I have been searching DNA sequences on NCBI/ MouseBLAST Query/and http://asia.ensembl.org. But I could not find it. I am new in this field.
Can anyone help me?
Many thanks in advance.
Chances are slim that somebody sequenced the genome of this cell line (I didn't check the literature) but you can simply use the mouse genome as a reference for designing primers. Perhaps your gene will have a mutation or two, but usually it doesn't strongly affect primer binding. If want to be 100% sure about the sequence, use a 2nd pair of primers which flanks your 1st pair, sequence the PCR product and design your primers according to the sequence.
@maximilian peters
Thank you so much for your suggestion. By the way, I am planing to design primer for RT-PCR as following genes: GAPDH, myogenin, myoD1 and FAK (focal adhesion kinase). Can you please recommend me a software tool for those specific primers?
Try to find established primers in the literature, I am sure somebody did RT-PCR with those genes before. If not, try designing your own primer pairs. I have no experience with RT-PCR primers, so I can only recommend trying some public server and see if the suggest primers work.
Good luck!
For rapid primer design I frequently use the ncbi qprimer depot http://mouseprimerdepot.nci.nih.gov/
@Kristian Bruun Laursen
Thank you a lot for sharing information. It is very easy, quick and convenient to use.
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