Hi everyone, was wondering if I could run something by you all?
I need to identify promoter sequences in several genes of interest as we are interested in doing bisulfite sequencing to determine if CpG islands in the promoter regions are potentially methylated.
I have used ensemble ( ensemble.org) to find the gene sequence before the first exon, and have entered the sequence into UCSC BLAT to determine if the sequence matches with what is on the UCSC database. However I am very new to this kind of work and I am not sure exactly how to interpret results from BLAT. Would anyone be able to help me in identifying gene promoter sequences either through UCSC BLAT or any other recommended software?
I must also say that we are investigating genes in pigs, so most databases/software's that are used for humans and mice cannot be used by us.
Any help at all will be greatly appreciated, many thanks in advance.
Hi Adam,
Why don't you use the upstream 1k regions from TSS recorded in UCSC database (genome build # susScr3). Here is the link: http://hgdownload.soe.ucsc.edu/goldenPath/susScr3/bigZips/upstream1000.fa.gz
Good luck!
Dear Adam
Please check this Book:
Human Molecular Genetics Strachan (Chapter 17).
Best wishes
Mohammad Amin
First you have to detect the promoter sequence of your gene of interest in this data base (http://epd.vital-it.ch/). Then design your primers( Methylated and unmethylated primers) using this online software (http://www.urogene.org/methprimer/).
Hi Adam Clark,
You must use Regulation section of UCSC for your aim. This section show items such CpG Islands,Unmasked CpG, DNase HS ,DNase signal , DNase cluster , H3K27AC,H3K4Me3, H3K4Me1 and transcriptions for you that they are enough for finding promoter of genes .
so TRANSFAC Date base ( not free ) can useful for this aim.
good luck.
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