ERISdb: A Database of Plant Splice Sites and Splicing Signals
Open Access
- 7 January 2013
- journal article
- Published by Oxford University Press (OUP) in Plant and Cell Physiology
- Vol. 54 (2), e10
- https://doi.org/10.1093/pcp/pct001
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/.Keywords
This publication has 56 references indexed in Scilit:
- OMA 2011: orthology inference among 1000 complete genomesNucleic Acids Research, 2010
- U12 type introns were lost at multiple occasions during evolutionBMC Genomics, 2010
- Genome-wide analyses of alternative splicing in plants: Opportunities and challengesGenome Research, 2008
- U12DB: a database of orthologous U12-type spliceosomal intronsNucleic Acids Research, 2006
- Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal intronsNucleic Acids Research, 2003
- Splicing signals and factors in plant intron removalBiochemical Society Transactions, 2002
- Evolutionary Fates and Origins of U12-Type IntronsMolecular Cell, 1998
- Functional analysis of the polypyrimidine tract in pre-mRNA splicingNucleic Acids Research, 1997
- dbEST — database for “expressed sequence tags”Nature Genetics, 1993
- Basic local alignment search toolJournal of Molecular Biology, 1990