Abstract
We have constructed the Vertebrate Exon Evolution Database (VEEDB). Together with ASAP2 VEEDB provides extensive information (gene; gene structure; splicing; alternative splicing analyses in multiple vertebrate genomes; comparative genomics analysis of splice site conservation and exon sequence conservation) for exon creation and loss events in human, mouse, dog, cow and zebrafish exons. Our multi-genome approach provides a way for
- distinguishing creation and loss events on the large scale,
- uncovering details of the evolutionary mechanisms involved,
- estimating the corresponding rates over a wide range of evolutionary times and organisms, and
- assessing the impact of AS on those evolutionary rates.
We use previously unpublished independent analyses of alternative splicing in 5 species (Human, Mouse, Dog, Cow and Zebrafish) from the ASAP2 database combined with genome-wide multiple alignment of 17 genomes to analyze exon creation and loss of both constitutively and alternatively spliced exons in mammals, fish, and birds. Our analysis provides a comprehensive database of exon creation and loss events over 360 million years of vertebrate evolution, including tens of thousands alternative and constitutive exons. We find that exon inclusion level is inversely related to the rate of exon creation. In addition, we provide a detailed in-depth analysis of mechanisms of exon creation and loss, which suggests that a large fraction of non-repetitive created exons, are results of ab initio creation from purely intronic sequences. Our data indicate an important role for alternative splicing in creation of new exons and provides a useful novel database resource for future genome evolution research.
Key features
- Comprehensive genome wide datasets for Human, Mouse, Cow, Dog and Zebrafish exon conservation
- Integration with ASAP2, which allows quick access to gene structures
- Quick online query of the complete dataset
- XML formated output allows to quickly save results directly from the web browser
- Database schema and rows are fully available for download for local installation
Availability
Our data is available for online query at this website. We provide three types of query.
- Outgroup query
This view presents the summary of the number of conserved exons from the source organism in the target organism. The outgroup is used to establish the ancestral state and interpret divergence as either exon creation or exon loss. In the extended view the details for each exon are presented.
- Genome view
In the genome view the exons in the source organism are presented in tabular form, giving conservation in each of the other 16 organisms. In addition, conservation of the neighboring exon splice sites is coded into the table entries.
- Exon view
Here the detailed entries in the conservation table of VEEDB are presented. The results include the splice site di-nucleotide sequences, percent identity and coverage, as well as conservation inference for the specified exon.
In addition, all data and scripts can be downloaded. See the downloads page for details on installation.