2020
DOI: 10.1186/s12870-020-2312-y
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CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers

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… Show more

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Cited by 9 publications
(7 citation statements)
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References 48 publications
(27 reference statements)
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“…Alternative splicing (AS) is a significant mechanism for regulating the expression of genes in eukaryotes [ 22 ]. AS refers to one mRNA precursor producing diverse transcripts, which is thought of as an important post-transcriptional mechanism for increasing the diversity of transcripts and proteins [ 23 ]. AS plays a major role in affecting protein function; therefore, it is necessary to systematically identify AS events.…”
Section: Introductionmentioning
confidence: 99%
“…Alternative splicing (AS) is a significant mechanism for regulating the expression of genes in eukaryotes [ 22 ]. AS refers to one mRNA precursor producing diverse transcripts, which is thought of as an important post-transcriptional mechanism for increasing the diversity of transcripts and proteins [ 23 ]. AS plays a major role in affecting protein function; therefore, it is necessary to systematically identify AS events.…”
Section: Introductionmentioning
confidence: 99%
“…In recent years, tea plant multi-omics sequencing data have been published [ 32 , 33 ], but the integration and comprehensive utilization of these data is more difficult than other species due to the tea plant genome size of about 3 Gb and high heterozygosity [ 34 , 35 ]. In this study, we integrated more than 20 Tb of sequencing data from multiple data sources to build a powerful database of tea plant variation.…”
Section: Discussionmentioning
confidence: 99%
“…Numerous databases have been created to store, mine, analyze, and disseminate vast transcriptomic and genetic datasets and to provide a central portal for research and breeding communities. The genomics and functional genomics databases specially constructed for the Cucurbitaceae, including cucumber, include the Cucurbit Genomics Database (CuGenDB, http://www.cucurbitgenomics.org/, accessed on 15 December 2021) [61] and the cucumber alternative splicing (CuAS) database (http://cmb.bnu.edu.cn/alt_iso/index.Php, accessed on 20 December 2021) [62].…”
Section: Information Resources For Cucumber Researchmentioning
confidence: 99%
“…Meanwhile, the CuAS database includes AS transcripts from cucumber and annotations that include genomic information, AS events, isoform functions, isoform features, and tissue-specific splicing events. CuAS can be used to explore the relationships between functional features and predicted AS transcripts [62].…”
Section: Information Resources For Cucumber Researchmentioning
confidence: 99%