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 4unstable1.56
ChiTaRS - Chimeric Transcripts and RNA-Sequencing data Israel 48alive12.00
RNAcentral United Kingdom 31alive15.04
Rfam - RNA Families
United Kingdom 3329alive237.79
The tmRNA website - The tmRNA website United States 300alive15.79
tRFdb - Transfer RNA related Fragments Database United States 4alive1.98
miRDB - miRNA target prediction and functional annotations database United States 465alive51.67
DIANA-TarBase - DIANA-TarBase Greece 1513alive137.55
DoRiNA - Database of RNA Interactions in Post-transcriptional Regulation Germany 115alive22.77
lncRNAdb Australia 351alive57.91
LNCipedia - A comprehensive compendium of human long non-coding RNAs Belgium 168unstable30.66
LncRNAWiki - a wiki-based platform for community curation of human lncRNAs China 15unstable6.22
LncRNA2Target - LncRNA-target association database China 12unstable2.40
MeT-DB - The MethylTranscriptome DataBase China 3alive1.44
Viral Genomes - Viral Genomes United States 0unstable0.00
rrnDB - Ribosomal RNA Operons Database United States 988unstable16.67
MyMpn - The Mycoplasma pneumoniae database Spain 11unstable4.95
DB-AT - Database of Apicomplexa Transcriptomes Germany 2alive1.00
Ensembl - Ensembl United Kingdom 12662alive827.25
UCSC Genome Browser - University of California, Santa Cruz Genome Browser United States 6429alive459.21
Genomicus - Genomes in Evolution France 182alive25.74
FlyBase - Database of Drosophila Genes & Genomes United States 3836alive166.78
VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens United States 382unstable10.31
NHPRTR - Nonhuman Primate Reference Transcriptome Resource United States 31alive7.67
RGD - Rat Genome Database United States 60alive29.70
SuperFly Spain 0alive0.00
DBTMEE - Database of Transcriptome in Mouse Early Embryos Japan 2alive1.00
The UCSC Cancer Genomics Browser United States 187unstable6.31
BCCTBbp - Breast Cancer Campaign Tissue Bank Bioinformatics Portal United Kingdom 3alive1.44
YM500 - YM500 Taiwan 45alive11.14
EHFPI - Database of Essential Host Factors for Pathogenic Infection
China 1unstable0.41
PNRD - Plant Non-coding RNA Database China 10unstable4.65
Plastid-LCGbase - The Plastid Lineage-based Conserved Gene-pair Database China 2unstable0.69
CGH - Coffee Genome Hub France 3alive1.50
HGNC - HUGO Gene Nomenclature Committee United Kingdom 612unstable61.20
NCBI Taxonomy Database - NCBI Taxonomy Database
United States 13unstable3.18
diArk - Database for Eukaryotic Genome Research Germany 16alive1.60
ArrayExpress
United Kingdom 289unstable65.03
CODEX
United Kingdom 13alive6.43
GeneFriends - GeneFriends:RNAseq United Kingdom 31alive6.20
miRBase - microRNA dababase United Kingdom 11326alive853.81
miRNEST - miRNEST Poland 35alive6.93
miRTarBase - miRNA Target Database Taiwan 899alive149.83
PolymiRTS - Polymorphism in microRNAs and their TargetSites United States 264alive26.14
starBase - starBase China 491unstable63.83
NONCODE - Noncoding RNAs China 637unstable47.77
NPInter - ncRNA Interaction Database China 119alive10.60
RADAR - Rigorously Annotated Database of A-to-I RNA editing United States 52alive17.16
SMMRNA - Small Molecule Modulators of RNA
India 5alive1.67
DEG - Database of Essential Genes China 573alive44.08
EBI Metagenomics - EBI Metagenomics
United Kingdom 32unstable9.17
POGO-DB - Database of Pairwise-comparisons Of Genomes and universal Orthologous genes United States 4alive1.33
RDP - Ribosomal Database Project United States 11954alive450.57
SILVA - High quality ribosomal RNA databases Germany 3927unstable129.59
SporeWeb Netherlands 11alive3.67
MycoCosm - The fungal genomics resource United States 93unstable27.59
AspGD - Aspergillus Gene Database United States 117alive23.17
RefSeq - Reference Sequence Database United States 6794unstable195.83
WormBase - WormBase Canada 2150alive134.38
TISdb - translation initiation site database United States 16alive5.33
GeneProf - GeneProf United Kingdom 44unstable8.27
GEISHA - Gallus Expression In Situ Hybridization Analysis United States 113alive8.34
HMDD - Human MicroRNA Disease Database China 61alive20.33
SoyKB - Soybean Knowledge Base United States 26alive8.49
ENCODE - Encyclopedia of DNA Elements United States 2053unstable42.64
SpliceAid-F Italy 20dead0.00
Spliceosome Database United States 20alive4.85
ChIPBase China 199unstable28.36
BSRD - Bacteria Small Regulatory RNA Database Hong Kong SAR China 27alive6.62
DIANA-LncBase - Database on miRNA-lncRNA interactions Greece 98unstable20.83
miRGator - miRGator Korea Rep. 228alive24.32
Darned - DAtabase of RNa EDiting Ireland 128alive18.10
MODOMICS - A Database of RNA Modifications Poland 509alive45.81
PlantRNA France 13alive3.12
Voronoia4RNA - Voronoia for RNA
Germany 4unstable0.55
NPIDB - Nucleic acid-Protein Interaction DataBase
Russian Federation 46alive4.55
PR2 - Protist Ribosomal Reference Database France 80alive20.00
dictyBase - Database for Dictyostelium Discoideum United States 128alive16.00
WDDD - Worm Developmental Dynamics Database Japan 4alive1.00
FlyAtlas - Drosophila gene expression atlas United Kingdom 983alive98.30
WholeCellKB - WholeCellKB United States 16alive4.00
ZFIN - Zebrafish Information Network United States 899alive44.50
H-InvDB - H-Invitational Database Japan 109alive12.11
SomamiR United States 27alive6.68
LncRNADisease - Database on lncRNA-disease associations China 267unstable46.06
GenomeRNAi - A Database for Cell-based and In Vivo RNAi Phenotypes Germany 45alive11.03
TropGeneDB - tropical gene database France 34alive2.54
RiceXPro - Rice Expression Profile Database Japan 189alive30.56
SRA - Sequence Read Archive United States -unstable-
GeneDB - GeneDB United Kingdom 92alive18.22
mirEX - MicroRNA Expression Database Poland 16unstable2.40
NAPP - Nucleic Acids Phylogenetic Profiling France 8unstable1.49
VIRsiRNAdb - database of viral siRNA/shRNA India 17alive3.40
MINAS - Metal Ions in Nucleic Acids
Switzerland 15alive3.00
RNA CoSSMos - RNA Characterization of Secondary Structure Motifs Database
United States 18alive3.60
ViPR - virus pathogene resourse United States 57alive11.40
VFDB - Virulence Factor Database China 448alive37.33
FlyRNAi - Drosophila RNAi screening center database United States 104unstable8.23
Nematode - Nematode.net United States 163alive12.54
DPSC-Cancer - Donnelly - Princess Margaret Screening Centre Cancer Database Canada 24alive4.75
IGDB.NSCLC - Integrated Genomic Database of Non-Small Cell Lung Carcinoma Taiwan 10alive1.98
SpliceDisease China 27dead0.00
PlantNATsDB - Plant Natural Antisense Transcripts Database China 23alive4.51
LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes United States 27alive5.18
DNAtraffic - DNAtraffic Poland 3unstable0.52
ExoCarta - EXOSOME PROTEIN, RNA AND LIPID DATABASE
Australia 590alive73.75
EcoliWiki - EcoliWiki United States 24unstable4.27
AREsite - AU-rich Elements Site Austria 110alive18.15
GyDB - The Gypsy Database Spain 127alive13.83
WebGeSTerDB - Web Genome scanner fot terminators database India 33alive5.39
mESAdb - microRNA sequence and expression database Turkey 18alive3.00
PmiRKB - Plant microRNA Knowledge Base China 19alive3.10
RepTar - A Database of Inverse miRNA Target Predictions Israel 33unstable5.12
RNAMDB - RNA Modification Database United States 1297unstable34.40
tRNADB-CE - The tRNA Gene DataBase Curated manually by experts
Japan 69alive8.54
CLIPZ - Cross-linking and Immunoprecipitation
Switzerland 72unstable9.96
PRIDB - Protein-RNA Interface Database United States 49unstable7.35
RNA helicase database United States 30alive5.00
Full-parasites - Full-parasites Indonesia 13alive2.17
DroID - Drosophila Interactions Database United States 183alive20.33
BGD - Bovine Genome Database United States 42alive5.88
GreenPhylDB - GreenPhylDB France 130unstable4.04
TFGD - Tomato Functional Genomics Database United States 46alive7.67
GermOnline - GermOnline France 63unstable4.41
GeneCards - GeneCards Israel 900unstable27.00
SalmonDB - A Database for salmonids species Chile 14alive2.24
modENCODE - The model organism Encyclopedia of DNA Elements United States 18alive3.00
The strategies WDK United States 9alive1.49
BFGR - Biofuel Feedstock Genomics Resource United States 12alive2.40
HTS-DB - High-Throughput Screening DataBase United Kingdom 0alive0.00
lncRNome - long noncoding RNA knowledgebase India 37unstable8.79
ESCAPE - Embryonic Stem Cell Atlas from Pluripotency Evidence United States 23alive5.75
GnpIS - Genetic and Genomic Information System France 9unstable0.68
Eimeria TDB - The Eimeria Transcript DB Brazil 3alive0.75
pseudoMap Taiwan 10alive2.50
piRBase - piRNA database China 6unstable1.86
VIRmiRNA - Resource for experimental viral miRNA and their targets India 7alive2.33
CarrotDB China 14unstable3.73
miRBase Tracker - miRBase Tracker Belgium 14unstable4.25
APADB Germany 8alive2.64
miRror-Suite - A dual view on sets of microRNAs and their targets Israel 33alive4.62
RegulonDB - Regulon DataBase Mexico 2506alive130.58
PhylOPDb - phylogenetic oligonucleotide probe database France 24unstable4.18
EpimiR - Database of Curated Mutual Regulation Between epigenetic Modifications and miRNAs China 8unstable1.79
DBatVir - the Database of Bat-Associated Viruses China 5alive1.67
miRIAD - Intragenic MicroRNA Database Germany 4unstable0.77
WholeCellSimDB United States 4unstable1.20
ChiloDB - Chilo suppressalis Database China 11unstable2.05
MorusDB - the Morus Genome Database China 4unstable0.80
SoyFN - A Knowledge Database of Soybean Functional Networks China 3unstable0.83
StaphyloBase Malaysia 1unstable0.25
miRGate - miRGate Spain 3unstable1.39
CyanOmics - Cyanobacterial Omics Analysis Database China 0alive0.00
RNABP COGEST - RNA Based Pair Count Geometry and Stability
India 1alive0.50
AtmiRNET Taiwan 3alive1.49
GermlncRNA - Germ Cell Long non-coding RNAs Database Hong Kong SAR China 2alive1.00
NGS catalog - A Database of Next Generation Sequencing Studies in Humans United States 23unstable1.15
SeqDepot
United States 1alive0.33
Sinbase - Sesamum indicum database China 14unstable6.16
SM2miR
China 15alive3.60
RNA FRABASE 2.0 - RNA FRAgments search engine & dataBASE
Poland 60alive8.23
SyStemCell China 6unstable0.97
C-It Germany 11alive1.54
microPIR - microRNA-Promoter Interaction Resource Thailand 17alive3.37
MetaMetaDB - Meta- Metagenomic Data Base Japan 3alive1.00
MirSNP - A collection of human SNPs in predicted miRNA target sites. China 67unstable12.60
STPD - salinity tolerant poplar database China 0unstable0.00
miRvar - A comprehensive database for genomic variations in microRNAs India 22unstable3.48
MOROKOSHI - MOROKOSHI Sorghum transcriptome database Japan 5alive2.50
mirPub - A Database for Searching MicroRNA Publications
Australia 4alive2.00
miRdSNP - Database of Disease-associated SNPs and MicroRNA target Sites on 3'UTRs of Human Genes United States 59alive11.45
CircuitsDB Italy 59alive8.34
miRCancer - microRNA Cancer Association Database United States 80unstable15.00
UniVIO - Uniformed Viewer for Integrative Omics Japan 13alive3.22
LincSNP China 24alive7.68
ExportAid - Database of RNA elements regulating nuclear RNA export in mammals Italy 1alive0.50
OncomiRDB(Tsinghua) - A Database for Oncogenic & Tumor-Suppressive MicroRNAs China 18alive5.76
PocilloporaBase - Pocillopora Transcriptomics Database United States 37unstable4.63
SNP@lincTFBS - SNP in human lincRNA TFBS database China 3alive0.96
dbCerEx - database of Cervical Cancer Gene Expression China 0dead0.00
HIVsirDB - A database of HIV inhibiting siRNAs India 17alive2.83
DBBP - DataBase of Binding Pairs in protein-nucleic acid interactions Skip Navigation Links
Korea Rep. -unstable-
miR-EdiTar - miR-EdiTar
United States 11alive2.16
MGEx-Udb - Mammalian Gene Expression Uterus database India 6unstable1.14
lnCeDB - lnCeDB India 15dead0.00
ECgene - ECgene Korea Rep. 167unstable9.60
HuSiDa - human siRNA database Germany 43dead0.00
PolyA_DB United States 83alive6.92
RNAdb Australia 290unstable16.19
siRNAdb Sweden 55alive4.58
Small Subunit rRNA Modification Database United States 62dead0.00
UTRdb - UTRdb Italy 644unstable34.47
H-DBAS - Human-transcriptome Database for Alternative Splicing Japan 80alive8.00
TransmiR - TF–miRNA Regulatory Database
China 184alive26.29
deepBase - deepBase China 102unstable5.25
IRESite - Internal Ribosome Entry Site Czech Republic 126alive11.11
miRGen - Discover the connection between miRNAs and TFs
Greece 410unstable29.11
NNDB - Nearest Neighbor Database
United States 138alive19.71
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 9unstable1.07
Patrocles Belgium 114unstable14.98
ASRP - Arabidopsis Small RNA Project Database United States 293alive24.42
GeneFarm - GeneFarm France 22dead0.00
PMRD - Plant MicroRNA Database China 191unstable22.37
Transterm New Zealand 108alive6.91
HOLLYWOOD United States 71alive6.39
TRANSFAC - a database on transcription factors and their DNA binding sites Germany 7590unstable195.17
ARED Saudi Arabia 928unstable45.82
Argonaute Germany 88alive8.00
GRSDB - ‘G’-Rich Sequences DataBase United States 80alive6.98
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 359alive32.64
RNAi Codex United States 48alive4.36
snoRNA-LBME-db France 297unstable7.29
tmRDB - tmRNA database United States 168alive11.88
UCbase & miRfunc - Ultraconserved sequences data and miRNA function United States 58dead0.00
BPS
United States 32unstable2.32
fRNAdb - Functional RNA Database
Japan 214unstable19.26
GtRNAdb - Genomic tRNA Database United States 378alive47.25
miR2Disease - miR-Disease
China 537alive67.13
miRecords - An Integrated Resource for MicroRNA-target Interactions United States 745dead0.00
miROrtho - The catalogue of animal microRNA genes Switzerland 55alive6.88
NRED - Noncoding RNA Expression Database Australia 152alive19.00
PseudoBase++ - An extension of PseudoBase United States 38alive4.75
siRecords United States 20unstable0.23
sRNAMap
Taiwan 58alive7.25
RsiteDB - RNA binding site database
Israel 19alive2.38
microTranspoGene - The influence of Transposed Elements (TEs) on the biogenesis of microRNAs Israel 56alive6.22
TransfactomeDB - Yeast Transfactome Database United States 22alive2.44
microRNA.org - microRNA.org-Targets and Expression United States 1199alive131.89
TAIR - The Arabidopsis Information Resource United States 768unstable63.15
piRNABank - A web resource on classified and clustered Piwi-interacting RNAs India 111unstable11.22
3D RIBOSOMAL MODIFICATION MAPS DATABASE United States 69alive7.59
Vir-Mir - The viral miRNA prediction database Taiwan 60alive6.47
HPD - heme protein structure–electrochemical function database
United States 68dead0.00
RNAJunction - RNAJunction
United States 106dead0.00
dbRES - dbRES China 20unstable1.08
ncRNAdb - Noncoding RNAs database Poland 53alive5.30
REDIdb - The RNA Editing Database
Italy 44dead0.00
Sno/scaRNAbase - Sno/scaRNAbase
China 45unstable0.72
qPrimerDepot - qPrimerDepot
United States 105unstable7.45
CSRDB - Cereal small RNAs Database United States 91alive9.10
PlantTA - TIGR Plant Transcript Assemblies (TA) database United States 169alive16.90
ForestTreeDB - ForestTreeDB Canada 29unstable2.29
TomatEST - Tomato expressed sequence tag Italy 26alive2.52
EPConDB - EPConDB United States 15alive1.50
GeneSpeed - GeneSpeed database United States 10dead0.00
WormBook - the online review of Caenorhabditis elegans biology United States 51alive5.10
TBestDB - Taxonomically Broad EST Database Canada 84alive8.32
Comparasite Japan 27alive2.70
ViTa - ViTa Taiwan 56alive5.60
FLIGHT - FLIGHT United Kingdom 39dead0.00
ITTACA - Integrated Tumor Transcriptome Array and Clinical data Analysis France 43alive3.91
AOBase - database for antisense oligonucleotides selection and design
China 6dead0.00
ChloroplastDB - Chloroplast Genome Database United States 68alive6.06
OncomiRdbB - Oncogenic miRNA database India 1alive0.32
RBP-Var China 0alive0.00
BIGNASim - BIGNASim database structure and analysis portal for nucleic acids simulation data
Spain 1alive1.00
TCGASpliceSeq - TCGASpliceSeq United States 0alive0.00
MitoAge - A database for comparative analysis of mitochondrial DNA, with a special focus on animal longevity Israel 1alive1.00
DIANA-miRGen - DIANA-miRGen Greece 303unstable27.57
EBI - The European Bioinformatics Institute United Kingdom 610unstable23.87
probeBase - probeBase Austria 804unstable51.69
piRNA cluster db - piRNA cluster database Germany 29alive5.80
HGTree - Database of Horizontally Transferred Genes Determined by Tree Reconciliation Pakistan 1alive0.96
InsectBase China 1unstable0.88
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 1alive1.00
NCBI - National Center for Biotechnology Information United States 16174unstable447.16
miRNASNP - microRNA-related Single Nucleotide Polymorphisms China 145alive27.84
MtiBase - MiRNA-target interactions database
China 0unstable0.00
miRSponge - Experimentally validated miRNA Sponges database China 1unstable0.47
LncReg - database for LncRNA regulating
China 2unstable0.92
G4RNA
Canada 0alive0.00
OCDB - Obsessive-Compulsive Disorder Database Italy 1unstable0.29
READDB - RNA Binding Protein Expression and Disease Dynamics database
United States 0alive0.00
5SRNAdb - Database of of ribosomal 5S RNAs Poland 9alive9.00
sRNATarBase - sRNATarBase China 32unstable3.70
rVarBase China 28alive9.24
CircNet
Taiwan 0alive0.00
RPFdb - ribosome protected mRNA fragments database
China 1unstable0.92
RMBase - RNA Modification Base China 2unstable1.68
Lnc2Cancer China 2unstable1.88
CRISPRz United States 0unstable0.00
dPORE-miRNA - Dragon Database of Polymorphic Regulation of miRNA genes Saudi Arabia 25unstable3.96
CANTATAdb - A database of long non-coding RNAs in plants Poland 1alive0.99
piRNAQuest - searching the piRNAome for silencers India 4alive1.32
GSA - Genome Sequence Archive China 4alive4.00
BIG Data Center - BIG Data Center for Life & Health Sciences China 12alive12.00
LNCediting United States 0unstable0.00
miRPathDB - miRNA Pathway Dictionary Database Germany 1dead0.00
RAID - RNA Association Interaction Database China 34alive11.33
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 54unstable2.85
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 1unstable0.92
PmiRExAt - plant miRNA expression atlas database India 0unstable0.00
IRNdb - Database of immunologically relevant non-coding RNAs New Zealand -alive-
SlideBase Denmark 0alive0.00
PGD - Pangolin Genome Database Malaysia 0unstable0.00
Reefgenomics Saudi Arabia 4alive4.00
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 8alive7.92
EpimiRBase Ireland 4unstable3.56
Cas-Database Korea Rep. 1alive1.00
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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