Zebrafish pseudogenes

Q:
I have a question regarding Zebrafish pseudogenes. I searched few
zebrafish genes to check if they have any pseudogenes existing in the
pseudogene.org, I found that there are 15779 zebrafish pseudogenes.
But when I read the nature reference that you mentioned in your blog
has total 154 zebrafish pseudogenes! Could you please let me know how
can one see those 154 pseudogenes, if I want to know whether my genes
of interest having pseudogenes or not?

A:
Pseudogene.org provides a set of pseudogenes resulted from automatic annotation. Zebrafish is a peculiar genome. It was subjected to numerous large scale genome duplication and thus is full of repeats. As such the automatic annotation overstates the number of pseudogenes present. We followed up the automatic annotation with manual curation that resulted in a subsequent much smaller number of pseudogenes. The continuous improvements in the genome annotation result in further improvements in pseudogenes annotation. I attach here the latest set of zebrafish pseudogenes.

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