Viewing RNAcentral sequences

All sequence report pages include: 

• ncRNA sequence
• cross-reference(s) to the databases where this sequence is annotated
• its unique accession number

Depending on the ncRNA type, organism, and the source database, the report pages may include one or more additional sections: 

• RNA secondary structure
• an embedded genome browser
• Rfam classification⁴
• Gene Ontology (GO) terms⁵
• orthologs and paralogs from Ensembl Compara⁶
• microRNA targets from TarBase and LncBase 
• modifications from Modomics⁷
• literature references
• sequence feature viewer
• AI generated summaries¹¹
• expression data
• molecular relationships according to RNA-KG¹⁰
• and more

View basic information about ncRNA sequence

1. Starting from the RNAcentral homepage (Figure 2), search for human miR-181b-1 stem-loop microRNA by entering URS000067427D_9606 in the search box located at the top of the page.

2. The search returns a result for the sequence and its Rfam family. Click on the single search result to view the sequence report. Let’s explore a sequence report page for the hsa-mir-431 precursor microRNA URS000067427D_9606 (Figure 3). You can see the RNA type, source databases, and genomic neighbourhood and view several interactive visualisations. For example, you can click on the RNAcentral transcripts in the genome browser to find what database these sequences come from, or you can visualise the GO term hierarchy by clicking on the tree icons.

3. Under the Annotations heading follow the links to the source databases to find additional information about this RNA. For example, in miRBase you can find deep sequencing data supporting this microRNA as well as >20 papers discussing this RNA, while in MalaCards you can read about the association of this microRNA with autism spectrum disorder.

4. Identify other sequences in the same genomic locations. The embedded genome browser (Figure 3) shows the sequence in the context of the reference genome, including other ncRNAs as well as protein-coding genes and pseudogenes found in the genomic neighbourhood.  It is important to view sequence reports for all ncRNAs in a genomic region of interest. For example, the genome browser shows another precursor microRNA sequence (URS0000EFD35A_9606) in the same region provided by MirGeneDB. This discrepancy is caused by the differences in the annotation methods between the two databases. 

Figure 3 A sequence report page for human hsa-mir-431 precursor microRNA.