Exploring a SNP in Arabidopsis
The Arabidopsis ATCDSP32 protein is chloroplastic drought-induced stress protein proposed to participate in a process called cell redox homeostasis.
(a) How many variants have been identified in the gene that can cause a change in the protein sequence?
(b) What is the ID of the variant that changes the residue 60 from Alanine to Threonine? What is the location of this SNP in the Arabidopsis genome? What are its possible alleles?
(c) Download the flanking sequence of this SNP in RTF (Rich Text Format). Can you change how much flanking sequence is displayed on the browser?
(d) Does this SNP cause a change at the amino acid level for other genes or transcripts?
(a) Search for ATCDSP32 on the Arabidopsis page in Ensembl Plants. On the left hand side menu of the Gene tab, click on Variant table.
Click on Consequences: All then select only missense variant. This button also indicates that there are 18 of these.
(b) Follow down the AA coord column to find a variant at residue 60. The ID of this variant is ENSVATH05153232, located at position 28549171 on chromosome 1. The two possible alleles at this locus are C and T.
(c) Click on the link ENSVATH05153232. Then click on Flanking sequence in the left hand side menu. Now click on Download sequence and select 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.
(d) Click on ‘Genes and regulation’ to find out this SNP does not cause a change at the amino acid level for any other genes or transcripts in that genome.