[ensembl-dev] Transcript Biotype

[Vito Flavio Licciulli]

Hi,
the following is a mapping between non-coding biotypes and Sequence 
Ontology from a couple of years ago. It was built by biology experts for 
our non-coding database ncRNAdb.

BIOTYPE    SO_TERM
antisense    SO:0001904
antisense_RNA    SO:0000644
guide_RNA    SO:0000602
lincRNA    SO:0001463
lncRNA    SO:0001877
processed_transcript    SO:0001877
retained_intron    SO: 0001877
sense_intronic    SO:0001903
sense_overlapping    SO:0001877
miRNA    SO:0000276
miRNA_primary_transcript    SO:0000647
misc_RNA    SO:0000483
Mt_rRNA    SO:0000737
Mt_tRNA    SO:0000737
piRNA    SO:0001035
precursor_RNA    SO:0000483
RNase_MRP_RNA    SO:0000385
RNase_P_RNA    SO:0000386
rRNA    SO:0000252
scRNA    SO:0000013
snoRNA    SO:0000275
snRNA    SO:0000274
SRP_RNA    SO:0000590
telomerase_RNA    SO:0000390
tRNA    SO:0000253
Y_RNA    SO:0000405

Please, if anyone can increase/update this list, it's welcome.

Flavio

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Vito Flavio Licciulli        e-mail: flavio.licciulli at ba.itb.cnr.it
Bioinformatics Researcher
C.N.R. - ITB Sede di BARI         Phone (39) 080-5929664/680
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Il 11/04/2019 12:36, Olson, Andrew ha scritto:
> 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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>>
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