Is it possible to obtain all the RefSeq transcripts of Ensembl genes for GRCh37 ?
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18 months ago
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Hello,

Using Biomart, it is possible to obtain the matching RefSeq transcripts for GRCh38. I would like to know if there is a way to obtain that information for GRCh37.

Ensembl RefSeq transcripts genes • 472 views
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use grch37 mart.

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thanks for reply but I tried that already, they don't have this option

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Hi badredda, there is absolutely no need to remove a question after it has been answered. This might still be useful for others. Thanks for adding the solution you found!

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@WouterDeCoster I actually deleted it because it was a wrong answer ... the transcript version is that of Ensembl and not RefSeq... I am sorry for my inattention :(

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If you are using biomaRt in R, you can use grch37 mart and get refseq entries with refseq_mrna filter.

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18 months ago

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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18 months ago
caggtaagtat ★ 1.5k

Hi,

here is the link for biomart of the GRCh37 genome, in case someone did not find the link. You can get to every version through ensembl archives.

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I know, that there was a mixup in your question. I just wanted to answer it anyway, in case someone needs it. From the link, you get to the old biomart with transcript coordinates in reference to the GRCh37 genome. Like in the normal biomart, you can select as attributes, the RefSeq ID per ENSEMBL ID.