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. Fur...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-03-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12870-020-2312-y |
| _version_ | 1818446512489758720 |
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| author | Ying Sun Quanbao Zhang Bing Liu Kui Lin Zhonghua Zhang Erli Pang |
| author_facet | Ying Sun Quanbao Zhang Bing Liu Kui Lin Zhonghua Zhang Erli Pang |
| author_sort | Ying Sun |
| collection | DOAJ |
| description | 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 . |
| first_indexed | 2024-12-14T19:48:54Z |
| format | Article |
| id | doaj.art-021bc884aabe4a4ea84402d405189318 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-14T19:48:54Z |
| publishDate | 2020-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-021bc884aabe4a4ea84402d4051893182022-12-21T22:49:28ZengBMCBMC Plant Biology1471-22292020-03-012011710.1186/s12870-020-2312-yCuAS: a database of annotated transcripts generated by alternative splicing in cucumbersYing Sun0Quanbao Zhang1Bing Liu2Kui Lin3Zhonghua Zhang4Erli Pang5MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal UniversityMOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal UniversityMOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal UniversityMOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal UniversityKey Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesMOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal UniversityAbstract 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 .http://link.springer.com/article/10.1186/s12870-020-2312-yCucumberAlternative splicingIsoform-level functionIsoform-level featuresTissue-specific alternative splicing events |
| spellingShingle | Ying Sun Quanbao Zhang Bing Liu Kui Lin Zhonghua Zhang Erli Pang CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers BMC Plant Biology Cucumber Alternative splicing Isoform-level function Isoform-level features Tissue-specific alternative splicing events |
| title | CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers |
| title_full | CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers |
| title_fullStr | CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers |
| title_full_unstemmed | CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers |
| title_short | CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers |
| title_sort | cuas a database of annotated transcripts generated by alternative splicing in cucumbers |
| topic | Cucumber Alternative splicing Isoform-level function Isoform-level features Tissue-specific alternative splicing events |
| url | http://link.springer.com/article/10.1186/s12870-020-2312-y |
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