Question

Pseudogene - scarce info

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12 hours ago

mf810 • 0

Hi everyone! First post here ever, hope I'm not doing anything too wrong.

TLDR: I'm trying to find info on a pseudogene (RNA5SP352) and simply can't. Any help or indications would be greatly appreciated.

So, I'm currently studying a master's degree related to Biology, and in a Bioinformatics class we've been assigned some genes to do a quick project about. The thing is, these genes are of a wide range of complexity and were assigned at random, so while some have very typical (should I say 'characteristic-looking'?) genes - with all their introns and exons, RNA translations and protein traductions, functionalities, relation to disease, etc -, others - like me - got weird-looking ones that don't seem to check out all these boxes. My issue is not so much - not at all, really - that they are of varying complexity, but that the layout for the project pretty much is to expose the mentioned 'typical' things about a gene, which mine doesn't seem to have.

I've got the honor to be tasked with RNA5SP352 (Ensembl code: ENSG00000200278.1). Working with Human Genome (GRCh38.p14) btw. It is a ribosomal pseudogene of about 140kb, with 81 alleles, 1 RNA transcript and non-coding for proteins.

I've scavenged the Internet and a bunch of databases but there doesn't seem to be much info available aside from the fact that it is in fact there in its described position in the genome. I would mention the databases I've searched just because I know how frustrating it feels when someone asks a generic question showing no work on their part, expecting others to do it for them. But tbh, I've searched all that I could find and I don't see the point of mentioning over 20 databases just to make a point. Just as examples, I've of course used Ensembl, GenomeDataViewer, UCSC's Genome Browser, HGNC and every crosslinked database and resource on any of these. A vast majority of them seemingly have a decent amount of info available between the basic name, position, etc and the links to other sites, but that ofuscates the fact that they all link to each other but add no useful information as such.

From what I've gathered it is completely UTR, but also very little studied, hence why there's so little info about it. Maybe it simply is irrelevant and that's all there's to it, but that feels cheap to put on a uni project. Although I'm starting to convince myself of it.

The only - potential - connections to other genes or conditions I've managed to put together are:

SIAE: two genes encoding for enzymes that participate in some kind of acetylation. In some events of that process failing, susceptibility of autoimmune disease 6 is an observed outcome. These are the first - and almost only - bet of there being anything interesting at all about my pseudogene cause their exons occupy the whole region of the pseudogene, so my guess is maybe affectations on the RNA5SP352 region in the DNA, or some kind of interaction with its mRNA transcript, can effect the SIAE gene transcription in some significant way. Haven't found evidence of that in the literature tho.
TRIM25: a gene only related to my pseudogene by grace of NCBI's National Library of Medicine in this link-,Interactions,-Products). The gene plays a pivotal role in some pathways of the immune response, but tbh I could'nt find any mention of my pseudogene on the linked article, although it was referenced on its NLM page.
TBRG1: on the upstream of my pseudogene. Not related in any way I am aware of, but it is the closest one in that direction.
SPA17: same thing but downstream.

Now, if anyone knows of specific databases I can check for this kind of "gene", or interesting things about it/them, or has any other suggestion, I would appreciate that SO much.

That's all, sorry for the boring read.

pseudogene mastersdegree • 119 views

ADD COMMENT • link 2 hours ago by mf810 • 0

score 0 · Answer 1 · 2025-10-08

The gene plays a pivotal role in some pathways of the immune response, but tbh I could'nt find any mention of my pseudogene on the linked article, although it was referenced on its NLM page.

TRIM25 seems to be an RNA-binding proteins with many targets. I imagine somewhere in the supplemental info there is a full list of its binding partners, and RNA5SP352 is likely to be one of them. You will get the same information if you click on the BioGRID link of the NCBI page you cited, or if you go directly to BioGRID and search for your pseudo-gene.

https://thebiogrid.org/3189464/summary/homo-sapiens/rna5sp352.html

The thing is, these genes are of a wide range of complexity and were assigned at random

I like helping people who invest time to explain their problem, so you qualify. The thing is, I should be much better than you in finding gene/protein functions, and I really can't find much more than what you did already. It is best summarized on this page:

https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000200278;r=11:124636459-124636592;t=ENST00000363408

So this is a non-coding RNA of the 5S rRNA variety, which is deduced by sequence search methods. It is not stated why it is a pseudo-gene, but that usually means that something in its sequence is out of whack and that it normally doesn't transcribe. That goes against the TRIM25 findings, which seemingly binds a transcript of this protein. That's about it.

In technical terms, you are royally a recipient of the shortest straw (a PG-13 version of the actual expression). If possible, I would go to whoever assigned this to you, show them that you have invested a good deal of time, and that simply there isn't much to be found. You can quote me on this last part if you wish. Then hopefully you get a more exciting project, or if not at least you tried.