detecting splicing sites

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linda-2010's picture
detecting splicing sites

recently ,I am researching the technical methods about detecting splicing sties.but I am not clear its technique developing.can you help me ? how many methods are there? who is the powerful man in this area? thank you !!

Jon Moulton
Jon Moulton's picture
By comparing genomic sequence

By comparing genomic sequence and cDNA sequence, you can determine where a transcript was spliced. 

Detecting potential splice sites not currently in use is more difficult.  There are many software packages that claim to identify splice sites, but putting a given sequence though several of these programs will often produce different results.  People working with these systems write that they often run a sequence though several of the programs and look for sites that the programs agree on.

You can manipulate splicing using steric-blocking antisense oligos to interfere with binding of splicing components to the RNA.  You can do targeted exon excision by blocking a splice junction (and its snRNP binding site) with an oligo.  There are some papers on blocking the binding sites of splice regulatory proteins wiht oligos, but these techniques are not as well developed and are not used routinely.

Sometimes blocking a splice site with an oligo will activate a cryptic splice site, causing splicing to a new and unexpected location in the RNA.  For an example, see Draper:
Draper BW, Morcos PA, Kimmel CB.  Inhibition of zebrafish fgf8 pre-mRNA splicing with morpholino oligos: A quantifiable method for gene knockdown.  Genesis. 2001 Jul;30(3):154-6.