A UBL Interactive

Peter Jankay

pjankay@calpoly.edu

 

Non-major freshman students begin this interactive after they isolate DNA from their cheek cells, perform PCR, run a gel (like the one above), and determine their genotype with respect to a particular jumping gene (pv92). Through discussions, students learn that the jumping gene resides within a "particular intron." The DNA band in the lane notched above is the "particular intron" from a student who does not have the jumping gene (homozygous without). The DNA band in lane immediately to the left is the "particular intron" from a student who is homozygous with pv92.

 

The students' task, and yours if you accept the challenge, is to determine the name and function of the gene the housing the "particular intron." It takes just a few minutes. How? There is an online database containing the human genome, and recently a couple of undergraduate students in our department sequenced 500 bases of the "particular intron." Find a computer with internet access.

 

1. First, obtain the intron sequence by visiting www.bio.calpoly.edu/ubl.

 

2. Click on "protocols", then on "Alu sequence." Copy the entire sequence.

 

3. Next visit the database www.ncbi.nih.gov.

 

4. Click on "BLAST" in the toolbar above the search box.

5. Then, Click on "Human" under Genomes. See below.

 

 

 

 

 

 

 

 

6. Paste the intron sequence you obtained from UBL into the search box.

 

 

 

7. Hit BEGIN SEARCH.

 

The database compares your submitted sequence to all others in the database, and records matching sequences!

 

An estimated time is given.

 

8. Hit FORMAT! to see the results.

 

 

9. Hit "Genome View"

 

What comes up next is really cool! Inspect each of the chromosomes shown for a red tick. What chromosome number is it?

 

10. Click on the chromosome number.

 

This brings you to part of a map showing the exact location of the "particular intron", AND, it gives you the name of the gene.

 

11. Click on the name of the gene (which is CDH13). This brings you to a page giving you the name of the gene, a summary of its functions, and kinds of problems that can come about if the gene malfunctions.

 

Students are highly motivated by the entire exercise (including the interactive) during which various questions are to be solved. Students learn gene structure and regulation, DNA synthesis, RNA processing, jumping genes, and they gain some experience witha few tools of science, e.g., how to find a gene.