Dear all, 

please would you advise, what is the easiest way to get the SEQUENCES of 3'UTR and the GENE_NAMES for all mouse or human genes  ? After glancing through previous posts, I think I shall start with : 

refSeq             <- makeTxDbFromUCSC(genom="mm10",tablename="knownGene")                     
threeUTRs          <- threeUTRsByTranscript(refSeq, use.names=TRUE)

many thanks, 

-- bogdan

This sort of thing continues to amaze me:

refSeq <- makeTxDbFromUCSC(genom="mm10",tablename="knownGene")

Is it not clear that the TxDb.Mmusculus.UCSC.mm10.knownGene package is the same thing, and you can just download that rather than spending the time to make your own? I see people doing that all the time, and I wonder if it's an informational problem on our end.

Anyway, I believe you want

library(BSgenome.Mmusculus.UCSC.mm10)

seqs <- getSeq(Mmusculus, threeUTRs)

See for example, ?getSeq, as well as the annotation workshop from BioC2018, particularly slide 3.4.39