I search ncbi for rora gene of mice and find mrna accesion numer (nm).I can't accesion number nm in rat but 3 xm accesion numbers were found.
Can I designprimers for this gene in rat based on the xm accesion number?
usually,the NCBI results are based on homology and similarity. But primers require specificity in design. so to be sure, if you cannot find the exact sequence you're interested in on NCBI then you will have to isolate and sequence the gene yourself. You may isolate it using RFLP enzyme assay. And to confirm if its the right gene you may include a nucleotide sequence of a known primer as the left and right flanking sequences. then your sequence will be longer than your target gene, but will have the gene in it. so during sequencing you can identify your target gene.Then you will know its exact sequence and can design primers based on the first hand information you have.
or you can just order the primers to be made industrially and sent to you.
i use clc genomics workbench, and the NCBI sequence for designing my primers. You can enter the specification for the primers such as GC%, Tm, etc. I have used NM sequences but also XM sequences, i really don't know the difference between them.
oh i see, well i guess it would depend on how well is predicted. I double checked and my primers are from NM seq only, sorry for the mistake.
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