Displaying genes in genome browsers

Question

[dominik.saburo]

Hi there!

Meybe it's a silly question but I can't find any good information about that...

So the problem is why (for example in IGV ) my genes are sometimes displayed from right to left order? I've noticed that mostly it is from left to right but from time to time I'm finding opposite situation.

Thanks for help!

[BioinfGuru]

what do you mean by right to left order?

If you could show an example image of both "left to right" and "right to left" orders, that would help alot.

[dominik.saburo]

Unfortunately I don't have an image of that right now but I will try to describe my problem in the simpliest way.

We have a sequence of random gene for example

AAAGGGTTTCCC -> Mostly software shows me this sequence in 5' to 3'.

But sometimes I see:

AAAGGGTTTCCC <- The arrow suggest me to read this in diffrent direction.

So the question is why genome browsers display such things? What is the reason of having diffrent direction of this sequence?

Answer 1

[BioinfGuru]

You are thinking correctly but just to clarify: The arrow indicates the direction of transcription which is always toward the 3' end.

Using your example, lets assume the full gene sequence of gene X given by genbank is AAAGGGTTTCCC. This is telling you that AAA is the 5' codon and CCC is the 3' codon.

If you see > on IGV when looking at this gene, then the sequence you see will be AAAGGGTTTCCC and will be transcribed as expected from left to right (toward the 3' end). However if you see <, then the sequence you see will be THE REVERSE COMPLEMENT (i.e. GGGAAACCCTTT) and will be transcribed from right to left (also toward the 3' end!!).

Example 1: left to right Example 2: right to left

We usually refer to these as being transcribed in the forward (left to right) or reverse (right to left) direction.

So you must remember whenever comparing/analyzing sequences in vivo, that gene sequence reference databases (e.g. genbank) only store the forward direction of the sequence (i.e. it assumes all genes are transcribed in the forward direction). If the gene is actually transcribed in the reverse direction, then you must convert the reference sequence to its reverse compliment to find it in vivo (or IGV).

[dominik.saburo]

Thanks a lot your answers!

So if it is a reverse complement why IGV shows me it instead of normal transcript? Are there any reasons why he shows exactly this complement?

[BioinfGuru]

You must remember that the database you get the sequence from only stores the sequence of the gene as if it was transcribed in the forward direction.

For example: If a gene is transcribed in the reverse direction (GGGAAACCCTTT) the database will still only store AAAGGGTTTCCC as if it is transcribed in the forward direction. But, in the real species genome AAAGGGTTTCCC does not actually exist... only GGGAAACCCTTT does. Databases do this to prevent duplication i.e. 2 sequence entries for the same gene. It is left up to the user to realize that the sequence stored, may exist in either forward or reverse form in the real species genome. IGV knows this. So IGV will always look for the "normal transcript" and the reverse complement.....and show you which one it found.

[dominik.saburo]

Once again thx for your help!