Ensembl Highlighted Exons Don't Match Coordinates

Question

[bioinformatics2020]

Hi all,

I'm looking at specific transcript (which can be found at this link: https://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000103876;r=15:80444832-80479288;t=ENST00000561421)

According to the Ensembl Table, this transcript has 14 exons, and their positions are all denoted. However, when I go click on the actual sequence, and configure the sequence page to highlight the exons, I notice what is being highlighted does not correspond to the sequence positions. At first I thought this was because I included some additional 600bp flanking, but even with those removed, the highlights don't match.

Any ideas?

[Emily]

What do you mean by "actual sequence"? Can you add the link?

[bioinformatics2020]

Hi Emily, sorry I meant when I click on the "sequence" of the gene associated with the transcript of interest:

https://grch37.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000103876;r=15:80444832-80479288;t=ENST00000561421

Is this sequence that is showing have highlights for exons from ALL potential transcripts?

[i.sudbery]

Yes, the sequence shows all exons of all transcripts.

[i.sudbery]

The transcript record you link to is on the old version of the genome (grch37/hg19) are you sure you are not look at the "actual sequence" on current version (grch38/hg38).

[bioinformatics2020]

Unfortuantely, for this specific task, I must stick with the older reference. Otherwise, I would completely agree with you.

[i.sudbery]

This wasn't supposed to be a criticism of the version you were using, just a suggestion to check you were using the same version throughout.

Answer 1

[Emily]

The highlighting on the gene sequence page shows all the exons of the gene, whereas the transcript exons page shows just the exons of that transcript. Looking at the graphical display of the gene you can see that there are more exons of the gene than in that transcript.