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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

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