | Too Long | 133bp (with extra frame-shift base) |
3.Terminator | rrnA | rrnA Biobrick | Dr. Jan-Willem Veening (Newcastle University) | Too Long | 132bp (with extra frame-shift base) |
Terminator 1 | Short Artificial (BBa_B1002) | See main page --> | BBa_B1002 Main Page | Checking | 34 |
Terminator 2 | Less Short Artificial (BBa_B1006) | See main page --> | BBa_B1006 Main Page | Checking | 39 |
RBS | |||||
2.RBS - Strong | RBS-spoVG | RBS-spoVG Biobrick |
Paper (reference only) DBTBS | Sequence incorrect, alternate sequence correct | 68bp |
3.RBS - Strong | RBS-PBS | RBS-PBS Biobrick |
Dr. Jan-Willem Veening (Newcastle University), Paper | Too short | |
4.RBS - Strong | RBS-ctc | Biobrick | Alt paper reference | J | 57 |
2.RBS | RBS-ctc | Biobrick | Alt paper reference | J, C, QQ | 51 |
Gene | |||||
3.Gene | sinR | Protein Biobrick |
NCBI GENE | QQ, J, C J- Changed the start codon to ATG for optimisation, needs double checking again | 377 |
9.Signal Peptide | Epr | Biobrick | Paper for signal peptide | QQ, C, J | 131 |