title: In silico study of breast cancer associated gene 3 using LION Target Engine and other tools.
abstract: Sequence analysis of individual targets is an important step in annotation and validation. As a test case, we investigated human breast cancer associated gene 3 (BCA3) with LION Target Engine and with other bioinformatics tools. LION Target Engine confirmed that the BCA3 gene is located on 11p15.4 and that the two most likely splice variants (lacking exon 3 and exons 3 and 5, respectively) exist. Based on our manual curation of sequence data, it is proposed that an additional variant (missing only exon 5) published in a public sequence repository, is a prediction artifact. A significant number of new orthologs were also identified, and these were the basis for a high-quality protein secondary structure prediction. Moreover, our research confirmed several distinct functional domains as described in earlier reports. Sequence conservation from multiple sequence alignments, splice variant identification, secondary structure predictions, and predicted phosphorylation sites suggest that the removal of interaction sites through alternative splicing might play a modulatory role in BCA3. This in silico approach shows the depth and relevance of an analysis that can be accomplished by including a variety of publicly available tools with an integrated and customizable life science informatics platform.
authors.affiliation: LION Bioscience, San Diego, CA, USA. darryl.leon@lionbioscience.com
authors.forename: Darryl A
authors.initials: DA
authors.lastname: León
authors.forename: Jaume M
authors.initials: JM
authors.lastname: Cànaves
mesh_terms: D048868:Adaptor Proteins, Signal Transducing; D000465:Algorithms; D003198:Computer Simulation; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D014644:Genetic Variation; D006801:Humans; D008956:Models, Chemical; D009363:Neoplasm Proteins; D009687:Nuclear Proteins; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: C471621:AKIP1 protein, human; D048868:Adaptor Proteins, Signal Transducing; D009363:Neoplasm Proteins; D009687:Nuclear Proteins; D011506:Proteins