Mutations in the rhodopsin gene
Base sequences can be easily compared to each other with the use of a desktop computer. This is called aligning. In bioinformatics the programme called CustalOmega is used.
In the picture depicted above a schematically display of an alignment is shown. The base sequences of two pieces of DNA are laid next to each other and compared with one another. Parts that differ are colored red.
Proceed using the next steps:
1. Go to the website of EMBL-EBI.
2. All custom settings can be used. The field we will use today is the entry field. Copy both genes (title + base sequence) after each other, without a blank line, in the entry field.
3. Hit submit and wait till the programme shows the results.
The results open on the same page. Click on ‘Show Colors’.
Below the headline Alignment three lines are shown. The first line displays the entered base sequence of the normal rhodopsin gene. The second row shows the entered base sequence of the rhodopsin gene of the child. The third row depicts the differences and similarities between the first two sequences. A star means both bases are similar. If the bases differ, no star is shown.
A. How many differences can you find between the two base sequences?
B. Find the second difference. What is the codon of the healthy rhodopsin gene? And what is the codon of the child? (Every line starts with a new codon)
C. For which codon does this codon code in the normal rhodopsin gene? To answer the question use the codon table
D. For which amino acid codes this codon in the rhodopsin gene of the child? Use the codon table to answer the question.
E. The other in the base sequences are given in a table on the answer sheet.
A. At the bottom of the alignment you can find that the healthy rhodopsin gene and the gene of the baby consists out of 1047 bases. Three bases code for 1 amino acid. Out of how many amino acids is the rhodopsin protein composed?
B. What is the number of the mutated amino acid of the first mutation? Answer in the table of exercise 4.
C. Complete the empty fields of the table. The complete table is later needed for entering the mutations in the 3D-software.