Difference between revisions of "Part:BBa K390002"
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This part can serve as a general RBS for ''Synechocystis'' sp. PCC 6803, until a library of RBS strengths in PCC 6803 is assembled. The consensus RBS was determined by aligning the 9 nucleotides on the 3' end sequence of the 16S rRNA to the 20 nucleotides preceding the start codon of every gene in PCC 6803. The most frequently represented nucleotide at each location along the alignment was considered to be the consensus. (Note: the alignment was done in relation to the 16S rRNA sequence, and not the start codon, as the spacing between RBS and the start codon varied considerably from gene to gene). | This part can serve as a general RBS for ''Synechocystis'' sp. PCC 6803, until a library of RBS strengths in PCC 6803 is assembled. The consensus RBS was determined by aligning the 9 nucleotides on the 3' end sequence of the 16S rRNA to the 20 nucleotides preceding the start codon of every gene in PCC 6803. The most frequently represented nucleotide at each location along the alignment was considered to be the consensus. (Note: the alignment was done in relation to the 16S rRNA sequence, and not the start codon, as the spacing between RBS and the start codon varied considerably from gene to gene). | ||
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| + | This part contains the Shine-Delgarno core consensus sequence. Approximately half of the genes in Synechocystis sp. PCC 6803 are preceded by the core SDS (Sazuka T and Ohara O. 1996. Sequence features surrounding the translation initiation sites assigned on the genome sequence of ''Synechocystis'' sp. strain PCC6803 by amino-terminal protein sequencing. DNA Research 3: 225-232), with the rest utilizing either matches with other sites on the 16S rRNA or binding of the fMet-tRNA to the start codon to align the mRNA with the ribosome. The consensus RBS contains this core SDS. | ||
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Latest revision as of 00:52, 2 August 2010
5'UTR and consensus RBS from psbA2 in Synechocystis sp. PCC 6803
This is the 5'UTR and RBS region from gene psbA2 in Synechocystis sp. PCC 6803. It covers the entire region from the end of the promoter (as reported in Imamura S and Asayama M. 2009. Sigma Factors for Cyanobacterial Transcription. Gene Regulation and Systems Biology 3: 65-87) to immediately before the start codon of the psbA2 gene.
The RBS region has been mutated from the native RBS "taaggaatta" to the consensus RBS "aaaggaggtt" for Synechocystis sp. PCC 6803.
This part can serve as a general RBS for Synechocystis sp. PCC 6803, until a library of RBS strengths in PCC 6803 is assembled. The consensus RBS was determined by aligning the 9 nucleotides on the 3' end sequence of the 16S rRNA to the 20 nucleotides preceding the start codon of every gene in PCC 6803. The most frequently represented nucleotide at each location along the alignment was considered to be the consensus. (Note: the alignment was done in relation to the 16S rRNA sequence, and not the start codon, as the spacing between RBS and the start codon varied considerably from gene to gene).
This part contains the Shine-Delgarno core consensus sequence. Approximately half of the genes in Synechocystis sp. PCC 6803 are preceded by the core SDS (Sazuka T and Ohara O. 1996. Sequence features surrounding the translation initiation sites assigned on the genome sequence of Synechocystis sp. strain PCC6803 by amino-terminal protein sequencing. DNA Research 3: 225-232), with the rest utilizing either matches with other sites on the 16S rRNA or binding of the fMet-tRNA to the start codon to align the mRNA with the ribosome. The consensus RBS contains this core SDS.
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Unknown
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Unknown
- 23INCOMPATIBLE WITH RFC[23]Unknown
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]