DBASS5 - Record Details
| Gene |
MUTYH (Ensembl) |
Location of Aberrant 5' Splice Site | Exon |
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| Phenotype |
Lung cancer cell line (OMIM) |
Distance between Authentic and Aberrant 5' Splice Site (nt) |
+237
|
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| Mutation | IVS1+5G>C | Change in the Reading Frame |
0
|
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| Reference(s) |
Yamaguchi, S., Shinmura, K., Saitoh, T., Takenoshita, S., Kuwano, H. and Yokota, J. (2002) A single nucleotide polymorphism at the splice donor site of the human MYH base excision repair genes results in reduced translation efficiency of its transcripts. Genes Cells, 7, 461-474. Pub Med Article # 12056405 |
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| Nucleotide Sequence[a] | GTAATCTTTC TCTCCTGCTC TCGCGGCGGG AACGCGGGGC CTCCGTGTTC TGCTGTCTTC ATCAGCGTGG GCCGCGGgta g(g/c)gggt agtggggtgg ctgggtttgg gctttccaga gaaggtgacg ctgcctgagc tgagcttaaa gcacgcccag gagttagact aggagagggt cgtgtggggg aaagaagggc gttctgggca tcggtaaatt cccagagagg atggagagct cagtgatctc cagaaagtga aagaggcggg gagtgggcca tcggaggagg ctgcccaggg tgtaagagcg accgattg/g tagggaagct tttgtaataa tccaatcaag tgataatgtg aacttgaatt aaggctggca gtatggatgg cgaggaaggg acaaattgtg aagcagctag gcggtatagt cgacctagag | ||||
| Percent Utilisation | 100 | ||||
| Terminal Exon? | No | ||||
| Splice Site Strength[b] | Authentic Site |
Aberrant Site |
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| Maximum Entropy Model [1] |
6.74
|
2.16
|
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| Maximum Dependence Decomposition Model [2] |
10.68
|
8.08
|
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| First Order Markov Model [1] |
6.92
|
4.95
|
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| Weight Matrix Model [1] |
3.65
|
3.65
|
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| Genomic Co-ordinates (hg38) | |||||
| Aberrant Splice Site |
chr1:45339661/45339662 chr1:45339894/45339895 |
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| Mutation |
chr1:45339893 |
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| Comments | The C allele creates cryptic 5'ss associated with lower translation (~30%) | ||||
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.