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Human  RCAN3  (regulator of calcineurin 3) belongs to the human  RCAN  gene family.  In this study we provide, with  in silico  and  in vitro  analyses, the first detailed description of the human multi-transcript  RCAN3  locus. Its analysis revealed that it is composed of a multigene system that includes at least 21  RCAN3  alternative spliced isoforms (16 of them identified here for the first time) and a new  RCAN3  antisense gene ( RCAN3AS ). In particular, we cloned  RCAN3-1,3,4,5  (lacking exon 2),  RCAN3-1a,2,3,4,5 ,  RCAN3-1a,3,4,5 ,  RCAN3-1b,2,3,4,5 ,  RCAN3-1c,2,3,4,5 ,  RCAN3-1c,2,4,5  and  RCAN3-1c,3,4,5 , isoforms that present a different 5′ untranslated region when compared to  RCAN3 . Moreover, in order to verify the possible 5′ incompleteness of previously identified cDNA isoforms with the reference exon 1, ten more alternative isoforms were retrieved. Bioinformatic searches allowed us to identify  RCAN3AS , which overlaps in part with exon 1a, on the opposite strand, for which four different  RCAN3AS  isoforms were cloned.  In order to analyze the different expression patterns of  RCAN3  alternative first exons and of  RCAN3AS  mRNA isoforms, RT-PCR was performed in 17 human tissues.  Finally, analyses of  RCAN3  and  RCAN3AS  genomic sequences were performed to identify possible promoter regions, to examine donor and acceptor splice sequences and to compare evolutionary conservation, in particular of alternative exon 1 or 1c - exon 2 junctions in different species.  The description of its number of transcripts, of their expression patterns and of their regulatory regions can be important to clarify the functions of  RCAN3  gene in different pathways and cellular processes.

Complexity of Bidirectional Transcription and Alternative Splicing at Human RCAN3 Locus