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Open Access Open Badges Research article

Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function

Thomas F Clarke and Patricia L Clark*

Author Affiliations

Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA

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BMC Genomics 2010, 11:118  doi:10.1186/1471-2164-11-118

Published: 18 February 2010



The process of translation can be affected by the use of rare versus common codons within the mRNA transcript.


Here, we show that rare codons are enriched at the 5' and 3' termini of genes from E. coli and other prokaryotes. Genes predicted to be secreted show significant enrichment in 5' rare codon clusters, but not 3' rare codon clusters. Surprisingly, no correlation between 5' mRNA structure and rare codon usage was observed.


Potential functional roles for the enrichment of rare codons at terminal positions are explored.