Download all NCBI gene names, synonyms, and gene ID for an organism

Question

[Patrick]

I would like to download all NCBI genes, synonyms and gene ID #s for mouse, and then human. Ive tried downloading lists of gene names, and then searching NCBI to get gene ID, however I run into problems with NCBI having a different official name compared to what I input. Is there a way to get all of the gene IDs easily in one go? Thanks!

Answer 1

[skbrimer]

Do you mean, you would like to download the complete reference from NCBI from the RefSeq FTP site?

like here for mouse and her for human

[Patrick]

I am only looking for a table or list. Something along the lines of:
Symbol Entrez Gene ID
Pzp 11287
Aanat 11298
Aatk 11302
Abca1 11303
Abca4 11304

(That has all Gene IDs)

[lessismore]

Quite straightforward. For Mus musculus gene: go to the NCBI gene page >> https://www.ncbi.nlm.nih.gov/gene/?term=Mus+musculus and go to "send to" >> file >> tabular (text). Then open the file and select the column 3 and 6 and save to new table:

cat gene_result.txt  | cut -f3,6 > Mus_mus_gene_id.txt

[Patrick]

Wow, that was too easy. Exactly what I was looking for, Thank you!