Computational prediction of splicing regulatory elements shared by Tetrapoda organisms

BMC Genomics

Table 5 Average PU for the predicted octamer elements surrounded by ± 30 nt context analyzed in various segments as shown in Figure 2.

Elements	Next to 5'SS		Next to 3'SS		Inside intron		Inside exon
	Number	Average PU	Number	Average PU	Number	Average PU	Number	Average PU
5'SS ISEs	3,946	0.100/0.100	3,954	0.185/0.191	4,014	0.189/0.196	4,017	0.148/0.154
5'SS ISSs	1,361	0.174/0.184	700	0.241/0.247	3,993	0.182/0.173 (P = 0.0064)	1,744	0.157/0.144
3'SS ISEs	3,930	0.165/0.165	4,061	0.205/0.206	3,989	0.190/0.187	3,984	0.182/0.174
3'SS ISSs	3,954	0.144/0.163	3,987	0.120/0.127	4,039	0.194/0.185 (P = 0.0063)	4,050	0.133/0.132
All Other elements	4,004	0.128/0.130	3,966	0.163/0.160	4,053	0.152/0.146 (P = 0.0083)	4,024	0.134/0.123

We classified the predicted elements surrounded by ± 30 nt context according to segments of their location. The mean PU values calculated according to [2] for wild type and dinucleotide reshuffled contexts are followed by significant P-values obtained with the Wilcoxon two-sided rank-sum tests. Only the P-values rejecting the null hypotheses (P < 1%) that the distribution is similar in the two groups of PU values are shown.

ISSN: 1471-2164