downloading human rRNA.fasta

Question

[Sara]

I am trying to download human rRNA.fasta file. do you know where I can find this file? in one of the older post in this forum, someone said this file can be found on the UCSC but I did not manage.

[ATpoint]

https://www.gencodegenes.org/human/

Take the Transcript sequence fasta file and extract whatever you need. You could grep for rRNA or use the GTF on the same repository to filter for biotypes etc.

[Trivas]

Aren't rRNAs not annotated in reference genomes? For OP: I followed this site to generate my list of rRNA sequences.

[ATpoint]

Yes, so? I am referring to transcriptome fasta file.

[Trivas]

Either way, the rRNAs that comprise 45S rRNA (e.g. 18S and 28S) aren't annotated/included. Last I checked, even if you look at where those rRNAs are in the genome on let's say, IGV, you won't see an annotated track.

Using your method, you'll pull out a variety of 5S and 5.8S pseudogenes as well as the 12S and 16S mitochondrial rRNAs but not 18S and 28S which I'm assuming the OP would also want.

[ATpoint]

Did not know, thanks!

[hector3500]

For anyone who finds this who is still looking. The riboseq analysis tool ARF uses the rRNA sequences, and have therefore placed them into a fasta file with the 28S, 5S, 5.8S, and 18S rRNAs. It's very helpful.

https://github.com/fallerlab/ARF/blob/main/rRNAs/4V6X_human_rRNAs.fa

Answer 1

[GenoMax]

There are multiple copies of rDNA repeats (~ 400) in humans and they are on different chromosomes. Each of us may have a different complement.

Complete rDNA human repeat is available: how can i download human ribosomal reference ?