Finding promoter - (Feb/20/2005 )
How do I find the promoter for the gene of interest? Do I just keep going upstream of the sequence till I find a TATA box? ANd how do I know where does the promoter sequence finish?
Hi, eleceyes. Not all genes have a TATA box. To get the promoter of your gene yo need to obtain the 5' flanking region. You can go to the GenBank and do a search with the name of your gene and the words (promoter OR flanking) in the title. If it has been already described you would find it there. If that's not the case you can go to the GoldenPath webpage and browse it using your gene's name, or do a Blat with your gene sequence. I don't know if you're familiar with this webpage, but if you click on the alignment it will give you the option of download the genomic sequence (if known), including the 5' flanking region which should contain your promoter. You can test that flanking region using promoter prediction programs, such as those you can find at Genomatix (you have to register and they allow you to make several analysis every month for free).
Even if you get a negative prediction, it does not mean that the 5' flanking region does not contain your promoter... only that prediction programs are not 100% accurate.
Hope that helps
of course u can go by badcell's suggestion. alternatively u can also find the promoter of the gene through http://www.ensembl.org/.
search ur gene in the database u will find various links for the particular gene. on the Ensembl Gene Report clik on 'Sequence Markup- View genomic sequence for this gene with exons highlighted'
u will get the genomic seq of the gene with all loads of options. here u can find the promoter seq just before the first exon. usually promoter seq include 500bases upstream of first exon. u can experiment urself with the options esp with SNPs.
alternatively there is also another option of confirming the promoter seq in http://www.epd.isb-sib.ch/ where most of the promoter seq are well characterized and classified. however it does not include all genes.
compare the seqs from all searchs and decide which is best for u.
Yeah. You're right. Ensembl is another possibility. But I find the interface at Goldenpath much more user-friendly. You can get the exons highlighted in uppercase and the promoter and introns in lowervase, which is really useful if you're pasting the sequence into DNAstar or other similar program. And the graphs and sequence alignments give a lot more information, such as the transcription initiation sites of all the ESTs described, etc.. As for the sequence, you should get the same sequence from NCBI, Ensemb or Goldenpath. I stick with Goldenpath, but Ensembl is also quite useful.