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

    Author(s)
    Forrest, Alistair Raymond Russell
    Taylor, Darrin F
    Crowe, Mark L
    Chalk, Alistair M
    Waddell, Nic J
    Kolle, Gabriel
    Faulkner, Geoffrey J
    Kodzius, Rimantas
    Katayama, Shintaro
    Wells, Christine
    Kai, Chikatoshi
    Kawai, Jun
    Carninci, Piero
    Hayashizaki, Yoshihide
    Grimmond, Sean M
    Griffith University Author(s)
    Chalk, Alistair M.
    Year published
    2006
    Metadata
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    Abstract
    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 http://variant.imb.uq.edu.au webcite. 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 ...
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    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 http://variant.imb.uq.edu.au webcite. 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 peptide 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, Csf1r, Egfr, Epha1, 3, 5,7 and 10, Ephb1, Flt1, Flt3, Insr, Insrr, Kdr, Met, Ptk7, Ptprc, Ptprd, Ptprg, Ptprl, Ptprn, Ptprn2, Ptpro, Ptprr, Ptprs, and Ptprz1) and 13 transmembrane forms (four known and nine novel: Axl, Bmpr1a, Csf1r, 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.
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    Journal Title
    Genome Biology
    Volume
    7
    Issue
    1
    Publisher URI
    http://genomebiology.com/articles/browse.asp
    DOI
    https://doi.org/10.1186/gb-2006-7-1-r5
    Subject
    Environmental Sciences
    Biological Sciences
    Information and Computing Sciences
    Publication URI
    http://hdl.handle.net/10072/20563.1
    Collection
    • Journal articles

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