elements are a distinct group of grow Ty3/gypsy-like retrotransposons characterized by several specific features, one of which is a separation of the region into two non-overlapping open reading frames: ORF2 coding for Gag-Pro, and ORF3 coding for RT/RH-INT proteins. buy PHA-680632 region between ORF2 and ORF3 is usually spliced from transcripts and showed that this process is only partial, probably due to poor splice signals. This is one of very few known cases of spliced LTR retrotransposons and the only one where splicing does not involve parts of the elements coding sequences, thus resembling intron splicing found in most cellular genes. Electronic supplementary material The online version of this article (doi:10.1007/s00438-008-0376-8) contains supplementary material, which is available to authorized users. gene codes for proteins needed for an assembly of virus-like particles and RNA packaging. The gene encodes enzymes protease (Pro), reverse transcriptase/RNaseH (RT/RH) and integrase (INT). RT/RH and INT convert the retrotransposon RNA into DNA and integrate it into the genome, respectively. Translation of the region is initiated from a single site on full-length RNA and individual functional proteins are released from a precursor polyprotein by the action of protease (Kumar and Bennetzen 1999; Havecker et al. 2004). While the genes are common to all autonomous LTR retrotransposons, there are differences in the structure of their coding regions, which are arranged in single or multiple (overlapping or adjacent) reading frames. Since the structural proteins encoded in the region are required in higher numbers than the catalytic proteins encoded in region into two reading frames suggests the use of translational recoding mechanisms including ribosomal frameshifting and stop codon bypass (Gao et al. 2003; Forbes et al. 2007). A unique arrangement of the region has been described for elements, a family of LTR retrotransposons occurring in several genera of dicot plants where they often constitute a major fraction of repetitive DNA (Neumann et al. 2003; Neumann et al. 2006; Macas and Neumann 2007). elements represent a distinct group of Ty3/gypsy-like retrotransposons characterized by the extreme size of the elements (up to 25?kb, with LTRs up to 6?kb), PBS complementary to tRNAarg, the presence of an extra Copper PeptideGHK-Cu GHK-Copper open reading frame (ORF1) coding for an unknown protein upstream of region into two ORFs. The domains (ORF2) are separated from (ORF3) by a region of about 150C350?bp, which includes several stop codons and is surrounded by GT/AG dinucleotides typical of the 5 and 3 termini of most introns (Breathnach et al. 1978; Mount 1982; Burset et al. 2000). Although the nucleotide sequences of this region differ between elements from various grow species, its position within and the GT/AG boundaries are conserved. Moreover, removing the region including these boundaries leads to in frame fusion of and enabling correct translation of the latter domains. Thus, it has been buy PHA-680632 proposed that this region represents an intron that is removed by splicing to reconstitute the full-length coding region (Neumann et al. 2003). Although the splicing has been well documented for some groups of retroelements like retroviruses and LINEs (Rabson and Graves 1997; Belancio et al. 2006; Tamura et al. 2007), it has so far been reported for only a few LTR retrotransposons. It occurs in transcripts of the envelope-class retrotransposon where it generates a subgenomic RNA lacking almost the entire sequence, thus enabling expression of the downstream gene (Vicient et al. 2001). Option splicing buy PHA-680632 of RNA from retrotransposon was shown to be involved in the regulation of the ratio between Gag and Pol proteins, as the full-length RNA containing and regions is usually translated to protein at a far lower level than spliced subgenomic RNA encoding products only (Brierley and Flavell 1990). In contrast to these cases where splicing usually removes part of the coding region, the putatively spliced region within transcripts does not include any coding sequence. Our previous data from pea (sequences are transcribed in leaves, roots and plants and that a significant portion of the transcripts lacks the putative intron sequence (Neumann et al. 2003). However, since there is a buy PHA-680632 small fraction of copies in the pea genome that also lacks this region, whether the shorter transcripts are produced from these elements instead of the splicing of full-length RNA could not be ruled out. Thus, in this work we investigated transcription and processing of RNA in more detail employing two different, yet complementary strategies to study this phenomenon: (1) Taking advantage of the available genomic sequence from the model grow and of our previous characterization of the population in this species (Macas and Neumann 2007), we followed transcription patterns of individual subfamilies using RT-PCR with specific sets of primers. This sequence-specific assay enabled us to.