Pseudogenes have long been considered nonfunctional elements. The influx of large-scale sequencing projects over the last decade have provided rich sources of evidence that pseudogenes can play key evolutionary and regulatory roles, highlighting the need for high quality annotation for both human and key model organisms. To date, GENCODE has completed the manual annotation of pseudogenes in human and has undertaken the task to curate and characterize pseudogenes in the mouse reference genome. Capitalizing on available high-quality annotations as well as on the functional-genomics, evolutionary, and phenotypical data, we were able to create a comprehensive picture of both the human and mouse pseudogene complements' creation, development, and activity. Thus, we found that while human pseudogenes were created through a single burst of retrotransposition events, the active transposable element content in mouse allows for a continuous renewal of the pseudogene pool. Despite their differences, the two organisms share a number of similarities in terms of pseudogene activity, with ~10% of pseudogenes being transcribed. Finally, we highlight a variety of resources developed based on the available GENCODE annotations that help shed light on pseudogene biology.
Keywords: Functional genomics; GENCODE; Human; Mouse; Pseudogene.