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Exploring a genomic region in human

(a) Go to the region from 31,937,000 to 32,633,000 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)?

(b) Zoom in on the BRCA2 gene.

(c) 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?

(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: Human and type 13:31937000-32633000 in the text box (or alternatively leave the Search drop-down list like it is and type human 13:31937000-32633000 in the text box). Click Go.

This genomic region is located on cytogenetic band q13.1. It is made up of eight contigs, indicated by the alternating light and dark blue coloured bars in the Contigs track. Note that KF455761.1 is a tiny contig that splits AL137143.8 in two.

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

(c) 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

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.

(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.

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

(e) 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

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