Are there junction probes?
While junction probes provide additional information about the possible splice variants present, they do require a priori knowledge of those variants. Given that the best enumeration of splice variants to date is substantially incomplete, in particular on the whole-genome scale, the current exon arrays focus on global detection and quantification of transcribed segments which, provides a more exhaustive coverage of which regions of a gene are expressed. For a more focused custom array design, focusing on a subset of very well characterized genes that have more comprehensive information on the transcript structure and precise junction sequences, including such junction probes, in addition to all of the exon based probes, may be a good design strategy for more detailed expression analysis on these loci.