This database contains the latest annotation and characterization of pseudogenes in 18 related mouse strains. The pseudogene anotation was produced using a combination of automatic pipeline annotation using PseudoPipe and lift over of manually curated pseudogenes from the reference genome to each of the strains.

The resulting annotation set is characterised by 3 confidence levels. Level 1 pseudogenes are identified by both PseudoPipe and manual lift over, Level 2 pseudogenes are identified only by lifting over the manually curated set of the reference genome to the strain of interest; and Level 3 pseudogenes are curated using just the automatic annotation pipeline.

- Reference: Sisu, Muir et al. Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history. Submitted   

Reference Genome

Individual Strains

Pangenome Set

The current pangenome pseudogene set comprising 18 mouse strains is available in data-frame and list file format.

Unitary Pseudogenes

- Mouse: Annotated unitary pseudogenes in the mouse reference genome with respect to human .
- Human: Annotated unitary pseudogenes in the human reference genome with respect to mouse .
- Strains: Annotated unitary pseudogenes in the mouse strains with repsect to the reference laboratory strain C57BL/6NJ .

The pseudogene complement set in 18 mouse strains annoated with information regarding biotype, confidence level, PFAM family, GO terms, gene esentiality information, and adult brain tissue expression data is available here.

1 to 1 orthology relationship between the pseudogenes in any two strains is available here.

The mappability maps constructed with a window of 75bp are available here.

Query the mouse strain pseudogenes here.

• GENCODE
• Ensembl
• UCSC