Definition of the different DNA regions

Question

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?

• Oshima, Koichi, et al. "Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia." Proceedings of the National Academy of Sciences (2016): 201608420.

Answer 1

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

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)

Answer 2

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).

Answer 3

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