Noncoding RNA database

 

The noncoding RNA (ncRNA) database is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota.

The primary source of sequences included in the database was the GenBank. Additional annotation information for mouse and human ncRNAs was derived from FANTOM3 database and H-inviational Integrated Database of Annotated Human Genes version 3.4, respectively. Genome mapping information was derived from tha data available at the UCSC Genome Browser site. The sequences and annotations of small cytoplasmic RNAs from bacteria, for which annotation is lacking in the genome sequences, were derived from the Rfam database.

The microRNAs or snoRNAs which were available in previous editions, as well as other housekeeping (infrastructural) RNAs (e.g. rRNA, tRNA, snRNA, SRP RNA) are not included in our database to avoid redundancy with more specialized databases which emerged in recent years (see links below).

The data can be retrieved using links below:

Search search by organism name, RNA symbol or GenBank accession number

BLAST BLAST your sequence against the ncRNAdb (over 30,000 sequences; 66,4 MB)

Browse Information pages

Download Download the sequences in FASTA format

Other RNA databases

RNAdb: mammalian noncoding RNA database

fRNAdb: functional RNA database

Rfam: database of noncoding RNA families

miRBase: microRNA database

ASRP: Arabidopsis thaliana small RNA project

methylation guide snoRNA database

snoRNAbase: human H/ACA and C/D box snoRNA database

plant snoRNA database

yeast snoRNA database

tRNA database

tmRDB: database of tmRNA sequences

RNase P: RNase P RNA and protein database

SRPDB: Signal recognition particle database

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Last updated: Oct. 27, 2006