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   
- Supplementary inforamtion: All the supplementary information associated with the paper is available here.


Annotation

Reference Genome

The automatic pseudogene annotation for the mouse reference genome (Gencode vM12, Ensembl 87) is available here.

Individual Strains

129S1/SvImJ AKR/J A/J BALB/cJ C3H/HeJ C57BL/6NJ
Caroli/EiJ CAST/EiJ CBA/J DBA/2J FVB/NJ LP/J
NOD/ShiLtJ NZO/HlLtJ Pahari/EiJ PWK/PhJ SPRET/EiJ WSB/EiJ

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 .


Functional Characterization

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.


Mappability Maps

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


Search

Query the mouse strain pseudogenes here.


External Links