<p>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, <a href="ftp://ftp.ensembl.org/pub/release-69/fasta/mus_musculus/ncrna/">Ensembl provides a FASTA download of ncRNAs</a>. Luckily, the actual sequence data is rather short and the file contains full annotation.</p>

<p>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 – <a href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1TranscriptAdaptor.html#af8f7857ab263e9420a5c997e3d683b4f"><code>TranscriptAdaptor::fetch_all_by_biotype</code></a> but I cannot find a list of biotypes anywhere, and if I read <a href="http://www.ensembl.org/info/docs/genebuild/ncrna.html">the ncRNA documentation</a> correctly, Ensembl simply doesn’t annotate retrotransposons at all.</p>

<p>Is there any way to obtain that information?</p>

<p>Answering my own question:</p>

<p><strong>Ensembl Biomart</strong> actually allows filtering by <strong>Gene type: “retrotransposed”</strong>.</p>

<p>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.</p>
