Isoform 1 of my gene of interest encondes a 323aa protein while isoform 2 differs in the 5' UTR, lacks multiple 3' coding exons, and includes a different terminal exon compared to isoform 1 (16 AA that differs from isoform 2). Both Isoforms exactly share the same aa sequence of the first 3 coding exons, then isoform 1 continue until exon 9 while isoform 2 has this extra different terminal exon compared to isoform 1 (which is intron 3 in isoform 1).
In isoform 2, the intron between the shared or common Exon 3 in the 2 isoforms and the extra different terminal exon in isoform 2 is of only 89 bp. I was asking myself whether the mechanism regulating this alternative splicing that cause the Differential Gene Transcription may lie in this 89 bp intron and how could I reveal or predict it. Any ideas?
Should I look for Splice sites, cryptic splice sites, etc within this intronic sequence? Anyone could recommend me a database or a software in order to predict this elements in silico?
Thank You very much
Since multiple factors are known to be involved in generation of alternatively spliced transcripts it would be difficult to ask the question. A better but classical approach would be to delete the hypothesised sequences/region and examine the effect of such deletions on alternative splicing of the gene in consideration. Once involvement of a sequence or region has been ascertained/recognised one can search for the presence or the absence of cryptic splice sites, splicing enhancers, splicing silencers etc.
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