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Exploring a genomic region in Bos taurus (Cow)

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Exploring a genomic region in Bos taurus (Cow)

  1. Go to the region from 28,400,000 to 28,988,000 on cow chromosome 12.

  2. 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?

  3. Zoom in on the BRCA2 gene.

  4. Create a URL 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?

  5. Export the genomic sequence of the region you are looking at in FASTA format.

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

  1. Go to the Ensembl homepage. Select Cow from the drop-down menu in the blue box and enter 12:28400000-28988000 in the text box. Click Go.

  2. 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 search box in the top left-hand corner. Enable the CpG islands track. Click on the i button in the far right-hand side to open the track description.

    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 the check icon in the top right-hand corner or anywhere outside the pop-up window. There are CpG islands on either side of BRCA2, with values of 0.84 and 0.97.

  3. Make sure that your cursor action is set to Select a region. With your cursor, click and drag a box encompassing the BRCA2 transcripts. Click on Jump to region in the pop-up menu.

  4. Click Share this page in the left hand-side panel. Copy the URL, get your neighbour’s email address and send them the URL you copied. 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. You might see differences where they specified a slightly different region to you, or where they have added different tracks.

  5. Click on Export data in the left-hand menu. Leave the default parameters as they are. Click Next> and view the sequence in a new browser tab by clicking on Text. The sequence is in FASTA formatwhich comprises a header (beginning with >) that provides information about the genome assembly (primary_assembly:Sscrofa11.1), the chromosome, the start and end coordinates and the strand. For example:
    >primary_assembly:Sscrofa11.1:11:8805953-8858418:1 >12 dna:primary_assembly primary_assembly:ARS-UCD1.2:12:28628932:28694341:1

  6. Click on Reset configuration at the top of the Region in detail image.