Table 3.

Site-specific frequencies and position weight matrix (PWM) for 275 5′ ss. The consensus sequence (UAAAG ∣GUAUGUU UAAUU) can be obtained from those large site-specific PWM entries, with the most important sites in bold italics . The χ ² test is performed for each site against the background frequencies (A = 0.3279, C = 0.1915, G = 0.2043, and U = 0.2763). The nucleotide sites are labeled with the five exon nucleotides as −5 to −1 and the 12 intron nucleotides as 1 to 12. The PWM is nearly identical when the introns in 5′ UTR were excluded.

Site	A	C	G	U	χ 2	P	A	C	G	U
−5	94	32	57	92	11.798	0.0081088	0.0641	−0.7117	0.0245	0.2792
−4	119	47	48	61	14.117	0.0027505	0.4032	−0.1599	−0.2225	−0.3115
−3	139	38	43	55	39.672	0.0000001	0.6268	−0.4651	−0.3805	−0.4601
−2	138	40	36	61	38.899	0.0000001	0.6164	−0.3915	−0.6355	−0.3115
−1	91	45	88	51	27.270	0.0000052	0.0174	−0.2223	0.6492	−0.5685
1	0	1	274	0	1060.426	0.0000004	−8.1042	−5.4675	2.2855	−8.1044
2	0	9	0	266	658.096	0.0000003	−8.1042	−2.5200	−8.1048	1.8081
3	268	1	2	4	522.754	0.0000003	1.5723	−5.4675	−4.6732	−4.1523
4	17	29	1	228	428.607	0.0000002	−2.3805	−0.8528	−5.5454	1.5859
5	2	0	272	1	1041.047	0.0000004	−5.2765	−8.1049	2.2750	−5.8967
6	10	8	2	255	583.545	0.0000003	−3.1271	−2.6862	−4.6732	1.7472
7	97	18	39	121	55.570	0.0000001	0.1092	−1.5351	−0.5206	0.6734
8	95	54	35	91	11.363	0.0099180	0.0793	0.0397	−0.6759	0.2635
9	123	45	34	73	22.172	0.0000601	0.4508	−0.2223	−0.7175	−0.0534
10	118	41	38	78	17.334	0.0006034	0.3911	−0.3560	−0.5579	0.0418
11	105	33	43	94	17.367	0.0005940	0.2232	−0.6676	−0.3805	0.3101
12	90	44	42	99	12.109	0.0070180	0.0015	−0.2546	−0.4142	0.3847