VastDB

VastDB provides genome-wide quantitative profiles of alternative splicing (AS) events across vertebrate cell and tissue types to support analysis of splicing regulation and function.

Key Features:

• Quantitative Profiles: Inclusion levels of AS events are quantified from RNA-seq data across genomes.
• Functional Associations: The database links AS events to functional associations that suggest potential roles in cellular processes and disease mechanisms.
• Diverse Biological Contexts: Data cover a wide range of vertebrate cell and tissue types and developmental stages for comparative analyses.
• Regulatory Relationships: Profiles reveal intergenic and intragenic regulatory relationships among different classes of AS events and map tissue-regulated exons.
• Isoform Diversity: At least 48% of multiexonic protein-coding genes express multiple splice variants in a cell/tissue-specific manner, and over 18% of genes simultaneously express multiple major isoforms across diverse cell and tissue types.
• Coexpression and Translation: Multiple major isoforms are generally coexpressed within the same cells and are often engaged by translating ribosomes.
• Functional Enrichment: Genes encoding multiple isoforms are significantly enriched for functions related to transcriptional control.

Scientific Applications:

• Functional Genomics: Enables analysis of the regulatory complexity introduced by alternative splicing to study gene function and regulation.
• Comparative Biology: Facilitates comparative studies across vertebrate species, developmental stages, and tissue types to assess conservation and divergence in splicing mechanisms.
• Disease Research: Supports identification of AS events linked to disease mechanisms, biomarkers, and potential therapeutic targets.
• Transcriptional Control Studies: Supports investigation of the role of AS in transcriptional control and gene expression networks.

Methodology:

Alternative splicing inclusion levels are quantified from RNA-seq data.