Open Access Highly Accessed Research article

Transcriptome analysis of the parasite Encephalitozoon cuniculi: an in-depth examination of pre-mRNA splicing in a reduced eukaryote

Cameron J Grisdale1, Lisa C Bowers23, Elizabeth S Didier23 and Naomi M Fast1*

Author Affiliations

1 Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada

2 Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA

3 Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA

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BMC Genomics 2013, 14:207  doi:10.1186/1471-2164-14-207

Published: 28 March 2013

Additional files

Additional file 1:

Gene expression levels. Expression levels in FPKM are shown for all 1985 E. cuniculi genes at three post-infection time-points.

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Additional file 2:

Intron motifs. (A) Weblogo of 34 E. cuniculi intron motifs, showing strict 5' splice site, branch point, and 3' AG. (B) Weblogo of three recently discovered introns, with intron motifs that are consistent with currently annotated introns. (C) Combined old and new data for a total of 37 introns, showing very little change from (A).

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Additional file 3:

Splicing levels in two fungal species. Levels of splicing found for 46 Saccharomyces cerevisiae introns (A) and 48 Candida albicans introns (B). Splicing level was measured by counting the number of spliced and unspliced transcripts and then dividing spliced by total transcripts to give a percentage of splicing.

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Additional file 4:

RNA decay genes. Table of six key RNA decay pathway genes found in E. cuniculi. Gene names in yeast and are shown, as well as the protein BLAST e-values.

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