Challenges in Microarray Design for Splice Variant Detection However, it only provides only a limited view of the gene structure, is labor-intensive, and does not easily scale to thousands of genes or hundreds of tissues. This is a powerful approach and can be effectively used for analyzing a small number of genes. Another commonly used method for discovering of novel gene isoforms is RT-PCR followed by sequencing. A number of novel gene transcripts were detected using microarray based methods that were not detected by ESTs using computational methods. Microarray based methods for detecting splice variants provide a robust, scalable platform for high-throughput discovery of alternative gene splicing. The highly parallel and sensitive nature of microarrays make them ideal for monitoring gene expression on a tissue-specific, genome-wide level. Microarray based splice variant detection is the most popular method currently in use. Currently, the most efficient methods for large scale detection of splice variants include computational prediction methods and microarray analysis. Gene splicing leads to the synthesis of alternate proteins that play an important role in the human physiology and disease. In this kind of gene splicing, two or more alternative 5' splice site compete for joining to two or more alternate 3' splice site. The gene splicing mechanism retains the non-coding (junk) portions of the gene and leads to a demornity in the protein structure and functionality.Īlternative 3' Splice Site and 5' Splice Site: Alternative gene splicing includes joining of different 5' and 3' splice site.
In humans 2-5 % of the genes have been reported to retain introns. Intron Retention: An event in which an intron is retained in the final transcript. The exons are the coding regions of a gene and are responsible for producing proteins that are utilized in various cell types for a number of functions.
These are the events that can simultaneously occur in the genes after the mRNA is formed from the transcription step of the central dogma of molecular biology.Įxon Skipping: This is the most common known gene splicing mechanism in which exon(s) are included or excluded from the final gene transcript leading to extended or shortened mRNA variants. There are several types of common gene splicing events.
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