I have a list of UniProt codes and I am trying to fetch the genomic coordinates through the API from programmatic access to UniProtKB (https://www.ebi.ac.uk/proteins/api/doc/).

Moreover, I read that UniProt in collaboration with Ensembl have mapped the protein sequences on the GRCh38 genome (doi: 10.1093/nar/gkw1099)

However, it is true that the number of protein codes in UniProt is updated more frequently than the GRCh38 assembly.

Considering only the protein genomic coordinates data: It is possible that a new submission in UniProt (in TrEMBL for instance) does not have any correspondence with Ensembl, due to the possibility that the genomic coordinates of a new protein do not match any gene model stored in GRCh38?

If not: It is possible to say that all the protein genomic coordinates in UniProt have been mapped on the GRCh38 (in connection with Ensembl) and it is impossible that a new submission in UniProt lacks of this data?



1 Answer 1


If you look at this query https://www.uniprot.org/uniprot/?query=NOT%20database:(type:ensembl)&fil=organism:%22Homo%20sapiens%20(Human)%20[9606]%22&sort=score

and restrict it to the reference proteome (by using the link on the left hand side): https://www.uniprot.org/uniprot/?query=NOT%20database:(type:ensembl)&fil=proteome%3AUP000005640+AND+organism%3A%22Homo+sapiens+%28Human%29+%5B9606%5D%22&sort=score

you will see that there are "only" 1100 entries, and that they are all in UniProtKB/Swiss-Prot, but none in UniProtKB/TrEMBL, the unreviewed section.

The manual review of sequences for human and other proteomes is one of our most important and crucial tasks but as you can imagine this is an ongoing process. First because it represents an immense work, second because knowledge is still evolving, the human reference genome being for instance constantly improved by the Genome Reference Consortium. For the human proteome, there are still a small but non negligible number of UniProtKB/Swiss-Prot entries for which the sequence is not identical or is not represented at all by Ensembl sequences. We are constantly collaborating with Ensembl and other genome annotation resources trying to agree on identical sequences to fill the gaps. UniProtKB human entries are automatically mapped to the latest Ensembl release but you have to take into account that UniProtKB and Ensembl releases are not synchronized.

Starting with release 2022_01, we will have cross-references from relevant UniProtKB/Swiss-Prot entries to MANE-Select (Matched Annotation from NCBI and EMBL-EBI, see https://www.ensembl.org/info/genome/genebuild/mane.html and https://www.ncbi.nlm.nih.gov/refseq/MANE/)


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