snoRNABase, a comprehensive database of
human H/ACA and C/D box snoRNAs.
The GenBank accession numbers for the rRNA sequences used are:
28S rRNA: U13369 nts 7935-12969
18S rRNA: X03205
5.8S rRNA: U13369 nts 6623-6779
These sequences, and the numbering of nucleotides, differs from those used in the previous version of the database, and from those used by certain authors.
If you make use of the data presented here, please cite the following article in addition to the primary data sources:
- Lestrade, L., and Weber, M. J. (2006). snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 34, D158-162.
The human-yeast snoRNA section has been modified to use the same yeast rRNA sequences (U53879) as the Yeast snoRNA database at UMass-Amherst.
Section Find guide RNA contains two new tables containing a list of modified bases in human 18S and 28S rRNAs with the corresponding guide snoRNAs. Mapped modifications without known snoRNA guide are included, as well as in the Find guide RNA sequences.
Thanks to the HUGO Gene Nomenclature Committee, all human snoRNAs have now approved names and symbols, and RefSeq IDs. In agreement with experts in the field, the list and names of snoRNAs of the HBII-52 and HBII-85 (SNORD115@ and SNORD116@) clusters have been revisited. The SNORD115@ cluster is composed of 42 snoRNAs numbered 1-48 following their chromosome order. Numbers 22, 27, 28, 45, 46 and 47 were left unassigned. These correspond to divergent cluster members that might not be processed as stable snoRNAs. The SNORD116@ cluster is composed of 29 members numbered 1-29 following their chromosome order.
You can now perform a Blastn search against the human sno/scaRNAs from snoRNABase.
Links to the UCSC Genome Browser are for the March 2006 (hg 18, NCBI Build 36.1) human reference sequence.
Phylogenic aligments are now available for scaRNAs.
We are progressively adding to each snoRNA page a phylogenic alignment of putative orthologues in vertebrates (and yeast for some of them).
For the moment, this has been performed only for C/D box snoRNAs of the HBII series with identified targets.
Note that the alignments have been extended to include the inverted sequences that bracket the snoRNA gene. They might thus not correspond to the actual 5 and 3 ends of the mature snoRNA.
In addition, it has not been systematically verified if the putative snoRNA orthologues reside in the orthologous host gene.
We thank Hiram Clawson (Genome Bioinformatics Group of UC Santa Cruz) for providing us with an alignment of 17 vertebrate genomes.
This site is featured in: NetWatch - Science 310:27 (2005) [doi: 10.1126/science.310.5745.27d]