Due to the composition of the exon microarrays and the nature of the splicing detection algorithm, the current study describes primarily the alternative skipping and inclusion of individual exons.
This observation suggested a cost-effective method of regulation: the cells do not have to produce completely new exons and proteins, but merely change the composition of the existing exons [ 46].
We summarized the nucleotide composition, length of the exons, and intron phase patterns bordering respective exons in tables, and genic structures to scale and exons to its translated protein regions in schematic figures.
To test for this possibility, for each exon end, we calculated the difference (Eenrich) between the observed ESE density (Eobs) and the expected ESE density (Eexpect), given the base composition of that exon end.
The complex structure of Dscam1 gene may have evolved along two possible evolutionary pathways: 1) changing the number of alternative exons by exon duplication and deletion; 2) changing the composition of individual exons by point mutations (including substitution, insertion and deletion).
To calculate the expected number of ESE sites found in an exon end, given its base composition, the sequence of the exon end was randomly shuffled 100 times and the expected number of ESE sites was taken to be the mean over these 100 shuffled sequences.
Hemi and homozygous genomic deletions encompassing FHIT and WWOX exons were targeted to reflect the exon dosage composition of the genes.
Codonic composition of coding exons has particular probabilistic properties that allow gene finders to synchronize their prediction engines with gene structure and efficiently stitch exons in frame-consistent fashion [ 2].
This study describes the value of an innovative approach using an MLPA assay specifically designed to scan the exon intragenic composition of the FHIT and WWOX genes involved at fragile sites, here evaluated in the setting of ESCC South African cell lines and primary tumor specimens.
In addition, previous studies suggest that the order of intron removal can influence the final mRNA transcript composition of exons and introns.
