Currently, we have successfully identified parents for 9369 pseudogenes of the manually annotated pseudogenes, whereas the parents for the remaining 1847 pseudogenes are still ambiguous and may require further investigation. It is important to note, however, that it is not always possible to identify the true parent of a pseudogene with certainty, for example, when a pseudogene is highly degraded and is derived from a parent gene with highly similar paralogs or when the parent contains a common functional domain. We have added this information to the pseudogene annotation if known (based on protein alignments), and it is also available from the pseuodgene decorated resource (psiDR described in Pei et al. 2012) http://www.pseudogene.org/psidr/psiDR.v0.txt.
