[ensembl-dev] rRNA genes

[Sergei Manakov]

hi Giulieta,

thanks for your reply.

> Select 'Gene type' 'rRNA'

Is this equivalent to gene_biotype rRNA in Mus_musculus.GRCm38.68.gtf file?

> Clicking 'Count' shows me there are 339 Ensembl rRNA genes in the latest
> mouse genome.

There are 341 gene_biotype rRNA genes in the aforementioned gtf file,
does this difference of 3 genes make sense?

> You will see all the rRNA genes in the output file - including 5S and 5.8S.

I followed your instructions and selected Associated gene name as one
of the attributes. I see many gene names that have 5s and two genes 5S
and 5_8S. Can I assume that these are 5S and 5.8S rRNAs? Is this
correct?

As for the others rRNAs, it is not immediately obvious which genes
correspond to 28S and 18S rRNAs, because I only see genes that have
names like:

AC110744.1
AC113124.1
AC119801.1
AC122872.1
...

Is there a way to understand which ones are 18S and 28S?


thanks,
Sergei




On 28 August 2012 05:29, Giulietta <gspudich at ebi.ac.uk> wrote:
> Hello Sergei,
>
> You can find the rRNA genes with BioMart.  The tool is here:
>
> http://www.ensembl.org/biomart/martview
>
> I set up a query as follows:
> Database: Ensembl Genes 68
> Dataset: Mus musculus genes (GRCm38)
>
> Filters: Expand the GENE panel
> Select 'Gene type' 'rRNA'
>
> Clicking 'Count' shows me there are 339 Ensembl rRNA genes in the latest
> mouse genome.  Add columns to the output table as such:
>
> Click 'Attributes'
> Expand the 'GENE' panel
> In addition to the default selections ('Ensembl Gene ID' and 'Ensembl
> Transcript ID'), add 'Associated Gene Name', 'Gene Start (bp)', and 'Gene
> end (bp)'
>
> Click 'Results'.  Click 'Go' to export a full result file.
>
> You will see all the rRNA genes in the output file - including 5S and 5.8S.
>
> We do have an online tutorial for BioMart:
>
> http://www.youtube.com/watch?v=DXPaBdPM2vs&feature=share&list=PLA5333E28D1193B6B
>
> This can also be done using the Core Perl API:
>
> http://www.ensembl.org/info/docs/api/core/index.html#api
>
> I hope this helps?
>
> Best wishes,
> Giulietta
>
>
> On 20/08/2012 03:18, Sergei Manakov wrote:
>>
>> hello,
>>
>> I apologize in advance if this this question was asked already many
>> times, but I can't find the answer.
>>
>>
>> Is there a way to get genomic locations of genes for rRNAs other than
>> 5S and 5.8S? I am interested in mm10 genome.
>>
>> thanks,
>> Sergei
>>
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>
>
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