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Gene Definition #272

Closed AlasdairGray closed 5 years ago

AlasdairGray commented 5 years ago

We need a descriptive definition for the Gene Type

deniseOme commented 5 years ago

@ljgarcia, one issue raised at the Paris biohackathon by the lady whose name I can't remember (from Canada? Or US?) is the DNA versus RNA genomes. The majority of the genomes out there from virus to mammals are DNA-based, but there are a few classes of virus that have RNA genomes.

I can see that from NCBI genomes resource they provide RNA genomes in the DNA nucleotide format (A, C, G, T) instead of RNA nucleotides (out with T, in with U) e.g. https://www.ncbi.nlm.nih.gov/nuccore/701219395

We should seek input from virologists if we want to include RNA genomes or do more research ourselves. Alternatively we may make the deliberate decision to define genes as per DNA genomes only.

For the time being, this is a suggestion:

gene = discrete unit of nucleotide sequences. When in DNA genomes, genes will get transcribed into RNAs, and the mostly translated into proteins.

ens-ap5 commented 5 years ago

Amendment to above definition: a discrete locus of heritable, genomic sequence which affect an organism's traits https://en.wikipedia.org/wiki/Gene

ens-ap5 commented 5 years ago

Examples: protein-coding: FOXP2 (Forkhead box protein P2); RNA gene: SCARNA21 (small Cajal body-specific RNA 21).

No examples of viral gene at present.

folago commented 5 years ago

At the F2F meeting this definition was agreed upon: A discrete unit of inheritance which affects an organism's traits, typically associated with a genomic locus https://en.wikipedia.org/wiki/Gene. Examples include FOXP2 (Forkhead box protein P2), SCARNA21 (small Cajal body-specific RNA 21), A- (agouti genotype).

ens-ap5 commented 5 years ago

Small tweak to make more generic:

A discrete unit of inheritance which affects one or more biological traits, typically associated with a genomic locus https://en.wikipedia.org/wiki/Gene. Examples include FOXP2 (Forkhead box protein P2), SCARNA21 (small Cajal body-specific RNA 21), A- (agouti genotype).

deniseOme commented 5 years ago

I'd recommend refraining from using "genomic locus" in this definition. Locus in genetics and genomics is a location for other entities as well, not only genes. Eg. the word locus can also be applied to SNPs, CNVs or any other region containing one or more genes...

AlasdairGray commented 5 years ago

@deniseOme would you suggest just omitting the final part of the sentence so that it would become:

A discrete unit of inheritance which affects one or more biological traits https://en.wikipedia.org/wiki/Gene. Examples include FOXP2 (Forkhead box protein P2), SCARNA21 (small Cajal body-specific RNA 21), A- (agouti genotype).

@ens-ap5 @folago what do you think of this alternative?

deniseOme commented 5 years ago

Yes @AlasdairGray, I think this alternative is a safer bet.

folago commented 5 years ago

@AlasdairGray @deniseOme yes the suggested edit looks good to me.