Exercise: Finding genes in human DNA (Thalassemia)

• Check whether the gene represents an ORF gene



• Open http://www.dnai.org/geneboy/.
• Click Genic 2, then Find Genes, ORFs.
• Record the position and length of ORFs and the length of their protein products.
• Go to http://www.ncbi.nlm.nih.gov/.
• Find and click BLAST.
• Find and click BLASTN.
• Paste your sequence into the window, click BLAST.
• Record the request ID.
• Click Format!.
• Using the output from the BLAST search identify the gene/protein. How long is the protein?


• Is the ORF determined above capable of encoding this protein?



• Determine the gene structure by aligning the protein sequence with the translated nucleotide sequence.



• Use a gene prediction tool to identify the gene in the human sequence above.
  
  
  • Highlight and copy the sequence.
  • Go to http://www.softberry.com/berry.phtml?topic=gfind&prg=FGENESH.
  • Paste the sequence into the window, click PERFORM SEARCH.
  • What structure does FGenesH (Find Genes Human) predict for the gene in this sequence?
  • Align the mRNA sequence displayed in the FGenesH result window with the human DNA sequence above using the tool at http://pbil.univ-lyon1.fr/sim4.php/.
  • What is the structure of the gene?
  • Where would the ORF be located that was identified by the ORF Finder?
  • Which is the true ORF for this gene?
  
  
• Identify the nature of the gene by performing a BLAST search of the human genome using Map Viewer.



• Open http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606.
• Find and click BLAST search the human genome, paste the sequence into the window, click Begin Search.
• Record request ID.
• Then, click Format.
• Click Genome View.
• How many hits? What chromosome is/are the hit/s located on?
• Click the number underneath the chromosome.
• How many genes are shown as hits?
• What type of gene?
• Find the gene that matches with the query sequence to 100%.
• Move the cursor over this gene and zoom in (left mouse-click on vertical line, click Zoom 4x. Zoom in approximately 16 times.
• How does the structure of the gene match the FGenesH gene prediction?
• Note the arrow next to the gene; what does it denote?
• For a nucleotide view of the gene click on sv.
• Identify the various structural elements of the gene, including introns, exons, start codon, stop codon, polyA-signal, and TATA-Box.