We have determined the full protein kinase (PK) complement (kinome) of mouse. This set of 540 genes includes many novel kinases and corrections or extensions to >150 published sequences. The mouse has orthologs for 510 of the 518 human PKs. Nonorthologous kinases arise only by retrotransposition and gene decay. Orthologous kinase pairs vary in sequence conservation along their length, creating a map of functionally important regions for every kinase pair. Many species-specific sequence inserts exist and are frequently alternatively spliced, allowing for the creation of evolutionary lineage-specific functions. Ninetyseven kinase pseudogenes were found, all distinct from the 107 human kinase pseudogenes. Chromosomal mapping links 163 kinases to mutant phenotypes and unlocks the use of mouse genetics to determine functions of orthologous human kinases. E ukaryotic protein kinases (PKs) constitute one of the largest of mammalian gene families and are key regulators of a wide variety of conserved cellular processes including cell cycle, cell growth and death, metabolism, transcription, morphology and motility, and differentiation. By adding phosphate groups to substrate proteins, kinases alter the activity, location, and lifetime of a large fraction of proteins and coordinate complex cellular functions. Most PKs belong to a single superfamily containing a conserved eukaryotic PK (ePK) catalytic domain. The remaining, atypical PKs (aPKs), for the most part lack sequence similarity to the ePK domain but are known to have catalytic activity. Fifty-one distinct kinase subfamilies are conserved from yeast to human, reflecting the ancient diversity of kinase functions (1). The recent publication of a comprehensive catalog of 518 human kinases (2) includes scores of novel or poorly understood kinases. The draft mouse genome now provides a key to better understand each human kinase, by comparative analysis of protein and regulatory DNA sequences, and by use of mouse genetics and functional assays to probe the shared functions of mouse kinases and their human orthologs. The detailed comparison of such a large superfamily also casts light on the current state and utility of the draft mouse genome.The Ϸ70 million years that separate mouse from human have allowed evolution to test the functional effect of mutations throughout the sequence of every gene. This allows a mapping of functionally important conserved regions within most genes. Initial analysis of the mouse genome (3) showed that within protein coding regions, synonymous nucleotide substitutions (those that do not change protein sequence) occur at a rate [synonymous substitution rate (Ks)] of Ϸ0.6 substitutions per base between mouse and human orthologs, whereas nonsynonymous substitutions are selectively reduced, to a rate [nonsynonymous substitution rate (Ka)] of Ϸ0.01-0.1 per base, indicating that most protein sequence changes are rejected by evolution. Accordingly, protein sequence conservation ranges from an average of 71% for regions outside of known domains, to 9...