[Genome] Zebrafish gene predictions

[Karin Kassahn]

Hi UCSC,

I am in the process of downloading zebrafish and other fish gene
predictions. I have noticed that the number of Ensembl genes differs between
the UCSC and Ensembl genome browsers. For example, Fugu has 38,510 Ensembl
genes in the UCSC database, but only 22,008 genes (719 known genes and
21,289 novel genes) on the Ensembl site. I was hoping to download from the
UCSC page since I am also intending to get other data from UCSC. Also, for
zebrafish there are RefSeq and ZGC gene tracks, but not Ensembl gene tracks
(while the Ensembl site indicates there are Ensembl genebuilds for
zebrafish). 

I would appreciate any comment as to why the number of Ensembl gene
predictions differs between the two browsers and where I could get more
information about the difference between zebrafish RefSeq, ZGC, and Ensembl
genes.

Your help is greatly appreciated.

Kind regards,
Karin.


Karin Kassahn
ARC Centre in Bioinformatics
Institute for Molecular Bioscience
The University of Queensland
Brisbane, QLD 4072
Australia

ph:  +61 7 3346 2606
fax: +61 7 3346 2101