URL: | http://www.rnairport.com/ |
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Description: | A 5'-leader, known initially as the 5'-untranslated region, contains multiple isoforms due to alternative splicing (aS) and alternative transcription start site (aTSS). Therefore, a representative 5'-leader is demanded to examine the embedded RNA regulatory elements in controlling translation efficiency. The representative 5'-leader-contained gene models and 5'leaderP can be accessed at RNAirport (http://www.rnairport.com/leader5P/). |
Year founded: | 2024 |
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Country/Region: | China |
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University/Institution: | Wuhan University |
Address: | Wuhan University, 299 Bayi Road, Wuchang District, Wuhan, Hubei, P.R. China |
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Country/Region: | China |
Contact name (PI/Team): | Guoyong Xu |
Contact email (PI/Helpdesk): | guoyong.xu@whu.edu.cn |
RNAirport: a deep neural network-based database characterizing representative gene models in plants. [PMID: 38518981]
A 5'-leader, known initially as the 5'-untranslated region, contains multiple isoforms due to alternative splicing (aS) and alternative transcription start site (aTSS). Therefore, a representative 5'-leader is demanded to examine the embedded RNA regulatory elements in controlling translation efficiency. Here, we develop a ranking algorithm and a deep-learning model to annotate representative 5'-leaders for five plant species. We rank the intra-sample and inter-sample frequency of aS-mediated transcript isoforms using the Kruskal-Wallis test-based algorithm and identify the representative aS-5'-leader. To further assign a representative 5'-end, we train the deep-learning model 5'leaderP to learn aTSS-mediated 5'-end distribution patterns from cap-analysis gene expression data. The model accurately predicts the 5'-end, confirmed experimentally in Arabidopsis and rice. The representative 5'-leader-contained gene models and 5'leaderP can be accessed at RNAirport (http://www.rnairport.com/leader5P/). The Stage 1 annotation of 5'-leader records 5'-leader diversity and will pave the way to Ribo-Seq open-reading frame annotation, identical to the project recently initiated by human GENCODE. |