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Exons in Refseq-hg19

Hi,

I was working with the refseq genes hg19 file to define genomic regions and I downloaded 4 files from the UCSC table browser

  1. with all exons
  2. 5'UTR exons
  3. 3'UTR exons
  4. Coding exons

I realised that the no. of records in 2+3+4 are more than that in 1. It doesnt strike me at the moment, why should this be the case. Shouldn't 5 UTR+3UTR+Coding exons add up to total no. of exons in the genome ? Or am I missing something obvious?

Thanks!

Aditi

gene
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updated by Ram Ram • written by aditi.qamra aditi.qamra

1 answer

One of possibility is that the UTR can be represented in the multiple exons. So the some of exons in coding exons file may have UTRs embedded in the coding exons You need to find coordinates of UTRs and check it, whether is is represented in coding exons or not.

• 1 views • link
updated by Ram Ram • written by Renesh Renesh

I can guarantee that this is the case. UTRs will commonly share exons with coding sequence.

• 1 views • link
written by Devon Ryan Devon Ryan

To add to this there's also noncoding RNA in refseq, which have a 5'UTR sequence and no coding exons.

• 1 views • link
written by Vivek Vivek

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