snOPY mainly provides three types of infromation: snoRNAs, snoRNA gene
loci, and target RNAs.
- snoRNA: The major function of snoRNAs is to guide nucleotide
modification of rRNA or snRNA. snoRNAs are divided into two
classes based on highly conserved motifs, i.e., box C/D and box H/ACA.
The box C/D snoRNAs contain two sequence motifs (box C: TGATGA;
box D: CTGA) and direct 2'O-methylation of target RNAs.
In this class of snoRNAs, the region upstream of box D or box D' is
complementary to the target RNA and modification occurs 5-nt upstream
of these boxes. The box H/ACA snoRNAs also contain two sequence
motifs (box H: ANANNA; box ACA: ACA), and they guide pseudouridylation
(conversion of uridine to pseudouridine) of the target RNA.
A modification site is located at the pseudouridylation pocket,
which is formed by an RNA:RNA antisense interaction between
complementary sequences of the snoRNA and target RNA. The snoRNA data were collected from public databases according to the sequence annotation and manually curated.
- snoRNA gene locus: There are three types of snoRNA gene locus,
intronic, polycistronic, and monocistronic. In an
intronic locus, the snoRNA gene is located within the
intron of a protein-coding gene (host gene). It is
transcribed simultaneously with its host gene using the
host gene promoter.
A polycistronic locus contains multiple snoRNA genes
that are organized into a cluster transcribed from a
single promoter. A monocistronic locus contains a single
snoRNA gene that is expressed using its own promoter.
- target RNA: rRNA and snRNA are the major targets for
snoRNAs. In general, the number of modified nucleotides
depends on the length of RNA. However, there are many orphan snoRNAs
whose targets remain to be determined.
- Orthologue: snOPY also contains information about snoRNA orthologues. The identification of the orthologues using common homology search techniques such as BLAST is difficult because the sequence conservation between snoRNAs from different species is very low. Although there are some short conserved motifs, BLAST often fails to identify the correct counterparts. Therefore, we focused on the sequence conservation between the target RNAs such as rRNAs rather than the snoRNA sequences themselves to identify the orthologues. We performed sequence alignment of the target RNAs from different species using ClustalW, then mapped the modification sites on that alignment. If the modified nucleotide is aligned at the same position, we assumed the snoRNA that guides this modification as an orthologue.
- Academic users may freely use the snOPY website at
http://snoopy.med.miyazaki-u.ac.jp/, freely link to
the snOPY website.
- Non-academic users may use the snOPY website as end users for
academic purposes, but any other use requires contact us.
snOPY is an original database product, copyright Kenmochi Laboratories.
Although best efforts are always applied when developing snOPY products,
Kenmochi Laboratories makes no warrant nor assumes any legal responsibility
for the accuracy or usefulness of snOPY or any information contained therein.
Yoshihama M, Nakao A, Kenmochi N
snOPY: a small nucleolar RNA orthological gene database
BMC Research Notes, 6: 426. 2013