I work on metallothionein gene in catfish Rita rita but there gene sequence is not available.
Dear Dinesh,
I am not an expert in Fish molecular biology. However, I suppose that there might be MT sequences available in the GenBank from other fishes which are phylogenetically related to Rita rita (same Genus/Family/Order). In such case you can download sequences from those related species, along with MT sequences with unrelated fishes also, align them (preferrably using MUSCLE algorithm) and find a conserved region and design your primers targeting those conserved regions. Using this approach you might be able to amplify and generate sequence data for R. rita.
Would like to know if works for you,
best wishes,
SD
I agree with Sibnarayan. Should search for related species. You can search in another data base
I´m Agree, you can use sequences from different species, just keep in mind that it could present more more polymorphic sites, and it could affect the specificity of the primers for the spice that you are studying !!!
Another important point is to adjust your PCR parametres, might require several runs to amplify your gene.
I am agreed with Dr. Sibnarayan Datta. In that case, if you can't identify 100% conserved region, then try to make degenerate primers with ambiguous bases.
- Badges
- Science method