22 Aug 2018

RNAcentral release 10

A new version of RNAcentral (release 10) is now available. This release features 10x more sequences with genomic coordinates, GO annotations from QuickGO, as well as new data from FlyBase, miRBase, LNCipedia, ENA, Ensembl, HGNC, PDB, and WormBase.

Genome mapping for >200 species

RNAcentral now provides genomic locations for sequences from over 200 organisms. The locations are based on a newly developed blat based alignment procedure. Details and an analysis of the method will be in an upcoming NAR paper. In short, sequences without known genome locations are aligned to the respective reference genomes using blat. The improved genome browser displays how the alignment was found. Here is an example of an human miRNA precursor URS000018AA08_9606 that is mapped with 99% identity to a single location in chromosome 17:
Browse all sequences with genome mapping or find your favourite organism in the genome browser.

Importing manual GO annotations

We are now displaying manual GO annotations imported from QuickGO. These annotations are based on the careful work of researchers like Rachel Huntley and colleagues (more details in their recent paper). The GO annotations are fetched from QuickGO and displayed as a table that includes an overview of the annotation terms. The ancestors of GO terms can be shown by clicking on the tree button. For example here is a snapshot for annotations for URS0000759B6D_9606.

Additionally, the search terms are searchable in the text search. For example searching for involved_in:"GO:1905563" finds all sequences annotated as being involved in negative regulation of vascular endothelial cell proliferation. You can also search for the names of GO terms, not just the term id, so searches like involved_in:"negative" are possible as well. The search isn’t yet ontology aware, so you can only search for direct annotations. You can browse all sequences with annotations with: has_go_annotations:"True". Read more in the documentation and try exploring the data to see what you can learn about your favourite sequence!

Updates for miRBase and LNCipedia

miRBase and LNCipedia recently had major new releases (versions 22 and 5.0 respectively). These updates to miRNA and lncRNA data have been one of the most requested features by our users.

Other data updates

The following database have also been updated:
  • ENA (release 136)
  • Ensembl (release 92)
  • FlyBase (FB2018_03)
  • RefSeq
  • PDB
  • HGNC
  • WormBase

Upcoming migration to https

On Monday, September 3rd, RNAcentral will switch to the https protocol which means that the main website URL will become https://rnacentral.org (note the “s” after http). Most people do not need to do anything, but if you use the RNAcentral API or provide links to the RNAcentral site, please replace “http” with “https” in the URL. Find out more about https in Google documentation or let us know if you have any questions about the migration.

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 September, 2018. 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!