downloading human rRNA.fasta
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8 months ago
Sara ▴ 220

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.

rRNA • 684 views
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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.

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

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

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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.

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Did not know, thanks!

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8 months ago
GenoMax 125k

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 ?

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