In the exon but not the coding sequence - exon 4 seems a long way in (Nov/16/2006 )
Hi guys,
I have a sequence in one of my clones that is found in exon 4 of my gene, but is not part of the coding sequence, i.e. the mRNA sequence (according to NCBI). Would someone mind explaining how a sequence may be found in an exon but not in the coding sequence? I always thought that exons = mature mRNA = polypeptide. I understand that outside exons may not code for the polypeptide but exon 4 seems a long way inside the outside exons. The gene is ADCY9 (Homo sapiens) if anyone is interested. My knowledge in this area (splicing) is not great I have to admit.
Cheers, Rob
Hi Rob,
Is the extra bit very long? It might be an insertion that is in your clone but not in others. It could be a case of alternative splicing. Have you aligned your sequence with genomic sequence? Does your extra bit disrupt translation (is it a multiple of three in length), or introduce a stop codon?
Good day Rob,
If the extra bases are at the edge of the exon, then there is a good chance that a cryptic splice site in a flanking intron was activated, whether by mutation or alternative splicing regulation, and the part of the intron between the original splice site and the newly-activated intronic splice site was expressed with the exon.
If the extra bases are entirely within the exon, flanked on both sides by sequence from exon 4, then the hypothesis above is not reasonable.
Regards,
- Jon
Is the extra bit very long? It might be an insertion that is in your clone but not in others. It could be a case of alternative splicing. Have you aligned your sequence with genomic sequence? Does your extra bit disrupt translation (is it a multiple of three in length), or introduce a stop codon?
Hey wbla,
Thanks for the input. The insert is 57 bp long, it codes for a 19 a.a. in-frame insertion and contains no nonsense mutations. The insert is found in exon 4 of my gene so it is a splice variant. What I'm interested in though is how a sequence that is found in exon 4 is not already part of the coding sequence for the gene. I thought exon = mature mRNA = polypeptide but I'm missing something.
Cheers again,
Rob
If the extra bases are at the edge of the exon, then there is a good chance that a cryptic splice site in a flanking intron was activated, whether by mutation or alternative splicing regulation, and the part of the intron between the original splice site and the newly-activated intronic splice site was expressed with the exon.
If the extra bases are entirely within the exon, flanked on both sides by sequence from exon 4, then the hypothesis above is not reasonable.
Regards,
- Jon
Hey Jon,
Thanks for the input. That's an interesting idea. I need to look more closely at where this sequence is in exon 4 and confirm that the sequence is within exon 4. There is a chance that the sequence flanks exon 4 and is actually part of an intron. When I performed a BLAST search to identify the sequence, the contig it gave me was ADCY9 exon 4 and I assumed my sequence was part of exon 4, however I didn't check the exon boundaries to confirm that. I will do that on Monday and keep you updated.
Cheers again,
Rob
Keep in mind that lots of variation exists within populations that hasn't found its way into public (or private) databases. If you find something that doesn't match with the few clones in GenBank, don't assume that there's something wrong with your sequence. You may just have found something new (and potentially important).