Table 1.
A collection of recently developed or updated non-coding RNA databases containing NGS generated data. All URLs were accessed on 22 October 2021.
| Name | Species | Database Content | URL | Refs. |
|---|---|---|---|---|
| AlnC | 682 Angiosperms | lncRNA | http://www.nipgr.ac.in/AlnC | [34] |
| ASRA | 21 Vertebrates | Circulating sncRNA | https://ccb-web.cs.uni-saarland.de/asra/ | [35] |
| circ2Go | Human | circRNA | https://circ2go.dkfz.de/ | [36] |
| CircAtlas 2.0 | 6 Vertebrates | circRNA | http://circatlas.biols.ac.cn/ | [37] |
| circBank | Human | circRNA | http://www.circbank.cn/ | [38] |
| circBase | 3 Vertebrates 2 Invertebrates |
circRNA | http://www.circbase.org/ | [39] |
| circFunBase | 7 Plants 8 Vertebrates 1 Invertebrate |
circRNA | http://bis.zju.edu.cn/CircFunBase/index.php | [40] |
| CIRCpedia 2.0 | 4 Vertebrates 2 Invertebrates |
circRNA | https://www.picb.ac.cn/rnomics/circpedia/ | [41] |
| DeepBase v3.0 | 11 Vertebrates 2 Invertebrates |
ncRNA | https://rna.sysu.edu.cn/deepbase3/index.html | [42] |
| DIANA-lncBase v.3 | 2 Vertebrates | miRNA targets on non-coding transcripts | https://diana.e-ce.uth.gr/lncbasev3/home | [43] |
| DIANA-Tarbase v8 | 2 Viruses 7 Plants 2 Invertebrates 7 Vertebrates |
miRNA-gene interactions | http://www.microrna.gr/tarbase | [44] |
| EVAtlas | Human | Extracellular vesicle ncRNA | http://bioinfo.life.hust.edu.cn/EVAtlas/ | [45] |
| exoRBase 2.0 | Human | Exosome ncRNA | http://www.exorbase.org/ | [46] |
| GTEx version 8 | Human (tissue) | Transcriptome | https://gtexportal.org/home/ | [47] |
| Lantern | Human | lncRNA | https://sysbio.lab.iupui.edu/lantern/ | [48] |
| LncATLAS | Human | lncRNA subcellular localization | https://lncatlas.crg.eu/ | [49] |
| LncBook | Human | lncRNA | https://ngdc.cncb.ac.cn/lncbook/index | [50] |
| LncExpDB | Human | lncRNA | https://ngdc.cncb.ac.cn/lncexpdb/ | [51] |
| LNCipedia 5 | Human | lncRNA | https://lncipedia.org/ | [52] |
| lncRNAKB | Human | lncRNA | http://psychiatry.som.jhmi.edu/lncrnakb/ | [53] |
| LncSEA | Human | lncRNA | http://bio.liclab.net/LncSEA/index.php | [54] |
| MINTbase 2.0 | Human | tRF | https://cm.jefferson.edu/MINTbase/ | [55] |
| miRBase | 271 organisms | miRNA | https://www.mirbase.org/ | [56] |
| MiREDiBase | 4 Vertebrates | Editing events in miRNA | https://ncrnaome.osumc.edu/miredibase/ | [57] |
| MirGeneDB 2.0 | 22 Vertebrates 23 Invertebrates |
miRNA | https://mirgenedb.org/ | [58] |
| mirTarBase 9.0 | 16 Vertebrates 3 Invertebrates 5 Plants 3 Viruses |
miRNA-target interactions | https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/index.php | [59] |
| miRWalk | 6 Vertebrates | miRNA binding sites | http://mirwalk.umm.uni-heidelberg.de/ | [60] |
| NONCODE v6.0 | 23 Plants 1 Fungus 2 Invertebrates 13 Vertebrates |
ncRNA | http://www.noncode.org/index.php | [61] |
| riboCIRC | 2 Invertebrates 4 Vertebrates |
Translatable circRNA | http://www.ribocirc.com/ | [62] |
| Rfam 14.6 | Various | RNA families | https://rfam.org/ | [63] |
| RNA Atlas | Human (tissue and cell lines) | Transcriptome | http://r2platform.com/rna_atlas | [64] |
| piRBase 3.0 | 28 Invertebrates 16 Vertebrates |
piRNA | http://bigdata.ibp.ac.cn/piRBase/ | [65] |
| piRNAclusterDB 2.0 | 23 Invertebrates 28 Vertebrates |
piRNA clusters | https://www.smallrnagroup.uni-mainz.de/piRNAclusterDB/ | [66] |
| piRTarBase | 2 Invertebrates | piRNA targeting sites | http://cosbi6.ee.ncku.edu.tw/piRTarBase/ | [67] |
| PlantcircBase 6.0 | 20 Plants | circRNA | http://ibi.zju.edu.cn/plantcircbase/index.php | [68] |
| PtRFdb | 10 Plants | tRF | http://14.139.61.8/PtRFdb/index.php | [69] |
| snoDB | Human | snoRNA | http://scottgroup.med.usherbrooke.ca/snoDB/ | [70] |
| TarDB | 43 Plants | miRNA targets | http://www.biosequencing.cn/TarDB/ | [71] |
| TransCirc | Human | Translatable circRNA | https://www.biosino.org/transcirc/ | [72] |
| TSCD | 2 Vertebrates | circRNA | http://gb.whu.edu.cn/TSCD/ | [73] |