In human, highly expressed genes contain shorter and fewer introns and these have been attributed to selection for economy in transcription and translation. On the other hand, in plants, it has been shown that highly expressed genes tend to be longer than lowly expressed genes. Here, in this study, we analyzed compositional influence on genome organization in both rice and human. We demonstrated that, in GC rich rice genes, highly expressed genes are less compact than lowly expressed genes. In GC-poor class, there is no difference in gene compactness between highly and lowly expressed genes. However, the scenario is different for human as there is no influence of GC composition on gene compactness due to their expression levels. We also reported that, highly expressed rice GC-rich pre-mRNA tend to form less stable secondary structure than that of lowly expressed genes. However, on removing intronic sequences, highly expressed mRNA form a stable secondary structure as compared to lowly expressed GC-rich genes. We suggest that in GC-rich rice genes long introns are under selection for enhancing transcriptional efficiency by modulating pre-mRNA secondary structural stability. Thus evolutionary mechanisms behind genome organization are different between these two genomes (human and rice).