exon
Definition
An exon is a protein-coding or functional sequence within a gene that is retained in the mature messenger RNA (mRNA) after splicing. During gene expression, the initial RNA transcript (pre-mRNA) contains both exons and introns. Through RNA splicing, introns are removed and exons are joined together to form the final mRNA molecule that is translated into protein. Exons are fundamental to understanding gene structure and protein diversity, as alternative splicing allows different combinations of exons to be included or excluded, enabling a single gene to produce multiple protein isoforms. This mechanism significantly expands proteomic complexity beyond what the genome alone would suggest. Exon boundaries are defined by splice sites recognized by the spliceosome machinery, and mutations affecting these sites can lead to disease by disrupting normal protein production.
Visualize exon in Nodes Bio
In Nodes Bio, researchers can visualize exon-level networks to map alternative splicing patterns across conditions or tissues. Network graphs can connect exons to their resulting protein isoforms, regulatory splicing factors, and disease phenotypes. Users can analyze how specific exon inclusion/exclusion events create functional protein variants and trace causal relationships between splice variants and biological outcomes, enabling discovery of therapeutic targets in splicing-related diseases.
Visualization Ideas:
- Exon-isoform networks showing alternative splicing patterns across tissue types
- Splicing factor-exon regulatory networks mapping trans-acting elements to target exons
- Disease-exon association networks linking splice variants to phenotypes and clinical outcomes
Example Use Case
A cancer researcher investigating tumor heterogeneity discovers that a specific exon in the BRCA1 gene shows differential inclusion patterns between aggressive and non-aggressive breast cancer subtypes. By analyzing RNA-seq data, they identify that exon 11 skipping creates a truncated protein isoform associated with chemotherapy resistance. The researcher needs to map which splicing factors regulate this exon, identify downstream signaling pathways affected by the variant isoform, and determine if targeting the splicing machinery could restore normal BRCA1 function and improve treatment response.