Exercise - Gene Prediction and Regulation

First we are going to align the genomic and cDNA sequence of Rad1 (Arabidopsis DNA
repair endonuclease gene). The genomic sequence can be located in two ways:

• Rad1 reads backward on the complementary strand of GenBank entry no.
AB010072 from 66706 to 62831

o Open the above mentioned entry
o Locate the mentioned coding sequence
o Click CDS
o Find and use a tool to retrieve the complementary sequence

• One can use TAIR SeqViewer to retrieve thee sequence

o Open the TAIR homepage and choose SeqViewer
o Choose the gene models box and search for ATRAD1
o Choose an 80-kb viewing range, click on the gene location mark, and then
look for locus At5g41150
o Open CDS and cDNA sequences

• Use the lalign program to align genomic and cDNA sequence
Now, we will use the GenScan server to predict the coding regions from the genomic
sequence

• Locate the GenScan web site and paste the above genomic sequence into the
appropriate field (choose the correct organism)

• Compare the results obtained from GenScan with your own findings
Another tool is GeneSeqer at the plant genome database site. It is a method to identify
potential exon/intron structure in pre-mRNA by splice site prediction and spliced
alignment.

• Use the above genomic sequence to

o Predict the ATRAD1 mRNA sequence utilising the provided cDNA and
EST database
o Align it with the above cDNA sequence of ATRAD1

• Compare the results to the results from GenScan

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