snoRNA-LBME-db statistics

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Protocols

snoRNA-LBME-db specifications

Information


Unique identifier OMICS_09908
Name snoRNA-LBME-db
Alternative name snoRNABase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 3
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainers


  • person_outline snoDBwebmaster
  • person_outline Michel Weber

Publication for snoRNA-LBME-db

snoRNA-LBME-db citations

 (28)
library_books

High Throughput Sequencing of Small RNA Transcriptomes in Maize Kernel Identifies miRNAs Involved in Embryo and Endosperm Development

2017
Genes
PMCID: 5748703
PMID: 29240690
DOI: 10.3390/genes8120385

[…] e known miRNA and the expressional level was calculated by bowtie software []. The remaining unmatched sequences were blasted against annotated non-coding RNA sequences, including plant snoRNA (Plant SnoRNAbase v1.2; [], transfer RNA (tRNA) [] and ribosomal RNA (rRNA) (RFAM, v11.0) [] etc., using blast []. The remaining reads were screened against degradated transcripts using the bowtie2 software […]

call_split

Coding and noncoding landscape of extracellular RNA released by human glioma stem cells

2017
Nat Commun
PMCID: 5658400
PMID: 29074968
DOI: 10.1038/s41467-017-01196-x
call_split See protocol

[…] des were excluded. The remaining reads were mapped to spike-ins (UniSp2, UniSp4 and UniSp5; parameter: -v 1 --all), and other non-coding RNA classes including tRNAs (gtRNAdb), piRNAs (RNAdb), snoRNA (snoRNA-LBME-db), scRNAs (Genbank), and others (Rfam database) (parameter: -v 2 --all). Finally, the remaining reads were mapped to the hg19 human genome, and the reads mapped to exons, introns, interg […]

library_books

Control of box C/D snoRNP assembly by N6‐methylation of adenine

2017
EMBO Rep
PMCID: 5579392
PMID: 28623187
DOI: 10.15252/embr.201743967

[…] A full alignment of 262 of human box C/D sequences taken from snoRNABase (https://www-snorna.biotoul.fr//) was made using Jalview (Jalview 2.9) . The k‐turn region was aligned manually based on the known pattern of conserved nucleotides. A WebLogo plot showing […]

library_books

Profiling of 2′ O Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity

2016
Nucleic Acids Res
PMCID: 5027482
PMID: 27257078
DOI: 10.1093/nar/gkw482

[…] S3). Two new sites were detected by RMS analysis, one with a low RMS score (0.63 at LSU-C1868; Figure ) and one with a high RMS score (1.00 at LSU-G3771; Figure ). The former site is mis-annotated in snoRNABase, where snoRD48 is suggested to modify LSU-2279. The interaction has a mismatch at pos. 2 upstream of the D box followed by 11 consecutive base pairs. The methylation is supported by a parti […]

library_books

An updated human snoRNAome

2016
Nucleic Acids Res
PMCID: 4914119
PMID: 27174936
DOI: 10.1093/nar/gkw386

[…] among the predicted interactions as those interactions, for which a corresponding snoRNA-guided RNA modification has also been reported in human. Data on snoRNA-guided modifications was gathered from snoRNAbase and available literature, or from very recently conducted experiments that were designed to identify RNA modifications in high-throughput. In particular, we obtained data on pseudouridine m […]

library_books

Diverse human extracellular RNAs are widely detected in human plasma

2016
Nat Commun
PMCID: 4853467
PMID: 27112789
DOI: 10.1038/ncomms11106

[…] at did not align in any of the previous steps are mapped against a variety of small-RNA libraries including (with no significance to the ordering): tRNAs from gtRNAdb, piRNAs from RNAdb, snoRNAs from snoRNA-LBME-db and snRNAs and other RNA sequences from RFam. In both steps 3 and 4 reads were allowed to multi-map to different annotated transcripts and in cases where this occurred, the read was spl […]

Citations

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snoRNA-LBME-db institution(s)
Institut d'Exploration Fonctionnelle des Génomes IFR109, CNRS/Université Paul Sabatier, Toulouse, France; Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, CNRS/Université Paul Sabatier, Toulouse, France
snoRNA-LBME-db funding source(s)
Supported by grants from CNRS and La Ligue Nationale contre le Cancer.

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