Hi,
I am working with a lncRNA (uncharacterized ) which i found to be present within the intonic region of my gene in human. When i blast it with mouse genome i did not find any sequence corresponding to it, assuming that it is absent in mouse.
However, by mistake i used 2 mouse cell line cDNA and used the primers for my lncRNA, i got exact size band. I thought of sequencing it and to my surprise it came out to be my LncRNA.
My question is
1. Is it possible that i identified a new lncRNA from mouse and i am unable to detect it in mouse genome as only 95% of mouse genome is sequenced and lncRNA falls in non coding region?
2. What can be the other possibility for this weird observation.
Thanks
Atoshi
Hi,
It seems to me the lncRNA of yours may be a novel one and it may be a reason why it is not appearing in any database search and lncRNAs are poorly conserved (though it is debatable), so it doesn't appear weird to me. Moreover, lncRNAs are poorly characterized till date. All the best with your work.
Cheers
Pankaj
Hi Pankaj,
But it should be present in mouse chromosome for sure, if not transcripts.
or the genome itself is not characterized fully.
Thanks
Atoshi
Mice and other rodents are quite distant from humans and other primates. Many protein-coding genes and structural RNA genes can be recognized in all mammals, but many other protein coding genes and RNAs have diverged a lot since the common ancestor of rodents and primates (and other mammals) lived something like 100 million years ago. What percentage identity are you seeing between your mouse PCR product and the human sequence? If you are finding something identical or nearly identical to human, it is almost certainly a PCR contaminant and not genuine mouse sequence.
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