5 replies to this topic

[steven]

hi,  i am a new one here. i wanna study the methlyation level in the promoter of one gene, but from the genebank,  only around 100 bp region at 5' primer of than gene was showed up. how can i find more information of that gene, esp its 5' promoter region, so i can design the  MSP primers. Thanks

steven

[pcrman]

Hi Steven,

There are several ways of searching the promoter sequence of a gene.

1. Go to NCBI and search the nucleotide database using "gene name" and "promoter" or "5 flanking". You will probably end up with lot of sequences from your search because the Entrez search tool is not user friendly. Promoter sequences in NCBI GenBank are submitted by researchers and are usually characterized.

2. Alternatively (my approach), you can go to ensembl.org and search your gene. After you find it, go to geneview, click "View genomic sequence for this gene with exons highlighted". By default, 600 bp 5'-flanking sequence will be displayed with exons highlighted. For example, this URL displays human E-caderin gene genomic structure
http://www.ensembl.o...gene_sequence=1

The 5'-flanking sequences annotated by ensembl most likely contains the true promoter sequence of genes but not always due to potential misannotation. To further verify, you can copy that 5'-flanking sequence and do a blast search back to NCBI site to see if you can fish out the characterized (experimentally verified) promoter sequence. You can also analyze the sequence for CpG island and promoter features using some CpG island and promoter prediction programs.

Hope thtat helps.

Edited by pcrman, 26 September 2004 - 09:25 PM.

[steven]

hi, pcrman,

Thank you very much. i will try.

steven

[Red-eyed Rabbit]

hi all, what if I cannot find this gene on Ensembl? How can I in this case predict the promoter?

[Mighty Mouse]

Red-eyed Rabbit, on 21 February 2011 - 02:03 AM, said:

hi all, what if I cannot find this gene on Ensembl? How can I in this case predict the promoter?

Try another database.

Or it might be that your gene has another name...I find NCBI to have a pretty extensive database:

http://www.ncbi.nlm.nih.gov/

just choose "gene" from the drop down menu....I've also found the ECR browser to be really useful for finding promoter regions.

Hope that helps.

MM

[pcrman]

Red-eyed Rabbit, on 21 February 2011 - 02:03 AM, said:

hi all, what if I cannot find this gene on Ensembl? How can I in this case predict the promoter?

Sometimes Ensembl does not return hits if the query term is not right. You can first go to NCBI gene database to find the official symbol for your gene and then search Ensembl using the official symbol.