U6 snRNA sequence conservation in eukaryotes

The sequences for Human (H. sapiens, X07425), Mouse (M. musculus, X06980), Fly (D. melanogaster, X06669), Nematode (C. elegans, X07829), Nematode (C. elegans, X07828), Tomato (L. esculentum, X51447), SC (S. cerevisiae, X12565) and SP (S. pombe, X14196) are taken from NCBI . The sequences for KT (K. thermotolerans, AY0AA012H12TP1r), KL (K. lactis, BA0AB015B07LP1), PS (P. sorbitophila, AX0AA026E03CP1), and PA (P. angusta, BB0AA028D08DP1r) were extracted from the Génolevures RST libraries and the sequence for CA (C. albicans, Contig6_2500) from the Stanford's C. albicans sequence assembly 6 by using the SC U6 sequence as bait [Bon et al., 2003].

The snRNAs have been divided into four domains according to Guthrie & Patterson [Guthrie & Patterson, Annu. Rev. Genet., 1988, 22, 387-419]: 5' and 3' terminal, U4 interaction and central. Functional sites are indicated: The U4BP-box of the U4 interaction domain which is the region that base pairs to the U4 snRNA, the IBP-box is the region that interacts through base-pairing with the 5' splice site. The yeast equivalents of U6, like their metazoan counterparts lacks a SmBP-box.

Unlike U1, U2, and U5, the size and general organisation of U6 is highly conserved in all organisms, probably reflecting evolutionary constraints imposed by the interaction between U6 and U4 [Guthrie & Patterson, Annu. Rev. Genet., 1988, 22, 387-419] as evidenced the high conservation of the U4 base-pairing site sequence ?PuATPyAGCA' in the U6 snRNAs homologues.

(r) Reverse and complement sequence

CLUSTALX multiple alignment of U6 snRNA sequences

Last modified: Tue Feb 10 11:18:46 CET 2004