Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
APASdb - Alternative PolyAdenylation Sites Database China 4unstable0.96
ChiTaRS - Chimeric Transcripts and RNA-Sequencing data Israel 48alive9.60
RNAcentral United Kingdom 31alive10.02
Rfam - RNA Families
United Kingdom 3329alive221.93
The tmRNA website - The tmRNA website United States 300alive15.00
tRFdb - Transfer RNA related Fragments Database United States 4alive1.31
miRDB - miRNA target prediction and functional annotations database United States 465alive46.50
DIANA-TarBase - DIANA-TarBase Greece 1513alive126.08
DoRiNA - Database of RNA Interactions in Post-transcriptional Regulation Germany 115alive18.98
lncRNAdb Australia 351alive49.64
LNCipedia - A comprehensive compendium of human long non-coding RNAs Belgium 168unstable22.51
LncRNAWiki - a wiki-based platform for community curation of human lncRNAs China 15unstable4.20
LncRNA2Target - LncRNA-target association database China 12unstable1.44
MeT-DB - The MethylTranscriptome DataBase China 3alive0.96
Viral Genomes - Viral Genomes United States 0unstable0.00
rrnDB - Ribosomal RNA Operons Database United States 988unstable14.53
MyMpn - The Mycoplasma pneumoniae database Spain 11unstable3.34
DB-AT - Database of Apicomplexa Transcriptomes Germany 2alive0.67
Ensembl - Ensembl United Kingdom 12662alive775.55
UCSC Genome Browser - University of California, Santa Cruz Genome Browser United States 6429alive428.60
Genomicus - Genomes in Evolution France 182alive22.52
FlyBase - Database of Drosophila Genes & Genomes United States 3836alive159.83
VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens United States 382unstable8.68
NHPRTR - Nonhuman Primate Reference Transcriptome Resource United States 31alive6.14
RGD - Rat Genome Database United States 60alive19.40
SuperFly Spain 0alive0.00
DBTMEE - Database of Transcriptome in Mouse Early Embryos Japan 2alive0.67
The UCSC Cancer Genomics Browser United States 187unstable5.19
BCCTBbp - Breast Cancer Campaign Tissue Bank Bioinformatics Portal United Kingdom 3alive0.97
YM500 - YM500 Taiwan 45alive8.91
EHFPI - Database of Essential Host Factors for Pathogenic Infection
China 1unstable0.25
PNRD - Plant Non-coding RNA Database China 10unstable3.07
Plastid-LCGbase - The Plastid Lineage-based Conserved Gene-pair Database China 2unstable0.42
CGH - Coffee Genome Hub France 3alive1.00
HGNC - HUGO Gene Nomenclature Committee United Kingdom 612unstable50.80
NCBI Taxonomy Database - NCBI Taxonomy Database
United States 13unstable1.95
diArk - Database for Eukaryotic Genome Research Germany 16alive1.45
ArrayExpress
United Kingdom 289unstable47.97
CODEX
United Kingdom 13alive4.29
GeneFriends - GeneFriends:RNAseq United Kingdom 31alive5.17
miRBase - microRNA dababase United Kingdom 11326alive792.82
miRNEST - miRNEST Poland 35alive5.78
miRTarBase - miRNA Target Database Taiwan 899alive128.43
PolymiRTS - Polymorphism in microRNAs and their TargetSites United States 264alive23.76
starBase - starBase China 491unstable52.61
NONCODE - Noncoding RNAs China 637unstable44.59
NPInter - ncRNA Interaction Database China 119alive9.72
RADAR - Rigorously Annotated Database of A-to-I RNA editing United States 52alive12.87
SMMRNA - Small Molecule Modulators of RNA
India 5alive1.25
DEG - Database of Essential Genes China 573alive40.93
EBI Metagenomics - EBI Metagenomics
United Kingdom 32unstable6.32
POGO-DB - Database of Pairwise-comparisons Of Genomes and universal Orthologous genes United States 4alive1.00
RDP - Ribosomal Database Project United States 11954alive433.89
SILVA - High quality ribosomal RNA databases Germany 3927unstable107.10
SporeWeb Netherlands 11alive2.75
MycoCosm - The fungal genomics resource United States 93unstable19.07
AspGD - Aspergillus Gene Database United States 117alive19.31
RefSeq - Reference Sequence Database United States 6794unstable169.85
WormBase - WormBase Canada 2150alive126.47
TISdb - translation initiation site database United States 16alive4.00
GeneProf - GeneProf United Kingdom 44unstable6.89
GEISHA - Gallus Expression In Situ Hybridization Analysis United States 113alive7.83
HMDD - Human MicroRNA Disease Database China 61alive15.25
SoyKB - Soybean Knowledge Base United States 26alive6.37
ENCODE - Encyclopedia of DNA Elements United States 2053unstable36.66
SpliceAid-F Italy 20dead0.00
Spliceosome Database United States 20alive3.88
ChIPBase China 199unstable23.08
BSRD - Bacteria Small Regulatory RNA Database Hong Kong SAR China 27alive5.29
DIANA-LncBase - Database on miRNA-lncRNA interactions Greece 98unstable17.05
miRGator - miRGator Korea Rep. 228alive21.89
Darned - DAtabase of RNa EDiting Ireland 128alive15.84
MODOMICS - A Database of RNA Modifications Poland 509alive41.99
PlantRNA France 13alive2.50
Voronoia4RNA - Voronoia for RNA
Germany 4unstable0.46
NPIDB - Nucleic acid-Protein Interaction DataBase
Russian Federation 46alive4.14
PR2 - Protist Ribosomal Reference Database France 80alive16.00
dictyBase - Database for Dictyostelium Discoideum United States 128alive14.22
WDDD - Worm Developmental Dynamics Database Japan 4alive0.79
FlyAtlas - Drosophila gene expression atlas United Kingdom 983alive89.36
WholeCellKB - WholeCellKB United States 16alive3.20
ZFIN - Zebrafish Information Network United States 899alive42.38
H-InvDB - H-Invitational Database Japan 109alive10.90
SomamiR United States 27alive5.35
LncRNADisease - Database on lncRNA-disease associations China 267unstable33.64
GenomeRNAi - A Database for Cell-based and In Vivo RNAi Phenotypes Germany 45alive8.82
TropGeneDB - tropical gene database France 34alive2.36
RiceXPro - Rice Expression Profile Database Japan 189alive26.19
SRA - Sequence Read Archive United States -unstable-
GeneDB - GeneDB United Kingdom 92alive15.18
mirEX - MicroRNA Expression Database Poland 16unstable2.00
NAPP - Nucleic Acids Phylogenetic Profiling France 8unstable1.24
VIRsiRNAdb - database of viral siRNA/shRNA India 17alive2.83
MINAS - Metal Ions in Nucleic Acids
Switzerland 15alive2.50
RNA CoSSMos - RNA Characterization of Secondary Structure Motifs Database
United States 18alive3.00
ViPR - virus pathogene resourse United States 57alive9.50
VFDB - Virulence Factor Database China 448alive34.46
FlyRNAi - Drosophila RNAi screening center database United States 104unstable7.02
Nematode - Nematode.net United States 163alive11.64
DPSC-Cancer - Donnelly - Princess Margaret Screening Centre Cancer Database Canada 24alive3.96
IGDB.NSCLC - Integrated Genomic Database of Non-Small Cell Lung Carcinoma Taiwan 10alive1.65
SpliceDisease China 27dead0.00
PlantNATsDB - Plant Natural Antisense Transcripts Database China 23alive3.76
LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes United States 27alive4.32
DNAtraffic - DNAtraffic Poland 3unstable0.44
ExoCarta - EXOSOME PROTEIN, RNA AND LIPID DATABASE
Australia 590alive65.56
EcoliWiki - EcoliWiki United States 24unstable3.40
AREsite - AU-rich Elements Site Austria 110alive15.56
GyDB - The Gypsy Database Spain 127alive12.45
WebGeSTerDB - Web Genome scanner fot terminators database India 33alive4.62
mESAdb - microRNA sequence and expression database Turkey 18alive2.57
PmiRKB - Plant microRNA Knowledge Base China 19alive2.66
RepTar - A Database of Inverse miRNA Target Predictions Israel 33unstable4.43
RNAMDB - RNA Modification Database United States 1297unstable34.59
tRNADB-CE - The tRNA Gene DataBase Curated manually by experts
Japan 69alive7.59
CLIPZ - Cross-linking and Immunoprecipitation
Switzerland 72unstable8.64
PRIDB - Protein-RNA Interface Database United States 49unstable6.37
RNA helicase database United States 30alive4.24
Full-parasites - Full-parasites Indonesia 13alive1.86
DroID - Drosophila Interactions Database United States 183alive18.30
BGD - Bovine Genome Database United States 42alive5.14
GreenPhylDB - GreenPhylDB France 130unstable3.38
TFGD - Tomato Functional Genomics Database United States 46alive6.57
GermOnline - GermOnline France 63unstable4.14
GeneCards - GeneCards Israel 900unstable23.85
SalmonDB - A Database for salmonids species Chile 14alive1.92
modENCODE - The model organism Encyclopedia of DNA Elements United States 18alive2.57
The strategies WDK United States 9alive1.26
BFGR - Biofuel Feedstock Genomics Resource United States 12alive2.00
HTS-DB - High-Throughput Screening DataBase United Kingdom 0alive0.00
lncRNome - long noncoding RNA knowledgebase India 37unstable6.96
ESCAPE - Embryonic Stem Cell Atlas from Pluripotency Evidence United States 23alive4.60
GnpIS - Genetic and Genomic Information System France 9unstable0.50
Eimeria TDB - The Eimeria Transcript DB Brazil 3alive0.60
pseudoMap Taiwan 10alive2.00
piRBase - piRNA database China 6unstable1.41
VIRmiRNA - Resource for experimental viral miRNA and their targets India 7alive1.75
CarrotDB China 14unstable2.84
miRBase Tracker - miRBase Tracker Belgium 14unstable3.22
APADB Germany 8alive1.98
miRror-Suite - A dual view on sets of microRNAs and their targets Israel 33alive4.04
RegulonDB - Regulon DataBase Mexico 2506alive124.05
PhylOPDb - phylogenetic oligonucleotide probe database France 24unstable3.52
EpimiR - Database of Curated Mutual Regulation Between epigenetic Modifications and miRNAs China 8unstable1.40
DBatVir - the Database of Bat-Associated Viruses China 5alive1.25
miRIAD - Intragenic MicroRNA Database Germany 4unstable0.54
WholeCellSimDB United States 4unstable0.91
ChiloDB - Chilo suppressalis Database China 11unstable1.40
MorusDB - the Morus Genome Database China 4unstable0.64
SoyFN - A Knowledge Database of Soybean Functional Networks China 3unstable0.57
StaphyloBase Malaysia 1unstable0.17
miRGate - miRGate Spain 3unstable0.93
CyanOmics - Cyanobacterial Omics Analysis Database China 0alive0.00
RNABP COGEST - RNA Based Pair Count Geometry and Stability
India 1alive0.33
AtmiRNET Taiwan 3alive0.99
GermlncRNA - Germ Cell Long non-coding RNAs Database Hong Kong SAR China 2alive0.67
NGS catalog - A Database of Next Generation Sequencing Studies in Humans United States 23unstable0.88
SeqDepot
United States 1alive0.25
Sinbase - Sesamum indicum database China 14unstable4.15
SM2miR
China 15alive2.91
RNA FRABASE 2.0 - RNA FRAgments search engine & dataBASE
Poland 60alive7.20
SyStemCell China 6unstable0.74
C-It Germany 11alive1.35
microPIR - microRNA-Promoter Interaction Resource Thailand 17alive2.81
MetaMetaDB - Meta- Metagenomic Data Base Japan 3alive0.75
MirSNP - A collection of human SNPs in predicted miRNA target sites. China 67unstable10.50
STPD - salinity tolerant poplar database China 0unstable0.00
miRvar - A comprehensive database for genomic variations in microRNAs India 22unstable2.95
MOROKOSHI - MOROKOSHI Sorghum transcriptome database Japan 5alive1.67
mirPub - A Database for Searching MicroRNA Publications
Australia 4alive1.33
miRdSNP - Database of Disease-associated SNPs and MicroRNA target Sites on 3'UTRs of Human Genes United States 59alive9.54
CircuitsDB Italy 59alive7.30
miRCancer - microRNA Cancer Association Database United States 80unstable11.84
UniVIO - Uniformed Viewer for Integrative Omics Japan 13alive2.57
LincSNP China 24alive5.82
ExportAid - Database of RNA elements regulating nuclear RNA export in mammals Italy 1alive0.33
OncomiRDB(Tsinghua) - A Database for Oncogenic & Tumor-Suppressive MicroRNAs China 18unstable4.05
PocilloporaBase - Pocillopora Transcriptomics Database United States 37unstable4.07
SNP@lincTFBS - SNP in human lincRNA TFBS database China 3alive0.73
dbCerEx - database of Cervical Cancer Gene Expression China 0dead0.00
HIVsirDB - A database of HIV inhibiting siRNAs India 17alive2.43
DBBP - DataBase of Binding Pairs in protein-nucleic acid interactions Skip Navigation Links
Korea Rep. -unstable-
miR-EdiTar - miR-EdiTar
United States 11alive1.80
MGEx-Udb - Mammalian Gene Expression Uterus database India 6unstable0.95
lnCeDB - lnCeDB India 15dead0.00
ECgene - ECgene Korea Rep. 167unstable8.22
HuSiDa - human siRNA database Germany 43dead0.00
PolyA_DB United States 83alive6.38
RNAdb Australia 290unstable13.83
siRNAdb Sweden 55alive4.23
Small Subunit rRNA Modification Database United States 62dead0.00
UTRdb - UTRdb Italy 644unstable32.92
H-DBAS - Human-transcriptome Database for Alternative Splicing Japan 80alive7.27
TransmiR - TF–miRNA Regulatory Database
China 184alive23.00
deepBase - deepBase China 102unstable4.21
IRESite - Internal Ribosome Entry Site Czech Republic 126alive10.19
miRGen - Discover the connection between miRNAs and TFs
Greece 410unstable27.21
NNDB - Nearest Neighbor Database
United States 138alive17.25
GeneTide - Gene Terra Incognita Discovery Endeavor Israel 10dead0.00
H-ANGEL - Human Anatomic Gene Expression Library Japan 24dead0.00
MouseBook - An Integrated Portal of Mouse Resources United Kingdom 9unstable0.87
Patrocles Belgium 114unstable12.82
ASRP - Arabidopsis Small RNA Project Database United States 293alive22.54
GeneFarm - GeneFarm France 22dead0.00
PMRD - Plant MicroRNA Database China 191unstable19.82
Transterm New Zealand 108alive6.48
HOLLYWOOD United States 71alive5.86
TRANSFAC - a database on transcription factors and their DNA binding sites Germany 7590unstable200.10
ARED Saudi Arabia 928unstable43.12
Argonaute Germany 88alive7.33
GRSDB - ‘G’-Rich Sequences DataBase United States 80alive6.47
MeRNA - A Database of Metal Ion Binding Sites in RNA Structures
United States 49dead0.00
miRNAMap - A database of experimentally verified microRNAs and miRNA target genes Taiwan 359alive29.62
RNAi Codex United States 48alive4.00
snoRNA-LBME-db France 297unstable6.19
tmRDB - tmRNA database United States 168alive11.09
UCbase & miRfunc - Ultraconserved sequences data and miRNA function United States 58dead0.00
BPS
United States 32unstable1.88
fRNAdb - Functional RNA Database
Japan 214unstable17.70
GtRNAdb - Genomic tRNA Database United States 378alive42.00
miR2Disease - miR-Disease
China 537alive59.67
miRecords - An Integrated Resource for MicroRNA-target Interactions United States 745dead0.00
miROrtho - The catalogue of animal microRNA genes Switzerland 55alive6.11
NRED - Noncoding RNA Expression Database Australia 152alive16.89
PseudoBase++ - An extension of PseudoBase United States 38alive4.05
siRecords United States 20unstable0.18
sRNAMap
Taiwan 58alive6.38
RsiteDB - RNA binding site database
Israel 19alive2.11
microTranspoGene - The influence of Transposed Elements (TEs) on the biogenesis of microRNAs Israel 56alive5.54
TransfactomeDB - Yeast Transfactome Database United States 22alive2.20
microRNA.org - microRNA.org-Targets and Expression United States 1199alive118.70
TAIR - The Arabidopsis Information Resource United States 768unstable52.22
piRNABank - A web resource on classified and clustered Piwi-interacting RNAs India 111unstable10.21
3D RIBOSOMAL MODIFICATION MAPS DATABASE United States 69alive6.83
Vir-Mir - The viral miRNA prediction database Taiwan 60alive5.82
HPD - heme protein structure–electrochemical function database
United States 68dead0.00
RNAJunction - RNAJunction
United States 106dead0.00
dbRES - dbRES China 20unstable0.89
ncRNAdb - Noncoding RNAs database Poland 53alive4.82
REDIdb - The RNA Editing Database
Italy 44dead0.00
Sno/scaRNAbase - Sno/scaRNAbase
China 45unstable0.61
qPrimerDepot - qPrimerDepot
United States 105unstable6.30
CSRDB - Cereal small RNAs Database United States 91alive8.27
PlantTA - TIGR Plant Transcript Assemblies (TA) database United States 169alive15.36
ForestTreeDB - ForestTreeDB Canada 29unstable1.90
TomatEST - Tomato expressed sequence tag Italy 26alive2.29
EPConDB - EPConDB United States 15alive1.36
GeneSpeed - GeneSpeed database United States 10dead0.00
WormBook - the online review of Caenorhabditis elegans biology United States 51alive4.64
TBestDB - Taxonomically Broad EST Database Canada 84alive7.56
Comparasite Japan 27alive2.45
ViTa - ViTa Taiwan 56alive5.04
FLIGHT - FLIGHT United Kingdom 39dead0.00
ITTACA - Integrated Tumor Transcriptome Array and Clinical data Analysis France 43alive3.58
AOBase - database for antisense oligonucleotides selection and design
China 6dead0.00
ChloroplastDB - Chloroplast Genome Database United States 68unstable5.21
OncomiRdbB - Oncogenic miRNA database India 1alive0.24
RBP-Var China 0alive0.00
BIGNASim - BIGNASim database structure and analysis portal for nucleic acids simulation data
Spain 1alive0.50
TCGASpliceSeq - TCGASpliceSeq United States 0alive0.00
MitoAge - A database for comparative analysis of mitochondrial DNA, with a special focus on animal longevity Israel 1alive0.50
DIANA-miRGen - DIANA-miRGen Greece 303unstable25.34
EBI - The European Bioinformatics Institute United Kingdom 610unstable21.10
probeBase - probeBase Austria 804unstable48.78
piRNA cluster db - piRNA cluster database Germany 29alive4.83
HGTree - Database of Horizontally Transferred Genes Determined by Tree Reconciliation Pakistan 1alive0.48
InsectBase China 1unstable0.44
GREENC - Green Non-Coding Database Spain 0alive0.00
InterRNA - INTERactions in RNA structures database
Malaysia 0alive0.00
DASHR - Database of small human noncoding RNAs United States 1alive0.50
NCBI - National Center for Biotechnology Information United States 16174unstable395.36
miRNASNP - microRNA-related Single Nucleotide Polymorphisms China 145alive23.44
MtiBase - MiRNA-target interactions database
China 0unstable0.00
miRSponge - Experimentally validated miRNA Sponges database China 1unstable0.31
LncReg - database for LncRNA regulating
China 2unstable0.62
G4RNA
Canada 0alive0.00
OCDB - Obsessive-Compulsive Disorder Database Italy 1unstable0.18
READDB - RNA Binding Protein Expression and Disease Dynamics database
United States 0alive0.00
5SRNAdb - Database of of ribosomal 5S RNAs Poland 9alive4.50
sRNATarBase - sRNATarBase China 32unstable3.00
rVarBase China 28alive6.93
CircNet
Taiwan 0alive0.00
RPFdb - ribosome protected mRNA fragments database
China 1unstable0.46
RMBase - RNA Modification Base China 2unstable0.77
Lnc2Cancer China 2unstable0.94
CRISPRz United States 0unstable0.00
dPORE-miRNA - Dragon Database of Polymorphic Regulation of miRNA genes Saudi Arabia 25alive3.43
CANTATAdb - A database of long non-coding RNAs in plants Poland 1alive0.50
piRNAQuest - searching the piRNAome for silencers India 4alive1.00
GSA - Genome Sequence Archive China 4alive4.00
BIG Data Center - BIG Data Center for Life & Health Sciences China 12alive12.00
LNCediting United States 0alive0.00
miRPathDB - miRNA Pathway Dictionary Database Germany 1dead0.00
RAID - RNA Association Interaction Database China 34alive8.50
R-loopDB Singapore 0alive0.00
RNALocate China 0alive0.00
MRPrimerV Korea Rep. 3alive3.00
GenomeCRISPR Germany 0unstable0.00
REDIportal Italy 1alive1.00
dbDEMC - database of Differentially Expressed MiRNAs in human Cancers China 54unstable3.31
NSDNA - The Nervous System Disease NcRNAome Atlas China 0unstable0.00
PceRBase - Plant ceRNA database China 0alive0.00
PlaMoM - Plant Mobile Macromolecules Hong Kong SAR China 1unstable0.82
PmiRExAt - plant miRNA expression atlas database India 0unstable0.00
IRNdb - Database of immunologically relevant non-coding RNAs New Zealand -unstable-
SlideBase Denmark 0alive0.00
PGD - Pangolin Genome Database Malaysia 0unstable0.00
Reefgenomics Saudi Arabia 4alive2.00
TBro Germany 0unstable0.00
miRnalyze - Analyzing microRNA-pathway relationships
India 0alive0.00
KTCNlncDB Poland 0alive0.00
P-SAMS - Plant Small RNA Maker Site United States 8alive3.96
EpimiRBase Ireland 4unstable1.82
Cas-Database Korea Rep. 1alive0.50
MINTbase United States 23dead0.00
Tools4miRs - tools for miRNAs
Poland 2dead0.00
LncVar - genetic variation associated with long non-coding genes China 2alive2.00
FoldAtlas United Kingdom 1alive1.00
* Citations derived from Google Scholar.
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