Question

How to get all locations in the genome of the 5'end of genes (hg19) ?

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9.7 years ago

Zakaria Benmounah ▴ 50

Hello,

I'm looking for How to get all locations in the genome of the 5'end of genes (hg19) ?

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genome hg19 • 2.6k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Zakaria Benmounah ▴ 50

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9.7 years ago

CraigM ▴ 90

The UCSC genome table browser can be used for this http://genome.ucsc.edu/cgi-bin/hgTables?command=start

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by CraigM ▴ 90

Ram · Accepted Answer · 2015-03-30

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9.7 years ago

Saulius Lukauskas ▴ 540

Have a play with either ENCODE table browser or Ensembl BioMart. hg19 is equivalent to genome version 37 in the latter.

You would get more specific instructions if you google for "transcription start sites".

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Saulius Lukauskas ▴ 540

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In the Encode Table browser, which table I have to choose to get the 5'end position of genes?

cheers,

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Zakaria Benmounah ▴ 50

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I would say knownGene (i.e. literally the 'known genes') txStart and txEnd columns.

If I remember correctly they use txStart < txEnd convention meaning that txStart is 5' for + strand and txEnd is 5' for - strand genes. Somebody correct me if I'm wrong.

ADD REPLY • link 9.7 years ago by Saulius Lukauskas ▴ 540

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I think Ensembl gene annotations are considered to be cleaner though. Personally I would recommend going with them.

This is the biomart you want to look at http://grch37.ensembl.org/biomart/martview/73fdcb3d90ea2557c0e0b39f64ca752f