Exposure of cold-hardy Rubidoux trifoliate orange [Poncirus trifoliata (L) Raf.] plants to temperatures from 28 degrees C to -5 degrees C enabled us to isolate and characterize a novel citrus low-temperature gene (CLT) with two transcripts, called CLTa and CLTb, from leaves and stems. CLTa was produced when plants were subjected to low temperatures (starting at 10 degrees C), while CLTb was constitutively expressed. Both CLTa and CLTb have the same open reading frame (ORF) of 165 nucleotides and encode a small (54 deduced amino acid) protein. However, CLTa has an additional 98 nucleotides in the 3'-untranslated region (UTR) that are absent in CLTb. Expression analysis using relative quantitative RT-PCR demonstrated that CLTa is expressed exclusively at low temperatures, while CLTb is expressed constitutively (expression verified from 33 degrees C to -5 degrees C). A GenBank database search identified 61 nucleotides inside of the ORF that are highly similar to low-temperature-responsive genes from Arabidopsis thaliana and Solanum tuberosum. The deduced amino acid sequence revealed similarity with low-temperature-responsive proteins from A. thaliana, Oryza sativa, and S. tuberosum of 77%, 81%, and 73.9%, respectively. A genomic clone was isolated, and the genome organization revealed the presence of three exons and two introns, the second of which is in the 3' UTR and participates in alternative 3' splice site selection. One of the 3' splice sites of the second intron was located immediately before the additional 98-bp non-coding fragment of CLTa, and the second at the very end of the 98-bp fragment. Additionally, the presence of the tetranucleotides TCTT and TTCT, which are involved in the regulation of transcript processing in animals and possibly also active in peach, was found in this intron. Competition for splicing sites on the pre-mRNA in the spliceosome, which is induced by low temperature, may be involved in the production of the two transcripts of the CLT gene.