Exon level alternative splicing

The ExoPLOT toolkit is designed for the ultra-fast exploration and analysis of alternatively spliced TE exons in a collection of huge and informative RNAseq.

We minimize the time of the standard “annotation-quantification-normalization-comparison-visualization” pipeline to a simple query, which depends on genomic coordinates for input.

Thus, the choice of coordinates becomes the most crucial factor to define ExoPLOT’s behavior, and possibly will lead to different observations.

Here, we explain ExoPLOT’s coordinate input, and detail the corresponding output in relation to different common splicing patterns.

Alternative splicing often is as complex as illustrated for the LPIN1 gene below:


It is very common that a gene or locus contains different combinations of multiple alternative splicing events. Not all products will be included in all databases.

The ExoPLOT toolkit focuses on the exon level of alternative splicing.

Below we introduce different prototypical splicing events and the correct application of ExoPLOT tool corresponding to each category.

How ExoPLOT distinguishes

Following is one of the most common alternative splicing patterns overall and those origined from TEs: the Cassette Exon, or some also call it Exon Skipping.


In the chart above, we illustrate the two different kinds of cDNA-reads that are part of the ExoPLOT analysis.

Reads overlapping the TE exon boundary (colored in dark pink) are denominated and counted as “with TE”.

Reads skipping the TE exon (colored in light pink) are denominated and counted as “without TE”.

Both types of cDNA reads are required to calculate the TE exon expression level; thus the coordinates of the illustrated TE exon are most informative (and should be provided) for the analysis of this splicing event.

Alternative splicing and coordinate input

Below we define different splicing patterns and describe the fitting coordinate input for the analysis of each event.

Cassette Exon

Alternative 5’ Splice Site

Alternative 3’ Splice Site

Alternative First Exon

Alternative Last Exon

Additional Exon in Alternative First/Last Splicing