Hi to everyone. I have a question about Ensembl Exon Order.
Specifically:
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
Panagiotis
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?
each entry is one transcript and all spiceforms are taken care of (ie it has unique splicing)