[Genome] Danio Rerio annotation GFF file

[Rachel Harte]

Mayank,
That is possible to do through our Table Browser which may be reached by
clicking on the Tables link on the top blue menu bar. First, select
the genome as Zebrafish and the assembly as Mar 2006 to get the
latest assembly. Then elect the "Genes and Gene Prediction Tracks"
group and select the track that you are intereseted in and make sure that
the region is set to "genome" Then you can select GTF as the output type.
GTF is a refinement of the GFF file format:
http://genome.ucsc.edu/FAQ/FAQformat#format4

There are a couple of options for the gene annotations: RefSeq Genes and
Ensembl Genes. These are all protein-coding genes. In the future, we hope
to add the non-coding genes to our Genbank tracks. There are non-coding
Ensembl genes on our test server which you can view at:
http://genome-test.cse.ucsc.edu

Please note that some of the data on our test server may be wrong and it
has not yet undergone QA so it could change before being released to our
public servers.

If you are interested in the Ensembl Gene set, you can also download the
current version of this gene set directly from Ensembl at:
http://www.ensembl.org/biomart/martview/

I hope that this helps you. Please let us know if you have further
questions.

Rachel

 Rachel Harte UCSC
Genome Bioinformatics Group http://genome.ucsc.edu


On Thu, 26 Apr 2007, Mayank Maheshwary wrote:

> Hi,
>
> I was wondering if there is some way to get the annotation GFF file for Zebrafish v6 (containing ORF names, start and end locations, exons, ncRNAs, etc.).
>
> Thanks a lot.
>
> Regards,
> Mayank.
> --
> Mayank Maheshwary
> Huntsman Cancer Institute
> University of Utah
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>