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Exploring CRISPR sites in a human genomic region

You want to do some CRISPR manipulation of the human SMC3 gene. You’re looking for a CRISPR editing site within the locus 10:110578600-110578700.

(a) Go to the locus above and turn on the CRISPR track. How many CRISPR sites can you see in this locus?

(b) Do any of the CRISPR sites overlap any phenotype causing variants? What are the identifiers of these sites and variants?

(c) Mark the region of the negative strand CRISPR site that overlaps these variants, then zoom out to see the whole SMC3 gene. What exon number is your CRISPR site found in the SMC3-201 transcript?

(a) Go to the Ensembl homepage.

Select Search: Human and type 10:110578600-110578700 in the text box (or alternatively leave the Search drop-down list like it is and type human 10:110578600-110578700 in the text box). Click Go.

Click Configure this page. Type crispr in the Find a track text box. Select CRISPR Cas9 in Labels.

There are five positive strand and three negative strand CRISPR sites.

(b) Click on the variants and CRISPR sites to get their identifiers.

1074131234, 1074131235 and 1074131236 overlap rs113411202 and rs1064797151. 1074131234 and 1074131235 overlap rs779773957. 1074131234 and 1074131235 also overlap rs779773957

(c) Click and drag a box around the site, then select Mark region. In the overview above, click and drag a box around the SMC3 gene then select Jump to region. Count the exons to get the number where the marked region is found.

The site is found in exon 7.