We describe the isolation of cDNA clones for zebrafish Pax9. Pax9 expression was initiated at the end of the segmentation period in mesenchymal sclerotome cells on both sides of the notochord similarly to the corresponding mouse and chick genes. Two transcripts, Pax9a and -b, are generated by alternative splicing. The gene contains 4 exons with exon 3 being included in the Pax9a transcript and spliced out in the Pax9b transcript. The Pax9a and -b proteins are identical for 212 amino acids from the N terminus but contain distinct C-terminal regions of 131 and 58 amino acids, respectively. The paired domain of Pax9 displayed a binding-site specificity distinct from Pax6 but similar to Pax1 and -2. Both Pax9a and -b activated a promoter containing a paired domain binding site. However, this activation was observed when low amounts of Pax9 expression vectors were used. Higher amounts led to a sharp decrease in the activation and even turned into repression. Both the distinct C-terminal regions of Pax9a and -b harbored transcriptional activating domains of different potency not revealed in the context of the full-length proteins due to a negative influence of the N-terminal region including the paired domain.
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