The centrosome plays a key role in the formation of the mitotic spindle, cell polarity, and cell locomotion. Previously we identified a novel centrosomal associated protein hNinein using GSK-3beta as a bait in the yeast two-hybrid assay. In this report, the hNinein genome was found to correspond to 29 exons of genomic sequence on human chromosome 14q22. Promoter analysis predicts that hNinein contains a TATA, two CCAAT, and three GC boxes. The promoter exhibits the following potential transcription factor binding sites: Sp1, p300, and AP-1. In addition, an alternatively spliced isoform, encoded a 2041-amino-acid protein of 237,900 Da, which was designated hNinein-Lm (GenBank AF302773). The hNinein-Lm genome was found to correspond to 28 exons (2'-29). Amino acid sequence comparison with hNinein showed that hNinein-Lm exhibited an EF-hand Ca2+ binding domain in the N-terminus which similar to mouse ninein. Northern blot showed that this hNinein-Lm isoform was expressed more than hNinein in tissues examined. Differential RT-PCR combining Southern blotting also showed that hNinein-Lm is much more abundant compared to hNinein. Two forms of ninein may also imply the status of ninein associated with a pair of the centrioles in the centrosome structure. Furthermore, molecular characterization shows that human ninein is oligomerized at the C-terminal end which overlapped with GSK-3beta binding site, suggesting that oligomerization of ninein may be regulated by GSK-3beta phosphorylation.