Computational analysis of splicing errors and mutations in human transcripts

Kurmangaliyev, Yerbol Z; Gelfand, Mikhail S

doi:10.1186/1471-2164-9-13

BMC Genomics

Table 2 Properties of skipped exons (S-exons) and exons with cryptic sites (C-exons). For all exon parameters the medians are reported. The last column reports parameters of all internal exons in our dataset of RefSeq genes. MW: the statistical significance of the differences between the S- and C-exons by the Mann-Witney test; n/s – non significant.

From: Computational analysis of splicing errors and mutations in human transcripts

	S-exons	C-exons	MW	Internal exons
Set size
Mutated donor sites	67	42
Mutated acceptor sites	42	72
All	109	114		154846
Exon length (nucleotides)
Mutated donor sites	114	147	0,024
Mutated acceptor sites	112,5	130	n/s
All	114	136	0,020	123
Densities of cis-acting elements(candidate sites per nucleotide)
*ESEfinder: SC35*
Mutated donor sites	0,043	0,042	n/s
Mutated acceptor sites	0,038	0,045	n/s
All	0,042	0,043	n/s	0,038
*ESEfinder: SF2/ASF*
Mutated donor sites	0,025	0,037	0,048
Mutated acceptor sites	0,036	0,041	n/s
All	0,028	0,040	0,005	0,036
*ESEfinder: SRp40*
Mutated donor sites	0,034	0,043	0,006
Mutated acceptor sites	0,040	0,043	n/s
All	0,035	0,043	0,004	0,040
*ESEfinder: SRp55*
Mutated donor sites	0,028	0,024	n/s
Mutated acceptor sites	0,022	0,023	n/s
All	0,025	0,023	n/s	0,023
*RESCUE-ESE*
Mutated donor sites	0,090	0,108	n/s
Mutated acceptor sites	0,100	0,080	n/s
All	0,091	0,094	n/s	0,099
*PESE*
Mutated donor sites	0,048	0,082	0,007
Mutated acceptor sites	0,057	0,055	n/s
All	0,055	0,064	0,023	0,064
*PESS*
Mutated donor sites	0,012	0,008	n/s
Mutated acceptor sites	0,009	0,007	n/s
All	0,011	0,007	n/s	0,007
Splice site scores
*Mutated donor sites*
Authentic donor sites	18,52	18,49	n/s	18,82
Acceptor sites of the (upstream) exon	18,70	19,67	n/s	19,08
Acceptor sites of the (downstream) intron	19,37	18,98	n/s	19,09
*Mutated acceptor sites*
Authentic acceptor sites	19,59	18,72	0,05	19,08
Donor sites of the (downstream) exon	18,44	18,56	n/s	18,82
Donor sites of the (upstream) intron	18,48	18,51	n/s	18,79
Distance to the closest candidate site(nucleotides)
Mutated donor sites	220,5	75	0,067	289
Mutated acceptor sites	185	66	0,024	81

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ISSN: 1471-2164

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