Introns are mysterious entity in eukaryotic genomes in a sense that all eukaryotes carry introns as parts of genes but they are ultimately eliminated in the process of gene expression through elaborate and complicated splicing regulatory systems. Nevertheless, putative functional roles of introns in various cellular processes such as splicing, mRNA transport, NMD, and expression regulation were recently identified. In the present study, we show meaningful characteristics leading to the functional territories of introns. First, genes with longer intron sequences were significantly more essential and evolved more slowly than genes with shorter introns. Additionally, sequence conservations are highest in first introns compared to other downstream introns. Consistently, conservations in first introns are positively correlated with the presence of various regulatory signals including transcription factor binding, DNase I hypersensitivity, and various chromatin marks. Furthermore, most of the trait-associated SNPs (TASs) which are considered to reside in near sites of actual disease-causing mutations detected by GWAS have been mapped on intron regions rather than exonic or nonsysnonymous sites. The TAS-enriched introns tend to harbor more epigenetic signals as well. Taken all together, introns are clearly not junk, and they provide selective advantages to cells enough to be evolutionarily maintained nevertheless it needs the expensive energetic cost.