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Exploring assembly exceptions in human

(a) Go to the region 21:32630000-32870000 in human. What is the red highlighted region? What is its name?

(b) Can you see the assembly exceptions in the chromosome overview at the top? How many regions with assembly exceptions are there on chromosome 21?

(c) Can you compare this assembly exception with the reference? What is different between this assembly exception and the version on the primary assembly?

(a) Go to the Ensembl homepage.

Select Search: Human and type 21:32630000-32870000 in the text box (or alternatively leave the Search drop-down list like it is and type human 21:32630000-32870000 in the text box). Click Go.

You will see a red highlighted region in the middle of this region. Click on the thin dark red bar in any of the three views to see the label _CHR_HSCHR21_3_CTG1_1:32769079-32843731__. Click on _What are assembly exceptions? to open a new window which explains assembly exceptions.

(b) Assembly exceptions are marked in the chromosome view at the top.

There are seven haplotypes on chromosome 21 and one patch.

(c) Another option in the drop-down is Compare with reference. Click on this.

Scroll down the page to see the comparison between the haplotype and primary assembly. Aligned sequences are highlighted in pink and linked together in green.

The assembly exception CHR_HSCHR21_3_CTG1_1 contains an extra region compared to the primary assembly.