Biosequence Databases

• NCBI
• NCBI Entrez Nucleotide Database
• RefSeq
• UCSC Archaeal Genome Browser
• UCSC Genome Browser

Databases for Specific Species

• GeneDB
• MaizeGDB
• PlasmoDB
• RNA Virus Database
• TriTrypDB
• TubercuList

RNA Structure Databases

• PseudoBase
• RNA FRABASE: RNA FRAgments search engine & dataBASE
• RNAJunction Database (National Cancer Institute)
• RNase P Database
• RNA STRAND
• SCOR Database
• The comparative RNA web site (University of Texas at Austin)

microRNA Databases

• CoGemiR (Article)
• microRNA.org (Memorial Sloan-Kettering Cancer Center)
• miRBase (Sanger Institute)
• miRGator (Ewha Womans University)
• miRNAMap (National Chiao Tung University)
• Vir-Mir Database (Academia Sinica)

ncRNA Databases

• fRNAdb in Japan
• Genomic tRNA Database
• NONCODE (Chinese Academy of Sciences)
• Noncoding RNA Database in Poland
• piRNABank: classified and clustered Piwi-interacting RNAs
• Rfam (HHMI Janelia Farm)
• Rfam (Sanger Institute)
• Ribosomal Database Project
• RNAdb

UTR Databases

• GRS UTRdb: G-Rich Sequences UTR DataBase (Ramapo College)
• PACdb 3' UTR Database (The Jackson Laboratory)
• UTRdb
• UTRome.org for C. elegans (New York University)

mRNA Databases

• AU-rich Element-Containing mRNA Database

siRNA Databases

• MIT siRNA Database

Ontology Databases

• Gene Ontology