Table 4

In silico analysis of novel sequence variations.

Gene (exon/intron)

Nucleotide change

Method

Result

Comments

MSH2 (exon 7)

c.1276G > A

Human Splice Finder (v.2.4)

(HSF)

(*)

EIEs (Zhang et al) No

Rescue ESE change

PESE octamers/no

ESS (Wang et al) motif

PESS octamers found

IIEs (Zhang et al)

Other splicing motifs

(Goren et al)

"wt" donor site broken (84.7/73.68)

Scores predicted for the wt seq/score predicted for the mut seq

ESE Finder: c.1274 (SRp55)→ new site

Rescue ESE: c.1271/c.1272→ site broken

ESE from HSF: c.1273/c.1276 (9G8)→site broken

Silencer motifs (Sironi et al): c.1271/c.1272→site broken

Fas-Ess hexamers: c.1275→ site broken

hnRNP motifs: c.1273/c.1274 (hnRNP A1)→site broken

NNSplice (0.9)

"wt" donor site broken (0.91/-)

Scores predicted for the wt seq/score predicted for the mut seq

NetGene2 Server

"wt" donor site broken (0.83/-)

Scores predicted for the wt seq/score predicted for the mut seq

MSH2 (intron 3)

c.646/46delC

Human Splice Finder (v.2.4)

(HSF)

(*)

ESE Finder

Rescue ESE

PESE octamers

EIEs (Zhang et al) No

ESE from HSF change

Silencer motifs/no

(Sironi et al) motif

ESS (Wang et al) found

IIEs (Zhang et al)

hnRNP motifs

Other splicing motifs

(Goren et al)

Variation in one of the potential branch points (c.646-48) (79.39/23.83)

Scores predicted for the wt seq/score predicted for the mut seq

PESS octamers: c.646-49 (46.39/87.56)/c.646-46→ new site

NNSplice (0.9)

SD: 0.90/0.90 No

SA: 0.90/0.91 change

Scores predicted for the wt seq/score predicted for the mut seq

NetGene2 Server

SD: 0.76/0.76 No

SA: 0.23/0.25 change

Scores predicted for the wt seq/score predicted for the mut seq

(*) these algorithms are included in the HSF analysis

Thodi et al. BMC Cancer 2010 10:544   doi:10.1186/1471-2407-10-544