Organization of the ABCR gene: analysis of promoter and splice junction sequences

Gene. 1998 Jul 17;215(1):111-22. doi: 10.1016/s0378-1119(98)00269-8.


Mutations in the human ABCR gene have been associated with the autosomal recessive Stargardt disease (STGD), retinitis pigmentosa (RP19), and cone-rod dystrophy (CRD) and have also been found in a fraction of age-related macular degeneration (AMD) patients. The ABCR gene is a member of the ATP-binding cassette (ABC) transporter superfamily and encodes a rod photoreceptor-specific membrane protein. The cytogenetic location of the ABCR gene was refined to 1p22.3-1p22.2. The intron/exon structure was determined for the ABCR gene from overlapping genomic clones. ABCR spans over 100kb and comprises 50 exons. Intron/exon splice site sequences are presented for all exons and analyzed for information content (Ri). Nine splice site sequence variants found in STGD and AMD patients are evaluated as potential mutations. The localization of splice sites reveals a high degree of conservation between other members of the ABC1 subfamily, e.g. the mouse Abc1 gene. Analysis of the 870-bp 5' upstream of the transcription start sequence reveals multiple putative photoreceptor-specific regulatory elements including a novel retina-specific transcription factor binding site. These results will be useful in further mutational screening of the ABCR gene in various retinopathies and for determining the substrate and/or function of this photoreceptor-specific ABC transporter.

Publication types

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

MeSH terms

  • ATP-Binding Cassette Transporters / genetics*
  • Alternative Splicing / genetics
  • Base Sequence
  • Binding Sites / genetics
  • Conserved Sequence / genetics
  • DNA / chemistry
  • DNA / genetics
  • Evolution, Molecular
  • Exons / genetics
  • Genes / genetics*
  • Humans
  • Introns / genetics
  • Molecular Sequence Data
  • Mutation / genetics
  • Promoter Regions, Genetic / genetics
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • Sequence Analysis, DNA


  • ABCA4 protein, human
  • ATP-Binding Cassette Transporters
  • Abca4 protein, mouse
  • RNA, Messenger
  • DNA