The GeneChip Mouse Exon 1.0 ST Array is a single array with over 4.5 million unique 25-mer oligonucleotide features constituting approximately 1.2 million probe sets. Based on annotations against the May 2004 build of the mouse genome sequence, these 1.2 million probe sets can be grouped into just under 1 million exon clusters (1 or more overlapping exons) and over 80,000 transcript clusters (groups of putative alternatively spliced transcripts from the same gene) containing more than 1 probe set for the most comprehensive genome-wide expression profiling at the exon level. The design includes (not mutually exclusive):
* 266,791 probe sets with Ensembl transcript support
* 266,220 probe sets with putative full-length mRNA support
* 554,003 probe sets with EST support
* 214,763 probe sets with human or rat mRNA support
* 835,897 probe sets with gene prediction support
   The design of the Mouse Exon 1.0 ST Array adopts an inclusive design strategy by projecting both the publicly available, empirically obtained, cDNA based content and results from gene prediction algorithms on the mouse genome assembly from May 2004. Combining all of the input sequence information, boundaries of exons and probe selection regions (PSRs) are defined.
   Probe sets are then selected for the PSRs of 25 bases or more in length. Empirical sequences are obtained from sources such as mouse RefSeq, mRNAs, and dbEST. Human and rat cDNAs are mapped onto the GenBank
mouse genome using genome synteny information from the genome browser group at the University of California, Santa Cruz. Gene predictions include those from published algorithms such as GENSCAN, GENSCAN Suboptimal, Ensembl, geneid, sgp, and TWINSCAN. Other miscellaneous content on the array includes the microRNA Registry.