Where can I obtain the sequence of the E. coli ribosomal RNA precursor?

Question

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:

https://www.ncbi.nlm.nih.gov/nuccore/U00096.3?report=fasta

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

Answer 1

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
  /gene="rrsA"
rRNA  4035531..4037072    
  /gene="rrsA"
gene  4037141..4037217
  /gene="ileT"
tRNA  4037141..4037217
  /gene="ileT"
gene  4037260..4037335
  /gene="alaT"
tRNA  4037260..4037335
  /gene="alaT"
gene  4037519..4040423
  /gene="rrlA"
rRNA  4037519..4040423
  /gene="rrlA"
gene  4040517..4040636
  /gene="rrfA"
rRNA  4040517..4040636
  /gene="rrfA"

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,...