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. |
||||
|
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 |
|
|
||||
|
Kurmangaliyev and Gelfand BMC Genomics 2008 9:13 doi:10.1186/1471-2164-9-13 |
||||
