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

• Chris D Hirst 00:17, 30 July 2008 (UTC):Woah, waht the deuce is going on with this page? Was it just me or did it just get rolled back 10 mins?

• James- Man i hate the wiki, whats going on? man sequence checking sucks so bad

• Chris - I hear you on that one, thinking it sucks worse checking one you've made yourself though, spotted a gem of a mistake I'd missed earlier. The comC sequence in the .doc file was for the wrong strand....

• Just had a thought, can we reuse lacI from the registry, ill check operon binding sites but if its a hybrid i guess its the same

• Ok, the LacI gene i sunder control of the Phyper-spank promoter, it's just downstream of it, that's pretty neat thinking about it.... We could bung the whole section (EcoRI to BamHI in, and plug our bit in the middle somehow maybe?)

Part Class	Part Name	Sequence File	Papers/References	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, C	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 ust had a thought, can we reuse lacI from the registry, ill check operon binding sites but if its a hybrid i guess its the same	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	C	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	QQ, J	640
5.Biomaterial	EAK16-II	Biobrick	Paper	QQ, J	92
6.Signal Peptide	SacB	Biobrick	Paper	QQ, J Unsure how the length of the sequence was decided?	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
2.Terminator	rrnO	rrnO Biobrick	Dr. Jan-Willem Veening (Newcastle University)		133bp (with extra frame-shift base)
3.Terminator	rrnA	rrnA Biobrick	Dr. Jan-Willem Veening (Newcastle University)		132bp (with extra frame-shift base)