getting genome coordinates of gene lists

[Bogdan Tanasa]

Dear all, 

would you please me know, how could i get the genome coordinates of the genes, given a list of genes ? thanks a lot, 

-- bogdan

[Gerardo Perez]

Hello, Bogdan.

Thank you for your question about getting genomic coordinates with respect to genes.

Here are two gene tracks that we offer for human hg38/hg19 and mouse mm10/mm39:

• NCBI RefSeq: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=refSeqComposite
• GENCODE: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=knownGene

You can download these data from our download page:
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
https://hgdownload.soe.ucsc.edu/gbdb/hg38/gencode/gencodeV36.bb

You can extract the genomic coordinates using the Table Browser. For example, to query the NCBI RefSeq on hg38, navigate to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and make the following selections:
1.

clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: Genes and Gene Predictions
track: NCBI RefSeq
table: RefSeq All (ncbiRefSeq)

2. Set the region to “genome”
3. Click paste list next to “identifiers (names/accessions):” and enter your list of ID's. Then click submit.
5. Set the output format to “Selected fields from primary and related tables”. This will allow you to select fields of interest. Click get output.
7. Select “chrom”, “chromStart”, “chromEnd”, and “name” fields. These fields will give you the coordinates in the genome for the genes.
8. Click get output. The output will then give you all the genes coordinates for hg38.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Bogdan Tanasa]

Thank you very much, Gerardo. Thanks.