<p>Try the GRCh37 version of BioMart, and the External reference "RefSeq mRNA ID" / "RefSeq ncRNA ID":</p>

<p><a href="https://grch37.ensembl.org/biomart" rel="nofollow noreferrer">https://grch37.ensembl.org/biomart</a></p>

<p>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.</p>

<p>I feel compelled to add a caution to this, though. GRCh37 is a very old build, having been <em>replaced</em> by GRCh38 in <a href="https://en.wikipedia.org/wiki/Reference_genome#Human_reference_genome" rel="nofollow noreferrer">December 2013</a>. If possible, please find a way to use GRCh38 for your analysis instead, and don't create any <em>new</em> software that depends on GRCh37. For example, gnomAD v3 supports GRCh38 (see <a href="https://bioconductor.org/packages/release/data/annotation/html/MafDb.gnomAD.r3.0.GRCh38.html" rel="nofollow noreferrer">bioconductor</a>, or <a href="https://macarthurlab.org/2019/10/16/gnomad-v3-0/" rel="nofollow noreferrer">here</a>).</p>

CC BY-SA 4.0
2020-01-22T10:23:58.170Z
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.
user324810
CC BY-SA 4.0
2020-01-22T04:48:40.857Z
2020-01-22T20:47:01.650Z
2020-01-22T20:47:01.650Z
gringer
<p>The RefSeq match option in BioMart is from the <a href="http://www.ensembl.org/info/genome/genebuild/mane.html" rel="noreferrer">Matched Annotation from NCBI and EBI (MANE)</a> 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.</p>

CC BY-SA 4.0
2020-01-21T22:31:21.807Z
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 ?
user324810
CC BY-SA 4.0
2020-01-22T09:46:26.627Z
No, we don't have the versions on the old verion of the database.
Emily_Ensembl
CC BY-SA 4.0
2020-01-21T15:44:20.883Z
2020-01-21T15:44:20.883Z
Emily_Ensembl
<p>I know that with GRCh38, it is possible to extract the matching RefSeq transcripts for Ensembl genes/transcripts/proteins using Biomart from Ensembl. </p>

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

<pre><code>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';"
</code></pre>

<p>Also, I was trying to play around with the <a href="https://www.ensembl.org/info/docs/api/core/diagrams/Core.svg" rel="nofollow noreferrer">databases schema</a> but I am not able to find any solution to problem.</p>

<p>Ultimately, I wish to obtain a table like the following:</p>

<pre><code>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
</code></pre>

<p>Thank you in advance.</p>

<ensembl><refseq>
Is it possible to obtain RefSeq transcripts from Ensembl database for GRCh37 to match Ensembl Genes?
# Is it possible to obtain RefSeq transcripts from Ensembl database for GRCh37 to match Ensembl Genes?

(Asked by: username_0 on 2020-01-21)

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.

**Tags:** ensembl, refseq

---

## 2 answers

### Answer by username_2 on 2020-01-21. Score: 6 | Accepted answer

The RefSeq match option in BioMart is from the [Matched Annotation from NCBI and EBI (MANE)](http://www.ensembl.org/info/genome/genebuild/mane.html) 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.

> **Comments:**
> **username_0**: 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 ?  
> **username_2**: No, we don't have the versions on the old verion of the database.  

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### Answer by username_1 on 2020-01-22. Score: 1

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](https://en.wikipedia.org/wiki/Reference_genome#Human_reference_genome). 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](https://bioconductor.org/packages/release/data/annotation/html/MafDb.gnomAD.r3.0.GRCh38.html), or [here](https://macarthurlab.org/2019/10/16/gnomad-v3-0/)).

> **Comments:**
> **username_0**: 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.  

---

