News for Vega Release 29

Display of mouse Knockout genes

The display of mouse Knockout (KO) genes has been rationalised as follows.

• KO genes designed for the EUCOMM and the KOMP projects are now shown in separate gene tracks.
• Whereas Vega previously showed all KO genes designed by the process of manual annotation, it now shows only those that have been succesfull, ie where constructs have been introduced into embryonic stem cells and targetting has been confirmed. Since only some of the designs are succesfull by this criteria there is consequently a decrease in the number of KO genes shown on the site from previous releases.
• The 'critical exons' track showing the location of the exons that are being removed in the KO genes has been renamed 'knockout deletions'.

Versions and modification dates

This release of Vega has changes to the way in which the versions of genes, transcripts and translations are recorded. This has subtle consequences in that the versions of such a feature in this release may actually be lower than in a previous release.

The creation and modification dates of (human) transcripts are now recorded correctly.

Importantly the version of an object is now incremented only when the underlying sequence is changed. So for example if a transcript edit affects only a remark and leaves the sequence unchanged, then although the modified date will reflect this change, the version of the transcript itself is not modified.

These changes will be rolled out to other species as new releases are made.

Gene Classification (, , , , )

The grouping of genes has been simplified and is now done on the basis of biotype only. So whereas protein coding genes with KNOWN and NOVEL status had previously been shown in different tracks, they are now all shaded the same shade of blue and shown in just the one track. As well has having relevance to the appearance of genes on location based views such as ContigView, MulticontigView etc, this also impacts on the BLAST/SSAHA search options and the files available for download from the FTP site.

Update to Vega Mouse

This update to mouse shows an increase in the amount of annotated sequence to about 900 Mbp and a rise in the number of annotated genes to over 17000.

Update to Vega Human

This release of human has a general update of annotation with an overall increase of 6Mb of annotated sequence. A major addition is a large increase in the amount of Havana annotation on chromosome 22.