spots
 
Ares lab Yeast Intron Database
Version 3.0
Created and maintained by Leslie Grate, Angela Telerski, Tyson Clark, Ross Centers and Manny Ares

Departments of Molecular, Cell & Developmental Biology and Computer Science in the Division of Natural Sciences and the Jack Baskin School of Engineering, University of California, Santa Cruz, CA  95064
Supported by the W. M. Keck Foundation, the Packard Foundation, and the National Institutes of Health.
Yeast Spliceosomal Introns

Intron Table

Extras

Links

Update History

Acknowledgments



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Welcome

               This site contains information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Introns present special problems for the annotation of eukaryotic genomes.  Splice sites are information-poor, and their recognition by the splicing apparatus is highly context-dependent and regulated, making identification by computational gene prediction programs a challenge.  At present we do not understand splice site context well enough to predict which potential splice sites will be used, and thus how the genomic sequences will be expressed.

               Understanding the how and why of introns will require genome level information about splicing.  One element of this will involve understanding splicing patterns and how they are regulated globally.  Another element will involve understanding how splicing patterns change during evolution.  To begin we study yeast, since it has the simplest known eukaryotic genome.  In these pages we have listed known spliceosomal introns in the yeast genome and documented the splice sites actually used.  Through the use of microarrays designed to monitor splicing, we are beginning to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition.

                  In this edition (version 3.0), we include expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors.  These data are displayed on each intron page for browsing and can be downloaded for other types of analysis.

               We encourage corrections or additions to this site.  We are no longer supporting the earlier versions of the site.  Please contact Manny Ares with questions or comments. The documents below may provide useful literature references on this topic.


Grate, L., and Ares, M. (2002) Searching Yeast Intron Data at the Areslab Website. (In Guide to Yeast Genetics and Molecular and Cell Biology, Part B, C. Guthrie and G. Fink, eds) Methods Enz. 350: 380-392. [ pdf ]

Clark, T., Sugnet, C., and Ares, M. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296:907-10. [ pdf ][ Supplement ]

Davis, C., Grate L., Spingola, M., and Ares, M. (2000) Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. Nucl. Acids Res. 28: 1700-1706. [ pdf ]

Ares, M., Grate, L., and Pauling, M. H. (1999) A handful of intron-containing genes produce the lion’s share of yeast mRNA. RNA 5:1138-1139. [ pdf ]

Spingola, M., Grate, L., Haussler, D., and Ares, M. (1999)  Genome-wide bioinformatic and molecular analysis of yeast introns. RNA 5: 221-34. [ pdf ]



Page last updated July 5, 2002

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