Data Note

The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence

Jason M Bechtel , Preeti Rajesh , Irina Ilikchyan , Ying Deng , Pankaj K Mishra , Wang Qi , Xiaochun Wu , Kirill A Afonin , William E Grose , Wang Ye , Sadik Khuder and Alexei Fedorov

BMC Research Notes 2008, 1:3

Published:	26 February 2008

Abstract (provisional)

Background

Some mutations in the internal regions of exons occur within splicing enhancers and silencers, influencing the pattern of alternative splicing in the corresponding genes. To understand how these sequence changes affect splicing, we created a database of these mutations.

Findings

The Alternative Splicing Mutation Database (ASMD) serves as a repository for all exonic mutations not associated with splicing junctions that measurably change the pattern of alternative splicing. In this initial published release (version 1.2), only human sequences are present, but the ASMD will grow to include other organisms. The ASMD is available at http://mco321125.meduohio.edu/~jbechtel/asmd/. This relational database allows users to investigate connections between mutations and features of the surrounding sequences, including flanking sequences, RNA secondary structures and strengths of splice junctions. Splicing effects of the mutations are quantified by the relative presence of alternative mRNA isoforms with and without a given mutation. This measure is further categorized by the accuracy of the experimental methods employed. The database currently contains 170 mutations in 66 exons, yet these numbers increase regularly. We developed an algorithm to derive a table of oligonucleotide Splicing Potential (SP) values from the ASMD dataset. We present the SP concept and tools in detail in our corresponding article.

Conclusions

The current data set demonstrates that mutations affecting splicing are located throughout exons and might be enriched within local RNA secondary structures. Exons from the ASMD have below average splicing junction strength scores, but the difference is small and is judged not to be significant.