Hello everyone,
I want to proceed to quantification of methylation of RRM1 gene with restiction enzymes and Real-time PCR. I need to design primers for the CpG sequence.
RRM1 gene (ENSG00000167325) is located in Chr 11. CpG islands are located in Chr11: 4115689 – 4116489.
How can I find this sequence in genome browser, to design primers and pick the proper restriction enzymes. I usually use ENSEMBL for primer design, but I cannot find the CpG islands.
Thank you in advance
Hi Christina!
You can use methprimer (online primer designing tool) to identify and design primers for CpG islands.
Cheers
Hi Christina
The UCSC Browser is very useful, you can find the sequence of any CpG island using the regulation track “CpG islands”. When you find the position of the CpG island, you must click on it (green bar) and you can get the CpG island info, including the DNA sequence and then you can use it in a primer designing tool.
I give you an example:
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A4094260%2D4095459&hgsid=1211055865_rKpc4XGElsH81Cp2gARL8gCTUap1
Best wishes.
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