[ensembl-dev] Transcript Biotype

[Thibaut Hourlier]

Hi Beat,
Maybe the definition needs to be modified to be more precise, if you look in the glossary, antisense is in the lncRNA category.

In Ensembl, the biotype lncRNA represent a broad range of transcript, the biotype antisense can be seen as “antisense lncRNA”

Hope this helps,

Thibaut

> On 10 Apr 2019, at 19:13, Wolf Beat <Beat.Wolf at hefr.ch> wrote:
> 
> Hi,
> 
> 
> i'm trying to solve an issue where a (for us) important lncRNA changed biotype in ensembl since the oct 2018 release.
> 
> The gene in question, GATA6-AS1, can be found here:
> 
> https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000266010;r=18:22164886-22169878
> 
> 
> Here its stated that all its Transcripts are antisense.
> 
> 
> But in the archive:
> 
> 
> http://jul2018.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000266010;r=18:22166898-22168968
> 
> 
> Its a lncRNA.
> 
> 
> Now if i read the description of Antisense, that seems technically true. But lncRNA as a biotype seems much more precise.
> 
> 
> The only explanation i can find is that because of: GATA6-AS-208, which is new and actually does overlap GATA6-201, all transcripts of GATA6-AS1 lost their lncRNA status and became antisense.
> 
> Does that mean that in ensembl it is not possible to have lncRNAs that overlap other genes? To me that sounds like a bug, but i might just misunderstand the biotypes.
> 
> 
> Thank you for your clarifications
> 
> 
> Beat Wolf
> 
> 
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