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Table 1 Statistics on Transcript Pattern Variant Data presented in this work.

From: AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation

  Human Mouse
Genes 7669 5862
Splice patterns (& average number per gene) 41201 (5.4) 27132 (4.6)
Transcript patterns (& average number per gene) 12559 (1.6) 7755 (1.3)
PolyA sites as detected by AltTrans pipeline1 (& average number per gene) 10221 (1.3) 6976 (1.19)
AltTrans polyA sites that are "skipped" 2468 1113
ATD PolyA sites as detected by AltTrans and AltPAS2 pipelines (& average number per gene) 17104 (2.2) 9451 (1.61)
ATD polyA sites that are "skipped" 5459 2214
Genes showing splice events (as seen among the splice patterns) 5672 (74%) 3825 (65%)
Genes showing multiple polyA sites (considering the polyA sites from both AltTrans and AltPAS)3 4603 (60%) 2456 (42%)
Genes showing both splice events and multiple polyA sites (considering the polyA sites from both AltTrans and AltPAS) 3523 (46%) 1718 (29%)
Genes showing multiple polyA sites (considering only the AltTrans polyA sites)4 2053 (27%) 1026 (18%)
Genes showing both splice events and polyA events (considering only the AltTrans polyA sites) 1679 (22%) 736 (13%)
Genes showing >= 2 Splice Patterns 6859 4989
Genes showing >= 2 Transcript patterns 3179 1548
EST/mRNA sequences confirming Splice Patterns 837828 726916
EST/mRNA sequences confirming Transcript Patterns 38731 18045
  1. 1:AltTrans pipeline requires for a transcript pattern that the underlying splicing and the terminating polyA site are confirmed by the same set of EST./mRNA sequences.
  2. 2:AltPAS pipeline identifies polyA sites independent of the underlying splicing pattern.
  3. 3:A gene is considered as undergoing alternative polyadenylation if it multiple polyA sites (from the merged list of AltTrans and AltPAS polyA sites) are seen mapped to the gene.
  4. 4:Consideration of only the AltTrans polyA sites gives a conservative estimate for the extent of alternative polyadenylation. AltTrans polyA sites differ from AltPAS sites in the manner they are detected; AltTrans polyA sites are confirmed by the same set of EST/mRNA sequences that confirm the splice structure of transcript pattern.