Genomics | Chemical Biology of the Cell | Bioinformatics | Control of Gene Expression
The salmonid selenotranscriptome: Salmo salar and Oncorhynchus mykiss in silico and in vivo characterization
Francisco J Altimiras*, Rodrigo Pulgar, Verónica Cambiazo
*Corresponding author: Francisco J Altimiras
Laboratory of Bioinformatics and Gene Expression, INTA-University of Chile, Santiago, Chile
Center for Genome Regulation, FONDAP, Santiago, Chile
F1000Posters 2012, 3: 260 (poster) [English]
Poster [5.04 MB]
International Society for Computational Biology - Latin America 2012, 17 - 21 Mar 2012, P71
The selenotranscriptome is the set of selenoprotein transcripts (selenotranscripts). Selenoproteins are a diverse group of proteins implicated in immune and oxidative responses, and are present in all three domains of life: bacteria, archaea and eukaryota. Selenoproteins contain selenium (Se) in the form of the amino acid selenocysteine (Sec), which is encoded by the STOP codon (UGA). The presence of an RNA stem-loop structure, the Sec insertion sequence (SECIS) element in the 3' untranslated region (3’UTR) of eukaryotic mRNAs, differentiates the Sec or stop function of UGA codons. Due to the dual meaning of the UGA codon, selenoprotein genes and transcripts are often miss-predicted by standard annotation pipelines. Here we applied a series of bioinformatics tools to predict the salmonid selenotranscriptome from large collections of EST sequences.
The computational approach for selenotranscript prediction was successful in identifying the salmonid selenotranscriptome. This set of transcripts are larger than other fish selenoproteomes reported; however, the same core selenoprotein families were found, including several selenoproteins (fep15, selJ, selL) that are missing in mammals.
No relevant competing interests disclosed.
Fondap Center for Genome Regulation, 15090007
Fondecyt , 1090211
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