Welcome to the mouse strain pseudogene resource page!
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 GenomeThe automatic pseudogene annotation for the mouse reference genome (Gencode vM12, Ensembl 87) is available here.
- Mouse: Annotated unitary pseudogenes in the mouse reference genome with respect to human .
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.
|Cross Strain Pseudogene Orthology||
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.