Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases

Alistair R.R. Forrest*, Darrin F. Taylor, Mark L. Crowe, Alistair M. Chalk, Nic J. Waddell, Gabriel Kolle, Geoffrey J. Faulkner, Rimantas Kodzius, Shintaro Katayama, Christine Wells, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Sean M. Grimmond

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

36 Scopus citations


Background: Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook a systematic study to catalog the variant transcripts of every protein kinase-like and phosphatase-like locus of mouse Results: By reviewing all available transcript evidence, we found that at least 75% of kinase and phosphatase loci in mouse generate alternative splice forms, and that 44% of these loci have well supported alternative 5′ exons. In a further analysis of full-length cDNAs, we identified 69% of loci as generating more than one peptide isoform. The 1,469 pepticle isoforms generated from these loci correspond to 1,080 unique Interpro domain combinations, many of which lack catalytic or interaction domains. We also report on the existence of likely dominant negative forms for many of the receptor kinases and phosphatases, including some 26 secreted decoys (seven known and 19 novel: Alk, Csfr, Egfr, Ephal, 3,5,7 and 10, Ephbl, Fltl, Flt3, Insrr, Insrr, Kdr, Met, Ptk7, Ptprc, Ptprd, Ptprg, Ptprl, Ptprn, Ptprn2, Ptpro, Ptprr, Ptprs, and Ptprzl) and 13 transmembrane forms (four known and nine novel: Axl, Bmprla, Csfir, Epha4,5,6 and 7, Ntrk2, Ntrk3, Pdgfra, Ptprk, Ptprm, Ptpru). Finally, by mining public gene expression data (MPSS and microarrays), we confirmed tissue-specific expression of ten of the novel isoforms. Conclusion: These findings suggest that alternative transcripts of protein kinases and phosphatases are produced that encode different domain structures, and that these variants are likely to play important roles in phosphorylation-dependent signaling pathways.

Original languageEnglish (US)
Article numberR5
JournalGenome biology
Issue number1
StatePublished - Jan 26 2006
Externally publishedYes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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