GENOMIC STRUCTURE AND COMPLETE NUCLEOTIDE-SEQUENCE OF THE BATTEN-DISEASE GENE, CLN3

We recently cloned a cDNA for CLN3, the gene for juvenile-onset neuron al ceroid lipofuscinosis or Batten disease. To resolve the genomic org anization we used a cosmid clone containing CLN3 to sequence the entir e gene in addition to 1.1 kb 5' of the start of the published CLN3 cDN A and 0.3 kb 3' to the polyadenylation site. CLN3 is organized into at least 15 exons spanning 15 kb and ranging from 47 to 356 bp. The 14 i ntrons vary from 80 to 4227 bp, and all exon/intron junction sequences conform to the GT/AG rule. Numerous repetitive Alu elements are prese nt within the introns and 5'- and 3'-untranslated regions. The 5' regi on of the CLN3 gene contains several potential transcription regulator y elements but no consensus TATA-1 box was identified. CLN3 is homolog ous to 27 deposited human ESTs, and sequence comparisons suggest alter native splicing of the gene and the existence of transcribed sequences upstream to the start of the published CLN3 cDNA. (C) 1997 Academic P ress.