scTEA-db : a comprehensive database of novel terminal exon isoforms identified from human single cell transcriptomes

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Nucleic Acids Research. Oxford University Press (OUP). 2024, 52(D1), pp. D1018-D1023. ISSN 0305-1048. eISSN 1362-4962. Available under: doi: 10.1093/nar/gkad878
Zusammenfassung

The usage of alternative terminal exons results in messenger RNA (mRNA) isoforms that differ in their 3′ untranslated regions (3′ UTRs) and often also in their protein-coding sequences. Alternative 3′ UTRs contain different sets of cis-regulatory elements known to regulate mRNA stability, translation and localization, all of which are vital to cell identity and function. In previous work, we revealed that ∼25 percent of the experimentally observed RNA 3′ ends are located within regions currently annotated as intronic, indicating that many 3′ end isoforms remain to be uncovered. Also, the inclusion of not yet annotated terminal exons is more tissue specific compared to the already annotated ones. Here, we present the single cell-based Terminal Exon Annotation database (scTEA-db, www.scTEA-db.org) that provides the community with 12 063 so far not yet annotated terminal exons and associated transcript isoforms identified by analysing 53 069 publicly available single cell transcriptomes. Our scTEA-db web portal offers an array of features to find and explore novel terminal exons belonging to 5538 human genes, 110 of which are known cancer drivers. In summary, scTEA-db provides the foundation for studying the biological role of large numbers of so far not annotated terminal exon isoforms in cell identity and function.

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ISO 690BARQUIN, Miguel, Ian U. KOUZEL, Beat EHRMANN, Michael BASLER, Andreas J. GRUBER, 2024. scTEA-db : a comprehensive database of novel terminal exon isoforms identified from human single cell transcriptomes. In: Nucleic Acids Research. Oxford University Press (OUP). 2024, 52(D1), pp. D1018-D1023. ISSN 0305-1048. eISSN 1362-4962. Available under: doi: 10.1093/nar/gkad878
BibTex
@article{Barquin2024scTEA-68040,
  year={2024},
  doi={10.1093/nar/gkad878},
  title={scTEA-db : a comprehensive database of novel terminal exon isoforms identified from human single cell transcriptomes},
  number={D1},
  volume={52},
  issn={0305-1048},
  journal={Nucleic Acids Research},
  pages={D1018--D1023},
  author={Barquin, Miguel and Kouzel, Ian U. and Ehrmann, Beat and Basler, Michael and Gruber, Andreas J.}
}
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