DBASS5 - Record Details
| Gene |
MSH2 (Ensembl) |
Location of Aberrant 5' Splice Site | Exon |
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| Phenotype |
Hereditary nonpolyposis colon cancer (OMIM) |
Distance between Authentic and Aberrant 5' Splice Site (nt) |
-48
|
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| Mutation | IVS7+2T>A | Change in the Reading Frame |
0
|
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| Reference(s) |
Auclair, J., Busine, M.P., Navarro, C., Ruano, E., Montmain, G., Desseigne, F., Saurin, J.C., Lasset, C., Bonadona, V., Giraud, S., Puisieux, A., Wang, Q. (2006) Systematic mRNA analysis for the effect of MLH1 and MSH2 missense and silent mutations on aberrant splicing. Hum. Mutat., 27, 145-154. Pub Med Article # 16395668 |
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| Nucleotide Sequence[a] | ATTGAATTTA GTGGAAGCTT TTGTAGAAGA TGCAGAATTG AGGCAGACTT TACAAGAAGA TTTACTTCGT CGATTCCCAG ATCTTAACCG ACTTGCCAAG AAGTTTCAAA GACAAGCAGC AAACTTACAA GATTGTTACC GACTCTATCA GG/GTATAAA TCAACTACCT AATGTTATAC AGGCTCTGGA AAAACATGAA Gg(t>a)aac aagtgatttt gtttttttgt tttccttcaa ctcatacaat atatacttgg caatgtgctg tcctcataaa gttggtggtg gtgactcact cttaggacac attcagattt cttttttttt tttttttgag aaggagtctt gctccgttgc caaggctaga gtgcagtggc | ||||
| Percent Utilisation | 20 | ||||
| Terminal Exon? | No | ||||
| Splice Site Strength[b] | Authentic Site |
Aberrant Site |
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| Maximum Entropy Model [1] |
8.92
|
2.31
|
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| Maximum Dependence Decomposition Model [2] |
12.68
|
7.68
|
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| First Order Markov Model [1] |
6.99
|
3.77
|
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| Weight Matrix Model [1] |
2.68
|
2.68
|
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| Genomic Co-ordinates (hg38) | |||||
| Aberrant Splice Site |
chr2:47429893/47429894 |
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| Mutation |
chr2:47429943 |
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Legend
- [a] /, cryptic or de novo splice sites; > nucleotide substitutions; (), deletions; [], duplications or insertions. Intronic sequences are in lower case (in blue), exons are in upper case (in green)
- [b] Shapiro and Senapathy matrix scores were calculated according to an algorithm published previously (1). Maximum entropy and the first-order Markov and weight matrix models were computed as described (2)
References
- Shapiro, M.B. and Senapathy, P. (1987) RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res., 15, 7155-7174.
- Yeo, G. and Burge, C.B. (2004) Maximum entropy modelling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol., 11, 377-394.
- Burge, C. 1998. Modeling dependencies in pre-mRNA splicing signals. In Computational methods in molecular biology (eds. S.L. Salzberg et al.), chapter 8, pp. 129–164. Elsevier Science, Philadelphia, PA.