Skip to main content

Advertisement

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

From: Variation in alternative splicing across human tissues

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  
  1. 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.