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Exercise 3 - Characteristics of Exon/Intron Borders
Eukaryotic genes consist predominantly of exons and introns. Introns are DNA sequences that are removed from the
original (primary) transcript, exons are the regions that remain during the mRNA maturation process.
The borders between exons and introns are called splice sites. More specifically, exons-intron borders are called
donor sites, and intron-exon borders are called acceptor sites. To characterize genes in eukaryotes it is important
to be able to exactly identify the borders between exons and introns.
During this exercise you will determine whether splice sites (donor and acceptor sites) are
associated with patterns (motifs, consensus sequences) that could aid in their identification and, ultimately,
in the mapping of exons and introns in eukaryotic genomes.
Access your sequence set here:
#1,
#2,
#3,
#4,
#5,
#6,
#7,
#8,
#9,
#10,
#11,
#12.
Have a look at
this worksheet.
Each vertical line represents a splice site. Exon-intron borders (donor sites) are on the left half of
the page and intron-exon borders (acceptor sites) are on the right half of the page. Transfer the last and the first five nucleotides of exon and intron sequences into the appropriate spaces
of the worksheet. The five last nucleotides of exons would approach the donor side on the left half
of the page from the left page margin. The first five nucleotides of exons would start immediately behind the
acceptor side on the right half of the page and lead towards the right margin. Conversely, the first five nucleotides of introns would start immediately after the donor site on the
left half of the page. And the five last nucleotides of introns would approach the acceptor site on the right
half of the page from the page center. You do not need to pay any attention to the order of introns and exons, they have
been chosen at random from genes from these model organisms. Once you have transferred the sequence stretches onto the worksheet get together with a team that has
worked on sequences from the same model organism. Compare your results and try to define a consensus sequence
for each, donor and acceptor splice sites in your organism.
How do your results jive with this image about alternative splicing? Discuss how computer software could identify splice sites. Why not try it out? Highlight and copy
this human nucleotide sequence
and paste into the submission window for this splice site prediction program.
Select 'Submit'. Interpret the output. (Should you experience problems with the program, view the results here.)
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