[ensembl-dev] mapping a gene and its exons to the underlying clone

[Andrea Edwards]

Hi

I was trying to find the sequence of a gene and its exons in the 
underlying clone using the ensembl api and not getting very far. I was 
doing this to get used to the api more than anything else and trying to 
map between a gene which is on the reverse strand, and a clone 
containing the forward strand.

I was able to retrieve the coordinates of the exons in the genomic sequence.

exon 1
start: 128,684,354
end: 128,684,488

exon 2
start: 128,664,422
end: 128,664,818

I have to flip the start and end round in my head

forward  5' ===========================================3'
reverse  3' ===========================================5'

                  126,664,422-128,664,818    128,684,354 -128,684,488
<=========E2 <=============E1

But i then was lost how to map these to a clone. I looked for something 
equivalent to the TranscriptMapper but couldn't find anything.

The total length of the sequence (including the intron in the middle is):
128,684,488 - 126,664,422 = 202066 bases

I then want to find out how these entire region maps to the underlying 
clone (AC112484.8). I would then like to print out, from the clone, the 
appropriate subsequence in both the forward and the reverse direction.

I hope that makes sense. I don't think it should be difficult but I 
can't find the appropriate methods

Many thanks