Technical Abstract: Comparative genomic analysis at the level of a genetic-map has demonstrated the extensive conservation of the synteny of genes in different species. We report our investigation of the microcolinearity at sh2-a1 region and identification of a gene in maize in comparison with sorghum and rice. We synthesized a pair of primers based on the homologous sequence region of sh2 and a1 loci in sorghum and rice. Using this pair of primers, we amplified and cloned a PCR product with molecular weight of 1.4 kb from maize leaves. The DNA sequence of the cloned PCR product had more than 90% homology with the 5'-end sequence of the putative transcriptional regulator gene in sorghum and 80% to the X-gene in rice. We detected a gene transcript (1 kb) in leaves, cobs, and silks using RT-PCR with this primer. Northern analysis also revealed the X-gene transcript of about 2.3 kb in leaves, cobs, and silks. This X gene identified in maize is a single copy gene and mapping of the maize genome revealed that this X gene is closely linked with sh2 and a1. Therefore, the X gene homologous to rice and sorghum exists in the maize genome. The position of the X gene in maize is closely linked with sh2 and a1 on chromosome 3. The functional feature of this X-like gene identified in sh2-a1 region in maize should be investigated in the future.