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Exploring a SNP in Arabidopsis

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Exploring a SNP in Arabidopsis

The Arabidopsis thaliana ATCDSP32 protein is a chloroplastic drought-induced stress protein proposed to participate in a process called cell redox homeostasis. Go to Ensembl Plants and answer the following questions:

  1. How many variants have been identified in the gene that can cause a change in the protein sequence (i.e. missense variant)?

  2. What is the ID of the variant that changes the amino acid residue 60 from Alanine to Threonine (hint: refer to an amino acid codon table)? What is the location of this SNP in the A. thaliana genome? What are its possible alleles?

  3. Download the flanking sequence of this SNP in RTF (Rich Text Format). Can you change how much flanking sequence is displayed on the browser?

  4. Does this SNP cause a change at the amino acid level for other genes or transcripts?

  1. Click on Arabidospsis thaliana on the Ensembl Plants homepage. Search for ATCDSP32 on the species page and in the search results, click on the Gene ID AT1G76080. In the left-hand side menu of the Gene tab, click on Variant table. Click on Consequences: All then select only missense variant.

    The missense variant button indicates that there are 18 of these. Alternatively, you can count the number of variants in your filtered list.

  2. An amino acid codon table can be found on Wikipedia. Sort the AA coord column by clicking on the header and scroll down to find a variant at residue 60. The ID of this variant is ENSVATH05153232.

    The variant is located at position 28549171 on chromosome 1. The two possible alleles at this locus are C (reference) and T (alternative).

  3. Click on the link ENSVATH05153232, then click on Flanking sequence in the left-hand side menu. Now click on Download sequence and select File format > Rich Text Format (RTF).

    If you want to change how much flanking sequence is displayed on the browser, go back to the Flanking sequence page, click on the Configuration button and change the length of the sequence. The default settings is 400 bp.

  4. Click on Genes and regulation in the left-hand side menu.

    This SNP does not cause a change at the amino acid level for any other genes or transcripts in A. thaliana.