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Exploring a genomic region in cow

(a) Go to the region from 28,400,000 to 28,988,000 on cow chromosome 12.

(b) Configure this page to turn on the CpG islands track in this view. What is this track? Are there any CpG islands near the BRCA2 gene? What are their values?

(c) Zoom in on the BRCA2 gene.

(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) Turn off all tracks you added to the Region in detail page.

(a) Go to the Ensembl homepage.

Select Search: Cow and type 12:28400000-28988000 in the text box (or alternatively leave the Search drop-down list like it is and type cow 12:28400000-28988000 in the text box). Click Go.

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

Type cpg in the Find a track text box. Select CpG islands. Click on the (i) button to find out more.

The CpG islands track shows regions with high density of adjacent cystosine-guanine pairs on the same strand.

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

There are CpG islands on either side of BRCA2, with values of 0.84 and 0.97.

(c) Draw with your mouse a box encompassing the BRCA2 transcripts. Click on Jump to region in the pop-up menu.

(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 (ARS-UCD1.2), the chromosome, the start and end coordinates and the strand. For example:

>12 dna:primary_assembly primary_assembly:ARS-UCD1.2:12:28628932:28694341:1

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