The Tomato small RNA Database

RNA Type: small RNA
Overview: The Tomato small RNA database is a repository small RNAs obtained from published experimental data and from in-house bioinformatics analysis. It stores information related to expression profiling, mapping of sRNAs and target gene. A target prediction tool is available on the website.
Search Methods:
  • Keyword: search by small RNA ID (e.g. S0000001), by sequence, by miRNA ID, miRNA name or by gene name.
  • TAG: search by highly abundant sRNAs.
Source: Published Experimental data (Pilcher et al., 2007; Itaya et al., 2008; Moxon et al., 2008), Dr. Blake Meyer's small RNA Labs data (site at University of Delaware); miRBase, In- house pipeline (RNAfold, mirCheck and based on Jones-Rhoades and Bartel parameters/matrix targets gene), SGN unigenes (SOL Genomics Network), ITAG predicted cDNAS (International Tomato Annotation Group).
Information Source: Experimental, In silico annotation.
Information Content: Alignment, Annotation, Folding Energy, Sequence, Structure, Target, Tissue.
Reference: Fei et al., 2010
PubmedID: 20965973.
Year: 2011
Multiple search: Yes
Download: FASTA.
Genomic Overview: Yes
Organism: Solanum lycopersicum (Tomato ), Solanum pennellii, Solanum lycopersicum x S. pennellii.

June 2018: Release 3.0