Archived Comments for:
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity
Gerard Manning, Salk Institute for Biological Studies
3 August 2006
Milanesi et al present in Table 1 a set of 5 protein kinase genes that they state are absent from the KinBase database (http://kinase.com/kinbase/) and the Manning et al (2002) reference. This is not fully correct, as one is a previously annotated kinase, two are previously annotated kinase pseudogenes, and one is a lipid rather than protein kinase:
Gene 1 (PIK4CB) is a lipid kinase whose phylogeny makes it highly unlikely that it would have protein kinase activity.
Gene 2 (LOC283155) is annotated in KinBase as a pseudogene, BMPR1Aps2.
Gene 3 (MGC75495) is the same as annotated kinase Nek5.
Gene 4 (LOC161635) is the same as KinBase psueodgene CK1a_ps2.
Gene 5 is indeed novel, and represents one of a number of recent duplications in the human genome that result in duplicated (and probably functionally identical) protein kinases. Another such case is the PITSLRE kinase, known in UniProt as CDC2L1, which in the current human genome assembly appears as a tandem duplication, with the copy annotated as CDC2L2. aCGH studies indicate that many other genomic regions have been duplicated in human or other primate lineages (Fortna et al, 2004 PLoS Biol 2(7): e207), of which the authors specifically cite two kinases, ROCK1 and PAK2, indicating that many kinases may be duplicated, though unlikely to have separable functions.
Errors in novel kinases table
3 August 2006
Milanesi et al present in Table 1 a set of 5 protein kinase genes that they state are absent from the KinBase database (http://kinase.com/kinbase/) and the Manning et al (2002) reference. This is not fully correct, as one is a previously annotated kinase, two are previously annotated kinase pseudogenes, and one is a lipid rather than protein kinase:
Gene 1 (PIK4CB) is a lipid kinase whose phylogeny makes it highly unlikely that it would have protein kinase activity.
Gene 2 (LOC283155) is annotated in KinBase as a pseudogene, BMPR1Aps2.
Gene 3 (MGC75495) is the same as annotated kinase Nek5.
Gene 4 (LOC161635) is the same as KinBase psueodgene CK1a_ps2.
Gene 5 is indeed novel, and represents one of a number of recent duplications in the human genome that result in duplicated (and probably functionally identical) protein kinases. Another such case is the PITSLRE kinase, known in UniProt as CDC2L1, which in the current human genome assembly appears as a tandem duplication, with the copy annotated as CDC2L2. aCGH studies indicate that many other genomic regions have been duplicated in human or other primate lineages (Fortna et al, 2004 PLoS Biol 2(7): e207), of which the authors specifically cite two kinases, ROCK1 and PAK2, indicating that many kinases may be duplicated, though unlikely to have separable functions.
Competing interests
None declared