Is there anything with a poly-A tail that isn't included in Ensembl's cDNA reference?

Question

[ericbrenner]

Like lncRNA's or pre-mRNA's that have a polyA tail but still have introns?

Thanks

[Jean-Karim Heriche]

The answer is: probably. But what are you looking for ? Or more precisely, where do you want to look for these things ? Are you interested in a species in particular ? Are you interested in cDNAs that have been already annotated or in raw sequences ?

[ericbrenner]

I was thinking things like lncRNA's or miRNA intermediates that haven't finished being processed. I've since learned that miRNA's are not included. Not sure about the rest. Basically, if I have raw RNA-seq data (corresponding to everything with a polyA tail), what reference(s) should I use for annotation if I want to make sure I don't leave out anything. I think annotating using the Ensemble cDNA reference and then using the Ensemble ncRNA reference should cover everything. I could also use a genome reference, but that wouldn't work with the speedy programs like Kallisto :/

[Jean-Karim Heriche]

I would think that mapping your reads to the Ensembl transcriptome would take care of this. Ensembl annotates all sorts of non-coding RNAs including miRNAs.