Sequence differences between Ensembl and Uniprot

Question

[jergosh]

As part of an analysis I'm doing, I mapped 17000 Ensembl IDs to Uniprot and noticed that in over 3'000 cases, the amino acid sequence differs between the two databases. Is this expected behaviour?

Answer 1

[Jean-Karim Heriche]

Yes. Ensembl's proteins correspond to the translation of the underlying transcripts, the sequences of which depend on the particular genome assembly used as reference. Uniprot's sequences come mostly from translations of GenBank coding sequences and from other sources (e.g. PDB).

[Emily]

We (Ensembl) endorse this reply.