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. 2020 Mar 18;20(1):119.
doi: 10.1186/s12870-020-2312-y.

CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers

Ying Sun  1 , Quanbao Zhang  1 , Bing Liu  1 , Kui Lin  1 , Zhonghua Zhang  2 , Erli Pang  3
Affiliations

CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers

Ying Sun et al. BMC Plant Biol. .

Abstract

Background: Alternative splicing (AS) plays a critical regulatory role in modulating transcriptome and proteome diversity. In particular, it increases the functional diversity of proteins. Recent genome-wide analysis of AS using RNA-Seq has revealed that AS is highly pervasive in plants. Furthermore, it has been suggested that most AS events are subject to tissue-specific regulation.

Description: To reveal the functional characteristics induced by AS and tissue-specific splicing events, a database for exploring these characteristics is needed, especially in plants. To address these goals, we constructed a database of annotated transcripts generated by alternative splicing in cucumbers (CuAS: http://cmb.bnu.edu.cn/alt_iso/index.php) that integrates genomic annotations, isoform-level functions, isoform-level features, and tissue-specific AS events among multiple tissues. CuAS supports a retrieval system that identifies unique IDs (gene ID, isoform ID, UniProt ID, and gene name), chromosomal positions, and gene families, and a browser for visualization of each gene.

Conclusion: We believe that CuAS could be helpful for revealing the novel functional characteristics induced by AS and tissue-specific AS events in cucumbers. CuAS is freely available at http://cmb.bnu.edu.cn/alt_iso/index.php.

Keywords: Alternative splicing; Cucumber; Isoform-level features; Isoform-level function; Tissue-specific alternative splicing events.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Overview of the construction of the CuAS database
Fig. 2
Fig. 2
Search tools of CuAS
Fig. 3
Fig. 3
Web interface of CuAS. (a) JBrowse. (b) At the gene level. (c) At the transcript level. (d) At the isoform level
Fig. 4
Fig. 4
Isoform features of CuAS
See this image and copyright information in PMC

References

    1. Lopez AJ. Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu Rev Genet. 1998;32:279–305. doi: 10.1146/annurev.genet.32.1.279. - DOI - PubMed
    1. Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S. Function of alternative splicing. Gene. 2013;514(1):1–30. doi: 10.1016/j.gene.2012.07.083. - DOI - PMC - PubMed
    1. Staiger D, Brown JW. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell. 2013;25(10):3640–3656. doi: 10.1105/tpc.113.113803. - DOI - PMC - PubMed
    1. Lee Y, Rio DC. Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem. 2015;84:291–323. doi: 10.1146/annurev-biochem-060614-034316. - DOI - PMC - PubMed
    1. Berget SM, Moore C, Sharp PA. Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci U S A. 1977;74(8):3171–3175. doi: 10.1073/pnas.74.8.3171. - DOI - PMC - PubMed