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Additionally, alternative splicing plays a key role in gene regulation through regulated production of splice variants with a premature termination codon that are degraded in nonsense-mediated decay ( Palusa and Reddy 2010). Protein isoforms produced in this way may possess altered functions ( Stamm et al. In the process of alternative splicing, primary transcripts from intron-containing genes are spliced by differential selection of splice sites in a spatiotemporal manner, leading to production of multiple mature mRNAs from a single gene ( Pan et al. It therefore does not seem surprising that introns play fundamental roles, being key elements in the process of alternative splicing, which is a critical contributor to the transcriptome and proteome complexity in most eukaryotes. For instance, the primary transcripts are longer, up to hundreds of thousands of bases, than the actual coding sequence, which requires a lot more substrates and energy in the process of transcription. The presence of introns has notable functional consequnces for the cell. In photosynthetic eukaryotes, the vast majority of protein-coding genes (up to 90%) contain introns ( Barbazuk and McGinnis 2008, Labadorf et al. One of the most prominent features of eukaryotic genes is that they possess quite a complex structure, which is attributed to the presence of spliceosomal introns. All the data are stored in a novel database called ERISdb and are freely available at. We also provide experimental evidence for plant splice sites in the form of expressed sequence tag and RNA-Seq data. Additionally we identified putative intronic and exonic cis-regulatory motifs, U12 introns as well as splice sites in 45 microRNA genes in five plant species. The analyses included identification of orthologous splice sites, polypyrimidine tracts and branch sites. Keeping this in mind, we performed a large-scale analysis of splice sites in eight plant species, using novel algorithms and tools developed by us. Unfortunately, there is still little known about splicing in plants and, consequently, further research in some fields of plant molecular biology will encounter difficulties.
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There are numerous factors that affect the process, but splice sites themselves along with the adjacent splicing signals are critical here. Splicing is one of the major contributors to observed spatiotemporal diversification of transcripts and proteins in metazoans.