The UCSC Genome Browser database

RNA Type: Multiple classes

Overview: The University of California Santa Cruz Genome Browser (UCSC Genome Browser) is a database concentrated mainly on genomics and annotation information. Even being a general scope resource, it contains much data specific for non-coding RNA. UCSC contains a system to retrieve various types of information (dataset) on non-coding RNA (e.g. experimental, prediction) for several organisms. The community can download de information in several fromats. Also, fRNAdb 3.0 database has a UCSC browser (mirror) with a larger number of tracks and richer features of ncRNA. The ncRNA dataset is also available for non-Eukaryote genomes in the UCSC Microbial Genome Browser.

Search Methods:

• Similarity: search sequences against genomes by using BLAT program.
• Keyword: search by gene name/symbol, forward/reverse primer.
• TAG: search by clade, genome, assembly, group, track, table.
• Genomic Location: choosing for a clade, genome, assembly and chromosome location or gene name.

Source: NCBI (e.g. genomes assemblies, GenBank, RefSeq, MGC, dbSNP), Ensembl, UniProt, Vega, miRBase, snoRNA-LBME-DB, GO, OMIM, DECIPHER, Catalog of Published Genome-Wide Association Studies, DARNED, Tools (e.g. BLAT, Fgenesh++, Genscan, Augustus, Evofold, RNAz), Consortium/Project dataset (e.g. ENCODE, CCDS, HapMap, HGDP, 1000 Genomes Project), Expression data (e.g. GNF Atlas, Affymetrix Transcriptome Project).

Information Source: Experimental, In silico annotation.

Information Content: Alignment, Annotation, Expression, Gene, Gene Ontology, Localization, mRNA, Orthologs, Polymorphism, Protein, Repeat, Sequence, SNP.

Reference: Karolchik et al, 2011; Dreszer et al., 2011; Chan et al., 2011; Fujita et al., 2010; Sanborn et al., 2010; Rhead et al., 2009; Karolchik et al., 2009; Mangan et al., 2009; Kuhn et al., 2008; Zweig et al., 2008; Karolchik et al., 2007; Karolchik et al., 2007; Kuhn et al., 2006; Hinrichs et al., 2006; Hsu et al., 2005; Karolchik et al., 2003

PubmedID: 12519945, 15608236, 16381938, 17142222, 18086701, 18428780, 18514479, 18996895, 19816931, 19906737, 19957273, 20959295, 21059681, 21975940, 22080555, 22086951.

Year: 2011; 2011; 2011; 2010; 2010; 2009; 2009; 2009; 2008; 2008; 2007; 2007; 2006; 2006; 2005; 2003

Multiple search: Yes

Download: BED, GTF, FASTA, Other.

Genomic Overview: Yes

Organism: Homo sapiens (Human), Rattus norvegicus (Norway Rat), Canis familiaris (Dog), Mus musculus (House Mouse), Macaca mulatta (Rhesus Monkey), Bos Taurus (Cattle), Ovis aries (Sheep), Pan troglodytes (Chimpanzee), Cavia porcellus (Guinea Pig), Equus caballus (Horse), Galago moholi (Mohol Bushbaby), Gorilla gorilla (Gorilla), Hylobates lar (Lar gibbon), Papio hamadryas (Baboon ), Pongo pygmaeus (Orangutan ) and 31 others.

Url: http://genome.ucsc.edu/