## Description

This track summarizes the alternative splicing seen in the mRNA and EST tracks. The blocks represent exons and the lines are the possible splice junctions. When the track is in full mode and the resolution is approximately gene level the exons are laid out such that alternative exons don't overlap each other and are easier to see. The more ESTs and mRNAs that contain that exon or splice junction the darker they are drawn.

To help filter out the noise present in the EST libraries both exons and splice junctions were filtered. ESTs and mRNAs were removed if the first and last exon were not within the transcription start and end sites for the RefSeq sequence from that region. Only those exons and splice junctions which have an orthologous exon or splice junction present in the mouse transcriptome, or are present three or more times, were kept. This process is similar to that presented in C.W. Sugnet, W.J. Kent, M. Ares Jr., and D. Haussler. Transcriptome and Genome Conservation of Alternative Splicing Events in Humans and Mice.

## Methods

The outline for generating this track is:

- mRNAs and ESTs were aligned to the genomic sequence using blat. A near-best-in-genome filter was applied where only alignments with 97% identity over 90% of the transcript and with a score no more than 0.5% lower than the best score were kept.
- Genomic sequence was retrieved and used to orient ESTs and mRNAs using consensus splice sites, GT->AG, and the less common GC->AG.
- Alignments were clustered together by sequence overlap in exons. As new splice sites were discovered, they were entered into the graphs as vertices, and the exons, introns, and splice junctions connecting them were recorded as edges. Each graph was considered to be a single locus, although they may be fragments of an actual gene structure. The supporting mRNA and EST accessions for each edge were also stored.
- Truncated transcripts were extended by overlap with other transcripts to the next consensus splice site. This avoided keeping vertexes in the graph that were not true splice sites.

## See Also:

Please note the Frames based index view of all the alt-splice sites.