ERISdb: A database of plant splice sites and splicing signals

Authors:

• Michał Szcześniak,
• Michal Kabza,
• Rafal Pokrzywa,
• Adam Gudyś,
• Izabela Makałowska

Abstract

Splicing is one of the major contributors to observed spatiotemporal diversification of transcripts and proteins in metazoans. There are numerous factors that affect the process, but splice sites themselves along with the adjacent splicing signals are critical here. Unfortunately, there is still little known about splicing in plants and, consequently, further research in some fields of plant molecular biology will encounter difficulties. 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. The analyses included identification of orthologous splice sites, polypyrimidine tracts and branch sites. 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. We also provide experimental evidence for plant splice sites in the form of expressed sequence tag and RNA-Seq data. All the data are stored in a novel database called ERISdb and are freely available at http://lemur.amu.edu. pl/share/ERISdb/. © The Author 2013. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved.