gene coordinates in refGene.txt

[Lin Pei]

Hi

I have download the file refGene.txt.gz from UCSC[1]

Could you please tell me in this file which two columns represent the start and end coordinates of a gene ?
Are the first two numbers just after the sign "+/-" ?

Also, where I can find the description for what was represented by each column ?

Thanks
Best,


[1] http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

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Lin Pei

[Jonathan Casper]

Hello Lin Pei,

Thank you for your question about data from the refGene table. Yes, the two numbers immediately after the strand information ("+" or "-") are the start and stop coordinates of transcription. You can find more information about what each of the columns mean by opening the track description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=refGene, also accessible by clicking the track name on the main browser page at http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19), or by selecting the table in the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables (under human assembly hg19, group "Genes and Gene Predictions", track "RefSeq Genes"). When you click on "describe table schema", you will be taken to a page that explains each of the fields in that table.

In this case, the refGene table is an extended form of the genePred table format. More information about this format can be found at http://genome.ucsc.edu/FAQ/FAQformat.html#format9.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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