Figure 6. Alternative 5′ and 3′ splice sites.

HMMSplicer results within 15 bp of RefSeq introns were analyzed to measure the number of bases added or removed from the spliced transcript. There were 997 instances where the intron had an alternate 5′ splice site (5′SS, shown in grey) and 2,577 instances of an alternate 3′ splice site (3′SS site, shown in black). The most common alternative splice was 3 bases removed or added to the exon at the 3′SS. TopHat results showed a similar pattern, though only 875 alternates (262 5′SS alternates and 613 3′SS alternates) are found, less than a quarter of the HMMSplicer results. WebLogos were constructed from the sequences at the 1,099 alternate 3′SS with three bases removed from the transcript and the 460 alternate 3′SS with three bases added to the transcript. For these, the green dashed line shows the alternate splice site while the red dashed line shows the canonical splice site. In both cases, a repetition of the YAG splice motif is evident.