plantintron

plantintron aggregates intron-splicing efficiency measurements from over 57,000 public RNA-Seq libraries across Arabidopsis, maize, rice, and soybean to enable comparative analysis of intron retention and splicing regulation.

Key Features:

• Extensive Database Coverage: Contains over 57,000 public RNA-Seq libraries (Arabidopsis: 25,283; maize: 17,789; rice: 10,710; soybean: 3,974) covering approximately 1.6 million introns.
• Curated Library Annotations: Libraries are annotated for mutant- and treatment-related conditions along with their matched controls to support precise comparisons of splicing efficiency.
• Intron-Splicing Ratios: Intron-splicing ratios are calculated from the aggregated libraries to quantify splicing efficiency across samples.
• Graphical Representation: Provides graphical displays of intron-splicing efficiency across tissues, developmental stages, and stress-related conditions.
• Comprehensive Condition and Mutant Data: Includes data from 3,313 distinct treatment conditions and 3,594 genetic mutants for analysis of condition- and genotype-specific splicing changes.

Scientific Applications:

• Differential Intron Retention Analysis: Identification of introns with differential retention across conditions and genotypes using calculated splicing ratios.
• Gene Regulation and Expression Studies: Investigation of how intron retention contributes to gene regulation and expression under diverse environmental signals.
• Developmental and Stress Response Research: Comparative analysis of splicing dynamics across tissues, developmental stages, and stress-related conditions, and in genetic mutants.

Methodology:

Aggregated public RNA-Seq data across four plant species; calculated intron-splicing ratios from these libraries; performed manual curation of library annotations to associate mutants, treatments, and matched controls.