29 Jan 2019

RNAcentral Release 11

We are pleased to announce that a new RNAcentral release is now available. Version 11 includes miRNA-target interactions from TarBase and LncBase, a new public Postgres database, data from Ensembl Plants, miRBase word clouds, and lots more.

Release 11 announcement

microRNA target interactions

We continue to expand the functional annotations available in RNAcentral by importing human and mouse miRNA-target interactions from LncBase and TarBase. These databases contain high quality, literature-based interactions between miRNAs and their lncRNA and protein targets. The interactions are displayed on sequences pages, for example human microRNA hsa-miR-1226-5p interacts with both lncRNAs and proteins:

You can also see when a lncRNA is targeted by a miRNA, for example:

The interactions are searchable, for example you can find sequences:
For more details see the help centre or browse the sequences in RNAcentral.

We would like to thank Artemis Hatzigeorgiou, Dimitra Karagkouni, Maria Paraskevopoulou and other present and former members of the DIANA lab for help with importing the data and developing the interface.

New website features

miRBase word clouds

Starting in version 22, miRBase began providing word clouds based on snippets from the open access literature mentioning miRBase accessions. Now the word clouds are available from the corresponding RNAcentral pages providing a quick insight into the function of a miRNA. For example, miRNA mir-100 is associated with cancer, with this term prominently featured in the word cloud:
Find out more about literature mining and word clouds in the latest miRBase paper.

Conserved regions

We now display conserved regions for 29 vertebrate species using data from the CRS website. The conserved structures were identified with CMFinder using vertebrate multiple sequence alignments (see the Genome Research paper for the description of the method).

The conserved regions are displayed in the sequence feature viewer alongside the Rfam annotations. Here is an example from URS0000BC44D5_9606.

We would like to thank Stefan Seemann and Jan Gorodkin (University of Copenhagen) for providing the data and enabling this integration.

New way of linking to RNAcentral

It is now possible to link to RNAcentral web pages without knowing the RNAcentral accessions. For example, if you would like to link to Ensembl transcript ENST00000365484, you can do so using a URL like /link/ensembl:ENST00000365484. See more examples in the documentation.

Public Postgres database

Following multiple user requests, we now provide a public Postgres database that provides the same data available on the RNAcentral website. The database is meant to help users who would like to access RNAcentral programmatically or are interested in tasks that are not yet supported by the website. The connection details, example queries, tips for quick start with Docker, and a sample Python script are found in RNAcentral Help.

You can now contribute new features or bug fixes for RNAcentral website by downloading the RNAcentral webcode and starting a local server using the public database. We welcome code contribution on GitHub. If you have any issues connecting to the database or have any questions please get in contact.

Data updates

We now import data from Ensembl Plants, a comprehensive source of plant gene annotations. Additionally we now import data from the Zasha Weinberg Database (ZWD), a recently established database of high-quality sequence alignments for a diverse range of habitats and organisms. Let us know if you see any other data sources for RNAcentral.

The following database have also been updated:
  • ENA (v137)
  • Ensembl (v95)
  • Ensembl Plants (v42)
  • FlyBase (fb_2018_05)
  • HGNC
  • LNCipedia (v5.2)
  • PDB
  • RefSeq
  • TAIR
  • WormBase (WS267)

Get in touch

The data are available on the RNAcentral website, via the API, and in the FTP archive. We plan to make the next release available in April, 2019. In the meantime, if you have any feedback please feel free to get in touch by email, on Twitter, or by submitting an issue on GitHub. We look forward to hearing from you!