Annotation For Retrotransposons

Question

[Konrad Rudolph]

I’m searching for a downloadable annotation file for different types of ncRNA: in particular, rRNAs and retrotransposons for mouse. Most ncRNAs are not a problem – for instance, Ensembl provides a FASTA download of ncRNAs. Luckily, the actual sequence data is rather short and the file contains full annotation.

Unfortunately, it doesn’t contain retrotransposons. I’m particularly interested in identifying LINEs and SINEs. Where could I get that information from? I tried Ensembl Biomart but was unable to find the appropriate filter there. The Ensembl API also contains a promising method – TranscriptAdaptor::fetch_all_by_biotype but I cannot find a list of biotypes anywhere, and if I read the ncRNA documentation correctly, Ensembl simply doesn’t annotate retrotransposons at all.

Is there any way to obtain that information?

Answer 1

[Konrad Rudolph]

Answering my own question:

Ensembl Biomart actually allows filtering by Gene type: “retrotransposed”.

However, this only works in the current build of Ensembl and I am unfortunately forced to use an archived build since I’m working on the genome version NCBIM37.

Answer 2

[nbartonicek]

This should help you with fetching the repeats: http://www.ensembl.org/info/docs/api/core/core_tutorial.html#repeats

I use:

my $registry = 'Bio::EnsEMBL::Registry';
$registry ->load_registry_from_url("mysql://anonymous\@ensembldb.ensembl.org/$ensembl");
my $ra_core = $registry->get_adaptor( $species, 'Core', 'RepeatFeature' );

[Konrad Rudolph]

Are LINEs and SINEs annotated in repeats though? Anyway, I’m gonna try this, thanks.

[JC]

the repeat track in Ensembl reports all repeats reported by RepeatMasker, so it includes LINEs/SINEs

Answer 3

[Ashwin]

Probably you should check Dfam

[SES]

That database only contains repeats from the human genome, for now anyway. It appears the OP is interested in repeats from mouse.

Answer 4

[nbartonicek]

The ribosomal RNA is a problem. See the discussion here: Where To Find Detailed Information On Genomic Location Of Rrna Genes?

Answer 5

[SES]

You can download all the repeats for a specific taxon, mouse for example, from Repbase. Just follow the "Browse RU" link, select the taxon you want, and download the file of repeats. It's free, but you will have to create an account.