I have predicted wheat introns and now I want to perform some type of analysis, may be functional, structural or else, using in-silico approaches. What can be done to infer maximum knowledge from them?
i think screening of new SSR markers for genes. or prediction of spliced variants from wheat.
Thank you very much Sir for the answer
But the intron sequences so predicted are from the splice variants so that rules out 1 thing and for the other one (SSR); I am on it.
1. Intron sequences might serve as binding sites for transcription factors. Therefore, such an analyses might give you insights into regulatory evolution!
2. Intron seqeunces from single copy genes are also being used as stand alone sequences for resolving phylogenetic relationships as well.
3. An analysis of methylation markers on these sequences might be of some consequence as well..
Good Luck!
Thank you very much Priyanka.
But could you please provide some literature on the same; I tried searching but couldn't get good resources.
Thanks!!
You can see if there is any conserved block in these intronic sequence. This can be done by aligning these intronic region with other species and finding the conserved motif sequences. This can also be a site for transcription factor if it has highly conserved blocks.
Secondly you can search for any miRNA or siRNA which may bind to this intronic region. Intronic region may act as a site for regulatory mechanism and target of different miRNA or siRNA.
Thirdly you can see evolutionary role of this intronic sequence.
Thanks Manmohan, but my approach only predicts the intronic sequences lying within the Coding region. And miR analysis is already on the cards.
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