Question: Need help understading gene representation in IGV browser
1
gravatar for Jordan
5.4 years ago by
Jordan1.1k
Pittsburgh
Jordan1.1k wrote:

CFTR gene

This is the structure of a gene called CFTR, present in Mouse. The screenshot was taken from a IGC browser.

I need help understanding some fairly trivial questions.

1. I think the vertical bars represent Exons and the rest is intronic region. Correct?

2. The arrow points to the direction of the gene. In this case it's 5'-3'?

3. Why does the starting and ending of the gene have regions of different vertical bar lengths. They seem to be shorter than the rest. Does this signify anything? Please scroll over to the right end to see what I mean. There is a long blue bar but shorter in size.

Thanks for the help.

igv gene • 3.3k views
ADD COMMENTlink modified 5.4 years ago by Devon Ryan92k • written 5.4 years ago by Jordan1.1k
2
gravatar for Devon Ryan
5.4 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

Yes, vertical bars represent exons. The taller bars are CDS within the exons (thus, the shorter vertical bars are UTR). Arrows are the 5'->3' direction (so if they pointed in the other direction, the gene would be on the - strand).

BTW, this is a standard representation of a gene, so you'll see this in the UCSC genome browser and many other places.
 

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Devon Ryan92k

I see. Thanks!

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Jordan1.1k

They're UTR. In this case, the 5' UTR is on the left and the 3' UTR on the right.

ADD REPLYlink written 5.4 years ago by Devon Ryan92k

Thank you for your answer to the question that I also had. In my data, I see UTRs not exactly on the extreme side of the mRNA, i.e., a coding region, UTR, and then CDS again. Is that possible?

ADD REPLYlink written 13 months ago by al.jal.abadi0
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