I have found separate sequences for 16S rRNA (from the small subunit) and 23S rRNA and 5S rRNA (from the large subunit). I need the full precursor rRNA sequence, which I cannot find.

However the complete annotated sequence of the E. coil genome is available:


Does changing the T to U of this sequence give me the complete rRNA sequence?


Generally most organisms have multiple copies of the genes/regions coding for ribosomal RNA (since it's needed quite a lot). Additionally these regions can be repetitive or otherwise similar to sequence or place correctly in the genome, therefore it's generally harder to find good genomic sequences for rRNA compared to other genes.

Based on your link, it seems that you are looking for the rRNA of E.coli; the GeneBank entry corresponding to the fasta file you linked contains the annotation of the full genome and has 7 entries for sets of ribosomal RNA (named rr[slf][A-H]*).
If you take any of the sequences spanning one of these regions you should get the sequence of the full precursor. However, there are things you should be aware of:

  • there will likely be minor sequence differences between all 7 regions
  • Apparently most of the e.coli rRNA operons also have tRNA genes mixed into them (these are different for all 7 operons)
  • replacing the genomic T with U will make the sequence look like RNA, however ribosomal RNA is often also edited post-transcriptionally, so the sequence you get may not fully match the mature rRNA sequence.

Another website that gives a better readable overlook over the rRNA operons in e.coli is this, it also contains source links & seems to match the genbank entry from what I can see.

Example on how to find rRNA region from the geneBank entry:

This is a (shortened) part of the annotation of the GeneBank entry, which shows the 'A' ribosomal genes :

gene  4035531..4037072
rRNA  4035531..4037072    
gene  4037141..4037217
tRNA  4037141..4037217
gene  4037260..4037335
tRNA  4037260..4037335
gene  4037519..4040423
rRNA  4037519..4040423
gene  4040517..4040636
rRNA  4040517..4040636

As you can see the genes in the region/opernoccur in order rrsA, ileT, >alaT, rrlA, rrF (the fact that this is an operon can not be inferred from the GeneBank entry) and if you take the corresponding region of the fasta sequence (nucleotides/characters 4035531 to 4040636) you'll get (most of) the primary transcript sequence.
Since promoter & terminator Sequences are not annotated in GeneBank (or any/most other genome assemblies), you can't easily get the sequence before the first and after the last gene. One potential source for these might be the other ressource I linked, which lists some sources for terminator sites.

* This is expressing all names as regex. i.e. for rRNA operon A there are rrlA, rrsA & rrfA; same for B,C,...

  • $\begingroup$ @User I added an example of what I meant with that paragraph $\endgroup$ – Nicolai Aug 13 '19 at 12:23
  • $\begingroup$ Thank you very much, this helps to find most of the operon sequence. @User $\endgroup$ – User Oct 16 '19 at 8:59

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.