Forum: RNA base modification
Hello,
Does anybody know if the transcribed spacers (external or internal) also get its base modified (methylation and ѱ formation) the same way as rRNA 18S, 5.8S and 28S get?
• 3,180 views
•
link
updated
by
Ram
•
written
by
kaur.devbio •
•
written
by
kaur.devbio •
1 answer
You can use RMBase to find the genome-wide RNA modification sites identified from 404 transcriptome sequencing datasets (Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq). You can check whether there are modifications in pre-rRNA.
RMBase contains more than 100 modification types, such as m6A, m5C, 2'-O-Me and pseudouridine etc.
Log in to answer this question.
More posts like this
-
ONT Methylation calling
written by Franci •
-
Collect ITS sequences from bacterial genomes
written by star715 •
-
Is it possible to retrieve STRING data base ids using Uniprot.ws in R?
written by ivansilbern •
-
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
written by contact •
-
HTseq-counts not counting correctly?
written by vm.higareda •
-
Difference between NAD and NOR
written by ankitplusplus •
-
Does GRCh38 reference genome contain 18S and 28S rRNA sequences?
written by zhangzhenyusz •
-
Intrastrand CpG Methylation Data
written by NGS-Newbie •
-
Could not find rRNA genes (28S, 18S, 5.8S and 5S) in human_genes.gtf file?
written by bioinforesearchquestions
-
Where To Find Detailed Information On Genomic Location Of Rrna Genes?
written by Nenad Bartonicek •
what do you mean by internal/external spacers?
Its external transcribed spacer (5'ETS and 3'ETS) of pre-rRNA and internal transcribed spacers.
so you are asking whether ETS and ITS in rRNA is also modified?
e.g. check this paper PMC232341
Thanks for writing Whetting,
The paper you mentioned, in this the ETS they were talking about was not the one of pre-rRNA , its related to Intronic part of K18 gene. I am looking if like 18s rRNA, the 5'ETS also get its base modified?