title: ERISdb: a database of plant splice sites and splicing signals.
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/.
authors.affiliation: Laboratory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland. izabel@amu.edu.pl
authors.forename: Michał Wojciech
authors.initials: MW
authors.lastname: Szcześniak
authors.forename: Michał
authors.initials: M
authors.lastname: Kabza
authors.forename: Rafał
authors.initials: R
authors.lastname: Pokrzywa
authors.forename: Adam
authors.initials: A
authors.lastname: Gudyś
authors.forename: Izabela
authors.initials: I
authors.lastname: Makałowska
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D020407:Internet; D007438:Introns; D035683:MicroRNAs / Q000235:genetics; D010944:Plants / Q000235:genetics; D022821:RNA Splice Sites; D012326:RNA Splicing; D018749:RNA, Plant / Q000235:genetics*; D038621:Regulatory Sequences, Ribonucleic Acid; D057386:Search Engine; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D012984:Software
chemical_list: D035683:MicroRNAs; D022821:RNA Splice Sites; D018749:RNA, Plant; D038621:Regulatory Sequences, Ribonucleic Acid