Intron/Exon Splice Site Exercise


 There are three parts to this exercise.

 1.  Use the program GENSCAN to identify a possible coding region within a genomic sequence
 2.  Use the program BLASTP to see how well your prediction matches with the actual coding region
 3.  Use the site UniGene to examine the location of this gene on a chromosmal map.

 The following four accession numbers identify genes that are relatively small (<10,000 bp) and contain just a few exons.  You could use other gene sequences or
 random segments of genomic DNA sequence as well.

                           J00265 Insulin
                           J00120 Myc
                           J00148 Human growth hormone
                           V00499 Beta globin

 PART 1.

 Use Entrez  to obtain the sequences of these genes.

 Select FASTA under Display to get just the DNA sequence.

 Copy the sequence and open GENSCAN.

 Paste your genomic sequence into the box and select Run GENSCAN.

 You will get results which predict the location of intron and exon splice sites and the predicted coding sequence.

 PART 2.

 Once you think you have identified the coding sequence of the gene, copy that amino acid sequence.

 Use the predicted amino acid sequence to perform a BLASTP alignment with other proteins to see how well your prediction matches with the correct cDNA sequence. Instructions on the use of BLAST are provided.

 In the BLAST program paste the amino acid sequence into the box and select blastp under program and then select search.

 You will get back an alignment of known sequences.   Compare these amino acid sequences with the sequence you predicted.

 PART 3.

 Go to the site UniGene to learn more about your gene.

 Paste the acession number into the search box and hit GO.