MEPDB: Database of microExons in plants.

Microexons, ≤ 51-nucleotide (nt), particularly ultra-short ones (1-15 nt), are challenging to identify due to their small size and frequent absence in genome annotations, which limits understanding of their biological roles. Using our developed pipeline, we identified 2398 small internal microexons across 10 diverse plant species, and most of them were not annotated in the reference genomes. These microexons are grouped into 45 conserved microexon clusters based on microexon-tags, which include the coding microexons and portions of flanking exon sequences. Leveraging these clusters, we developed a predictive method that identified 20 224 microexons across 132 plant genomes. For these microexons, we developed the Database of MicroExons in Plants (MEPDB), which includes genomic coordinates, sequences (nucleotide/amino acid), gene annotations, and updated CDS information for microexon annotations, as well as an integrated tool for RNA-seq-independent microexon prediction, thereby offering a comprehensive resource for plant microexon research.