How comprehensive is genode lncrna anotation for mouse?

Question

[piyushjo]

Hi,

I am working on a small paper to characterize lncrna in in vitro differentiated neural cells. I started with using gencode annotation file for quantifying lncRNA. Now I came across with several papers suggesting how to find novel lncRNA (lincScore). But then I realized that I am interested in working with annotated lncRNA particularly antisense and lincRNAs. If I find novel lncRNA how can annotate them for being endogenous? Is there an algorithm for mouse? Plus if I just stick with gencode how comprehensive is that annotation (I am using vM17 version)? How often it is used in the field?

P.S.: Sorry for a naive question. Just trying to build my concepts in lncRNA and Bioinformatics. Thanks for sugegstions!

Answer 1

[GenoMax]

It is impossible to judge if a database is complete since it represents a snapshot of our current understanding of the knowledge at the time the data was released. It is likely that GENCODE data is more reliable since it is supposed to be the official resource for all things related to human/mouse genomes.

For comparison if you look at RNAcentral these entries assigned to various species of mouse labeled lncRNA. Compare and contrast that with what you have.