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!
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Why cant you extract promoter regions (Ensembl genes) and CpG sites directly from UCSC table browser ??
https://genome.ucsc.edu/goldenpath/help/hgTablesHelp.html
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.