Additional file 1:

List of 87 synonymous and missense splice-affecting genome variants (SAVs) that cause exon skipping used for analysis in this study. The variants are derived from [12,13,37,41,44,47,48,54-56,65-103].

Format: PDF Size: 117KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 2:

List of 80 synonymous and missense variants that have been experimentally tested in mini-gene constructs and do not cause changes in splicing. The variants are derived from [74,104-106].

Format: PDF Size: 108KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 3:

(a) Full results of ESR changes and bootstrap analysis of exon skipping SAVs vs. hSNPs, (b) splice-neutral variants vs. hSNPs, (c) SAVs that cause exon inclusion vs. hSNPs, (d) ectopic SAVs vs. hSNPs and (e) ectopic-like hSNPs vs. hSNPs with a ΔSS of 0.

Format: PDF Size: 148KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 4:

Set of graphs illustrating that exon-skipping SAVs are significantly overrepresented within certain positions across the four ESEfinder matrices.

Format: PDF Size: 279KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 5:

Methods and results for an analysis on whether using local RNA secondary structure as a filter improves our ability to distinguish exon skipping SAVs from hSNPs. Our results suggest that using this filter does not improve our ability to predict SAVs although a small number of SAVs may arise from the indirect uncovering of ESS motifs by changes in local RNA secondary structure.

Format: PDF Size: 154KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 6:

List of 20 variants that cause increased exon inclusion. The variants are derived from [44,47,104,107,108].

Format: PDF Size: 78KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 7:

Two plots that show that mean RC score is negatively correlated with minimum distance from a splice junction (top) but not correlated with exon length (bottom).

Format: PDF Size: 89KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 8:

Only distributions of exon lengths up to 600 bp were plotted for clarity. Genome-wide exons were divided into constitutively spliced (CE) and alternatively spliced (AS) as defined by the Hollywood database [36]. A fifth, expected set of exons represents a set of exon lengths we would expect given the average distribution of hSNPs across the genome and fits the real distribution of HapMap exons closely.

Format: PDF Size: 101KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 9:

List of 54 variants that cause de novo 5' or 3' ectopic splice site activation. The variants are derived from [4,37,86,109-154].

Format: PDF Size: 98KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 10:

Base substitution distributions in hSNPs were used a background nucleotide substitution rates in calculating an expected distribution of ESE/ESS changes of the NI-ESR hexamer set (Figure 3). Significant differences in distributions between skipping SAVs and hSNPs (such as that seen in A->T, T->C and G->T) and ectopic SAVs (A->T, A->C, T->A, C->G) while potentially of biological interest, should be treated with caution due to small number of skipping and ectopic SAVs and large discrepancy in dataset size between these sets and HapMap SNPs.

Format: PDF Size: 175KB Download file

This file can be viewed with: Adobe Acrobat Reader