A pseudogene ontology was created to associate a variety of biological properties—such as sequence features, evolution, and potential biological functions—to pseudogenes and is incorporated into the GENCODE annotation file. The hierarchy of these properties is shown in Supplemental Figure 3. The ontology allows not only comprehensive annotation of pseudogenes but also automatic queries against the pseudogene knowledge database (Holford et al. 2010). The breakdown of the different biotypes within the GENCODE data set can be seen in Supplemental Table 4. A schematic to describe the different manually annotated pseudogene biotypes is presented in Figure 3. For example, unitary pseudogenes (i.e., genes that are active in mouse but pseudogenic in the human lineage) were all manually checked for false positives due to genomic sequencing errors or incorrect automated gene predictions in the mouse (Zhang et al. 2010).
