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Exploring a genomic region in zebrafish

(a) Go to the region from 54,400,000 to 54,900,000 bp on Danio rerio chromosome 7. How many contigs make up this region?

(b) Zoom in on the gene fgf4.

(c) Configure this page to turn on the Type II transposons track in this view. What tool was used to annotate the LTRs according to the track information? How many LTRs can you see within the fgf4 gene? Do any overlap exons?

(d) Create a Share link for this display. Email it to your neighbour. Open the link they sent you and compare. If there are differences, can you work out why?

(e) Export the genomic sequence of the region you are looking at in FASTA format.

(f) Reset the track configuration you changed in the Region in detail page.

(a) Go to the Ensembl homepage.

Select Search: Zebrafish and type 7:54400000-54900000 in the text box (or alternatively leave the Search drop-down list like it is and type zebrafish 7:54400000-54900000 in the text box). Click Go.

This genomic region is made up of five contigs, indicated by the alternating light and dark blue coloured bars in the Contigs track.

(b) Draw with your mouse a box encompassing the fgf4 transcripts. Click on Jump to region in the pop-up menu.

(c) Click Configure this page in the side menu (or on the cog wheel icon in the top left hand side of the bottom image).

Go into Repeats in the left-hand menu then select Type II transpoons. Click on the (i) button to find out more

Repeat Masker was used to annotate type II transpoons onto the genome.

Save and close the new configuration by clicking on ✓ (or anywhere outside the pop-up window).

There is one type II transposon in an intron of fgf4.

(d) Click Share this page in the side menu. Select the link and copy. Get your neighbour’s email address and compose an email to them, paste the link in and send the message.

When you receive the link from them, open the email and click on your link. You should be able to view the page with the new configuration and data tracks they have added to in the Location tab. You might see differences where they specified a slightly different region to you, or where they have added different tracks.

(e) Click Export data in the side menu. Leave the default parameters as they are. Click Next>. Click on Text.

Note that the sequence has a header that provides information about the genome assembly (GRCz10), the chromosome, the start and end coordinates and the strand. For example:

>7 dna:chromosome chromosome:GRCz10:7:54615489:54625923:1

(f) Click Configure this page in the side menu. Click Reset configuration. Click ✓.