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)

   CUCCU

323

   CUCCC

264

   CUCC

945

  CCUCCC

137

CCUC (41.0)

  CCUCC

363

  CCUC

1021

 GCCUCC

136

 GCCUC

375

 GCCUCA

122

GGCCUC

118

UGCCUC

108

SE/brain (BR2)

   GGGUU

97

GGGU (25.6)

   GGGU

411

  AGGGU

116

SE/brain (BR3)

  UGGGA

324

UGGG (47.2)

  UGGG

948

 CUGGG

426

CCUGGG

171

SE/brain (BR4)

   GGGAUU

58

GGGA (45.5)

   GGGAU

176

   GGGA

840

SE/brain (BR5)

  CUCA

925

CUCA (46.5)

  CUCAC

206

GCCUCA

122

GGCUCA

102

 GCUCAC

79

   CUCAGC

126

SE/brain (BR6)

  UAGC

269

UAGC (18.0)

  UAGCU

106

 GUAGC

96

 GUAGCU

51

AGUAGC

47

  UAGCUG

54

SE/brain (BR7)

  UAGG

186

UAGG (13.8)

 UUAGG

63

 UUAGGG

24

SE/testis (TE1)

  UAGG

99

UAGG (16.6)

 UUAGG

33

Core A5E/liver (LI1)

  AAAC

42

AAAC (53.3)

 AAAAC

18

Core A5E/liver (LI2)

 UAAA

29

UAAA (40.0)

 UAAACC

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.

Yeo et al. Genome Biology 2004 5:R74   doi:10.1186/gb-2004-5-10-r74