AP Biology, DNA Technology & Genomics
Pan – Homo Chromosome Breaks

In your lab notebook: 
	Table of Contents			2
	Title/Date				2
	Objectives				5
	Recorded Observations		15
	E-mail					5
	Conclusions				10

Objectives
1.	Practice using a bioinformatics database.
2.	Identify expressed sequences around the ends of Pan-Homo pericentric inversions.
3.	Relate closely linked expressed sequences to hypothetical 

Procedure
1.	Google: UCSC genome browser [Yes, you’re feeling lucky]
2.	Click on Genome Browser in the text.
3.	Record your assigned breakpoint in your lab notebook.
Settings
	Mapping and Sequencing Tracks: Base Position “dense”, all others “hide”
	Genes and Gene Prediction Tracks: MGC Genes “pack”, all others “hide”
	mRNA and EST Tracks: Human mRNAs “dense”, Spliced ESTs “dense” , all others “hide”
	Comparative Genomics: Chimp Chain “pack” , all others “hide”
	Variation and Repeats: SNPs “dense”, RepeatMasker “dense” , all others “hide”
	All others “hide”
4.	In the “position/search” window type “chr” immediately followed by the chromosome number. For example, “chr5”. Hit Return.
5.	Point to the approximate position of your breakpoint on the chromosome diagram in the window under the jump button. Click to zoom in.
6.	Look at the first two red lines in the diagram window. Use the left and right buttons to move back and forth on the chromosome. Find the place where the top red line goes from thick to thin and where the second red line goes from thin to thick. Those points should be aligned. That’s the breakpoint. It may not be in the chromosome band we read off of the diagrams but it should be within a few bands.

7.	Zoom in. Use the left and right buttons to keep the breakpoint centered. Zoom in all the way so you can read the base sequence at the break. Describe the structure of the breakpoint: is there a small gap, or overlap, or to the chimp sequences exactly abut? Record the base range at the breakpoint.
8.	Zoom out until you can see the human mRNA sequences (shown in green) on either side of the break. E-mail the URL for this view to kbjordan@wcpss.net.
9.	Click the mRNAs closest on either side of the breakpoint and record the identity of the protein coded for by the two mRNAs. 

Conclusion
For each expressed sequence write a paragraph about how a change in the expression of that sequence may account for a phenotypic difference between Pan and Homo.