Hi,
I have some Splice site mutation information. I had a doubt is that can we detect splicing mutations from cDNA sequence? Or else from the reference gene sequence.
If you're sequencing cDNA then you like have mostly mature RNA, which will have already undergone splicing. So you'll then be hard-pressed to discern splice-site mutations. You could, however, just directly assay changes in splicing. If you really want to look for the mutations then you need to sequence the DNA (or somehow purify the immature RNA, though I would think that whole exome sequencing would be simpler and the baits would likely capture most/all splice sites).
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version 2.3.6
I had a doubt that whether the splicing mutation will occur only in the intronic region as the exonic region or coding region mutations are classified as missense, nonsense, insertions and deletion mutations.Is there any tool to view the splice site mutation in a sequence.
You might want to read up a bit on splicing, generally splice sites are intronic. Any genome browser that can accept BAM files (e.g., IGV) would allow you to look at splice site changes.
how can we calculate the splice site distance for a gene sequence
bedtools closestcan probably help with that, as can the GenomicRanges package in R.