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. The track will draw itself such that no exons overlap each other making alternative events easier to see if the track is in full mode and the resolution is approximately gene level.

To help filter out the noise present in the EST libraries both exons and splice junctions are filtered using both orthologous mouse transcripts and number of times an exon or intron is seen in human transcript libraries. 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, are kept. Transcripts marked in GenBank as mRNA contribute an extra count to reflect the fact that they are usually of higher quality. This process is similar to that presented in: "Transcriptome and Genome Conservation of Alternative Splicing Events in Humans and Mice" C.W. Sugnet, W.J. Kent, M. Ares Jr., and D. Haussler.

Methods

This track was generated in the following manner:
  1. The splicing graphs for each genome were generated separately from their native EST and mRNA transcripts using the following process:
  2. Once the splicing graphs were constructed independently for both human and mouse they were mapped to each other using the the whole genome Mouse Net alignments (viewable on the browser as the Mouse Net track). Exons and splice junctions that were common to both or that occur three or more times in human are kept in the splicing graph and displayed. When counting the number of times an exon or splice junction were included in human transcripts those designated as mRNA are weighted more than those designated as EST.