In eucaryotes, alternative splicing can produce multiple mature mRNA isoforms from a single gene. In actual genome annotations, mature mRNAs contain one protein coding sequence only and code for a single protein. Proteins translated from different mRNA isoforms can be similar or different from each other.
We have reanalyzed the transcriptome of many organisms and detected thousands of non-annotated coding sequences. These new protein sequences are completely different from annotated coding sequences. They are termed alternative protein coding sequences. Proteins translated from alternative coding sequences can be detected by mass spectrometry and many of these new proteins are currently being studied in the laboratory to uncover there biological functions. The discovery that a single mature mRNA can code for multiple different proteins increases drastically the diversity of eukaryotic proteomes. For more information about this discovery, read the following articles (NAR, PLOS ONE).