Could not find rRNA genes (28S, 18S, 5.8S and 5S) in human_genes.gtf file?

Question

[bioinforesearchquestions]

Dear All,

I am searching for human 28S, 18S, 5.8S and 5S rRNA (RNA28S, RNA18S, RNA5-8S and RNA5S genes) and also 12S and 16S mitochondrial rRNA (MT-RNR1 and MT-RNR2) in human_genes.gtf file from UCSC.

I am unable to find these genes(RNA28S, RNA18S, RNA5-8S, RNA5S, MT-RNR1 and MT-RNR2 genes) in human_genes.gtf file. I am looking at gene_id or gene_name in gtf file.

How do I check these genes in gtf file or in any other resources.

Is it saved in some other name?

[glihm]

You can try to looking for in GENCODE resources. ;)

Answer 1

[Devon Ryan]

You can find 5S, 5.8S and MT_rRNA in the Ensembl/Gencode files. The others aren't in the reference genome (they're on an unplaced contig). If you need the sequences then you can get them from NCBI (the ones not in the reference genome come from 45S).

[bioinforesearchquestions]

Thanks Devon. I am using new kit which is expected to remove eukaryotic cytoplasmic rRNA, mitochondrial rRNA. In order to know the reads associated to these rRNA genes. I have the output from htseq-count. Only RNA5-8S5 alone is found in human_genes.gtf file and also in htseq output. Then how do I get the numbers of reads for other rRNA genes.

[Devon Ryan]

You might download the 45S sequence that I linked to, add it to your genome, and then map to that. Just add a line to the GTF file including either that whole contig or each of the constituent parts (the bounds of 28S and so on are noted on the NCBI site).

[bioinforesearchquestions]

I downloaded the hg19 whole genome fast sequence from UCSC. I built the bowtie2 index file based on the whole genome. I have a doubt here, then the 45S rRNA sequence is not present in the whole genome sequence file.

[Devon Ryan]

I know, that's why I said to add the sequence from NCBI to it.

Answer 2

[ivan.antonov]

Hi, guys!

I believe that some 45S genes are now present in the hg38 human reference genome, for example: https://www.ncbi.nlm.nih.gov/gene/106631777

Here is the location in UCSC GenomeBrowser -- chr21:8,433,222-8,446,572

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr21%3A8433222-8446572

It is annotated in NCBI, but not in GENCODE (as of version 31).