Exploring a genomic region in human

Go to Ensembl.

  1. Go to the region from 32,264,000 to 32,492,000 bp on human chromosome 13. On which cytogenetic band is this region located? How many contigs make up this portion of the assembly (contigs are contiguous stretches of DNA sequence that have been assembled solely based on direct sequencing information)?

  2. Zoom in on the BRCA2 gene.

  3. Configure this page to turn on the LTR (repeat) 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 BRCA2 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 homepage, select Human from the Species drop-down list and type 13:32264000-32492000 in the text box (alternatively leave the Search drop-down list as it is and type 13:32264000-324920000 in the text box). Click Go.

    This genomic region is located on cytogenetic band q13.1. It is made up of three contigs, indicated by the alternating light and dark blue coloured bars in the Contigs track.

  2. Draw with your mouse a box encompassing the BRCA2 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 Repeats in the left-hand menu then select LTR. Click on the (i) button to find out more information.

    Repeat Masker was used to annotate LTRs onto the genome.
    Save and close the new configuration by clicking on ✓ (or anywhere outside the pop-up window). There are ten LTRs overlapping BRCA2, none of them overlap exons.

  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.

    Here is the Share link from the video answer: https://may2021.archive.ensembl.org/Homo_sapiens/Share/71a173bba78f0dbe03e48d3240424943?redirect=no;mobileredirect=no

  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 (GRCh38), the chromosome, the start and end coordinates and the strand. For example:
    >13_dna:chromosome_chromosome:GRCh38:13:32311910:32405865:1

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

Exploring a genomic region in mouse

Go to the Ensembl homepage.

  1. Go to the region from 150,320,000 to 150,540,000 bp on mouse chromosome 5. How many contigs make up this portion of the assembly (contigs are contiguous stretches of DNA sequence that have been assembled solely based on direct sequencing information)?

  2. Zoom in on the Brca2 gene.

  3. Configure this page to turn on the LTR (repeat) 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 Brca2 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. Select Mouse from the Species search list and type 5:150320000-150540000 in the text box (or alternatively leave the Search drop-down list like it is and type mouse 5:150320000-150540000 in the text box). Click Go.

    It is made up of five contigs, indicated by the alternating light and dark blue coloured bars in the Contigs track. Note the tiny contig, AEKQ02165236.1, which splits AC084217.7 in two.

  2. Draw with your mouse a box encompassing the Brca2 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 to Repeats in the left-hand menu then select LTRs (Repeats (Mouse)). Click on the (i) button to find out more information.

    Repeat Masker was used to annotate LTRs onto the genome.

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

    There are seven LTRs overlapping Brca2, none of them overlap exons.

  4. 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.

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

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

Exploring a genomic region in Oryza sativa Japonica (rice)

Go to the Ensembl Plants homepage and do the following:

  1. Go to the region between 405000 and 453000 on chromosome 1 in Oryza sativa Japonica.

  2. Turn on the AGILENT:G2519F-015241 microarray track. Are there any oligo probes that map to this region?

  3. Highlight the region around any reverse strand probes you can see. Do they map to any Ensembl transcripts?

  1. Go to the Ensembl Plants homepage. Select Oryza sativa Japonica from the Species drop-down list and type 1:405000-453000. Click Go.

  2. Click on Configure this page to open the menu. You can find the AGILENT:G2519F-015241 track under Oligo probes in the left-hand menu, or by using the Find a track box at the top right. Turn on the track as Normal then save and close the menu. As the AGILENT:G2519F-015241 track is stranded, it appears at the top and bottom of the view.

    There are 5 probes mapped to this region on the positive strand and one probe on the reverse strand.

  3. Drag a box around the reverse strand probe then click on Mark region to highlight.

    The highlighted region maps to two transcripts: Os01t0107900-02 and Os01t0107900-01

Exploring a region in Coprinopsis cinerea okayama

Go to Ensembl Fungi. Let’s try to find some information about the region from 1,400,000 to 1,425,000 in chromosome 7 in Coprinopsis cinerea okayama:

  1. How many complete genes are found in this region? How many on the forward and how many on the reverse strand?

  2. Zoom in on the largest gene EFI27358. How many exons does this gene have?

  3. Export the genomic sequence in FASTA format for this region.

  1. In the Ensembl Fungi homepage, select Coprinopsis cinerea okayama from the Species search drop-down. Enter 7:1400000-1425000 in the Search bar and click Go. This will send you to the Location tab. Your region of interest is indicated by a red rectangle in the 50kb view. Look at the Genes track: each block represents a different gene. Count the number of complete genes within the rectangle.

    There are 7 complete genes in the region.

  2. Look at the Region in detail view (the most detailed view at the bottom of the page). You can zoom into a region by clicking and dragging your mouse (you can change your mouse action in the top right-hand corner of the view under **Drag/Select) and selecting Jump to region in the pop-up menu. Count the number of blocks you can see for EFI27358.

    The EFI27358 gene has 23 exons.

    Click on the transcript ID CZT99117 in the transcript table.

    It has 4 exons.

  3. We want to export the genomic sequence for our original region (not just the EFI27358 gene). You can reset the view by entering 7:1400000-1425000 in the Location bar above the Region in detail view or hitting the Back button on your internet browser. Click on Export data in the left-hand panel. In the pop-up menu, select FASTA from the drop-down and click Next >. You can export the sequence as is (text) or as a compressed file (.gz).

    If you choose to download the sequence as text, your browser might open the FASTA file in a new tab. In this case, just right-click on any white space and select Save As… from the menu.

Exploring a genomic region in Salmonella enterica

Go to Ensembl Bacteria and do the following:

  1. Search for the Salmonella enterica subsp. enterica serovar Typhi str. Ty2 (GCA_000007545) (Hint: type Ty into the Search for a genome box).

  2. Go to the region Chromosome:2000605-2009742.

  3. How many genes are annotated in this region? How many are on the forward strand? How many are on the reverse strand?

  1. Go to the Ensembl Bacteria homepage. Type Ty2 into the Search for a genome box. Click on the auto-completed genome name to navigate to the species information page.

  2. Type Chromosome:2000605-2009742 into the search box. Click Go.

  3. There are 8 genes annotated in this region, all on the reverse strand.