Klee, E.W., Ekker, S.C., and Ellis, L.B.M. (2001) Target selection for Danio rerio functional genomics. Genesis (New York, N.Y. : 2000). 30(3):123-125.
Secreted proteins are of interest as targets for morpholino technology since they frequently mediate cell-cell interactions. Most are identified through the presence of an N-terminal signal sequence. Proteins from the zebrafish Danio rerio containing such signal sequences will be easy to detect with the publication of the complete genome, expected by the end of 2003 (Sanger Centre, 2000). Until then, most zebrafish proteins are only available as translated Expressed Sequence Tags (ESTs) that often lack N-terminal residues. Interim innovative techniques for the identification of EST-derived proteins predicted to contain signal sequences are needed. Here we describe the use of genetic homology among eukaryotes as a basis for selecting a subset of zebrafish sequences with high probability of encoding secreted proteins. We estimate there are 1,000-2,000 gene families encoding these proteins in the zebrafish genome.