What is the most common notation for indicating genomic binding sites of primers relative to an ORF?

For instance, if I want to indicate a primer like so:

         [ Primer           ]        [ Hs ACTB coding sequence   ]

Should the location of this primer be indicated as -8 or -28 (from ACTB start codon) or something else?

  • $\begingroup$ Personally, I would say something about the forward primer spanning nucleotides -28 to -8 from the ATG codon, and perhaps give a reference to the nucleotide positions in either the genomic sequence NC_000007.14 (ACTB is on the reverse strand) or the mRNA sequence NM_001101.3. $\endgroup$ – MattDMo Sep 4 '15 at 21:52

There is no such convention. People, mostly name their primers arbitrarily (or just FP and RP) and mention in the text about their binding sites.

In general, in the context of specific genes, the positions are described with respect to the transcription start site (TSS).


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.