starBase

RNA Type: miRNA

Overview: starBase (small RNA target base) is a database of Argonaute interaction sites and miRNA cleavages sites, based on new high-throughput methods (public CLIP-Seq and Degradome data) and target prediction tools. It also integrates thousand of binding sites of other RNA-binding proteins.

Search Methods:

• Similarity: search sequences using the authors program (ClipSearch or DegradomeSearch). Both tools help identify small RNAs in CLIP-Seq and Degradome-Seq data.
• Keyword: search by gene symbol and RefSeq Accession.
• TAG: search by organism, clade, gene symbol, miRNA name, target prediction tool, CLIP-Seq number of reads or site type (e.g. 8mer).
• Genomic Location: search by chromosome location, database (e.g. hg19) and organism.
• Density of ncRNAs: search by clade, genome and database.

Source: Literature and NCBI GEO database, Target Prediction Tools (TargetScan, PicTar, miRanda, PITA, RNA22, RNA22, miRanda and CleaveLand), miRBase, UCSC, GO ontology, KEEG pathways, BioCarta, Ensembl, TIGR, MSU Rice Genome Annotation Website and Grapevine genome sequences (Genoscope website).

Information Source: Experimental, In silico annotation.

Information Content: Annotation, Argonaute sites, Cleavage sites, CLIP-Seq, Cluster, Degradome-Seq, Expression, Gene, High-throughput sequencing, Next-generation data, Reads, RefSeq, Sequence, Target site.

Reference: Yang et al, 2010

PubmedID: 21037263.

Year: 2011

Multiple search: Yes

Download: BED.

Genomic Overview: Yes

Organism: Homo sapiens (Human), Mus musculus (House Mouse), Caenorhabditis elegans, Arabidopsis Thaliana (Thale Cress), Oryza sativa (Rice), Vitis vinifera.

Url: http://starbase.sysu.edu.cn/