I'm using the biomaRt R packages (bioconductor) to retrieve the 3'UTR sequences of a list of genes. I've the entrezgene Id for each of them and I've differences between the biomaRt result and the ensembl biomart DB.
Here's an example :
For the ENSBTAT00000014489 transcripts (I'm working with Bos Taurus sequences)
In R :
library("biomaRt") ensembl <- useMart("ensembl") ensembl <- useDataset("btaurus_gene_ensembl",mart=ensembl) getSequence(seqType="3utr",mart=ensembl,type="entrezgene",id=522265) 3utr entrezgene 1 No UTR is annotated for this transcript 522265
In biomart ensembl : In "export Data", only check 3'UTR :
So, where's the problem ? How can the biomaRt package not retrieve this sequence ?
Thanks a lot,
ok thanks ! so biomaRt works great :)
FYI, this is the best browser page to check whether a transcript contains a UTR or not:
On this page the CDS is in black, UTRs in purple, introns in blue and flanking sequence in green. So, indeed this transcripts has no UTRs annotated.