I am a little confused as to what you are asking, perhaps you can elaborate. 

Do you mean that in one of them (e.g rice) there is an tandem duplication upstream of the gene in question, while in the other there is not? If this is the case then are you asking for suggestions to analyze the different effects the upstream region has relative to downstream sequences, or have I misunderstood?

hi

thanks for the interest. The tandem repeat is present in rice and wheat. In wheat this gene is found in chromosomes 7AL, 7BL and 7DL (so 3 copies). The tandem repeat is found on rice, 7BL and 7DL. I have attached the alignments. My question is if this is simply a tandem repeat or if I have misunderstood. Could it be a transposon effect ???

best regards

Chandima

I see, though I don't know what you are searching for, and I am not to sure what to make of the alignment you attached because it is not labelled. 

Assuming it is a duplication...

It could be transposons/repeats which facilitated ectopic recombination and gene duplication, but if you mean to ask it it is transposon movement that causes it, then there should be flanking inverted repeats (See link).

Retrotransposition can be a cause for repeated genes, though I know plants tend to enjoy DNA transposon more. If this is the case you likely would have noticed something funny already, since retrogenes result in the poly A being re-integrated into the genomic sequence.

Best of luck with the analysis.

http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::palindrome