Finding the parent gene of pseudogene in mouse

Question

[pyKey]

Hello everybody,

I have a list of ENSEMBLE mouse genes and I wnat to investigate if some of the pseudogenes are mutations of some genes, for example: if 'ENSMUSG00000084349' has been extracted from 'ENSMUSG00000060036'. Is there any systematic structure to check this?

Thank you very much,

[pyKey]

Thank you!

Could you elaborate a bit? Are there any published hierarchical information out there? Sorry I am not from bioinfo background :)

Answer 1

[Juke34]

Catch all genes similar to your pseudogene using blast, then perform an alignment with all the sequences, your pseudogene sequence included ; then create a phylogenetic tree. The closest sequence to your pseudogene Will probably be the parental sequence.

Answer 2

[Juke34]

Hello,

To check this kind of assumption I guess using a phylogeny approach would be one of the best way.

[niuyw]

Hi Juke, if I want to find the parent gene of lots of pseudogenes using phylogeny method, is it acceptable using some simple method to infer the relations of sequences, such as a NJ tree? The ML tree needs a lot of computing resources. Comparing with a rigorous blast search (perform a blast search to find the parent gene of pseudogene using rigorous filters), is the NJ tree method more accurate?

[Juke34]

I would definitely prefer to use ML tree if I had the possibility. And between NJ tree and rigorous Blast, I will turn without hesitation to the NJ tree.

[niuyw]

Thanks, Juke. It is very helpful.

Answer 3

[vkkodali_ncbi]

For NCBI RefSeq GeneIDs, you can query the gene_group.gz file located at the FTP path: https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_group.gz

This file has the following columns:

     #tax_id [  1]: 3847
      GeneID [  2]: 100527391
relationship [  3]: Related pseudogene
Other_tax_id [  4]: 3847
Other_GeneID [  5]: 100777546

If you have a list of GeneIDs for the mouse pseudogenes you are interested in, you can find the parental mouse genes as shown below. In this example, my query (GeneID: 100043000) is the Rpl3-ps1 gene you have mentioned above and the related functional gene (GeneID: 27367) is Rpl3 parental gene.

$ zgrep '100043000' gene_group.gz | column -t -s $'\t'
10090  27367      Related pseudogene       10090  100043000
10090  100043000  Related functional gene  10090  27367