This is the -20 to -1 region of T7 gp0.7, which contains the native RBS region for this gene. The physical instantiation of this part does not exist. This part is not compatible with Standard Biobricks assembly methods, as the scar created during assembly would interrupt the spacing between the RBS and the start codon of the CDS. Individuals wishing to use this RBS sequence in their assembles should refer to part XXXXX. (Information forthcoming)
The -20 to -1 region was chosen to be representative of the RBS region of the T7 genes for the following reasons: 1) The Shine-Delgarno region is contained within this defined region for all T7 genes. 2) Current literature suggests that when bound to the Translation Start Site (0), the Ribosome covers positions -20 to +13.
Genome of wild-type bacteriophage T7, positions 2001-2020. Includes the -20 to -1 region of gp0.7.
This is the native ribosome binding site of crtE (geranylgeranyl pyrophosphate synthase) from Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321) Accession: D90087.
This is a virtual part to be added, blunt ended, to the coding sequence.
Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321) Accession: D90087.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene II message (BBa_M13002). The part aligns with base pairs 8252-8267 in M13K07 genome. It was identified as the RBS for gene II message by Wezenbeek et al in Gene (1980) 11: 129-148
New England Biolabs M13K07. Sequenced in 2002 by L. Panganaban
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene VII message (BBa_M13007). The part aligns with base pairs 1092-1107 in M13K07 genome. It was identified as the RBS for gene VII message by Wezenbeek et al in Gene (1980) 11: 129-148
Modified version of B0031 from the Voigt Lab. Not currently available as an independent part (only in a tet inverter).
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene IV message (BBa_M13004). The part aligns with base pairs 4204-4219 in M13K07 genome. It was identified as the RBS for gene IV message by Wezenbeek et al in Gene (1980) 11: 129-148
This is the -20 to -1 region of T7 gp0.5, which contains the native RBS region for this gene. The physical instantiation of this part does not exist. This part is not compatible with Standard Biobricks assembly methods, as the scar created during assembly would interrupt the spacing between the RBS and the start codon of the CDS. Individuals wishing to use this RBS sequence in their assembles should refer to part B2103.
The -20 to -1 region was chosen to be representative of the RBS region of the T7 genes for the following reasons: 1) The Shine-Delgarno region is contained within this defined region for all T7 genes. 2) Current literature suggests that when bound to the Translation Start Site (0), the Ribosome covers positions -20 to +13 of the gene.
Genome of wild-type bacteriophage T7, positions 1476-1495. Includes the -20 to -1 region of gp0.5.
GsiB ribosome binding site (RBS) for B. subtilis
GsiB is an endogenous ribosome binding site from ''B.subtilis''. The sequence of the gsiB ribosome binding site is '''AAAGGAGG''' which is complementary to the sequence '''UUUCCUCC''' from the 3' region of the 16s rRNA from ''B.subtilis''. GsiB is an endogenous ribosome binding site (RBS) from ''B.subtilis''. The sequence of the gsiB ribosome binding site is '''AAAGGAGG''' which is complementary to the sequence '''UUUCCUCC''' from the 3' region of the 16s rRNA from ''B.subtilis''. Previous research showed that the predicted binding energy of the 16s rRNA to the RBS is -9.3kcal.
In order to ensure that the RBS is functional the actual ribosome binding site was maintained and the distance between the RBS and the start codon maintained. In order to conform to the biobrick standard the sequence flanking the RBS had to be changed but the distance between the promoter and RBS, and start codon and RBS was maintained.
The sequence was taken from a previous research paper [1] and was constructed by Geneart
Test RBS from T7 that may be used in E.coli
The ribosomal binding site of the creD gene in the E Coli creD operon.
Synthetic ribosome binding site added by Son of Babel procedure
This is a 4bp synthetic ribosome binding site which can be added by fusion PCR using a reverse primer and the Son of Babel cloning system.
The part can be added by fusion PCR using a Son of Babel reverse primer.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene III message (BBa_M13003). The part aligns with base pairs 1563-1578 in M13K07 genome. It was identified as the RBS for gene III message by Wezenbeek et al in Gene (1980) 11: 129-148 New England Biolabs M13K07. Sequenced in 2002 by L. Panganaban
Native ribosome binding site for crtZ (beta-carotene hydroxylase) from Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321). Accession: D90087.
A virtual part to be added to the coding sequence blunt (without a scar).
Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321). Accession: D90087.
This part is the natural RBS associated with the invJ protein in Salmonella Typhimurium LT2.
This part was not designed with compliance to biobrick standard assembly in mind.
ribosome binding site for transcription initiation
This part is the natural RBS for the sopB gene in the Salmonella Type III Secretion System.
This part was not designed with consideration for biobrick standard assembly in mind. This RBS hasn't been explicitly tested for expression rate in a Fluorescence or B-Gal assay.
This RBS is recognized by ribosomes carrying the modified anti-Shine Dalgarno sequence as found in Brink et al. (see below)
Brink MF, Verbeet MP, de Boer HA (1995). Specialized ribosomes: highly specific translation in vivo of a single targetted mRNA species. Gene, 156, pp. 215-222
Specialized RBS modified from that of B0036 (Brink et al.)
This RBS has the modified Shine-Dalgarno sequence, it has a reduced secondary structure relative to using the actual Brink sequence with mixed connective sites flanking it. the spacing between the SD and the ATG is the same as that used by Brink et al. even though it is non-optimal for E. coli
strong synthetic E. coli ribosome binding site with SacI site.
This is a strong synthetic E. coli ribosome binding site. It is synthesised as two complementary oligonucleotides rather than being incorporated into a biobrick plasmid. It incorporates a SacI site overlapping the XbaI site, which is preserved when it is added to any other biobrick. This allows easy detection of the RBS after it has been added upstream of a biobrick coding sequence in a plasmid vector.
Note the presence of a SacI site overlapping the XbaI site, which is preserved when this biobrick is added to any other biobrick. At the time of writing, this biobrick is added as a short piece of DNA composed of two complementary oligonucleotides rather than being incorporated into a biobrick cloning vector by itself. It can be added upstream of a biobrick coding sequence, and its presence can easily be detected in miniprep DNA on a gel by using a SacI-SpeI or similar digest.
This part is the natural invI RBS from Salmonella Typhimurium LT2.
This part was not designed with consideration for biobrick standard assembly in mind. This RBS has not been explicitly tested for expression level in a fluorescence or B-Gal assay.
Native ribosome binding site of crtY (lycopene cyclase) from Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321). Accession: D90087.
This is a virtual part to be added, blunt-ended, to the coding sequence.
Natural RBS sequence for Bacillus Subtilis, described in the literature as a strong RBS for this bacteria.
From genomic sequence Bacillus Subtilis.
Sequence comes from the natural gene 5 RBS. Using gene 5 as a strong RBS is from initial results from experiments characterizing all natural T7 RBSs.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene VIII message (BBa_M13008). The part aligns with base pairs 1285-1300 in M13K07 genome. It was identified as the RBS for gene VIII message by Wezenbeek et al in Gene (1980) 11: 129-148
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene I message (BBa_M13001). The part aligns with base pairs 8252-8267 in M13K07 genome. It was identified as the RBS for gene II message by Wezenbeek et al in Gene (1980) 11: 129-148
Native rbs from crtI (phytoene dehydrogenase) of Pantoea ananatis (formerly Erwinia uredovora) DSMZ 30080 (ATCC 19321). Accession: D90087.
Virtual part to be added to the coding sequence.
Reverse RBS (RBSrev) -- corresponds to BBa_B0030
Repeats in oligos caused unusual products during cloning
This is the natural RBS from the sicA chaperone (BBa_J6021) in the Salmonella Type III Secretion System.
This part was not designed with standard biobrick assembly in mind.
This is the naturally-occurring RBS found in the regulatory region of the DntR gene. gataaaaacaagaggaaaacaa
The expression level of this RBS has not been quantified.
This is the natural RBS associated with the sopA effector protein in the Salmonella SPI-1 system.
This part was not designed with compliance to biobrick standard assembly in mind. This RBS hasn't been explicitly tested in an expression assay such as GFP fluorescence or B-Gal expression.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene XI message (BBa_M13011). The part aligns with base pairs 3900-3915 in M13K07 genome. It was NOT identified as the RBS for gene XI message by Wezenbeek et al in Gene (1980) 11: 129-148
Christian Jacob (hijacked by Patrick King)
This is the naturally-occurring RBS found in the regulatory region of the DntR gene.
'''''This does not physically exist as a basic part due to time constraints; it was cloned as part of composite part which incorporates all of the components necessary for expression of a reporter gene under the control of DntR'''''. For this reason, the ends of the supplied sequence may not accurately represent the boundaries of the functional unit.
Cloned from a historical plasmid based on pQF52 carrying genomic sequences from ''Burkholderia cepacia''.
This is the naturally-occurring RBS found in the regulatory region of the DntA gene.
This is the consensus RBS for Bacillus subtilis.
The part must be 8 nucleotides away from the first methionine of the coding sequence, and so we added 'TGT' downstream of the actual binding sequence: AAAGGAGG. This, combined with the truncated non-CDS BioBrick prefix scar, gives exactly 8 'spacer bases' between the 3' end of the RBS and the start of the coding sequence.
This is the natural RBS for the sptP gene in Salmonella Type III Secretion
This part was designed without consideration for biobrick standard assembly. This RBS has not been explicitly tested for expression rate.
ribosome binding site for creA gene in the E Coli cre operon
Ribosome binding site for transcription initiation
Native ribosome binding site of sam8 (tyrosine ammonia lyase) from the bacterium Saccharothrix espanaensis DSM 44229.
Virtual part to be added to coding sequence I742142.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene IX message (BBa_M13009). The part aligns with base pairs 1190-1205 in M13K07 genome. It was identified as the RBS for gene IX message by Wezenbeek et al in Gene (1980) 11: 129-148
Strong RBS based on Ron Weiss thesis. Strength is considered relative to BBa_B0031, BBa_B0032, BBa_B0033 and BBa_B0034.
SpoVG ribosome binding site (RBS) for B. subtilis
Description: SpoVG is an endogenous ribosome binding site from B.subtilis. The sequence of the spoVG ribosome binding site is AAAGGUGGUGA which is complementary to the sequence UUUCCUCCACU from the 3' region of the 16s rRNA from B.subtilis. Previous research showed that the predicted binding energy of the 16s rRNA to the RBS is -19kcal 1
The sequence was taken from a previous research paper [1] and was constructed by Geneart.
RBS specific to dedicated ribosomes. This RBS is a modified version of B0036. The spacing between the SD sequence and the start codon has been increased by 5 bases to give the same spacing as used by Brink et al. The 5 bases are the same as those used by Brink. That means they form the first five bases of an XbaI site and no negative affects of using these bases are known at present.
This is the native ribosome binding site for sam5 (4-coumarate-3-hydroxylase) of the bacterium Saccharothrix espanaensis.
This is a virtual part to be added to coding sequence I742141.
This part is the natural RBS from the sipC protein in Salmonella Type III Secretion.
This part was not designed with biobrick standard assembly in mind. This RBS has not been explicitly measured for expression rate using fluorescence or B-Gal assay.
Sequence comes from the natural B0030. Using B0030 as a medium strength RBS is from initial results from experiments characterizing all natural T7 RBSs.
This is the weak version of the consensus RBS for Bacillus subtilis. The sequence is present in front of some B. subtilis operons, but is expected to give weaker expression than the consensus sequence. The consensus sequence AAAGGAGG (BBa_K090505) was changed to AGAGGTGG for this part.
The part must be 8 nucleotides away from the first methionine of the coding sequence, and so we added 'TGT' downstream of the actual binding sequence: AGAGGTGG. This, combined with the truncated non-CDS BioBrick prefix scar, gives exactly 8 'spacer bases' between the 3' end of the RBS and the start of the coding sequence.
The ribosomal binding site for gene creC in the E Coli cre operon.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene X message (BBa_M13010). The part aligns with base pairs 480-495 in M13K07 genome. It was identified as the RBS for gene II message by Wezenbeek et al in Gene (1980) 11: 129-148
Weak1 RBS based on Ron Weiss thesis. Strength is considered relative to BBa_B0030, BBa_B0031, BBa_B0033.
This is the native ribosome binding site of ftsK, a DNA-translocating motor protein involved in cell division in Escherichia coli.
Virtual part to be added to coding sequence BBa_I742137.
DNA is double-stranded. To translate genes of both strands, you need RBSs in both strands.
Please refer to the original (BB_B0034).
'host-takover module' from B.subtilis Bacteriophage SPO1
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene VI message (BBa_M13006). The part aligns with base pairs 2840-2855 in M13K07 genome. It was identified as the RBS for gene VI message by Wezenbeek et al in Gene (1980) 11: 129-148
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene V message (BBa_M13005). The part aligns with base pairs 827-842 in M13K07 genome. It was identified as the RBS for the gene V message by Wezenbeek et al in Gene (1980) 11: 129-148
This is the natural RBS from the sopD gene in Salmonella Type III Secretion.
This RBS has the modified Shine-Dalgarno sequence, it has a reduced secondary structure relative to using the actual Brink sequence with mixed connective sites flanking it. This RBS is modified from B0071 by reducing the 3' sequence so that the SD to ATG spacing is closer to that which is optimal for E. coli.
This version of the T7 0.3 RBS is designed for construction via Heather Keller's alternative assembly plan using XbaI and SapI for RBS/CDS assembly without a mixed site. Contains the -20 to -1 region of gp0.4 from the wild-type T7 genome. Can also be used with Standard BioBricks assembly, although this will add a 7 amino acid fusion to the N-terminus of the resulting protein.
This RBS is designed to be compatible with Heather Keller's RBS assembly scheme for creating RBS/CDS junctions without a mixed site. For use in this scheme, this part should be cut with XbaI and SapI. It must be used with a coding sequence containing the SapI site at the 5' end. This part is not compatible with CDSs that use a GTG site and must be used with CDSs using an ATG start site. The two bp spacer on the 3' end also allows this part to be used in standard biobricks assembly and is necessary to maintain the reading frame of a downstream CDS. Note that Standard Biobricks Assembly with this part results in the creation of a new ATG start site, and a 7 amino acid fusion at the N terminus of the downstream protein. CDSs with alternative start sites are compatible with this part via Standard Assembly. This part was inadvertently constructed without the single base pair (G/C) that separates the XbaI site and the 5' end of the part.
The RBS is taken from the wild-type bacteriophage T7 genome. Please see part B2001 for more information.
This is the natural RBS for the sigE chaperone (BBa_J64025) in Salmonella Typhimurium LT2.
This part was not designed with compatibility to biobrick standard assembly in mind. This RBS has not been explicitly assayed for expression rate.
This is the natural RBS that drives the sipA effector protein in the Salmonella SPI-1 system
This part was not designed with compatibility to biobrick standard assembly in mind. This RBS has not been explicitly tested in an expression assasy such as B-Gal or GFP expression.