[ensembl-dev] TSL vs Gencode Basic

[Carlos]

Hi Beat,

The GENCODE basic gene set and the TSL flags are calculated separately.

The GENCODE basic aim is to provide a representative subset of the
GENCODE (comprehensive) transcript set based on full-length transcripts
covering the majority (>= 80%) of the exonic sequence [1] [2].

The TSL flags highlight how well the transcripts are supported based on
primary data (mRNAs and ESTs) [2].

There could be cases like the one you pointed out (SYNGAP1-230) which do
not have any TSL support because the fact that there is an associated
RefSeq NM does not mean there should be a TSL flag as well. TSLs are
based on primary data, not on NMs (which are also based on primary data
though).

I hope it helps.

Regards,
Carlos

[1] https://doi.org/10.1093/nar/gky955
[2] http://www.ensembl.org/Help/Glossary

On 11/09/18 14:47, Wolf Beat wrote:
> I'm trying to better understand the TSL for Human genes and some things i noticed with the Gencode basic annotation.
>
>
> Basically i wanted to know if there is any relation between the two. I have two examples:
>
>
> http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000197283;r=6:33419661-33457541
>
>
> Here we see SYNGAP1-230 which has the Gencode basic annotation, but no TSL support level at all. Is there a specific reason why? Considering that its protein coding, has a refseq, uniprot and ccds id and is in gencode basic, i would have intuitively assumed it to be TSL1, but certainly not without any TSL.
>
>
> A second example i don't fully understand is (but which is less confusing):
> http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000109063;r=17:10628526-10657309
>
> here the only protein coding transcript is in gencode basic, but has TSL5. If i understood gencode basic correctly, they are supposed to be transcripts of a good quality. TSL5 seems to indicate the contrary.
>
> So my main question is, why do some transcripts, even if they are in gencode basic, not have a TSL level? I would also be interested in the other questions raised in this email, but thats the one i'm most interested in.
>
> Kind regards
>
> Beat Wolf
>
>
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