Genomic structure and complete nucleotide sequence of the Batten disease gene, CLN3

Genomics. 1997 Mar 1;40(2):346-50. doi: 10.1006/geno.1996.4576.

Abstract

We recently cloned a cDNA for CLN3, the gene for juvenile-onset neuronal ceroid lipofuscinosis or Batten disease. To resolve the genomic organization we used a cosmid clone containing CLN3 to sequence the entire gene in addition to 1.1 kb 5' of the start of the published CLN3 cDNA 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 introns vary from 80 to 4227 bp, and all exon/intron junction sequences conform to the GT/AG rule. Numerous repetitive Alu elements are present within the introns and 5'- and 3'-untranslated regions. The 5' region of the CLN3 gene contains several potential transcription regulatory elements but no consensus TATA-1 box was identified. CLN3 is 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 published CLN3 cDNA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Cloning, Molecular
  • DNA, Complementary / genetics
  • Exons / genetics
  • Gene Expression
  • Genes / genetics*
  • Humans
  • Introns / genetics
  • Membrane Glycoproteins*
  • Molecular Chaperones*
  • Molecular Sequence Data
  • Neuronal Ceroid-Lipofuscinoses / genetics*
  • Proteins / genetics*
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Restriction Mapping
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid

Substances

  • CLN3 protein, human
  • DNA, Complementary
  • Membrane Glycoproteins
  • Molecular Chaperones
  • Proteins

Associated data

  • GENBANK/D20292
  • GENBANK/F09095
  • GENBANK/F10019
  • GENBANK/F11432
  • GENBANK/F12401
  • GENBANK/H08689
  • GENBANK/H08690
  • GENBANK/H14184
  • GENBANK/H26783
  • GENBANK/H26893
  • GENBANK/N30094
  • GENBANK/N40884
  • GENBANK/R12998
  • GENBANK/R40387
  • GENBANK/R66835
  • GENBANK/R67932
  • GENBANK/T08995
  • GENBANK/T47968
  • GENBANK/T47969
  • GENBANK/T61330
  • GENBANK/T74504
  • GENBANK/T97772
  • GENBANK/W19672
  • GENBANK/W37752
  • GENBANK/W37753
  • GENBANK/X99832