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!
Photo
- - - - -

Finding region of interest in a gene

transcript variant

  • Please log in to reply
2 replies to this topic

#1 Tabaluga

Tabaluga

    Making glass out of shards

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 400 posts
49
Excellent

Posted 17 April 2012 - 02:55 PM

Hi, got the following problem:

I have got a gene with several transcript variants. By blasting, I've found a region of interest on a transcript variant, but I only know the base numbers (for example, from base number 700 to base number 720) from the mRNA of the respective transcript variant. How can I see where this region is with regard to the whole gene ? I guess what I need is a sort of map of the whole gene with all introns and exons and the whole sequence, but somehow I don't get along with the NCBI or Ensembl databases. I've looked at the gene maps there, I somehow cannot solve it....

Anyone who can help me ? Been stuck on this problem for days... :(
Thanks !

Il dort. Quoique le sort fût pour lui bien étrange,
Il vivait. Il mourut quand il n'eut plus son ange;
La chose simplement d'elle-même arriva,
Comme la nuit se fait lorsque le jour s'en va.

 


#2 bob1

bob1

    Thelymitra pulchella

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 5,799 posts
406
Excellent

Posted 18 April 2012 - 01:39 PM

Try the BLAT site at UCSC. Note that the region of interest is usually in an exon and the cDNA sequences on the NCBI website are probably what you are really looking for, as the intron can be of any random length without telling you anything about the protein produced.

#3 Tabaluga

Tabaluga

    Making glass out of shards

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 400 posts
49
Excellent

Posted 23 April 2012 - 08:25 AM

Thanks for your answer, and sorry for my late reply !
The region I'm interested in contains in all probability an exon-exon junction, and this being the case I realised that I cannot BLAST or BLAT this sequence against the genomic sequence...

Il dort. Quoique le sort fût pour lui bien étrange,
Il vivait. Il mourut quand il n'eut plus son ange;
La chose simplement d'elle-même arriva,
Comme la nuit se fait lorsque le jour s'en va.

 





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

©1999-2013 Protocol Online, All rights reserved.