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

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, 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