The microtubule-associated proteins STOP are essential for synaptic plasticity and integrated brain function. The STOP gene (Mtap6) is composed of 4 exons and presents different developmental and tissue specific alternative transcripts resulting in the neuronal isoforms E- and N-STOP, and in the fibroblastic F-STOP isoform. We now characterize the transcription initiation sites for neuronal and non neuronal STOP transcripts. Our results show that there is a single neuronal specific promoter for transcription of E- and N-STOP mRNAs. F-STOP mRNA transcription is regulated by a distinct promoter. A remarkable feature of this promoter is that it lies within coding sequences expressed in neuronal E- and N-STOP isoforms. (C) 2003 Elsevier Science (USA). All rights reserved.