Reading from Oshima et al. (2016):

We identified 3,868 noncoding mutations including 394 located <5 Kb downstream, 1,762 intergenic, 1,621 intronic, 81 <5 Kb upstream, 7 UTR 3′, 2 UTR 5′, and 1 intragenic variants.

How upstream, downstream and intragenic variants are defined? Shouldn't intragenic variants be classified within intronic variants, and upstream/downstream within intergenic variants?

Edit: By adding the different numbers it seems they are mutual exclusive. While upstream/downstream variants can be defined as intergenic variants that lie close to genes, I haven't found a definition to tell the intragenic variants from the intronic ones.

Edit 2: The only explanation I could think of for intragenic variant is that it is located in a coding region which is not transcribed due to alternative splicing. Can it be possible?

  • 1
    $\begingroup$ You could try sending them a quick email. $\endgroup$
    – canadianer
    Nov 3 '17 at 17:21

We can take a look at the following picture (from wikipedia):

Gene structure

The regions are then:

  • intergenic: everything outside of the shown gene region
  • <5 Kb downstream: outside of the transcribed region, but possibly part of the promoter or an enhancer (yellow boxes before coding region).
  • UTR 5′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box before coding region).
  • intronic: In the Introns, as shown in the picture (grey boxes)
  • intragenic: These have to be mutations inside the coding region (red boxes), which is confusing since the authors specifically describe them as 'non-coding' mutations. If you read that as 'mutations that don't change the protein sequence', these could be silent mutations
  • UTR 3′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box after coding region)
  • <5 Kb upstream: outside of the transcribed region, but possibly part of an enhancer (yellow boxes after coding region)
  • $\begingroup$ Intragenic is not coding (as it's CDS and introns). Intragenic is region from TSS to TTS. $\endgroup$
    – pogibas
    Nov 5 '17 at 19:30
  • $\begingroup$ @SEwontLetMeDeleteProfile can you elaborate more on that? Also, what is a TTS? $\endgroup$
    – gc5
    Nov 29 '17 at 17:04

The Sequence Ontology project defines an intragenic variant as "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." source

Intragenic means the variant is located within the same gene, which only implies that the sequence analysis assigned a certain variant to a gene. So, there is incomplete data regarding the gene product (such as different splice forms).


You can look up the mutation locations here: http://grch37.ensembl.org/index.html


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.