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Open Access Open Badges Research article

Effect of 5'UTR introns on gene expression in Arabidopsis thaliana

Betty YW Chung14, Cas Simons23, Andrew E Firth1, Chris M Brown1 and Roger P Hellens2*

Author Affiliations

1 Biochemistry Department, University of Otago, Dunedin, New Zealand

2 HortResearch, Auckland, New Zealand

3 Institute of Molecular Biosciences, Brisbane, Australia

4 Bioscience Institute, University College Cork, Cork, Ireland

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BMC Genomics 2006, 7:120  doi:10.1186/1471-2164-7-120

Published: 19 May 2006



The majority of introns in gene transcripts are found within the coding sequences (CDSs). A small but significant fraction of introns are also found to reside within the untranslated regions (5'UTRs and 3'UTRs) of expressed sequences. Alignment of the whole genome and expressed sequence tags (ESTs) of the model plant Arabidopsis thaliana has identified introns residing in both coding and non-coding regions of the genome.


A bioinformatic analysis revealed some interesting observations: (1) the density of introns in 5'UTRs is similar to that in CDSs but much higher than that in 3'UTRs; (2) the 5'UTR introns are preferentially located close to the initiating ATG codon; (3) introns in the 5'UTRs are, on average, longer than introns in the CDSs and 3'UTRs; and (4) 5'UTR introns have a different nucleotide composition to that of CDS and 3'UTR introns. Furthermore, we show that the 5'UTR intron of the A. thaliana EF1α-A3 gene affects the gene expression and the size of the 5'UTR intron influences the level of gene expression.


Introns within the 5'UTR show specific features that distinguish them from introns that reside within the coding sequence and the 3'UTR. In the EF1α-A3 gene, the presence of a long intron in the 5'UTR is sufficient to enhance gene expression in plants in a size dependent manner.