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

Question

[Zakaria Benmounah]

Hello,

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

Best

Answer 1

[Saulius Lukauskas]

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".

[Zakaria Benmounah]

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

cheers,

[Saulius Lukauskas]

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.

[Saulius Lukauskas]

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

[Zakaria Benmounah]

Many thanks Saulius,

Answer 2

[CraigM]

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