function of unknown gene

[rasing02]

If you have a gene sequence which is known to be expressed but does not have a biochemical or physiological function, then how can one determine the function and prove it, lets say in a plant system? Also consider the fact that you have to work from scratch no database (gene bank, blast,etc) is avaliable???

[Bonnie]

A couple ways to approach it:
1) Look for homologous genes in a species for which you do have a database available.
2) Overexpress it and look for phenotype changes.
3) Knock it down with siRNA or similar and look for phenotype changes.
4) Cross-link and immunoprecipitate it, then use mass spec to identify proteins it interacts with to determine processes it's involved in.

[rasing02]

Thanks a lot for the response. What if the unknown gene is invovled in a biochemical pathway and is responsible for synthesis of some intermediate, or phytochemical,etc...then how will overexpression in this case help, because I think these internal biochemical changes wouldnt be seen in phenotype (plants)....I hope I am thinking in right direction. Thanks !

[Anastasiya]

Why no database is available? It is a strange constrain.