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Protein-based analysis of alternative splicing in the human genome

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4 Author(s)
Loraine, A.E. ; Affymetrix Inc., Emeryville, CA, USA ; Helt, G.A. ; Cline, M.S. ; Siani-Rose, M.A.

Understanding the functional significance of alternative splicing and other mechanisms that generate RNA transcript diversity is an important challenge facing modern-day molecular biology. Using homology-based, protein sequence analysis methods, it should be possible to investigate how transcript diversity impacts protein structure and function. To test this, a data mining technique ("DiffHit") was developed to identify and catalog genes producing protein isoforms which exhibit distinct profiles of conserved protein motifs. We found that out of a test set of over 1,300 alternatively spliced genes with solved genomic structure, over 30% exhibited a differential profile of conserved InterPro and/or Blocks protein motifs across distinct isoforms. These results suggest that motif databases such as Blocks and InterPro are potentially useful tools for investigating how alternative transcript structure affects gene function.

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Bioinformatics Conference, 2002. Proceedings. IEEE Computer Society

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