We have identified a 7.5 kb transcript from the dystrophin locus which encodes a novel 140 kDa protein (Dp140). Based on immunoblotting Dp140 consists of the distal rod domain and C-terminus of 427 kDa dystrophin and is found throughout the CNS. This protein is transcribed from an alternative promoter in the dystrophin locus upstream to exon 45. The unique 5' first exon is conserved between rat and human. The transcript has a 1 kb 5' untranslated region, and the first methionine initiation codon occurs in exon 51, predicting a protein of 140 kDa. Several studies report that Duchenne dystrophy patients with deletions in the exon 45-52 region have an increased incidence of cognitive impairment. Such deletions would affect expression of 427 kDa dystrophin and this shorter 140 kDa isoform but not the recently described small distal transcripts Dp116 or Dp71, suggesting particular importance to CNS function.