Gene Locus to ENSEMBL ID

Question

[Scott McKay]

Is there some way (biomaRt or not) that will allow me to convert the gene locus (NM_###) to it's ensembl gene id?

[Jean-Karim Heriche]

Assuming this is about RefSeq accession numbers, note that NM prefixes are used for curated protein-coding transcripts, not genomic loci. Associating an accession number with the wrong entity type may mislead you.

[Ram]

What have you tried? Did you look at listAttributes() etc in biomaRt? Search for other packages such as org.Hs.eg.db?

[Scott McKay]

I looked at searchAttributes(mart=ensembl, pattern=locus) and then searched the Attributes for some loci information but turned up nothing

Answer 1

[Kevin Blighe]

If you want to convert RefSeq 'NM' or 'NR' identifiers, then use refseq_mrna or refseq_ncrna attributes, repectively, as I mention at the end of my answer, here: A: Affymetrix Human Genome U133 Plus 2.0 Array

Also a practical example shown here by another user: A: biomaRt doesn't convert refseq_rna to flybase_gene_id