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Identification of the coding elements in the genome is fundamental to interpret the development of living systems and species diversity. Small peptides (length < 100 amino acids) have played an important role in regulating the biological metabolism, but their identification has been limited by their size and abundance. Serum is the most important body fluid and is full of small peptides. In this study, we have established a small ORF-encoded peptides (SEPs) database from mouse GENCODE release. This database provides about half a million putative translated SEPs in mouse. We also extract serum proteins from wild type and ob/ob mice, and collect the low molecular weight proteins for mass spectrometric analysis. More than 50 novel SEPs have been discovered. Several SEPs are further verified by biochemical method with newly raised antibodies. These novel SEPs enhance the knowledge about the complexity of serum and provide new clues for the annotation and functional analysis of genes, especially the noncoding elements in the genome.
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