Fig. 1

Suboptimal features of the BRAF intron 3 and intron 8. a The sequences of indicated 5′ splice sites in base-pairing with the 5′ end of U1 snRNA. The lines below the U1 sequences indicate six most important U1 5′end nucleotides (core) for base-pairing with each 5′ splice site during 5′ splice site recognition. The intron 5′ end sequences are bolded with the intron 5 end G as position 1 and the exon 3′ end nucleotide immediately upstream of the intron 5′ end G as position -1. b The sequences of intron 3 and intron 8 3′ splice sites with predicted 7-nt (red lines) and 5-nt BPS (green lines). The mammalian consensus 7-nt BPS sequence YNYURAC [23, 24] or 5-nt YUNAN [25–27] are shown for comparison. Red color A in the predicted 7-nt BPS and in the predicted 5-nt BPS indicates the putative BP adenosine A. Conservation value (CV) for each predicted 7-nt BPS is calculated by using Human Splice Finder (http://www.umd.be/HSF/), with indicated distance of the bulged A from the downstream 3′ splice site. Purines in the putative PPT are labeled in light blue or red