Hello everyone!
If I have a complete cds of a gene, according to this sequence can I predict its possible regulators and some related molecules(genes of proteins)? If you could would you recommend some tools or websites if there is any?
Which organism are you working on? If it's mouse or human, for example, have a look at Ensembl, we have used the ChIP-Seq data etc from ENCODE and other projects to annotate regulatory features on assays on different cell lines. So you can find out where the TFBS are and the regions with promoter/enhancer activities are. Have a look at the Ensembl tutorials on the Regulation theme but this is a nice example on our browser looking at the regulatory features in SMAD2 in two cell lines, GM12878 and K562.
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Hello @Devon Ryan and @Denise - Ensembl,
Our sample is one of the desert insects from xinjiang, west part of China. The region's winter daily temperature is really low, sometimes it can reach -30 degrees Celsius. our studies shows that the species can express antifreeze protein at this period of time, but we only have its complete cds​. So I wonder is there any means can predict its regulators and other related genes to it?
If you really want TF binding sites (i.e. possible transcriptional modulators) then you need genomic sequence. If you don't have any genomic sequence for your species, then you'll need to do 5' RACE and either genomic sequencing followed by assembly or make some BACs, screen them and then sequence the appropriate one. That'd be easier to assemble. You could then align the 5' UTR to that and then predict TF binding sites upstream of the TSS.
Thank you @Devon Ryan.
One of the isoforms of the antifreeze protein of the insect I got here have about 1000 bp 5' UTR, and I used TRANSFAC to predict TF binding sites. unfortunately, they don't provide their up to date database for free use.
I think there are other databases out there, though I would have checked transfac first too. In general, binding sites inside a UTR will be less informative than those in the promoter, for which you don't have sequence.
It depends on what level of regulation you're talking about. You can translate to the amino acid sequence and predict phosphorylation sites and such, but you can't predict transcriptional regulators.