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Figure 3 | BMC Bioinformatics

Figure 3

From: SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

Figure 3

Graphical output of Primer-Check for SEC23IP (P125) showing the discrepancy between variants targeted by the Affymetrix U133A array probe sets and Taqman (ABI) primer and probe sets[24]used by Dallas and co-workers[17]. Four distinct splice variants of SEC23IP are displayed. Orange vertical lines indicate the target positions of the microarray probes. Probe set 209175_at targets two of four variants, and probe set 216392_at targets three of four variants. The light blue vertical lines show the context sequence location for the qRT-PCR ABI Taqman primer/probe set that targets all splice variants. The dissimilarity of splice variant coverage between qRT-PCR primers and microarray probes creates the potential for discordant expression values, depending on which mix of variants is expressed in the sample being studied.

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BMC Bioinformatics

ISSN: 1471-2105

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