Difference between 'intergenic' and 'ncRNA' in annotation.
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3.2 years ago

Hi all.

I am confused about the concept of 'Intergenic' region in annotation. What's difference between ncRNA? ncRNA means only 'long' non-coding rna?

Thanks in advance.

annotation annovar intergenic ncrna • 1.0k views
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3.2 years ago

Intergenic is "between" genes, so not close to any known gene. ncRNA, non-coding, is just a gene which does not code for a protein.

On a not entirely unrelated note: I don't like the term "non-coding". It's non-protein-coding, but it's still coding for a functional RNA molecule. But that's an artefact from older times when only protein-coding genes mattered.

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Thank you for answer. But still confused. 'intergenic region means intron? And of course it doesn't code protein?? What's functional difference with intron??

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If you have gene-A from, say, chr1:10000-15000 and gene-B from chr1:20000-25000, then the range between the intervals, given that there is no additional gene in between, would be termed intergenic. This only means that no annotated gene is located there. Still, there can be other functional elements, like enhancers or insulators. This all comes, as Wouter said, from the time that the community considered genes as the one and only major players in the genome, considering the remaining 98% of DNA as junk or evolutionary remainings without function (which is of course non-sense as we know nowadays).

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An intron is a piece of non-protein-coding DNA between the start and stop nucleotide of a gene/transcript. The most important functional elements here are probably splice signals, splice enhancers and transcription factor binding sites.

Intergenic means non-protein-coding outside of genes, while intron is inside a gene.

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3.2 years ago

An intergenic region is one between genes. A ncRNA is a non-coding gene. An ncRNA could be either long or short, it's sort of a catch-all grouping.

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