Question: How to distinguish if a gene is a paralogue or an isoform?
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gravatar for DNAngel
4 weeks ago by
DNAngel20
DNAngel20 wrote:

I'm reading up on fish osmoregulation and have come across many papers talking about the expression levels for a very important gene, atpase alpha (NKAa or atp1a1); it has many names. There are different "versions" that are well known such as atpa1a, atpa1b, and atpa1c where each one is expressed differently depending on species/habitat/tissue.

But half the papers refer to these genes as isoforms, and the other half call them paralogues because of the whole genome duplication event.

I want to sequence these genes for my own species later on but as I write about it, how do I fully understand if these are indeed paralogues or isoforms? Looking up the data from the papers on Ensembl lists these genes as paralogues but why is there this difference between papers? These terms are not interchangeable in my book.

isoform paralogue gene • 159 views
ADD COMMENTlink modified 4 weeks ago by kashiff00750 • written 4 weeks ago by DNAngel20
2

Not a typical bioinformatics question, but I'll give it a try. Probably both are true. This gene must have experienced duplication events (eight local or whole genome) that generated paralogous copies. Each copy may also have multiple transcription isoforms. You'll have to find the conserved regions across all known copies, presumably in species related to your target species, and "fish" all copies out from whole genome sequences or by PCR with primer anchored to the conserved regions. Paralogous genes are at different physical genomic locations, while isoforms come from a single locus. You'll need to do RT-PCR or mRNA-Seq to confirm all isoforms.

ADD REPLYlink written 4 weeks ago by Vitis2.0k
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gravatar for kashiff007
4 weeks ago by
kashiff00750
Cologne
kashiff00750 wrote:

According to the basic definition isoforms are coming from same gene, so their location should be same in the genome. At least, in most cases TSS and TTS are usually same for all transcript. While paralogs are the result of duplication so their position differ from the original gene. Technically paralogs are different genes and so their location. For sequencing, you may have to look for the region before the gene start; upstream.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by kashiff00750

True! When I dug into it deeper and looked up their genomic regions they are indeed located at different points along the chromosome (but still close to each other). Even when reading deeper into a big paper that calls them isoforms, they actually described them as potential paralogs in a figure caption..sigh lol.

ADD REPLYlink written 4 weeks ago by DNAngel20
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