IGEM:IMPERIAL/2008/Sequence

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	99
2.Promoter - σB	PgsiB	PgsiB Biobrick	Paper DBTBS	J	81
3.Promoter - ComK upregulated	PcomC	PcomC Biobrick	DBTBS	Wrong - needs to be 94 bp sequence	137
4.Promoter - Constitutuive	P43	P43 Biobrick	Paper Paper2	C,J	99
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?	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	40-44bp (83-87bp Biobrick)
7.Promoter - Contitutive (high)	Pveg	Pveg Biobrick	Dr. Jan-Willem Veening (Newcastle University), DBTBS	C, J - Checked on NCBI and the veg gene promoter is different NCBI think its fine but can someone check	87
RBS
1.RBS - Stong	RBS-gsiB	RBS-gsiB Biobrick	Paper DBTBS		27bp (54bp biobrick, 343bp with promoter)
2.RBS - Strong	RBS-spoVG	RBS-spoVG Biobrick	Paper (reference only) DBTBS	C	37bp (68bp Biobrick)
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 (start codon AUG)
2.Gene	ytvA	Protein Biobrick	Partial sequence (LOV domain)	QQ, J	786 (start codon AUG)
3.Gene	sinR	Protein Biobrick	-	QQ, J	377 (start codon UUG)
4.Biomaterial	EP24-20-20	Biobrick	Paper	QQ	640 No start Codon
5.Biomaterial	EAK16-II	Biobrick	Paper	QQ	92
6.Signal Peptide	SacB	Biobrick	Paper	QQ	139
7.Signal Peptide	LipA	Biobrick	Paper	QQ	145
8.Signal Peptide	Epr	Biobrick	Paper	QQ	133
Terminator
1.Terminator	TermI-VI Consensus of 6 terminators	6NSCT Protein Biobrick	Search for additional replication terminators in the Bacillus subtilis chromosome		30bp