title: The abundance of short proteins in the mammalian proteome.
abstract: Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown. Current catalogues of mammalian proteins exhibit an artefactual discontinuity at a length of 100 aa, so that protein abundance peaks just above this length and falls off sharply below it. To clarify the abundance of short proteins, we identify proteins in the FANTOM collection of mouse cDNAs by analysing synonymous and non-synonymous substitutions with the computer program CRITICA. This analysis confirms that there is no real discontinuity at length 100. Roughly 10% of mouse proteins are shorter than 100 aa, although the majority of these are variants of proteins longer than 100 aa. We identify many novel short proteins, including a "dark matter" subset containing ones that lack detectable homology to other known proteins. Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway.
authors: Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.
authors: Martin C
authors: MC
authors: Frith
authors: Alistair R
authors: AR
authors: Forrest
authors: Ehsan
authors: E
authors: Nourbakhsh
authors: Ken C
authors: KC
authors: Pang
authors: Chikatoshi
authors: C
authors: Kai
authors: Jun
authors: J
authors: Kawai
authors: Piero
authors: P
authors: Carninci
authors: Yoshihide
authors: Y
authors: Hayashizaki
authors: Timothy L
authors: TL
authors: Bailey
authors: Sean M
authors: SM
authors: Grimmond