Ribosomal Binding Sites

Ribosomal Binding Site (RBS)

This site, located at the 5' untranslated region (UTR) of the mRNA transcript, regulates protein synthesis based on its sequence and structure. There are two consensus sequences, named Kozak and Shine Dalgarno (after their discoverers), which are known to facilitate efficient translation in Eukaryotes and Prokaryotes respectively. See chart for more details.

Name Type of Organism Description

Kozak Sequence Eukaryote Preferred sequence context which allows effective ribosomal binding at initiation site. The favored context is:
-6 -5 -4 -3 -2 -1 1 2 3 4
G C C A C C A U G G
around the initiating methionine (AUG), with the A at the -3 being the most important, and a purine at +4, preferably G being next most influential. [Kozak, M. (1991) J. Biol. Chem. 266, 19867-19870.(pdf)

Shine Dalgarno (SD) Sequence Prokaryote The SD sequence is complementary to the 3' end of the 16S rRNA. Its consensus sequence is 5'-UAAGGAGG-3' which is followed by an initiation codon, most commonly AUG. (About 8% of start sites use GUG, whereas UUG and AUU are rare initiators present in autogenously regulated genes). The optimal spacing between the SD sequence and the start codon is 8 nt, but translation initiation is severely affected only if this distance is reduced below 4 nt or increased above 14 nt. [Shine, J. and Dalgarno, L. (1975) Eur. J. Biochem. 57, 221.]
An additional mRNA feature affecting translation initiation is the downstream box (DB), located after the initiation codon and complementary to bases 1469-1483 of the 16S rRNA. DBs consensus sequence is: 5'-AUGAAUCACAAAGUG-3'.

Related Bioinformatics Tools

RBS Calculator - tunable control of translation initiation rate (Salis lab)

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Name	Type of Organism	Description
Kozak Sequence	Eukaryote	Preferred sequence context which allows effective ribosomal binding at initiation site. The favored context is: -6 -5 -4 -3 -2 -1 1 2 3 4 G C C A C C A U G G around the initiating methionine (AUG), with the A at the -3 being the most important, and a purine at +4, preferably G being next most influential. [Kozak, M. (1991) J. Biol. Chem. 266, 19867-19870.(pdf)
Shine Dalgarno (SD) Sequence	Prokaryote	The SD sequence is complementary to the 3' end of the 16S rRNA. Its consensus sequence is 5'-UAAGGAGG-3' which is followed by an initiation codon, most commonly AUG. (About 8% of start sites use GUG, whereas UUG and AUU are rare initiators present in autogenously regulated genes). The optimal spacing between the SD sequence and the start codon is 8 nt, but translation initiation is severely affected only if this distance is reduced below 4 nt or increased above 14 nt. [Shine, J. and Dalgarno, L. (1975) Eur. J. Biochem. 57, 221.] An additional mRNA feature affecting translation initiation is the downstream box (DB), located after the initiation codon and complementary to bases 1469-1483 of the 16S rRNA. DBs consensus sequence is: 5'-AUGAAUCACAAAGUG-3'.