A new version of RNAcentral (release 9) is available. This features the Rat Genome Database (RGD) as a new Expert Database as well as updated data from ENA, RefSeq, Ensembl, PDBe and HGNC. Additionally, we have added more search options, provided a feature viewer for sequences and improved the display of genomic locations.
Another request we’ve gotten has been for sorting options. Now you can control sorting so it isn’t just our default sorting. We allow sorting by popular species and descending length or just length in descending or ascending order. Let us know what sortings you would want, or new search features!
Here are a few interesting examples. Can you find any others?
This helps clarify the localizations when a sequence is found in many databases or locations. For example, human hsa-mir-10a precursor is only found on chromosome 17, while the human hsa-mir-3648 precursor appears twice in chromosome 21. Without the summary table you would have to carefully read the entire cross reference table to learn this. Additionally, this table provides links to viewing this region in the Ensembl and UCSC genome browsers. We are working on other improvements to our genomic locations, so stay tuned for big changes!
We have imported another Model Organism database, RGD. This database serves as the primary resource for genomic, phenotype and disease data generated from Rat research.
More search options
One common request for our search has been to make it easy to search by length. It has been possible using the advanced syntax documented in our help; but this wasn’t intuitive, so we added the length slider.
Sequence feature viewer
Now that RNAcentral shows Rfam annotations of sequences, we want to ensure these results are easy to understand. To do this we added a feature viewer for sequences, which we use to show the Rfam annotations of sequences and any modifications or non-standard bases. This viewer is particularly nice in cases where a sequence is composed of several Rfam models, like:
Here are a few interesting examples. Can you find any others?
- An incomplete sequence
- A complex sequence
- A simple, well annotated sequence
- An example that shows the evolutionary history of the 5.8S
More useful genomic location display
RNAcentral displays the genomic location of ncRNAs in selected organisms. For example, the genome browser shows human HOTAIR in chromosome 12. Now, RNAcentral has a table that summarizes all known locations, additionally the current sequence is highlighted.
This helps clarify the localizations when a sequence is found in many databases or locations. For example, human hsa-mir-10a precursor is only found on chromosome 17, while the human hsa-mir-3648 precursor appears twice in chromosome 21. Without the summary table you would have to carefully read the entire cross reference table to learn this. Additionally, this table provides links to viewing this region in the Ensembl and UCSC genome browsers. We are working on other improvements to our genomic locations, so stay tuned for big changes!
Welcome RGD
- Browse 21,672 ncRNA sequences from RGD
- View RGD summary page
- Find out more about RGD in their most recent paper
Other data updates
The following database have also been updated:
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 June, 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!- ENA (release 134)
- Ensembl (release 91)
- RefSeq
- PDB
- HGNC
- WormBase