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Table 4 Counting number of conserved octamers in the exonic proximity

From: Computational prediction of splicing regulatory elements shared by Tetrapoda organisms

Intronic flanks next to 5'SS

Intronic flanks next to 3'SS

5'SS ISEs

3'SS ISEs

 

Conserved

Non-Conserved

 

Conserved

Non-Conserved

Elements

4,024

6,800

Elements

4,272

8,363

Non-

elements

251,842

518,369

Non-

elements

261,387

578,106

Fisher 2-tail test: 1.81 × 10-22

Fisher 2-tail test: 1.59 × 10-10

5'SS ISSs

3'SS ISSs

 

Conserved

Non- Conserved

 

Conserved

Non- Conserved

Element

399

648

Element

6,537

11,385

Non-

elements

251,842

518,369

Non-

elements

261,387

578,106

Fisher 2-tail test: 0.00025

Fisher 2-tail test: 3.46 × 10-51

  1. Set of all other possible elements was obtained by excluding the ISEs and ISSs supporting either 5' or 3' SSs from the set of all possible octamers. We counted cases where oligonucleotides stay entirely conserved versus changing in at least one nucleotide position between the pairs of sequences from multiple sequence alignments, where only the motifs containing no gaps were considered. In case of 5'SS elements we considered window of size 20 nt starting 16 nt downstream from 5' exonic boundary in human sequence, where in case of elements supporting 3'SS we considered 20 nt window ending 63 nt upstream of 3' exonic boundary.
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BMC Genomics

ISSN: 1471-2164

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