RNAcentral Release 19

 

We are pleased to announce that RNAcentral release 19 is now live. Version 19 features a new intermolecular interaction database, PSICQUIC, improved genome mapping, updated Rfam annotations, and CPAT-based protein detection. Read on to learn more or browse >31 million non-coding RNAs in RNAcentral.

Welcome to PSICQUIC

RNAcentral welcomes PSICQUIC (pronounced ‘psychic’) as a new member database. This database provides manually curated intermolecular interactions and we have imported the ncRNA-protein interaction data produced by UCL functional gene annotation team. This adds 4,420 new RNA-protein interactions to RNAcentral, for example human hsa-miR-27a-5p has 42 new interactions:

Future updates to PSICQUIC will be added to RNAcentral as part of our release process. You can browse all sequences with PSICQUIC annotations here.

Updated Rfam Analysis

Since RNAcentral started annotating sequences with Rfam models in release 8, Rfam has updated and improved hundreds of families. RNAcentral always uses the latest Rfam models on the new sequences, but will only yearly reanalyze all sequences. As part of this release we reanalyzed all sequences with current Rfam models. We will continue to ensure RNAcentral keeps sequence annotations up-to-date with Rfam.

Visualisation of ORFs predicted by CPAT

RNAcentral is committed to providing a high quality set of ncRNAs. To that end we have started analyzing all sequences from human, fly, zebrafish, and mouse with CPAT, which predicts possible open reading frames. We found that only 6% of sequences from scanned organisms contain a possible ORF. For example, Homo sapiens long non-coding RNA NONHSAT212870.1, contains a possible and it is displayed in the feature viewer as:

We have added a new QA check, possible ORF, to ensure users are aware of these issues, and these can be browsed here.

Database updates

We have updated 11 databases, bringing the total number of sequences to 31 million. The updated databases are:

• ENA (as of 3 September 2021)
• FlyBase (FB2021_04)
• GeneCards/MalaCards (5.5)
• GtRNAdb (release 19)
• HGNC (as of 3 September 2021)
• IntAct (as of 3 September 2021)
• PDBe (as of 3 September 2021)
• PSICQUIC (as of 3 September 2021)
• PomBase (as of 2 September 2021)
• QuickGO (as of 3 September 2021)
• RefSeq (208)

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. The next release is scheduled for January 2022. In the meantime, 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!