Genomic structure and complete nucleotide sequence of the Batten Disease Gene, CLN3

Abstract

We recently cloned a cDNA forCLN3,the gene for juvenile-onset neuronal ceroid lipofuscinosis or Batten disease. To resolve the genomic organization we used a cosmid clone containingCLN3to sequence the entire gene in addition to 1.1 kb 5′ of the start of the publishedCLN3cDNA and 0.3 kb 3′ to the polyadenylation site.CLN3is organized into at least 15 exons spanning 15 kb and ranging from 47 to 356 bp. The 14 introns vary from 80 to 4227 bp, and all exon/intron junction sequences conform to the GT/AG rule. Numerous repetitiveAluelements are present within the introns and 5′- and 3′-untranslated regions. The 5′ region of theCLN3gene contains several potential transcription regulatory elements but no consensus TATA-1 box was identified.CLN3is homologous to 27 deposited human ESTs, and sequence comparisons suggest alternative splicing of the gene and the existence of transcribed sequences upstream to the start of the publishedCLN3cDNA.