How to trace exon number in genome sequence? - (Mar/13/2012 )
I am working on a fusion oncogene (BCR-ABL) causing blood cancer. The problem is that I don't exactly know the product size of my pcr product (amplifying the fusion-oncogene).
I know the exons of both genes involved (e13 & 14 of BCR) and (a2 of ABL1) in the chromosomal translocation. but when I try to trace these exons in "ensemble" sequence I get confused. as there are many small exons not shown in the gene map of translocation.
Please help me out of it.
Presuming that you are looking for the p210bcr-abl fusion protein and that you are looking for the full lenght, you will have a product of approximately 5.25 kbp, based on the average kDa-basepairs conversion of approximately 40 kDa/kbp.
Translocation map shows BCR transcript with 23 exons (c1 - c23, the two before the last one are omitted in drawing). That correspond to transcript variant 1, ENST00000305877.
ABL1 has two transcripts with an alternate first exon (1b, 1a), since your breakpoint is before a2 you don't need to worry about them, just pick any of the two.