[ensembl-dev] Transcript Biotype

[Olson, Andrew]

Is there a mapping between biotypes and Sequence Ontology terms?

Andrew

> On Apr 11, 2019, at 5:23 AM, Thibaut Hourlier <thibaut at ebi.ac.uk> wrote:
> 
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.ensembl.org_Homo-5Fsapiens_Gene_Summary-3Fdb-3Dcore-3Bg-3DENSG00000266010-3Br-3D18-3A22164886-2D22169878&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=ic-pQ08gnhTpvpqfp3_6Uw&m=J2Ysxscv8-Scd9FZ03cQLdh0JfGGsXkZsBGebFWurTc&s=ja6tkV7Ot0pZPJnnPEMpkiZh2gYPcK7Rn2c__eXAXXE&e=
>> 
>> 
>> Here its stated that all its Transcripts are antisense.
>> 
>> 
>> But in the archive:
>> 
>> 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__jul2018.archive.ensembl.org_Homo-5Fsapiens_Gene_Summary-3Fdb-3Dcore-3Bg-3DENSG00000266010-3Br-3D18-3A22166898-2D22168968&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=ic-pQ08gnhTpvpqfp3_6Uw&m=J2Ysxscv8-Scd9FZ03cQLdh0JfGGsXkZsBGebFWurTc&s=WbU16oG4qUFLQdp7jJ7xrtM1BVgyocXGrtkSAmznh2A&e=
>> 
>> 
>> 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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