PlantAPAdb

PlantAPAdb catalogs alternative cleavage and polyadenylation (APA) sites across multiple plant species to support investigations of APA-mediated regulation of gene expression.

Key Features:

• Comprehensive Data Collection: PlantAPAdb includes APA sites from six plant species: Oryza sativa (japonica and indica), Arabidopsis thaliana, Medicago truncatula, Trifolium pratense, Phyllostachys edulis, and Chlamydomonas reinhardtii.
• Sequencing-derived Annotations: APA site annotations are derived from diverse 3' sequencing protocols and biological samples.
• Genomic Coordinates and Heterogeneity: Provides detailed genomic locations of APA sites, including heterogeneous cleavage sites and sample-specific expression levels.
• Poly(A) Signal Profiles: Contains poly(A) signal data associated with APA sites across different genomic regions, reflecting cis-element profiles.
• 3' UTR Dynamics: Documents 3' untranslated region shortening and lengthening events resulting from APA.
• Evolutionary Conservation: Includes information on conservation of APA sites across plant species to support comparative analyses.

Scientific Applications:

• Gene Expression Regulation: Enables analysis of APA as a regulatory mechanism affecting transcript isoforms and expression levels.
• Developmental and Tissue-specific Studies: Supports investigations of developmental stage–specific and tissue-specific APA patterns.
• Environmental and Stress Response: Facilitates study of APA changes in response to environmental stimuli.
• Comparative and Evolutionary Analyses: Allows cross-species comparisons of APA site conservation and cis-element evolution.

Methodology:

APA sites were identified from diverse 3' sequencing protocols applied to multiple biological samples.