mirbase does not have miRNA annotation of my species, what are the alternatives?

Question

[demoraesdiogo2017]

Hello

I have been trying to align E. coli mirnome data. For other species, I see that many people have suggested to use the data available on mirbase to use as reference, but it doesn't have a reference for E. coli. When I used the gft available on NCBI, no counts were given by featurecounts. I looked over the gtf file and could not find any miRNA annotation, so I thought this might be the issue. I have considered perhaps using the supplementary data given from this 2013 article to align my data. Is this the correct course of action?

[GenoMax]

RNACentral has plenty of E coli RNA's: https://rnacentral.org/search?q=Escherichia%20coli

Limit the search based on what kind of RNA you are looking for (filters in left column).

[demoraesdiogo2017]

thanks! however, shouldn't it also have a gtf/gff file with the annotations?

Answer 1

[i.sudbery]

E. coli does not have miRNAs. miRNAs are a eukaryotic phenomenon. The paper you reference is about miRNA-sized RNAs. That is, RNAs that are in the 19-27nt size range. In prokaryotes these are usually referred to as "sRNA"s. In general these RNAs do not function in the same way as eukaryotic miRNAs.