Danio rerio tRNA annotation table

[Leonardo M Martin]

Dear Genome Bioinformatic Group,

I am trying to download tRNAs annotation using the Table Browser. I selected the following options:

Clade: vertebrate

Genome: Zebrafish

Assembly: Jul. 2010 (Zv9/danRer7)

Group: Genes and Gene Predictions

Track: tRNAs

Region: genome

Output format: GTF

Output file: <my file name>

File type returned: gzip

The rest of options were kept to default

 

Using these options above I got a file with tRNAs annotation, so it works well. However that file does not contains annotations for tRNAs pseudogenes.

There is a way to download tRNA pseudogenes annotation for zebrafish using the table browser??

Can you please suggest how to get such annotations in case it could not be possible using table browser?

 

Sincerely,

Leonardo.

 

Leonardo Martin Martin, PhD student.

Norwegian University of Life Science.

Oslo.

Norway.

 

[Jonathan Casper]

Hello Leonardo,

Thank you for your question about obtaining annotation for tRNA pseudogenes in the zebrafish danRer7 genome assembly. We do not have a track specifically devoted to tRNA pseudogenes, but the tRNA track that you name does contain pseudogene information mixed in with the real genes. The tRNA Genes track actually displays tRNA genes predictions from the tRNAscan-SE software package - a score is assigned to each gene according to how likely it is to be a real copy instead of a pseudogene. More information on this process, along with suggested values for cutoff scores, can be found on the track description page at http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer7&g=tRNAs. tRNAscan-SE and the Genomic tRNA Database (http://gtrnadb.ucsc.edu/) are provided and maintained by Todd Lowe (http://lowelab.ucsc.edu/). His lab might have additional suggestions for obtaining tRNA annotation.

You may also be interested in the RepeatMasker track for danRer7, which includes some annotation for repetitive elements like tRNA sequences. You can obtain a list of these items from the Table Browser by using the following steps:

1. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables?db=danRer7
2. Select the following settings:

Clade: vertebrate
Genome: Zebrafish
Assembly: Jul. 2010 (Zv9/danRer7)

Group: Variation and repeats
Track: RepeatMasker
Table: rmsk
Region: genome

3. Click the "filter: create" button.
4. Filter by setting either repClass or repFamily to "does" match "tRNA". repFamily = tRNA is a superset of repClass = tRNA. It includes all elements where repClass = tRNA, but also includes some items where repClass = SINE.
5. Click "submit".
6. Click "get output".

The result will be a list of repeats from the RepeatMasker track that are marked as tRNA elements. You can find more information about the RepeatMasker track on the description page at http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer7&g=rmsk, including links to the RepeatMasker program and the Repbase Update library of repeats. You can also browse Repbase's collection on their site at http://www.girinst.org/repbase/update/browse.php, which allows you to specifically look at the repeat class of tRNA pseudogenes.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

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