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How to identify exon sequences

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

utrs exon genome
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updated by tes.to • tes.to • written by Ak • Ak

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.

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written by Tm Tm

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.

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written by Ak • Ak

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

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written by tes.to • tes.to

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.

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written by Ak • Ak

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