I'm trying to identify the promoter and 5'UTR of a rice gene namely LOC_Os11g43830. However, I have never done this kind of identification before, I have found some results but I'm not sure if I really identified the right sequences.
I used PlantPAN 2.0 to find the sequence with X = 2000 and Y = 500 (please see attachment "Sequence PlantPAN"), and this sequence is predicted to have a large number of TF binding sites. However, I want the full upstream sequence of the gene and I'm not sure if I can do this with PlantPAN 2.0. Therefore I looked up the gene on rap-db, and indentified the total upstream sequence (until the CDS of the next gene). However, when I enter this sequence in PlantPAN I don't get any predicted TF binding sites (please see attachment "Sequence rapdb" for the sequence).
Finally, I BLASTed these 2 sequences, but as it turns out my promoter + 5'UTR in the case of my PLANTPan sequence are in the first exon of my gene. So I'm a little confused by these results, I also included the images of my BLAST search in the attachment (please see "PLANTPan BLAST" and "Rapdb BLAST").
My apologies for the very long question, but would anyone be able to help me with the right methodology?
Thanks you very much in advance!
Kind regards, Jonas De Saeger
I just ran your sequence on PlantPAN 2.0 and i got quite a few predicted TF binding sites. Once i have the results from promoter analysis, then i looked for TFs near TATA box region. Once you have found a potential TF binding site near the TATA box then you can look if the sequence of the TF is conserved or not. May be you can use JASPAR for that.
Just to make sure if we used the same parameters. I ran promoter analysis of your sequence by choosing all species.
Dear Mr. Khan,
Thank you very much for looking into it! I also found a lot of predicted TF binding sites using PlantPAN 2.0, but I would like to get the full sequence of my promoter and 5'UTR (in PlantPAN 2.0 itself only a part of the sequence can be selected), and I'm not sure how to go about this.
In any case, thank you for your help!
Kind regards, Jonas
Dear Kun Lu,
Thank you for your answer! I was hoping to avoid RACE but if we can not use a bioinformatic approach maybe we'll have to; or alternatively I think we'll first try with a promoter of an arbitrary length of 2 kbp and see where it will get us.
In any case, thank you for your answer!
Kind regards, Jonas
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