The human genome contains about 24 % introns and only 1-2 % exons. Why such large amount of intron RNA is produced is not known. This paper exemplifies a putative function of an intron RNA, the alternatively spliced intron 5, exon 6 and intron 6 (i5e6i6) of the U2 small nuclear ribonucleoprotein particle (U2 snRNP) A' specific protein (U2A') pre mRNA. The U2 snRNP is a central component of the spliceosomes and very abundant in human nucleus. The U2 snRNP genes are tandemly repeated in the RNU2 locus which occasionally co-localize to Cajal bodies in a transcription dependent process not very well understood. We have earlier found that U2A' exon 6 that is skipped in alternative splicing, is highly conserved in its nucleotide sequence. In this paper I have searched for a possible function of the U2A’i5e6i6 RNA.

The U2A'i5e6i6 contains conserved sequence cassettes that are complementary to cassettes of the U2 snRNA. A possible RNA-RNA structure, based on RNA helices that may form by these complementary sequences, is presented. The structure, which is conserved in vertebrates, suggests a role of U2A'i5e6i6 in the 3'end processing of U2 snRNA primary transcript.

I predict a function of the U2A' i5e6i6 RNA in the 3’end processing of the U2 snRNA primary transcripts, a process that most probably occur during the RNU colocalization to Cajal Bodies. The production of U2 snRNPs would, thus be autoregulated by coupling of splicing efficiency of one of its components (U2A') to transcription of another (U2 snRNA). Such autoregulatory function may well be a common feature of introns.