Hi,
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 :
result :
So, where's the problem ? How can the biomaRt package not retrieve this sequence ?
Thanks a lot,
N.