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

Question

PLEASE 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 chr11:83063393-84063392 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) There are more than 200 protein coding genes in the region

b) Approximately 10% of 1Mb makes the protein coding region

c) About 0 - 10% if these genes are exons

d) No the genes are not similar in terms of their structure.

e) Yes there are non coding genes in the region, It also contains retrotransposones

f) Yes there are retrotransposones in the region. Their parental genes are from

Dog (canFam3)97Mouse (mm10)13Rhesus (rheMac3)34

g) 30 - 60% of the window is made of transposable elements

h) There are so many genes in this small region of the chromosome. Each and every transposable element have a very different score for their parental gene. The origin varies widely for each and every single gene.

Related Questions

Navigate

• Browse (All)
• Browse P
• Subjects

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.