Where To Find Detailed Information On Genomic Location Of Rrna Genes?

Question

[Nenad Bartonicek]

Hello,

I'm trying to identify genomic locations of individual rRNA genes in mouse. It seems that some rRNAs are fine - 5 and 5.8 for example. However, other large ribosomal rRNAs usually come in batches (LSU rRNA - combined 5S, 5.8S and 28S) which are quite useless.

I've tried ENSEMBL (only 5 and 5.8), repbase (LSU and SSU, but no detail), rFam (the sum of previous two), UCSC (only mitochondrial rRNA), Silva (LSU only 28s) to no avail - all lacking an rRNA or two.

Am I missing something? Is LSU in fact a short name for 28S!? Where is the phantom 45S rRNA (pol1 transcript) coming from as well?

Thanks for any info!

Nenad

[David Quigley]

Are you searching using the official gene symbols? Common names are often reused between genes, and it's hard enough to distinguish the rRNA family members as it is.

Answer 1

[Larry_Parnell]

In eukaryotes, the 60S ribosomal subunit contains a 5 S, 5.8 S and 28 S RNA moities, while the small subunit (40 S) contains an 18 S RNA (RNA = associated proteins make this a 40 S subunit). The mouse 28 S entry is here, mapping ot mouse chromosome 3, 6, 8, 9. The entry for mouse 18 S is here. As the smaller rRNAs were fine, in your words, I did not locate those.

[Nenad Bartonicek]

Thanks a lot for the information. Unfortunately, I wish it were that simple. This is the quote from the pubmed reference on human RN28S1: "The sequences coding for ribosomal RNAs are present as rDNA repeating units, designated RNR1 through RNR5, in the p12 region of chromosomes 13, 14, 15, 21 and 22. A 45S rRNA which serves as the precursor for the 18S, 5.8S and 28S rRNA, is transcribed from each rDNA unit by RNA polymerase I. The number of rDNA repeating units varies between individuals and from chromosome to chromosome, although usually 30 to 40 repeats are found on each chromosome."

[Nenad Bartonicek]

The problem is that these regions were difficult to assemble into the reference genome because of their repetitiveness. So they are lying around the unplaced supercontigs, unannotated.

[Larry_Parnell]

OK, I better understand your situation now. Sometimes, the monomer of the repetitive sequence, the 45S, might be found in older, pre-whole genome sequencing data. I have seen this for other organisms where the rDNA unit was sequenced in the 1970's to early 1990's.