Where can I find the DNA sequence of the C. elegans rRNA cluster?

Ideally, I would be able to do it using the command-line.

I've tried using NCBI but the results are unsatisfactory. I am interested in the DNA sequence that is in the current reference genome of WormBase.

I have tried using the Bioconductor biomaRt package and create a table containing the description but when I grep 'rRNA', I only get proteins doing things with rRNA. I used the following code:

ensembl <- biomaRt::useMart('ensembl', dataset = 'celegans_gene_ensembl')
wormGenes <- biomaRt::getBM(attributes = c('external_gene_name', 'chromosome_name', 'start_position', 'end_position', 'gene_biotype', 'description'), mart = ensembl)
wormGenes[grep('rRNA', wormGenes$description), 6]

[1] "rRNA 2'-O-methyltransferase fibrillarin  [Source:UniProtKB/Swiss-Prot;Acc:Q22053]"      
[2] "Pre-rRNA-processing protein pro-1  [Source:UniProtKB/Swiss-Prot;Acc:Q22006]"            
[3] "Pre-rRNA-processing protein TSR1 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q19329]"     
[4] "rRNA methyltransferase 2, mitochondrial  [Source:UniProtKB/Swiss-Prot;Acc:O62251]"      
[5] "Probable rRNA-processing protein EBP2 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q09958]"
[6] "Putative rRNA methyltransferase  [Source:UniProtKB/TrEMBL;Acc:Q5CCJ2]" 

1 Answer 1


The info is actually in the gene_biotype column of my wormGenes data frame. I could select the rRNA genes using dplyr::filter(wormGenes, gene_biotype == 'rRNA'). Unfortunately, no description is available for the genes, so I will have to get it using the gene IDs.


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