Where to download the Refseq gene definition file?
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Entering edit mode
7.6 years ago
moxu ▴ 510

I am looking for the coordinates of the genes for hg19. In hg17/hg18, there used to be a file with the following format:

name    chrom   strand  txStart txEnd   cdsStart    cdsEnd  exonCount   exonStarts  exonEnds    name2   hg17.refLink.product    hg17.refLink.protAcc    
hg17.refLink.geneName   hg17.refLink.locusLinkId
NM_001005484    chr1    +   58953   59871   58953   59871   1   58953,  59871,  OR4F5   olfactory receptor, family 4, subfamily F,  NP_001005484    184539  
79501
NM_001005224    chr1    +   407521  408458  407521  408458  1   407521, 408458, OR4F3,OR4F3,OR4F3,  olfactory receptor, family 4, subfamily F,  NP_00100
5224    184653  26683
...

I am looking for something similar if not identical to the above.

Thanks in advance.

gene • 1.2k views
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Entering edit mode
7.6 years ago
Shicheng Guo ★ 9.4k

Download it from:

https://yunpan.cn/cMiAu5SfzaqFK

with passwd: 69a5

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7.6 years ago
microfuge ★ 1.9k

You can use the UCSC table browser selecting the chosen genome version. In output you can use "Selected fields from primary and related tables" and then choosing related ids.

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Thank you, microfuge! I thought there was something that one could download from NCBI.

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