Question: Promoter regions of genes to find CpG island sites
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gravatar for birdnerd
2.8 years ago by
birdnerd0
birdnerd0 wrote:

Hi!

I'm trying to use online tools to find the promoter regions of selected genes within a genome (upstream from TSS), and then to find the corresponding CpG island/sites. I'm using the Ensembl tool. I search for selected gene > click matched gene > summary page opens > click 'sequence' on left side in table titled 'gene-based displays' > red highlighted areas are exons, and i've been told that the unhighlighted sequence above is the promoter region? Is this correct?

Link is of Ensembl page showing what I described above: https://postimg.org/image/x6km1d8dz/

I'm searching for CpG sites, but when I copy and paste this into a UCSC BLAT to see if it matches, or a methylation-primer-designer tool and CpG Island finder (e.g. MethPrimer), there are no matches. So is Ensembl providing me with the correct promoter regions, or is there something I'm missing/doing incorrectly?

Thanks!

genome gene • 1.6k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 2.8 years ago by birdnerd0

Why cant you extract promoter regions (Ensembl genes) and CpG sites directly from UCSC table browser ??

https://genome.ucsc.edu/goldenpath/help/hgTablesHelp.html

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by EagleEye6.5k

Thank you! The TSS and promoter regions of my targeted genes haven't been defined in any bird species - only sometimes in humans, mice etc. Solution has been to use MethPrimer and design primers upstream from islands.

ADD REPLYlink written 2.5 years ago by birdnerd0
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