lesser-than:
So I’ve been studying this one gene in my bioinformatics class, At5g07730, that codes for a protein of unknown function in Arabidopsis thaliana. The goal of the class has been to explore different bioinformatic tools to understand the query gene. I think it was pretty cool, so I thought I would share it with you.
The direction I was heading in was to understand the function of my gene and its protein product. The above pictures are my results (a small handful of it), and the following is my interpretation.
At5g07730 is a relatively new gene that is, so far, found in plants only. There are some residues that have absolute conservation suggesting an important function in those locations. Phylogenetic trees showed that most of the residues were under negative selection, but a couple of residues were undergoing positive selection, where mutations were favoured, which makes sense because the gene is new. It was discovered to interact with membrane proteins that were associated with vesicular transport from the ER to the Golgi. Protein domains associated with the ER transport were also found to be conserved in organisms like yeast and humans - however it seems that At5g07730 does not share these regions and simply interacts with them. Our query gene was also found to be co-expressed with At5g19000 which is known to be expressed in mature pollen. It’s responsible for cellular responses to salt stress and osmotic stress and functions in protein binding. Cis-elements were identified in At5g07730 that matched previously characterised motifs found in endosperm and flower development. This may suggest that At5g07730 is involved in ER to Golgi vesicular transport during salt/osmotic stress in mature pollen/plant reproduction pathways.
Anyway, I thought this was a pretty cool thing to do and I encourage everyone to take a bioinformatics class! It is INCREDIBLY frustrating, but strangely rewarding.
It is exceedingly rewarding :D
Source:
lesser-than