What is the definition of splice-junctions detected by splice-junction mappers

[kanewong]

Hi all,

I know this question may be too general to ask in a forum, but I have searched on the net for a while but still can't get a good definition.

I have run several splice-junction tools such as TopHat, SpliceMap...etc. The results are splice-junctions in bed format. Each junction contains two important information, chr start and chr end.

My question is:
Is chr start to chr end equivalent to intron? Or it means intron + a part of the two neighbour exons(acceptor + donor sites)?

Also, I will need a citation for my thesis. I would appreciate a lot if you could provide me a website which gives the definition of splice junction given by mappers.
Many thanks

[mastal]

My question is:
Is chr start to chr end equivalent to intron? Or it means intron + a part of the two neighbour exons(acceptor + donor sites)?

Have a look at a few of the 'chr start end' positions (in the .bed files output by the splice junction mappers you have been using) on the tracks of the UCSC genome browser, and you should be able to figure out the answer.

[kanewong]

Have a look at a few of the 'chr start end' positions (in the .bed files output by the splice junction mappers you have been using) on the tracks of the UCSC genome browser, and you should be able to figure out the answer.

Thanks, but the organisms I am investigating is Arabidopsis Thaliana. UCSC genome browser doesn't support a numbe of plant genome, including this one.

[GenoMax]

Thanks, but the organisms I am investigating is Arabidopsis Thaliana. UCSC genome browser doesn't support a numbe of plant genome, including this one.

http://epigenomics.mcdb.ucla.edu/

http://atensembl.arabidopsis.info/index.html

http://plants.ensembl.org/index.html