many genes can be alternatively spliced in different tissues or at different times in development ( there are only about 30000 genes but many times that number of translated protein products) and these are not all due to post translational modification .

alternative splicing?

I agree with you dear sir ...but my query is disease related not in general. we have one patient where we found deletion of two exons in cDNA but not in gDNA. its well documented that mutation at splice site junction present in genomic DNA of any gene may lead to exon spiking at  RNA level subsequently at cDNA level. 

Alternative splicing is a controlled mechanism. There is no alternative splicing mechanism for the gene in which i am looking for the mutation. So deletion of two exons due to defective alternative splicing is less likely to be the cause in this patient.

i wanted to know that other than mutation at spice site or defective alternative splicing mechanism, is there any other way by which exon skiping or exons deletion may occur?

Thank you Dr. Paul for your prompt response.

new alternative splicing can arise in a disease contexte. That's why in a RNAseq study you can analyse differential expression but also alternative mRNA splicing patterns differences in samples compared to controls.

see the SplceSeq tool for example (http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview).

fred

 That's a new concept for me ...thanx Dr, Frederic. 

What is the gene under scrutiny?

BTK (Bruton Tyrosine Kinase)

To which domains of the kinase do the spliced exons correspond?

Spliced exons are correspond to SH2 domain..