20 Oct 2022

RNAcentral Release 21

We are pleased to announce RNAcentral release 21, featuring two new expert databases, PLncDB and Expression Atlas, a new visualisation, and updates to LitScan.

Welcome PLncDB

PLncDB is a comprehensive database of long non-coding RNAs found in plants, featuring data on 80 species.

PLncDB have gone to considerable lengths to ensure confidence in their annotations, more details on which can be found in the paper. To explore their data, start here.

Welcome Expression Atlas

Expression atlas is a resource that allows users to find out where genes are expressed, and how the expression changes when disease is present. In this release, we have imported cross-references to all RNAs that have expression data, so that users can find which sequences have expression data. To explore the data imported from Expression Atlas, have a look at all Expression Atlas entries, or for a single example look at the URS below:

We plan to extend our expression data to include visualisations in the future. Please let us know if you have any suggestions for expression data in RNAcentral.

Visualise locations

We have included SwissBioPic visualisations into RNAcentral. These provide a simple and clear way to visualise the locations of RNA molecules in a cell. Here we show MALAT1 as an example:

We have used the gene ontology annotations provided by groups like the Functional Gene Annotation team at UCL, as the source for these figures.

LitScan updates

LitScan is our text mining tool and is used to associate papers with the RNA sequences they mention. We use our comprehensive collection of RNA names to associate sequences with papers. It has been updated with 5.6 million new RNA names leading to 545,244 papers connected to 2.5 million sequences. Please reach out to us if we have missed any names!

Additionally, we are preparing exports of LitScan results. In future releases this will be part of our FTP export. Get in contact if you would like to hear about the export as soon as it is ready.

FTP export updates

RNAcentral is powered by a PostgreSQL database, which is publicly available. We are now making dumps of the latest release publically available in our FTP site. We intend to keep only the latest dump available. Power users interested in large scale analysis with RNAcentral can fetch and use our database dumps now. Take a look at some documentation, details on our schema, or reach out if you have any questions!

Database updates

  • ENA (snapshot as of October '22)

  • Ensembl (version 107)

  • FlyBase (2022_04)

  • GeneCards (5.12)

  • gtRNAdb (19)

  • HGNC (snapshot as of September '22)

  • IntAct (1.0.3)

  • PDBe (snapshot as of September '22)

  • PSICQUIC (snapshot as of September '22)

  • PomBase (2022-08-24)

  • QuickGO (snapshot as of September '22)

  • RefSeq (213)

  • Rfam (14.7)

  • SILVA (138.1)

  • ZFIN (2022-08-25)

  • ZWD (1.1)

Get in touch

As always, all data are freely available on the RNAcentral website, via the API, our public database, and in the FTP archive. If you have any feedback, please get in touch by email, on Twitter, or by submitting an issue on GitHub. We look forward to hearing from you!