How to get coordinates from UCSC Genome Browser
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5.7 years ago
fk566938 ▴ 10

Hello, I am trying to get coordinates for a gene on the ucsc genome browser. I have zoomed in but once you zoom in by holding shift and click it can only zoom in so much.

coordinates ucsc genome browser • 2.8k views
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5.7 years ago

You can do a mysql query of the UCSC Genome Browser for a specific gene and build, e.g., human "CTCF":

$ gene="ctcf"
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e "SELECT k.chrom, kg.txStart, kg.txEnd, x.geneSymbol FROM knownCanonical k, knownGene kg, kgXref x WHERE k.transcript = x.kgID AND k.transcript = kg.name AND x.geneSymbol LIKE '${gene}';" hg19
+-------+----------+----------+------+
| chr16 | 67596309 | 67673088 | CTCF |
+-------+----------+----------+------+

Just replace the value of gene with your gene-of-interest, and modify the build (hg19) if you're interested in a different reference genome or organism.

Some genes have more than one transcript. You can add LIMIT 1 to the SQL query to just grab the first hit:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e "SELECT k.chrom, kg.txStart, kg.txEnd, x.geneSymbol FROM knownCanonical k, knownGene kg, kgXref x WHERE k.transcript = x.kgID AND k.transcript = kg.name AND x.geneSymbol LIKE '${gene}' LIMIT 1;" hg19

Or you could post-process the query output with awk or similar to get the first result's start and last result's end coordinates, to get the overall interval of the gene.

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5.7 years ago
5utr ▴ 350

When you enter the gene name genome browser offers you with a list of genes and transcripts that match your query, each one has the coordinates for the assembly that you selected.

Alternatively you can go to Table browser and download a flat table that you can customize: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=454971717_SwAPqe5Nq2wP5DA8laA6PO1XcxiE

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