Mouse Knockout Genes
EUCOMM and KOMP are projects designed to produce comprehensive libraries of mouse embryonic stem (ES) cells containing null mutations in every gene in the mouse genome. Some of the gene structures designed for these projects are shown in Vega.
- Manual annotation is used to identify the exons required for correct translation of the longest transcript of the target loci (known as 'critical exons'). With this knowledge constructs can be designed for gene targetting experiments, one of the approaches being used for knocking out of target genes. The annotation is being performed by the Havana group at the WTSI for the EUCOMM project, with previous contributions from the Washington University Genome Center for the KOMP project.
- Vega shows the locations the critical exons in the 'Knockout Deletion' track on Location based views. Note that this track is not shown by default so will need enabling via 'Configure this Page' -> 'Transcript features'.
- The site also contains 'KO' genes, the artificial genes arising from the removal of the these exons. To distinguish these from the standard Vega genes they are shown in separate tracks coloured red or orange (for EUCOMM and KOMP respectively), and the gene and transcript names are prefixed with 'KO:'.
- KO genes will be found in the results of text searches, for example using gene names, but will not be found with sequence (ie BLAST and BLAT) searches. They are not present in FASTA files downloaded from the FTP site, although lists of their stable IDs are available from here. They are not present in Ensembl.