snoRNA Database

Browse snoRNA gene identifications

Methylation Guide snoRNA Database

We have developed an algorithm for searching genomic sequence for 2'-O-ribose methylation guide snoRNA genes. Here we provide our predictions, many of which have been experimentally verified. We also include information on previously identified methylation guide snoRNAs. Please don't hesitate to contact us (see below) if you have comments or notice errors in our annotation or attribution of previous snoRNA work.

Papers describing our computational identification of snoRNAs have been published:

For budding yeast (Lowe & Eddy, Science 283: 1168-1171, 1999 [Feb 19])
For Archaea (Omer, Lowe, Russel, Ebhardt, Eddy, & Dennis, Science 288: 517-522, 2000 [Apr 21]),
a collaborative effort with Pat Dennis' lab at the University of British Columbia
For Arabidopsis thaliana: A collaboration between John Brown of the Scottish Crop Research Institute (jbrown@scri.sari.ac.uk), and Todd Lowe: Brown, Clark, Leader, Simpson, & Lowe, RNA 7:1817-32, 2001 [Dec].

Sections below have sequences and additional annotations corresponding to these publications.

Saccharomyces cerevisiae Methylation Guide snoRNAs

SnoRNA Annotation organized by:

Archaeal snoRNA-like C/D Box Small RNAs

For original gene predictions submitted with the April 2000 Science paper, and supplemental text, click here.

For most current predictions, including additional information from other sources, see links below:

Crenarchaeotes

Sulfolobus solfataricus sRNAs (13) [alignment] [annotation][sequences]
Sulfolobus acidocaldarius sRNAs (29) [alignment] [annotation][sequences]
Aeropyrum pernix sRNAs (23) [alignment][annotation][genomic loci] [sequences]

Euryarchaeotes

Methanococcus jannaschii sRNAs (8) [alignment] [annotation] [genomic loci] [sequences]
Archaeoglobus fulgidus sRNAs (4) [alignment] [annotation] [genomic loci] [sequences]
Pyrococcus horikoshii sRNAs (51) [alignment] [annotation] [genomic loci] [sequences]
Pyrococcus furiosus sRNAs (52) [alignment] [annotation] [genomic loci] [sequences]
Pyrococcus abyssi sRNAs (56) [alignment] [annotation] [genomic loci] [sequences]

Extras:

Table mapping Gaspin et al. Pyrococcus sRNA names onto our those we previously identified and assigned
Alignment of individual Pyrococcus homolog groups (57 from Omer et al., 3 additional from Gaspin et al.)

Arabidopsis thaliana snoRNAs

FASTA sequence file listing the sequences detailed in Brown et al..
SnoRNA alignment [PDF] (created by J. Brown)
SnoRNA annotation table (not yet active)

Experimental Methods

The snoRNA database is curated by Todd Lowe,
If you have questions (technical/scientific) regarding the contents of these pages, please email lowe@soe.ucsc.edu

Last updated January, 2002