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PCR primers


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#1 ninez

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Posted 08 May 2004 - 02:22 AM

I'd just like to know if PCR primers originally meant for RT-PCR of
cDNA of TRBV2 can be used for the genomic sequence. I ran our
forward primer (the one that's supposed to anneal to the variable
region) on BLAST and it matched with a sequence in the middle of the
TRBV20-1 sequence. The primer, however, also matched with cDNA
sequences of TRBV2. Why do the sequences differ so much? Does
anyone know of recent papers which have the rearranged sequences for
the TRB locus?
Thanks for any help...

#2 sage

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Posted 11 May 2004 - 07:35 AM

It depends.

If RT-PCR primers span introns, and used for genomic DNA, the difference is only the size of the product. If the RT-PCR primers were designed to bridge exon-exon boundary, it may not work for genomic DNA.

Regarding your 2nd question, check NCBI latest genome assembly.




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