GENETICS HELP!! Go to www.genome.ucsc.edu Click on “Genomes” in the upper left c

Question

GENETICS HELP!!

Go to www.genome.ucsc.edu

Click on “Genomes” in the upper left corner. From the pulldown menus, choose “mammal”, “human”, and “Dec. 2013”

Then type in the genomic location chr10:49146204-49177003 in the window, and click “submit".

Among the dozens of pull down menus in the bottom half of the window, turn everything to “hide” except the following: “Base position”, “GENCODE v22", RetroGenes V9 and “Repeat Masker” should be set to “full”.

In the top of the browser window there is a little cartoon of your chromosome, where the red line shows you where your region is. Below that is a window showing you the genes (“GENCODE v22”) and the transposable elements (“Repeating elements”) in your 1Mb region. The vertical bars or boxes on the gene represent exons, while the line connecting them represent introns. The thicker vertical bars represent protein-coding portions of exons. The arrows on the introns tell you in which direction the gene is transcribed. If it looks like some genes have multiple copies on top of each other, they likely represent multiple splice variants.

Question

Protein coding genes

a. How many protein coding genes are in your region?

b. Just using your eyeball, approximately what percent of the 1Mb is made up of protein coding genes (introns and exons)?

c. Just using your eyeball, about what percent of these genes, in general, appear to be exons?

d. How do you feel about the protein coding genes in your region? That is, is your region fairly typical of the

human genome? Are most of these genes typical, in terms of structure, number of exons, introns, UTRs,

etc.? Are there any protein coding genes in your region that seem atypical?

RNA genes

e. Are there any noncoding genes in your area? If so, what are they?

Retrotransposed genes

f. Are there any retrotransposed genes? If so, what is the "parent gene" from which the retrotransposed gene was transcribed? Is the retrotransposed gene functional?

Transposable elements

g. Transposable elements (TEs) are shown under the track called “Repeating elements”. Each little vertical black and gray bar in the “Repeating Elements” track represents an independent transposable element. Click the “Zoom in 10X” button twice. Your window should now be showing you 10,00bp.Justusingyoureyeball,aboutwhat percent ofthis windowdoyou estimate tobemadeupof transposable elements?

h. Find three (3) interesting things in your 1Mb region. What are they? Explain what you are seeing and what the track is showing.

Explanation / Answer

a. 8 protein coding regions are seen

b. approximately 60percent will be exons [8exons]and 40percent are introns [7introns are present]

c. 60 percent of the genes are appered to be exons

d. the thick vertical lines are the coding regions of the genome . yes these regions seems to be the typical for the human genome such as exons,inrons and UTR ,but there are no genes which are atypical and diseasecausing

e. non coding regions are the introns there are total 7 genes which are non coding regions .

f. no,there is no retrotransposon genes in the gene .

g. i dont know the answer for that

h. i dont know the answer for this question

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