Neural salient serine/arginine-rich protein 1 (NSSR1, alternatively SRp38) is an important splicing factor that can repress pre-mRNA alternative splicing in cells during heat shock and mitosis. We show here that NSSR1 protein is dephosphorylated when cells are heat shocked or incubated with kinase inhibitor K252a. Both heat shock and K252a treatment increase the truncated splicing isoform of the GluR-B minigene pre-mRNA. We also investigated the roles of the RRM motif and three RS domains of NSSR1 in in vivo pre-mRNA splicing. The results show that deletion of the RRM motif did not affect GluR-B minigene pre-mRNA splicing, but deletion of any one of the three RS domains increases the truncated splicing isoform of the GluR-B minigene. We further show that an SRSRSK sequence in the RS3 domain may play an important role in the function of NSSR1 in pre-mRNA splicing.