We cloned AGN-1, which interacted with protein phosphatase 6, as a molecule highly expressed in nephritic rat kidney. Our previous studies revealed that in neuronal cells (Neuro2a cells), AGN-1 was co-localized with U1-70K, a constitutive protein of U1snRNP, and splicing factor SC35 which participates in the synthesis of tau alternative splicing variants, 4R-tau and 3R-tau. Moreover, our study showed that AGN-1 knock-down decreased mRNA expression ratio of 4R-tau to 3R-tau in Neuro2a cells. In this study, to clarify the mechanism underlying the change in the expression pattern of the tau alternative splicing variants, we investigated whether AGN-1 binds to 4R-tau and 3R-tau mRNAs. RNA immunoprecipitation assay using anti-AGN-1 antibody and cytosol fraction of Neuro2a cells resulted in PCR fragments derived from 4R-tau and 3R-tau mRNAs. In vitro synthesized 4R-tau and 3R-tau mRNAs bound to AGN-1 protein prepared by immunoprecipitation, and the binding affinity of 3R-tau mRNA seemed to be higher than that of 4R-tau mRNA. Additionally, AGN-1 was co-immunoprecipitated with U1snRNP constitutive proteins. These results suggest that AGN-1 protein interacts with 4R-tau and 3R-tau mRNAs, and U1snRNP constitutive proteins including AGN-1 may involve in the interaction.