How to Convert Ensembl Gene and Transcript IDs to RefSeq mRNA and Gene IDs from isoforms data?

Question

[mauricio.1313]

Hi everyone,

I'm currently working with a dataset that contains Ensembl gene IDs and Ensembl transcript IDs, and I need to map these to RefSeq mRNA IDs and RefSeq Gene IDs. Here's a snippet of my dataset:

> head(isoform.ensembl)

         gene_stable  transcript_stable
1 ENSMPUG00000000002 ENSMPUT00000000002
2 ENSMPUG00000000003 ENSMPUT00000000003
3 ENSMPUG00000000004 ENSMPUT00000000004
4 ENSMPUG00000000005 ENSMPUT00000000005
5 ENSMPUG00000000006 ENSMPUT00000000006
6 ENSMPUG00000000007 ENSMPUT00000000007

I’ve tried using the getBM() function with Ensembl gene and transcript IDs as filters and retrieving the corresponding RefSeq mRNA and RefSeq transcript. However, I keep getting empty results, even for human data. For example, I focus on ferret first:

# Connect to the Ensembl BioMart database for ferret
ensembl.mu <- biomaRt::useMart("ensembl", dataset = "mpfuro_gene_ensembl")
#
getBM(
    attributes = c("ensembl_gene_id", "ensembl_transcript_id", 
                   "refseq_mrna", "refseq_peptide"),
    filters = "ensembl_transcript_id",
    values = isoform.ensembl$transcript_stable,
    mart = ensembl.mu
)

The code works, however, I just got empty results:

ensembl_gene_id ensembl_transcript_id refseq_mrna refseq_gene
1   ENSMPUG00000000002    ENSMPUT00000000002            
2   ENSMPUG00000000003    ENSMPUT00000000003            
3   ENSMPUG00000000004    ENSMPUT00000000004            
4   ENSMPUG00000000005    ENSMPUT00000000005            
5   ENSMPUG00000000006    ENSMPUT00000000006            
6   ENSMPUG00000000007    ENSMPUT00000000007            
7   ENSMPUG00000000008    ENSMPUT00000000008

Even If I tried using humans, I still got empty columns.

I know that there is a lot of different post related to the same idea, however, not of them worked so far.

Please, any comment to solve this issue will be really appreciated!