Both unclustered olfactory receptors and olfactory receptor pseudogenes can be expressed
We were interested in whether olfactory receptors need to be part of a cluster in the genome in order to be transcribed, or if the clustered genomic organization of olfactory receptors is simply a consequence of the fact that local duplication is the major mechanism for expanding the gene family [1]. 'Singleton' olfactory receptors (defined as full-length olfactory receptors without another olfactory receptor within 0.5 Mb) are more often pseudogenes than are olfactory receptors in clusters (8 out of 16 versus 271 out of 1,358; χ2 = 8.8, P < 0.005). Of the eight intact singleton olfactory receptors, two have matching cDNAs in our collection, a similar proportion as found for olfactory receptors in clusters, showing that clustering is not an absolute requirement for olfactory receptor expression. However, it is possible these two expressed singleton genes are part of 'extended' olfactory receptor clusters - their nearest olfactory receptor neighbors are 1.7 Mb and 2.6 Mb away, respectively.
We also find that some olfactory receptor pseudogenes are expressed, albeit with a lower probability than intact olfactory receptors. Considering the 1,392 olfactory receptor gene sequences for which reliable full-length data are available, 15 out of 285 (5%) apparent pseudogenes are represented in our cDNA collection, compared to 393 out of 1,107 (36%) intact olfactory receptors. However, three of these 15 'expressed pseudogenes' are intact genes in the public mouse genome sequence. The defects in Celera's version of these genes may be due to sequencing errors or true polymorphism. Publicly available mouse sequence confirms that 11 of the 12 remaining expressed pseudogenes are indeed pseudogenes. No public sequence matches the 12th 'expressed pseudogene' with 99% identity or more.