Next Article in Journal
The Role of Gamma Delta T Cells in Autoimmune Rheumatic Diseases
Previous Article in Journal
TRPC1 Regulates the Activity of a Voltage-Dependent Nonselective Cation Current in Hippocampal CA1 Neurons
Open AccessArticle

Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites

by Katharina Frey 1,2,* and Boas Pucker 1,3
1
Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
2
Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615 Bielefeld, Germany
3
Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
*
Author to whom correspondence should be addressed.
Cells 2020, 9(2), 458; https://doi.org/10.3390/cells9020458
Received: 20 January 2020 / Revised: 11 February 2020 / Accepted: 14 February 2020 / Published: 18 February 2020
Most protein-encoding genes in eukaryotes contain introns, which are interwoven with exons. Introns need to be removed from initial transcripts in order to generate the final messenger RNA (mRNA), which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides, which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5′ end and AG at the 3′ end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice site combinations, which have been known for years. Recently, various minor non-canonical splice site combinations were detected with numerous dinucleotide permutations. Here, we expand systematic investigations of non-canonical splice site combinations in plants across eukaryotes by analyzing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences, such as an apparently increased CT-AC frequency in fungal genome sequences. Canonical GT-AG splice site combinations in antisense transcripts are a likely explanation for this observation, thus indicating annotation errors. In addition, high numbers of GA-AG splice site combinations were observed in Eurytemora affinis and Oikopleura dioica. A variant in one U1 small nuclear RNA (snRNA) isoform might allow the recognition of GA as a 5′ splice site. In depth investigation of splice site usage based on RNA-Seq read mappings indicates a generally higher flexibility of the 3′ splice site compared to the 5′ splice site across animals, fungi, and plants. View Full-Text
Keywords: splicing; spliceosome; RNA-Seq; gene structure; mRNA processing; introns; sequence conservation; splice site analysis pipeline splicing; spliceosome; RNA-Seq; gene structure; mRNA processing; introns; sequence conservation; splice site analysis pipeline
Show Figures

Figure 1

MDPI and ACS Style

Frey, K.; Pucker, B. Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites. Cells 2020, 9, 458.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop