I have a gene which is having 10 transcript variants. However, only 4 transcripts are protein coding ORFs. I need to find out the level of expression of only one transcript out of 4 protein coding transcripts. I used NCBI Primer blast tool to design qPCR primers. however, designed primers not only detect expected transcript but also detect other transcripts variants. during primer designing with Primer BLAST i used these parameters. expected product length 70-200bp, from the Exon/intron selection I selected exon -exon junction.all the other parameters set as default.
I am happy if someone can help me to find out ONLY one transcript variant-specific primer for qPCR out of several other transcripts from the same gene.
0 answers
No answers yet.
Log in to answer this question.
-
Multiplex Primer Design to Distinguish 7 Bacterial Genomes
written by dirtees •
-
18S gene not present in genome assembly?
written by milesdavis •
-
qPCR primer design for multiple transcript variants
written by Jordan •
-
mRNA-based tissue typing: Which transcripts to choose for primer engineering?
written by milesdavis •
-
Tool to design Q-PCR primers with exon skipping?
written by gabriel.monteiro233 •
-
concat fasta sequences based on some common header string
written by mforthman •
-
How to design qPCR primers to validate RNA-seq experiment?
written by brett.vanderwerff •
-
ExAC ABO data
written by daehyuni1118 •
-
Is there a good site or software to see if a primer pair spans an exon junction?
written by gaelgarcia
-
Posting form data to NCBI Primer-BLAST
written by Tom Harrop
The target has no unique sequence that can distinguish it from the other transcripts? Take a look at my SOP for designing primers, written a number of years ago, if you need help: Designing a single set of primers and probe for a genomic region of interest.
In essence Primer3 is a good tool: http://primer3.ut.ee/