Animal, fungi, and plant genome sequences harbour different non-canonical splice sites

Frey K, Pucker B (2020)
Cells 9(2): 458.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Most protein encoding genes in eukaryotes contain introns which are interwoven with exons. After transcription, introns need to be removed in order to generate the final mRNA which can be translated into an amino acid sequence by the ribosome. 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 are known for many years. During the last few years, various minor non-canonical splice site combinations were detected with all possible dinucleotide permutations. Here we expand systematic investigations of non-canonical splice site combinations in plant genomes to all eukaryotes by analysing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences such as a substantially increased CT-AC frequency in fungal genomes. In addition, high numbers of GA-AG splice site combinations were observed in two animal species. 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.
Stichworte
non-canonical splice sites; plants; animal; fungi; genome-wide; RNA-Seq
Erscheinungsjahr
2020
Zeitschriftentitel
Cells
Band
9
Ausgabe
2
Art.-Nr.
458
ISSN
2073-4409
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2935311

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Frey K, Pucker B. Animal, fungi, and plant genome sequences harbour different non-canonical splice sites. Cells. 2020;9(2): 458.
Frey, K., & Pucker, B. (2020). Animal, fungi, and plant genome sequences harbour different non-canonical splice sites. Cells, 9(2), 458. https://doi.org/10.3390/cells9020458
Frey, Katharina, and Pucker, Boas. 2020. “Animal, fungi, and plant genome sequences harbour different non-canonical splice sites”. Cells 9 (2): 458.
Frey, K., and Pucker, B. (2020). Animal, fungi, and plant genome sequences harbour different non-canonical splice sites. Cells 9:458.
Frey, K., & Pucker, B., 2020. Animal, fungi, and plant genome sequences harbour different non-canonical splice sites. Cells, 9(2): 458.
K. Frey and B. Pucker, “Animal, fungi, and plant genome sequences harbour different non-canonical splice sites”, Cells, vol. 9, 2020, : 458.
Frey, K., Pucker, B.: Animal, fungi, and plant genome sequences harbour different non-canonical splice sites. Cells. 9, : 458 (2020).
Frey, Katharina, and Pucker, Boas. “Animal, fungi, and plant genome sequences harbour different non-canonical splice sites”. Cells 9.2 (2020): 458.
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Dissertation, die diesen PUB Eintrag enthält
Computational pangenomics and its application to sugar beet and crop wild relatives
Sielemann K (2023)
Bielefeld: Universität Bielefeld.

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PMID: 32085510
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Preprint: 10.1101/616565

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