Alternative Splicing Events in Exons Other Than Those Reported in RefSeq. The grey bars along the top of each diagram represent the RefSeq gene annotation. Traces in the upper region of each figure show average intensities of probesets representing exon regions for tumors (blue) and Cells (red). The lower insets show extensive annotatation provided by the H-InvDB. (a) The trace displays the average intensities for the probe sets representing the exons of the CECR5 gene. Expression differences are evident v for exons 4 and 5 and show higher values for the tumor. The 5' exon also shows differences whereby the CELLs express an alternative 5' isoform which has been reported in RefSeq (grey bars). The H-InvDB reports 27 alternative splicing events. The blue arrow highlights the transcript (HIT00075872) the tumor is expressing with exons 3 and 4 retained but the 5' exon is missing. The CELLs appear to be expressing a transcript with AS events at exons 3, 4, 6 and 7 indicated by the red arrow (HIT000279852. (b) The array has a probeset that maps to an intron between exons 9 and 10 in the UBXD5 gene and this region is retained in the tumor samples. The tumor appears to be expressing sequences from the intron between exons 9 and 10. RefSeq annotates 3 representative transcripts, while H-InvDB annotates 15 different transcripts but none of these include retention of this intron. The insert shows a map of the expressed sequenced tag sites ESTs that map to this region on chromosome 1. A collection of these (delineated by the arrow) have been placed in the exact position of the retained intron on UBXD5.
Mojica and Hawthorn BMC Genomics 2010 11:5 doi:10.1186/1471-2164-11-5