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How can I get a csv or a list of the gene symbol names for all the protein coding genes in mice? I have RNA sequencing data and I'm not interested in the non-coding stuff. I'm worried it could mess up my results. Can GEO or blast provide this?

Edit: I am not interested in EntrezID or Ensemble, I don't not want them I just am more interested in gene name like Fos or Penk. Etc. I work in RNA seq I don't need to map any fastq files to a genome that has been done already I just need to filter out genes that are not protien coding. If you are not familiar with what RNA seq data looks like it is simply rows of genes and columns of samples each entry giving the number of reads for that gene in that sample, single cell RNA seq is the same. Have a look at GEO if you want more examples: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145970

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  • $\begingroup$ So my answer should give you exactly what you need, right? If you don't want protein coding genes that do not have a "name" assigned, you can skip the "gene stable id" option. $\endgroup$
    – terdon
    Mar 9, 2023 at 9:40

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If you want all known mouse protein coding genes, you can get the list from Ensembl's BioMart.

First, select the mouse genome:

BioMart screenshot

Then, in "Filters" limit to protein coding genes only:

BioMart screenshot

And next, choose "Gene name" and, to have a more standardized and stable name and to ensure that you get allr esults (not all genes have a "name", but they will all have IDs), include the "Gene stable ID":

BioMart screenshot

Finally, click on "Results":

BioMart Screenshot

Select "File" and "CSV" and then click on "Go" to download the list:

BioMart screenshot

The end result is a file like this:

Gene stable ID,Gene name
ENSMUSG00000064341,mt-Nd1
ENSMUSG00000064345,mt-Nd2
ENSMUSG00000064351,mt-Co1
ENSMUSG00000064354,mt-Co2
ENSMUSG00000064356,mt-Atp8
ENSMUSG00000064357,mt-Atp6
ENSMUSG00000064358,mt-Co3
ENSMUSG00000064360,mt-Nd3
ENSMUSG00000065947,mt-Nd4l
ENSMUSG00000064363,mt-Nd4
ENSMUSG00000064367,mt-Nd5
ENSMUSG00000064368,mt-Nd6
ENSMUSG00000064370,mt-Cytb
ENSMUSG00000095019,
ENSMUSG00000094915,
ENSMUSG00000095041,
ENSMUSG00000095666,
ENSMUSG00000094741,Pramel39

With 21849 gene IDs, of which 21772 have a "name" as well.

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    $\begingroup$ Thanks, @RamRS, I blame my years living in France! :) $\endgroup$
    – terdon
    Mar 9, 2023 at 19:17

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