Hi !
i will work on specific gene and i have to search about methylation status for it , so how i can determine the promoter for this gene ? And define how many CpG islands there are or in total gene ?
An eukaryotic core promoter refers to the minimal set of sequence elements requiere for accurate transcription by RNApol II. This core is typically ~40-60 nucleo long (upstream or downstream from +1 site). Sites like BRE, TATA, Inr, DCE, DPE, have consensus sequences. I suggest you start search those common seq.
If the genome is sequenced then:
By definition, the promoter of any transcribed sequence is immediately surrounding the annotated or experimentally defined (by 5' RACE) 5' end of the gene. This can be viewed best with some very nice annotated tracks of ENCODE data (including methylation marks) at the above link.
If not then: Then use in silico prediction tools such as:
Promoter 2.0 Prediction Server
- Promoter Scan from the Bioinformatics and Molecular Analysis section of NIH.
- TFSearch from the Computational Biology Research Center of Japan.
- DRAGON Gene Start Finder from the DRAGON Genome Explorer site
t
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Enzymology
- Enzymes