Predict Splice Site Effect

This tool will analyze a variant track to determine whether the variants fall within potential splice sites. First select your variant track (figure 27.45) followed by a transcript track (see figure 27.46). As part of the dialog you can choose to exclude all variants that do not fall within a splice site.

Image predict_splice_site_effect1
Figure 27.45: Variant track selection.

Image predict_splice_site_effect2
Figure 27.46: Transcript track selection.

If a variant falls within two base pairs of an intron-exon boundary, it will be annotated as a possible splice site disruption (see figure 27.47).

Image predict_splice_site_effect3
Figure 27.47: Results of the Predict Splice Site Effect tool.