Ares Lab Yeast Intron Database

http://www.cse.ucsc.edu/research/compbio/yeast_introns.html

Telerski, A.¹, Centers, R. J.², Ares, M.²

¹Department of Computer Science Jack Baskin School of Engineering Universitiy of California, Santa Cruz Santa Cruz, CA 95064
²Center for Molecular Biology of RNA Sinsheimer Laboratories University of California, Santa Cruz Santa Cruz, CA 95064

Contact ares@biology.ucsc.edu

Database Description

This searchable database contains information about the location, structure, and function of spliceosomal introns in the nuclear genome of Saccharomyces cerevisiae. Searches produce reports for each intron satisfying the search criteria, showing key information, including a short gene description with links to the Saccharomyces Genome Database, estimated transcription rate, special features of the intron, literature or EST verification links, intron size, splice sites and branchpoint sequences and complete sequences of the intron and flanking exons, as well as the sequence generated by splicing. Expression measurements that profile the impact of mutations on the splicing of each intron are also included in the reports. The underlying data can also be downloaded in generic formats. We enjoy hearing suggestions, corrections, and new information and can update the information easily.

Recent Developments

The current version is 3.0 and has several added features not found in version 2.1. We now display expression data from splicing sensitive microarrays (Clark et al. 2002). In addition a newly added feature called the spliced sequence shows the sequence found after joining of the exon segments by conceptually splicing out the intron. We have also added a static page in which we present information that is hard to find in other databases, for example introns in non- protein-coding parts of RNA (SGD only annotates those introns that interrupt ORFs), or the locations of intron-encoded snoRNAs.

Acknowledgements

We thank Chuck Sugnet for help in displaying the expression data and Tyson Clark for catching many mistakes. Leslie Grate wrote the original version of the database. Evan Hurowitz (Stanford) and Joe DeRisi (UCSF) contributed information about specific introns in advance of publication.

REFERENCES

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.
Clark, T., Sugnet, C., and Ares, M. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296: 907-10.
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.
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.
Spingola, M., Grate, L., Haussler, D., and Ares, M. (1999) Genome-wide bioinformatic and molecular analysis of yeast introns. RNA 5: 221-34.