2 replies to this topic

[Tabaluga]

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 !

[bob1]

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.

[Tabaluga]

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...