DBASS5 - Record Details
| Gene |
RB1 (Ensembl) |
Location of Aberrant 5' Splice Site | Intron |
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| Phenotype |
Retinoblastoma (OMIM) |
Distance between Authentic and Aberrant 5' Splice Site (nt) |
+45
|
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| Mutation | del(E15-16_IVS15+37) | Change in the Reading Frame |
0
|
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| Reference(s) |
Shew, J. Y., Chen, P. L., Bookstein, R., Lee, E. Y., and Lee, W. H. (1990). Deletion of a splice donor site ablates expression of the following exon and produces an unphosphorylated RB protein unable to bind SV40 T antigen. Cell Growth Differ 1, 17-25. Pub Med Article # 1964074 |
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| Nucleotide Sequence[a] | gtgccatttc accccagcct ggcaacagag caagacacca tctaaaaaaa aaaaaaaaaa aaaaaaaaat tcaatgctga cacaaataag gtttcaatta aacaacttct tttttttttt ttaaattatc tgtttcagGA AGAAGAACGA TTATCCATTC AAAA(TTTTA Ggtaaatttt ttacttttag taaaaaattt ttttcttt)t tatagaa/gt aagtatttta taatcttttt ttttttcctt tagCAAACTT CTGAATGACA ACATTTTTCA TATGTCTTTA TTGGCGTGCG CTCTTGAGGT TGTAATGGCC ACATATAGCA | ||||
| Terminal Exon? | No | ||||
| Splice Site Strength[b] | Authentic Site |
Aberrant Site |
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| Maximum Entropy Model [1] |
6.62
|
9.82
|
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| Maximum Dependence Decomposition Model [2] |
10.68
|
13.98
|
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| First Order Markov Model [1] |
5.49
|
8.09
|
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| Weight Matrix Model [1] |
8.70
|
8.70
|
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| Genomic Co-ordinates (hg38) | |||||
| Aberrant Splice Site |
chr13:48380129/48380130 |
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| Mutation |
chr13:48380078 |
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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.