Could someone define "flanking region" for me please?

[cazmantis]

Hi,

 

Could I just check with someone if I have got this right please? My definition of a flanking region of a gene is the region x bp upstream from the start codon and the equivalent downstream from the stop codon? For the current gene I am looking at I am using about 500bp as my flanking region as it seemed a sensible figure (1,000 bp upstream is the end of another gene so I didn't want to go into that) but is there an official way to identify a flanking region or would my estimate be appropriate? I am BLASTING these regions to try and identify similarity.

 

Thanks so much!

 

Caz

[CharonY]

Flanking regions just means up and downstream from a given position. A flanking region of an ORF is precisely as you defined it. One could also take any other arbitrary region or position and define bp and and down from it. However, BLAST is a global alignment tool and non-coding regions often only have local similarities. Other alignment algorithm may serve you better (depending on what you intend to see).

[cazmantis]

That's great - thanks. Good to have a confirmation of what I had presumed!

 

I am just trying to ascertain that the gene which codes for a particular protein (in this case I'm looking at antigen 5) is a product of the same locus in two species. It has been suggested that looking for similarities in the non-coding regions will help identify that. I am using Clustal also to align these sequences but it is hard for me to tell (due to lack of experience) exactly how similar means "similar enough"! Thanks for your help!

 

Caz

[CharonY]

There are different ways to assign distances based on similarities, however, the usefulness of local regions to identify loci is dependent on how close the organisms are and how conserved the region is. For instance, it is possible that gene duplication resulted in multiple copies of that particular region in the genome, or the gene region itself may have undergone some kind of changes as e.g. inversions, relocation and so on. In these cases looking at synteny, which requires the addition of surrounding genes and not only the gene region may be of relevance.