[ensembl-dev] rRNA genes

[Giulietta]

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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