The developmental paired-type gene Pax7 is expressed in skeletal muscle and brain during development and in the adult mouse. In this study, RNA was isolated from the brains and skeletal muscles of the limbs of adult BALB/c and SJL/J mice to determine whether there were alternate transcripts which could account for the biological diversity of Pax7. Four alternate transcripts have been identified, each of which differs by the presence and/or absence of a trinucleotide or a hexanucleotide in the region of Pax7 which encodes the paired domain. Inclusion of the trinucleotide and the hexanucleotide results in insertion of the amino acids glutamine (Q) and glycine and leucine (G,L), respectively, into the paired domain. The insertion of GL is predicted to influence the binding specificity, whereas insertion of Q may affect the relative binding affinity of the N and C termini of the paired domain. The transcripts which include the hexanucleotide are more frequent in RNA from the hind-limb skeletal muscles of adult mice compared with the brain, suggesting that they may effect some form of myogenic function. By contrast, it is possible that transcripts which lack the hexanucleotide encode factors which are involved in neurogenesis. The proportion of the potential myogenic transcript Pax7b was found to be increased in RNA from limb skeletal muscles of adult SJL/J mice compared with that of BALB/c mice. These results provide a new basis for examination of the genetic control of skeletal muscle formation and neurogenesis. (C) 1998 Elsevier Science B.V. All rights reserved.