Entering edit mode
3.3 years ago
Ak
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60
I'm trying to identify exons of a gene family from a genomic DNA.
Initially, I've tried mapping the reference gene CDS to the genome to identify the exons. But then I won't be able to obtain the UTRs and only the coding regions.
So can someone suggest a better way for me to identify the exon sequences? Or should I just find a separate way to identify the UTRs, then only combine the UTRs and coding region together to form the exons
Don't you have genome annotation available in form of gtf/gff file for your genome of interest? If yes then it can have information which you are looking for.
No. Because it is my assembled genome. And since I'm only interested in that particular gene family, I did not annotate the genome. That is why initially I thought by mapping the reference gene sequence to my genome, I'll be able to identify my gene. But I missed out that exon include UTR.
Hi Ak, did you manage to find a solution to this problem? I am doing a similar thing so I was wondering if you could give me some advice. Thanks
Sorry tes.to I was still not able to identify the UTRs. I've shifted my focus on solely identifying the coding sequence (exon without UTRs) and the intron.
Ok, thanks anyway