[ensembl-dev] Mapping between Ensembl transcripts and Refseq, specifically for ENSG00000167131

Tony Håndstad tony.handstad at gmail.com
Mon Mar 4 13:23:35 GMT 2013

Dear Ensembl developers.

I am wondering if someone could explain how the mapping between Ensembl
transcripts and Refseqs is done in general, and specifically, for a
particular gene:

Ensembl Gene  ENSG00000167131 has five transcripts, two of these are
ENST00000417826  and ENST00000410006  which  both map to the same CCDS
When selecting the longest ENST00000417826 and looking at General
Identifiers under External References, I observe that this maps to five
Refseqs (NM_001258395.1, NM_001258396.1, NM_001258398.1, NM_001258399.1,
NM_213607.2). All of these are very similar, but with slightly different
However, for the other ENST00000410006, there are NO Refseqs that come up.

Is the reason that the shorter transcript does not overlap sufficiently
with the Refseq sequences in non-coding regions? Or could this be a bug,
or is my understand of this perhaps too incomplete?

Tony Håndstad
Oslo University Hospital

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