Sequence similarity between two genes

Question

[yunkyoung0225]

Can anyone explain what does it mean that two genes share similar non-coding sequences?

When I align two genes that I am interested in, there is particular sequences about 120 bp length that shares about 80% similarity. This small fragment is located in intron of both genes, I see it shows up repeatedly in intron and downstream region from end of the gene.

Is this common that genes are share non-coding sequences? Is it some part of functional DNA element? I just cannot figure what it means, and how to test whether it is functional or meaningful. Does anyone know good references or experiences?

Thank you very much..!!

[WouterDeCoster]

Could you be more specific with regard to the shared sequence? Is it by chance a repetitive element?

Answer 1

[joanneberghout]

Can you be a bit more specific about the two genes you're looking at? The best answers will depend on:

1. Are the two genes homologous within the same species (paralogs) or across two different species (orthologs)?
2. Is the similar region comprised of repetitive elements?
3. Have you checked these on a browser or similar to ensure that it is not a unique (also homologous) gene embedded within the sequence? Many miRNA genes or retrotransposons, for example are found within the introns of coding genes.
4. Have you looked to see if any of the ESTs or transcripts associated with either of these genes include that intron as an alternatively spliced exon?

Answer 2

[yunkyoung0225]

Thanks a lot Joanneberghout.

These two genes are located next to each other on same chromosome. They are only 6kb apart so I am wonder this short sequences are something important to regulate their transcription.

I've looked these two genes on genome browser, it seems unspliced EST exist on where I see this short sequences, but when I aligned these two genes, I see several regions has similarity in their introns. EST is only in one of them.. And, when I blasted these short sequences to whole mouse genome, got several matches on several genes, they are mostly in their non coding sequences or intergenic sequences.

And to answer Q2, I may need your helps.. How to know if it is comprised of repetitive elements?

Thanks!!

[WouterDeCoster]

Please use ADD COMMENT/ ADD REPLY to answer to earlier posts to keep the thread logically structured and easy to follow.

With regard to your question, if you could be more specific about which genes you have this finding you could get more specific answers. Don't make us guess.