Identification of the promoter sequence when the cDNA sequence is available
Hi,
I recommend to use the link below to find your answer.
https://signagen.com/blog/2015/10/14/how-to-locate-promoter-sequence-for-a-specific-gene/
Hi Chanuka
it depends mainly on which specs you're working on.
you need to access databases as UCSC or NCBI and see if TF have been identified, highlighting the promotor.
fred
If you only have the cDNA sequence then you can not identify the promoter, since the promoter will not be on the cDNA. If you have both the cDNA and the genome sequences then you can use appropriate tools to scan the regions generally upstream from the first exon in the cDNA
Hi Chanuka Fernando , Here is a tool for promoter identification and sequence retrieval. You can use NCBI BLAST for finding the exact promoter sequence in your interest of sequence if it has a promoter sequence.
https://epd.epfl.ch//index.php
Michael J. Benedik
Thank you very much ! I have the genomic sequence and I'd be delighted if you could provide me with an outline of the tools for identifying the promoter sequence !
I think the links that Atar Singh Kushwah and Marzieh Rostaminejad provide a good outline of how to identify the promoter (where possible). Note that bioinformatics tools are only going to be good guesses and are not the same as an experimental determination.
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