Both sequences are different versions of the same myc-tag containing plasmid. Usually, a linker sequence contains an endopeptidase tag for the removal of the particular affinity tag from the fusion protein. However, in this case, the linker sequence is actually a spacer sequence that segregates the myc and flag tags. Nevertheless, the DNA sequence of the linker/spacer sequence (AANDIL) contains a cleavage site for the restriction enzyme EcoRV, which may be beneficial for cloning. However, it is also speculated that such spacer sequences play role in governing protein solubility and folding.

Hi Francesca Pontanari

As Jatin said, both sequences are aimed for the same tag. If you check Origene site, you will see that the expression plasmid contains only EQKLISEEDLDYKDDDDK.

https://www.origene.com/catalog/vectors/mammalian-expression-vectors/ps100016/pcmv6-an-myc-ddk-mammalian-expression-vector

My guess is that the AANDIL linker was introduced during the cloning procedure. If I have a choice, I would not go with this linker. I do not want to have a higher proportion of hydrophobic amino acids in my linker/epitope.

The following review article might give you some insights.

https://pubmed.ncbi.nlm.nih.gov/23026637/

Cheers,

Chamara