CpG islands of FASN, CPT1, SOCS3 in liver of C57BL/6 mice.
Help to find the number of CpG in a specific gene.
Hi Rogerio,
you can use UCSC genome browser to look at the CpG Island.
Go to, https://genome.ucsc.edu/cgi-bin/hgGateway (to reach the browser).
Type in your gene of interest (ex. FASN).
Once in the browser, look at the bottom of the page for the ''Regulation'' option.
Enable the CpG Island track (choose show) and it refresh
and ta-da, you have all the annotation for your gene.
In this case, FASN has 9 CpG island.
The great thing of UCSC is that you can display other track at the same time and get a good feel of your gene of interest.
Best,
Nicolas
Thank you so much for your feedback Nicolas
I tried here for mouse and there is just 1 CpG island for FASN gene.
Hi Rogerio,
It seems that the CpG islands seen here in the UCSC genome browser, are in the transcribed genomic region of the gene. If you drag the cursor to the left you may see the promoter region upstream and there may be other CpG islands there that may be important for gene expression. For the FASN gene in mouse, as you mention, it seems to be that one that overlaps with the promoter.
Good luck!
Blanca
Hi Blanca L. Valle
I have other question but it looks like stupid but I am starting with this kind of analysis: How can I say that the CpG Island is in the promoter region (in the UCSC I mean)?
Thank you so much
Hi Rogerio,
The CpG island associated with your gene seems to be in the promoter and spanning the TSS, going into the transcribed region of the gene. It has a portion in the promoter and a portion in the gene. The promoter is located upstream of the gene, in the 5’ region adjacent to the transcription start site. In this case, the gene is read in direction to the left (indicated by the small arrows along the gene in the UCSC), so the promoter is the region to the right, in this case, adjacent to that 1st exon where the gene starts.
Good luck!
Blanca
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