Hi Mahmoud,

There are a ton of online promotor and cis-regulatory element prediction software tools available. Here's one site that summarizes a number of them and their key features: http://www.shodhaka.com/cgi-bin/startbioinfo/simpleresources.pl?tn=Promoter%20prediction

Tair also has a more concise list of plant-specific resources: https://www.arabidopsis.org/portals/genAnnotation/genome_annotation_tools/cis_element.jsp

I hope these help you get started with your analysis. Best wishes

Hi.

Typically, the region upstream of Transcription Start Site (TSS) should be of interest. Well, if you don't have an idea of the TSS for BR1, you can as well keep ATG as the 3' boundary of the promoter. Based on the genomic sequence move upstream up to 1.0 kilobase for Arabidopsis or about 1.5 kb incase of tomato. Once the putative upstream sequence has been demarcated then proceed for insilico analysis of specific cis-acting elements that you might expect to be present on this gene. The above step helps to narrow down the segment of the upstream sequence which would be taken up for further cloning and characterization. Also, you can plan deletion anlaysis if required.

PLACE database, TSSP tool on www.softberry.com  can help in bioinformatic analysis   

i am very pleased for your helping sir, thanks so much , these website it was so helpful with arabidopsis plant ,but not with tomato .please i ask help for another website

Hi Mahmoud,

These days most of the sequenced genomes utilize Gbrowse software (perl based, web interface) to display the components of Genome. If you have the ids of your gene its pretty easy to get the putative promoter region of the gene in question. Following are the steps to get the promoter sequences.

1. In the Gbrowse put your ID.

2. Get the coordinate of your gene and chromosome number. Let say it is on Chromosome 5 and it starts with A and Ending on B.

3. So to fetch the promoter you have to provide a coordinate in the search box like Chr5:A-1000..A-1.

4. This will show you the region on assemble pseudomolecule which you can easily save.

This apply to all the sequenced organisms which

1. Use Gbrowse (Toamto and Arabidopsis use it)

2. A pseudomolecule of super contig is assembled

You have to take care in case of a gene which is lying on the negative strand. For that you have to tweak with the coordinate give.

Do write back if you need any assistance further.

With best

Vinay

thanks so much vinay for the great advice i want to analyse the sequence

most of the wbesite it doesn't work 

Hi Mahmoud,

For Tomato and Arabidopsis it is working for sure..

https://solgenomics.net/locus/Solyc00g010750.1/view

Look here.

With best complements

Vinay

Hi Mahmoud,

Go to TAIR, browse your gene (e.g. https://www.arabidopsis.org/servlets/TairObject?id=127581&type=locus), scroll until "Map Links" and click on " Sequence Viewer", a new window opens (like this: https://seqviewer.arabidopsis.org/?action=accession&type=gene&id=2121898&chr=4) and click just above your highlighted gene (in yellow) in the white bar which has writen on it "Sequence ruler-click here...window" and another window will open (as: https://seqviewer.arabidopsis.org/servlets/sv?action=seq&start=12742783&length=10000&band=0) . There, you will find the genome sequence of arabidopsis with the gene sequence on the right and different highlights for UTR, introns exons...and you can navigate back and forward to find or delimit your promoters of interest.

I have never worked on tomato but I think you may have info also from TAIR, by going to e-FP browser (you can find it scrolling down to find "External Link" and clicking on "e-FP browser" or by Ctrl+F and writing "e-FP" to find it quicker). On the uToronto external link you have other links to homolog species ("expressologs" or "cis-elements"),  and I believe you may find info for Tomato. Another idea may be to BLAST the Arabidopsis promoter for Tomato and you may get some hits.

Bests in your search,

Mila

thanks so much Dr. mila  , the upstream sequence for promoter will be extended up to TAA for next gene yes

Hi

I recommend to go sol genomics for tomato and TAIR for arabidopsis it will helpful.