We have shown that the mCG density-CpG O/E correlation is the most marked in internal exons.
Most of the internal exons are of exactly the same lengths across a wide range of organisms from zebrafish to human (supplementary tables 2, 4, 6, 8).
GRB target genes are often associated with higher ratios between CGI length and transcript length (CpG-to-gene ratio), and the overlapping CGIs map not only to the promoter, as in most other genes, but also introns, internal exons, and in some cases, even cover the entire target gene [ 25].
This indicates that most of the intron-exon boundary regions in these internal exons have reduced CBI values, as shown in the whole genome analyses [ 20].
Although some strong ESEs can influence splicing at a distance of several kilobases [ 49], functional ESEs are most abundant in close proximity to splice junctions of internal exons [ 50].
In addition to the 3' most exons, polyadenylation sites (poly(A) sites) can also exist in introns and internal exons.
Within genes, the 5′ most exons show methylation which, like CpG island promoters, correlates with gene silencing, while both internal exons and introns show variable methylation (Brenet et al. 2011; Edwards et al. 2010).
A list of the novel internal exons is provided as Additional file 5. Exon skipping is reported to be the most common alternative splicing event [ 55].
Methylation at internal exons is suggestive of splicing.
Trans-splicing has been used to repair mutant RNA transcripts via competition for the spliceosome using pre-trans-splicing molecules, or "PTMs". Previous studies have demonstrated that functional PTMs can be designed for either 3'- or 5'-exon replacement, with a vast majority of the work to date focusing on repair of mutations within internal exons and via 3'-exon replacement.
