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I know that with GRCh38, it is possible to extract the matching RefSeq transcripts for Ensembl genes/transcripts/proteins using Biomart from Ensembl.

However, for GRCh37, this option does not exists. Using the following MySQL command returns Ensembl transcript IDs for matching RefSeq transcripts:

mysql -u anonymous -h ensembldb.ensembl.org -A -P 3337 -D homo_sapiens_core_99_37 -e "SELECT transcript.stable_id, xref.display_label FROM transcript, object_xref, xref,external_db WHERE transcript.transcript_id = object_xref.ensembl_id AND object_xref.ensembl_object_type = 'Transcript' AND object_xref.xref_id = xref.xref_id AND xref.external_db_id = external_db.external_db_id AND external_db.db_name = 'RefSeq_mRNA';"

Also, I was trying to play around with the databases schema but I am not able to find any solution to problem.

Ultimately, I wish to obtain a table like the following:

Gene stable ID      Transcript stable ID    Protein stable ID   RefSeq match transcript
ENSG00000120329     ENST00000239451         ENSP00000239451     NM_031947.4
ENSG00000164219     ENST00000419445         ENSP00000404676     NM_005023.4
ENSG00000150594     ENST00000280155         ENSP00000280155     NM_000681.4
ENSG00000113578     ENST00000337706         ENSP00000338548     NM_000800.5

Thank you in advance.

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The RefSeq match option in BioMart is from the Matched Annotation from NCBI and EBI (MANE) collaboration between RefSeq and Ensembl. It has only been calculated for the up-to-date gene annotation on GRCh38 so cannot be obtained on GRCh37. You can get mapping from Ensembl to RefSeq transcripts through BioMart as RefSeq mRNA ID (refseq_mrna in R) but this is not a perfect match like the MANE, it is a mapping based on sequence similarity and similar genomic location, and there can be mismatches between them.

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  • $\begingroup$ Thank you @Emily_Ensembl for your answer. I will continue discussing this topic here. Is it possible to obtain also the RefSeq mRNA ID with the versions using biomaRt ? $\endgroup$ – Law Jan 21 at 22:31
  • $\begingroup$ No, we don't have the versions on the old verion of the database. $\endgroup$ – Emily_Ensembl Jan 22 at 9:46
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Try the GRCh37 version of BioMart, and the External reference "RefSeq mRNA ID" / "RefSeq ncRNA ID":

https://grch37.ensembl.org/biomart

From the Perl code provided by BioMart, it looks like the field name should be "refseq_mrna" or "refseq_ncrna". I'm not sure how that translates to the SQL code.

I feel compelled to add a caution to this, though. GRCh37 is a very old build, having been replaced by GRCh38 in December 2013. If possible, please find a way to use GRCh38 for your analysis instead, and don't create any new software that depends on GRCh37. For example, gnomAD v3 supports GRCh38 (see bioconductor, or here).

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  • $\begingroup$ Thank you for your comment. Unfortunately, I have to use GRCh37 since gnomAD were annotated with this old version using VEP from Ensembl. So, doing a lift-over or annotating again would lose any supports that the paper had at that time. $\endgroup$ – Law Jan 22 at 10:23

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