Genomic mapping

Species with genomic mapping

The following species are annotated with genomic coordinates (where possible). Click on a species to view the sequences annotated with genomic coordinates.

Genome-specific functionality

Whenever genomic mapping is available, RNAcentral sequences can be viewed in their genomic context using a light-weight genome browser Genoverse and their genomic neighborhood can be interactively explored without leaving the page (e.g. URS00000B15DA).

External links are provided to the fully-featured genome browsers such as Ensembl, Ensembl Genomes, and UCSC genome browser.

The genomic coordinates of the RNAcentral entries can be downloaded in a variety of formats from the FTP site or through the REST API.

About genomic mapping

Viewing ncRNA sequences in their genomic context can often provide valuable information. For example, snoRNAs that are transcribed within the introns of protein coding genes become readily apparent when viewed in a genome browser (e.g. URS0000269B1D).

For a number of key species we establish a mapping between the RNAcentral entries and their genomic coordinates in reference genomes using the Ensembl Perl API.

Notably, the latest human genome assembly, GRCh38, is used for the mapping.

Currently the genomic coordinates are only available for RNAcentral entries that come from INSDC accessions used in reference genomes. In the future we plan to expand the mapping to sequences that are not part of reference genomes.

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