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Exploring a genomic region in Rainbow trout

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Exploring a genomic region in Rainbow trout

  1. Go to the region from 49,000,000 to 49,400,000 bp on Rainbow trout chromosome 3.

  2. Zoom in on the myo3b gene.

  3. Configure this page to turn on the CpG islands track in this view. What tool was used to annotate the CpG islands according to the track information? How many CpG islands can you see within the myo3b gene?

  4. 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?

  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 Rainbow trout from the Species drop-down list and type 3:49000000-49400000 in the text box. Click Go.

  2. Draw with your mouse a box encompassing the myo3b transcripts. Click on Jump to region in the pop-up menu.

  3. 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 Simple features in the left-hand menu then select CpG islands. Click on the (i) button to find out more information.

    The CpG islands are determined from the genomic sequence using a program written by G. Micklem, similar to newcpgreport in the EMBOSS package. Save and close the new configuration by clicking on ✓ (or anywhere outside the pop-up window). There is one CpG island overlapping myo3b.

  4. Click Share this page in the side menu. Copy the URL. 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.

  5. Click Export data in the side menu. Leave the default parameters as they are (FASTA sequence should already be selected). Click Next>. Click on Text. Note that the sequence has a header that provides information about the genome assembly (USDA_OmykA_1.1), the chromosome, the start and end coordinates and the strand. For example:
    >3 dna:primary_assembly primary_assembly:USDA_OmykA_1.1:3:49195318:49199101:1

  6. Click Configure this page in the side menu. Click Reset configuration. Click ✓.