I am evaluating hepato-toxicity of drugs in mice (Mus Musculus). Considering cytochrome 450 gene subtypes CYP2C19, 2C9, 2D6, 2E1 1A2 and 3A4. I got nucleotide sequence of some genes from NCBI and designed their primers. But I did not got nucleotide sequence of CYP2C19, 2C9, 2D6, 2E1 genes.
I tried to find homologous gene (Say, CYP2C9 of Homo Sapience) but it was showing 96% Query Cover value for another gene (CYP2C65) but not with my gene of interest ( CYP2C9 of Mus Musculus).
So should i consider CYP2C65 gene (Mice) function same as that of CYP2C9 (Human)?
or if not, please suggest me how to find nucleotide sequence of such genes and design primers for them?
Thanking all of you in advance.
Hi, previously I also faced similar situation when I needed to design a primer for a local edible mushroom: the data available on NCBI was scarce and in the end I tried to use different key words and finally I managed to find a suitable, correct nucleotide sequence on NCBI.
Apart from that, you may also try to widen your search to non-NCBI database as some nucleotide sequences were from unpublished work or article in press which had not yet being deposited onto the NCBI database.
Worst comes to worst, you have to choose a similar gene (with similar function) in other species, in hoping that the nucleotide sequence can be used to design a primer which can then amplify your gene of interest in another species.
Thank you Chong for your valuable suggestion.........I will to find nucleotide database search in library too...
You can limit your BLAST search to mouse or try related rodent species. Those should be closer than human. It can be really challenging to design primers that are specific when you are working with an expanded gene family. See if you can get the gene sequences from co-authors, RNAseq data, or other sources. Good luck!
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