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Exploring a genomic region in coffee

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Exploring a genomic region in coffee

Go to Ensembl Plants.

  1. Go to the region from 23,704,000 to 23,766,000 bp on coffee chromosome 1.

  2. Zoom in on the GSCOC_T00030044001 gene with transcript ID CDP09644.

  3. Configure this page to turn on the Repeats (Repbase) track in this view. What tool was used to annotate the repeats according to the track information? How many repeats can you see within the GSCOC_T00030044001 gene? Do any overlap exons?

  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 Plants homepage, select Coffea canephora from the Species drop-down list and type 1:23704000-23766000 in the text box. Click Go.

  2. Draw with your mouse a box encompassing the GSCOC_T00030044001 transcript (with ID CDP09644). 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 Repeat regions in the left-hand menu then select Repeats (Repbase). Click on the (i) button to find out more information.

    Repeats identified by RepeatMasker, using the Repbase library of repeat profiles.
    Save and close the new configuration by clicking on ✓ (or anywhere outside the pop-up window). There are no repeats from Repbase overlapping GSCOC_T00030044001.

  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, the chromosome, the start and end coordinates and the strand. For example:
    >1 dna:chromosome chromosome:AUK_PRJEB4211_v1:1:23755890:23764847:1

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