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. Tanscriptional activity and strain-specific history of mouse pseudogenes. Nature Communications 2020   
- Supplementary inforamtion: All the supplementary information associated with the paper is available here.
- Behind the paper: Dusting off the mouse molecular relics   
- Research highlights: A catalogue of pseudogenes in the mouse   

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, brain tissue expression data, and essentiality information is available here.

A matrix of enrichment values for Gene Ontology terms in the 18 mouse strains is available here.

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

The haplotype annotation for each pseudogene and the subspecies specific origin annotation for pseudogenes in the 12 laboratory mouse strains can be accessed here.

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

Query the mouse strain pseudogenes here.

• GENCODE
• Ensembl
• UCSC