how to design the primer from only the CDS sequence as i want to clone my gene into the expression vector?
There are some software for designing primers. For example: vector nti,primer premier, becoan designer and so on.for earning the cds of the gene you can retranslate the protein coded by gene or use the mrna sequence of the gene exit in ncbi cite. On the ncbi site, there is the cds of genes in genebank format.
Dear, you can design CDS sequence Primer using primer premier, Primer-BLAST or Primer3 online.
Dear Fahim
find attached an SOP I made for instruction purposes describing how to design primers using primer BLAST
In essence navigate to detailed transcript structures as followed (and as detailed in SOP):
Identifying NCBI transcript & associated primers
Go to the Entrez gene (‘Gene’) database (formerly ‘Locus Link’):
http://www.ncbi.nlm.nih.gov/gene
Click on the ‘RefSeqGene link’: ‘Resources_DNA & RNA_RefSeqGene’
This will take you to the portal for NCBI Reference sequences
Type the generic name of your gene into the search box_Search
Now select the link to your gene
This should provide a summary page of your gene:
On the right hand side you should see ‘NCBI Reference sequences’
Click on this and you will come to a page giving details of transcripts
Select the FASTA file for your transcript of interest and to the right you will see 2 headings, namely 'pick primers' and 'find in this sequence'
The former is primer BLAST and wil design primers based on the FASTA sequence provided. The latter allows you to narrow down the sequence against which you design primers against, e.g. your desired CDS
Select the CDS using 'find in this sequence' and then use 'pick primers'
For exact details see protocol attached
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