I was fetching small RNA like tRNA/rRNA/snRNA/snoRNA from the latest Ensembl, and then I noticed that there are a class of repeat in RepBase called 'RNA repeat', which contains various RNA, tRNA, rRNA, snRNA, scRNA, and srpRNA. I expected they are annotated, but actually when I intersect between them and I found a large number of RNA repeats are not annotated. Here is it:
$ grep rRNA $repeats_from_RepBase | intersectBed -a stdin -b $snRNAsnoRNAtRNArRNA_from_Ensembl -s -v | sort -u | wc -l
1557
Here is an rRNA example:
and a tRNA example:
Both are not annotated as a rRNA/tRNA gene, but as a RNA repeat.
So, what's the definition of RNA repeat for RepBase? pseudogene?
