Promoter recognization - to find core promoter, CAAT box, TATA box, 5' UTR,exons and 3'UTR (Sep/25/2005 )

Hi,

I am looking for a method to search core promoter, CAAT box, TATA box, 5' UTR, exons and 3'UTR in a complete eukaryotic gene. Can you please let me know how to do it. I am new to this form and also this subject is new to me. I will appreciate if you can help me out.

Thanx
peggi

hi peggi
which lab u are working in? and which eukaryotic gene you are talking about?
dilip

Hi,
I am doing Masters in Biotech in CA. Well I am talking about any eukaryotic gene, having complete genome in it. Since my professor has gone out assigning us this home work. I am not able to figure out how to do it.

Thanks
peggi

http://www.cbrc.jp/research/db/TFSEARCH.html
I think this should be helpful
dilip

Hi Dilip,

Thanks for the site. I think I am not able to access the site for the results I am looking for. I have the sequence of mouse gene with the accession number BC072600. My question is how to find the promoter region, CAAT box TATA box and 5'UTR, 3'UTR and exons in that sequence. I tried to look on NCBI for the following gene.

"BC072600.1| Mus musculus eukaryotic translation initiation factor 4 gamma, 3, mRNA"

Hope you understand what I am looking for.

Thanks
peggi

what dilip gave was for transcription factors. if u check the results it will mention abt presence of TATA box and CAAT box. u can also try this one
http://www.cbs.dtu.dk/services/Promoter/
which will just tell the region that is most probable to have promoter sequence. inorder to look for the exons, i would look for a software that can predict ORFs. just search in google for "ORF finder"

If you type the gene name in the ucsc genome browser and click on the correct mRNA it will give you the sequence with all introns and exons, you can direct it to give upstream and downstream sequences as well, you should search at least 1kb upstream from the 5' end of the gene to identify promoter sequences....

Hi all,

I came across your discussion on Promotor recognition, to find core promotor, CAAT box, TATA box, 5'UTR, exon and 3'UTR. In a reply to this discussion there is mention about software that can predict ORFs, Sim Vector 4.0 beta version which is about to be released by next week may help you search ORFs in gene of interest. Sim Vector ORF Search is a graphical analysis tool that finds all the ORFs in the chosen reading frame. I hope this feature will meet your research needs.

SimVector automates the production of publication quality graphics of vectors and analyzes sequences to assist in designing cloning experiments such as Gateway,TA and restriction cloning.

Link of the website : http://www.premierbiosoft.com/plasmid_maps/index.html


Hope this helps.

vedika

Hi all,

Thanks very much for pouring in so much of info. Some of the sites are really good. I got few hits on NCBI and it worked as well.

Thanks again
peggi

Remember that not all promoters are going to be like you see if the textbook. Sometimes the only way to figure this stuff out definitively is experimentally.