Variation in alternative splicing across human tissues

Table 2 Sequence motifs enriched in skipped exons (SEs) and alternative 5' splice site exons (A5Es)

AS type /tissue (motif name)	Oligonucleotides	Occurrences	Consensus (% of exons containing)
SE/brain (BR1)	CUCCUG	169	CUCC (45.3)
	CUCC U	323
	CUCC C	264
	CUCC	945
	C CUCC C	137	CCUC (41.0)
	CCUC C	363
	CCUC	1021
	GCCUC C	136
	GCCUC	375
	GCCUC A	122
	G GCCUC	118
	U GCCUC	108
SE/brain (BR2)	GGGU U	97	GGGU (25.6)
	GGGU	411
	A GGGU	116
SE/brain (BR3)	UGGG A	324	UGGG (47.2)
	UGGG	948
	C UGGG	426
	CC UGGG	171
SE/brain (BR4)	GGGA UU	58	GGGA (45.5)
	GGGA U	176
	GGGA	840
SE/brain (BR5)	CUCA	925	CUCA (46.5)
	CUCA C	206
	GC CUCA	122
	GG CUCA	102
	G CUCAC	79
	CUCA GC	126
SE/brain (BR6)	UAGC	269	UAGC (18.0)
	UAGC U	106
	G UAGC	96
	G UAGC U	51
	AG UAGC	47
	UAGC UG	54
SE/brain (BR7)	UAGG	186	UAGG (13.8)
	U UAGG	63
	U UAGG G	24
SE/testis (TE1)	UAGG	99	UAGG (16.6)
	U UAGG	33
Core A5E/liver (LI1)	AAAC	42	AAAC (53.3)
	A AAAC	18
Core A5E/liver (LI2)	UAAA	29	UAAA (40.0)
	UAAA CC	5

Sequence motifs of length four to six bases that are significantly over-represented (p < 0.002) in SEs relative to constitutively spliced exons from brain- or testis-derived ESTs are shown, followed by the number of occurrences in SEs in these tissues. Sequence motifs are grouped/aligned by similarity, and shared tetramers are shown in bold and listed in the last column, followed by the fraction of SEs that contain the given tetramer. Sequence motifs significantly over-represented (p < 0.01) in the core of A5Es from human liver-derived ESTs are shown at the bottom, followed by the number of A5E occurrences and the fraction of A5Es that contain the given tetramer. Statistical significance was evaluated as described in Materials and methods.

ISSN: 1474-760X