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Finding zebrafish genetic variation in Ensembl, demo

In any of the sequence views shown in the Gene and Transcript tabs, you can view variants on the sequence. You can do this by clicking on Configure this page from any of these views.

Let’s take a look at the Gene sequence view for smc3 in zebrafish. Search for smc3 and go to the Sequence view.

If you can’t see variants marked on this view, click on Configure this page and select Show variants: Yes and show links.

Find out more about a variant by clicking on it.

You can go to the Variation tab by clicking on the variant ID. For now, we’ll explore more ways of finding variants.

To view all the sequence variations in table form, click the Variation table link at the left of the gene tab.

You can filter the table to only show the variants you’re interested in. For example, click on Type: All, then select the variant consequences you’re interested in.

The table contains lots of information about the variants. You can click on the IDs here to go to the Variation tab too.

You can also see the phenotypes associated with a gene. Click on Phenotype in the left hand menu.

You can see other locations in the genome where any of these phenotypes have been associated. Click on caudal fin, aplastic.

Let’s have a look at variants in the Location tab. Click on the Location tab in the top bar.

Configure this page_ and open Variation from the left-hand menu.

There are various options for turning on variants. Turn on the following sequence variants:

  • dbSNP variants
  • Phenotype annotations (all types)
  • Larger Structural variants (all sources)

Click on a variant to find out more information. It may be easier to see the individual variants if you zoom in.

Let’s have a look at a specific variant. If we zoomed in we could see the variant rs180070657 in this region, however it’s easier to find if we put rs180070657 into the search box. Click through to open the Variation tab.

The icons show you what information is available for this variant. Click on Genes and regulation, or follow the link at the left.

This variant is found in two transcripts of the smc3 gene. It has not been associated with any regulatory features or motifs.

Let’s look at population genetics. Either click on Explore this variant in the left hand menu then click on the Population genetics icon, or click on Population genetics in the left-hand menu.