IGEM:IMPERIAL/2008/Sequence

From OpenWetWare

Jump to: navigation, search

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:

Strategy For Assembly


Construct Sequence (Updated Version)


[Sequence for Constructs]


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, QQ144
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.GeneXylR XylR Gene Biobrick NCBI GENE C, J 1094, 1097 with the extra stop codon
4. GeneLacI 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-IIBiobrick 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, J137
8.Signal Peptide LipA Biobrick Paper for signal peptide QQ, C ,J143
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 again377
9.Signal Peptide Epr Biobrick Paper for signal peptide QQ, C, J 131
Personal tools