Pucker, Boas ; Brockington, Samuel F.: Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. In: BMC Genomics. Jg.19 H. 1. 2018
Inhalt
- Methods
- Collection of data sets and quality control
- Classification of annotated splice sites
- Investigation of splice site diversity
- Analysis of splice site conservation
- Validation of annotated splice sites
- Phylogenetic tree construction
- Intron length analyses
- Comparison of non-canonical splice sites to overall sequence variation
- Results
- Genomic properties of plants and diversity of non-canonical splice sites
- Non-canonical splice sites are likely to be similar to canonical splice sites
- Non-canonical splice sites in single copy genes
- Intron analysis
- Conservation of non-canonical splice sites
- RNA-Seq-based validation of annotated splice sites
- Quantification of splice site usage
- Discussion
- Confirmation of bona fide splicing from minor non-canonical combinations
- Species-specific differences in minor non-canonical splice site combinations
- Putative mechanisms for processing of minor non-canonical splice sites
- Usage of non-canonical splice sites
- Limitations of the current analyses
- Future perspectives
- Conclusion
- Additional files
- Acknowledgements
- Funding
- Availability of data and materials
- Authors’ contributions
- Ethics approval and consent to participate
- Consent for publication
- Competing interests
- Publisher’s Note
- References