BARE-1 insertion site preferences and evolutionary conservation of RNA and cDNA processing sites

Genetica. 1997;100(1-3):219-30.


The BARE-1 copia-like retrotransposon constitutes nearly 7% of the barley (Hordeum vulgare L.) genome as a family of more than 2 x 10(4) mostly full-length copies dispersed on all chromosomes. BARE-1 elements are transcribed in barley tissues from promoters within the LTR (long terminal repeat). The predicted, translated polyprotein contains conserved domains for GAG, aspartic proteinase, integrase, reverse-transcriptase, and RNase H. Here, we have used inverse PCR with LTR-based primers to establish the consensus sequences for the terminal region of the LTR, the external dinucleotides of the cDNA integration intermediate, and the minus- and plus-strand priming sites. These key functional entities are well-conserved in the BARE-1 family, including wheat Wis2, but differ from those of other plant retrotransposons. The target site duplication was established as 5 bp. Of the 13 integration sites identified here, 8 were other BARE-1 elements and 1 another retrotransposon; 59% of the total 17 identified BARE-1 insertion sites are retrotransposons. This nested insertion pattern may represent a basic feature of plant retrotransposons.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cloning, Molecular
  • Consensus Sequence
  • Conserved Sequence*
  • DNA Primers
  • DNA, Complementary / genetics*
  • DNA, Plant / genetics*
  • Evolution, Molecular*
  • Genomic Library
  • Molecular Sequence Data
  • Polymerase Chain Reaction
  • RNA, Plant / genetics*
  • Repetitive Sequences, Nucleic Acid
  • Retroelements / genetics*
  • Sequence Homology, Nucleic Acid


  • DNA Primers
  • DNA, Complementary
  • DNA, Plant
  • RNA, Plant
  • Retroelements

Associated data

  • GENBANK/Z84536
  • GENBANK/Z84537
  • GENBANK/Z84538
  • GENBANK/Z84539
  • GENBANK/Z84540
  • GENBANK/Z84541
  • GENBANK/Z84542
  • GENBANK/Z84543
  • GENBANK/Z84544
  • GENBANK/Z84545
  • GENBANK/Z84546
  • GENBANK/Z84547
  • GENBANK/Z84548
  • GENBANK/Z84549
  • GENBANK/Z84550
  • GENBANK/Z84551
  • GENBANK/Z84552
  • GENBANK/Z84553
  • GENBANK/Z84554
  • GENBANK/Z84555
  • GENBANK/Z84556
  • GENBANK/Z84557
  • GENBANK/Z84558
  • GENBANK/Z84559
  • GENBANK/Z84560
  • GENBANK/Z84561
  • GENBANK/Z84562
  • GENBANK/Z84563
  • GENBANK/Z84564
  • GENBANK/Z84565