The Ensembl release 61 mouse gene set (released on 1 February 2011) includes updated automatic annotation for mouse NCBIM37 assembly. The automatically annotated transcript models match 94.6% of RefSeq proteins exactly.
We merged the results of this automated annotation with Havana’s manual annotation to produce the final gene set that you see displayed on our website. (We are currently merging in Havana’s mouse annotation every other release.) The final gene set has also been used as an input set for a new round of CCDS comparisons. As a result, the number of genes in the mouse CCDS set has increased.