Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
* - - - - 1 votes

How to trace exon number in genome sequence?

ensemble sequence exons oncogene

  • Please log in to reply
2 replies to this topic

#1 de ifz

de ifz


  • Active Members
  • Pip
  • 13 posts

Posted 13 March 2012 - 06:21 AM


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.

Attached Thumbnails

  • bcr-abl.gif

#2 bob1


    Thelymitra pulchella

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 6,509 posts

Posted 13 March 2012 - 11:47 AM

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.

#3 Trof


    Brain on a stick

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 1,360 posts

Posted 15 March 2012 - 07:52 AM

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.

Our country has a serious deficiency in lighthouses. I assume the main reason is that we have no sea.

I never trust anything that can't be doubted.

'Normal' is a dryer setting. - Elizabeth Moon

Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.