Question: Ensembl Exon Order
gravatar for Panagiotis Alexiou
8.5 years ago by
Athens, Greece
Panagiotis Alexiou200 wrote:

Hi to everyone. I have a question about Ensembl Exon Order.


I have used Biomart to download a file with all exon positions for each transcript (and some other information). An example header is:

11|ENSG00000166796|LDHC|1|ENST00000280704|18390429;18390832| 18390585;18390840|18429251|18429366|18429086;18390429;18416651; 18393307;18390832;18424333;18412863;18407860|18429366;18390585; 18416768;18393424;18390966;18424456;18413036;18408033|8;1;6;3;2;7;5;4

notice that the last 3 fields:

|18429086;18390429;18416651;18393307;18390832;18424333;18412863;18407860| 18429366;18390585;18416768;18393424;18390966;18424456;18413036; 18408033|8;1;6;3;2;7;5;4

contain exon starts and stops and a field called "Exon Order". Now the exon order field corresponds to the order of the exon coordinates (for example the "second" coordinates that have order = 1 are the smallest coordinates).

My question is:

does this mean that when splicing occurs and the cDNA is created the exons are put together in the order defined? To have cDNA do I have to take into account that order?

Hope this makes sense - thanks for anybodies help


ensembl exon • 1.6k views
ADD COMMENTlink modified 8.0 years ago by Alastair Kerr5.2k • written 8.5 years ago by Panagiotis Alexiou200

Since each entry corresponds to a different transcript, I'm assuming you don't have to worry about different splicoforms (resulting from alternative splicing) in the same entry?

ADD REPLYlink written 8.5 years ago by Daniel Standage3.8k

each entry is one transcript and all spiceforms are taken care of (ie it has unique splicing)

ADD REPLYlink written 8.5 years ago by Panagiotis Alexiou200
gravatar for Alastair Kerr
8.5 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

Exon splicing per transcript is always in sequence; lowest coordinate to highest coordinate (or highest to lowest if transcript is on the negative strand). So as you note the order number is consistent with your exon coordinates.

That said it is be easier to use biomart to pull out the cDNA directly rather than piece it together from the data you have.

A word of caution, if you check your transcript against the latest build: "ENST00000280704" the coordinates are not the same. You may be using an old assembly with biomart

ADD COMMENTlink written 8.5 years ago by Alastair Kerr5.2k

I have used biomart, to get the coding sequence of transcripts. Only to get the genome coordinates that correspond to my sequence I have to get the exon coordinates.

and yes it is an older assembly (thanks for pointing that out).

ADD REPLYlink written 8.5 years ago by Panagiotis Alexiou200
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