how we can identify CpG for specific gene?
pubmed give use the gene sequence from the transcription starting site(TSS) what about the upstream sequence how we can find it?and find CpG island in it ?
Try to use the program named "methyl primer express(mpe)". Open the upstream sequence of your target gene in the "nucleotide" in the pubmed. You should open about 1000 to 2000 b.p. around the TSS. CpG island is located near TSS. Than download your sequence in to the mpe. You can easy convert your sequence with this program and find all CpG sites. If you will see many sites located next to each other it means you've got an island. Good luck!
You can download upstream and gene sequences from BioMart at ENSEMBL easily if your organism is included in ENSEMBL. I'd suggest taking a sequence from -2000bp to +500bp for looking at CpG Islands in promoter regions. For intergenic CpG islands, you need a whole region, such as a chromosome (or a part of it). EMBOSS has a tool called cpgplot for identifying and visualisation of CpG islands in nucleotide sequences (http://emboss.open-bio.org/rel/rel6/apps/cpgplot.html).
Apart from this, you may want to check out some other tools at https://omictools.com/cpg-islands-category.
Lastly, if your genome is included in UCSC Genome Browser (http://genome.ucsc.edu) , there's a chance that CpG Islands are already in there. If there is one, you can download the list of regions and compare with your own data or if you are interested in some particular genes, you can directly search and look on the Genome Browser.
HTH,
Good luck!
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