I want to search the promoter sequence of a gene. Seeking an advice on where to look for it.
Besides using different bioinformatic tools to predict a promoter sequence, you can also determine its location experimentally, by sequencing its mRNA. You can identifiy the transcriptional start site (TSS), which is where the RNA polymerase starts reading a gene. The promoter should be immediately upstream of the TSS. You can sequence the mRNA in high-throughput and genome wide by using e.g. Illumina technology or for single transcripts with methods like 5'-RACE.
In a recent paper (see attachment), we have applied both methods to identify TSS.
Article The Pseudomonas aeruginosa Transcriptome in Planktonic Cultu...
here:
http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=187337415&clade=mammal&org=Mouse&db=0
Change genome if you need it.
You can look for a TATA or Pribnow box, or for a Shine-Dalgarno sequence, depending on the organism. Hope that helps.
Is your interest about vertebrates? Usually I look into ENSEMBL for vetebrate genomic DNA sequence then paste it into promotor finder softwares which are usually free from internet.
Dear Ru-Jeng, may I ask you which promoter finder software do you use?
This is the website that I used before
http://molbiol-tools.ca/Promoters.htm
Hope this can help.
1. go to http://genome-euro.ucsc.edu/cgi-bin/hgGateway
2. select your genome and search your gene
3. in the genome browser click your gene in the Refseq track to open refseq information page
4. search in the page "Links to sequence" and click on genomic sequence
5. now select the region of your gene you want to download
Besides using different bioinformatic tools to predict a promoter sequence, you can also determine its location experimentally, by sequencing its mRNA. You can identifiy the transcriptional start site (TSS), which is where the RNA polymerase starts reading a gene. The promoter should be immediately upstream of the TSS. You can sequence the mRNA in high-throughput and genome wide by using e.g. Illumina technology or for single transcripts with methods like 5'-RACE.
In a recent paper (see attachment), we have applied both methods to identify TSS.
Article The Pseudomonas aeruginosa Transcriptome in Planktonic Cultu...
The promotor sequence of the gene can be found at Eukaryotic Promotor Database http://epd.vital-it.ch/
And in case, you're looking for prokaryotic promoters, the Prodoric database provides valuable tools: http://www.prodoric.de/
I've often used http://linux1.softberry.com/berry.phtml for in silico analysis and the 5' RACE mentioned above for experimental confirmation.
Hi,
you can easily download the promoter sequence of many genes with EPD. It contains experimentally validated TSS coordinates for many organisms.
For example to download the promoter sequence of MAPK10 gene in human follow this link:
http://epd.vital-it.ch/cgi-bin/get_doc?db=epdNew_hg&format=genome&entry=MAPK10_1
and in the lower part of the page you can select the promoter region (eg. from -500 to 100 from the TSS) and get the corresponding sequence
Hope this help.
http://epd.vital-it.ch
I'm looking for the promoter and terminator sequence of a fusarium gene. Seeking an advice on where to look for it ? many thanks.
https://epd.vital-it.ch/human/human_database.php THIS WILL HELP.
http://www.protocol-online.org/forums/blog/4/entry-10-from-how-to-find-promoter-sequences/
This link will help
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