Ensembl 108

Mitochondrion is not visible and not present in dumped files for Sus scrofa Sscrofa11.1

Affects: Live site Expected Versions: Ensembl 107, Ensembl 108
Description: The mitochondrial sequence is absent for the files on the FTP (e.g. genomic FASTA file). The mitchondrion is not displayed on the karyotype view (whole-genome view from the Location tab) on the website. This only affects the Sus scrofa (pig) reference assembly Sscrofa11.1.

Genomic files can be downloaded from the Ensembl 106 archive site, as the assembly has not changed. The mitochondrion can be accessed on the website by either searching for ‘MT’ while restricting to Sus scrofa, or it can be directly accessed from the Location tab, by searching the location ‘MT:1-16613’

Alignment of External Feature – Unable to Retrieve Sequence from Uniprot/SwissProt

Affects: Live site, Mirrors Expected Versions: Ensembl 102, Ensembl 103, Ensembl 104, Ensembl 105, Ensembl 106, Ensembl 107, Ensembl 108
Description: The alignment of the external feature for MYH9-201 (ENST00000216181.11) page is unable to retrieve the sequence from UniProt/SwissProt. See this page.
The display_label field in the xref table contains the UniProt ID including a version (P35579.240) instead of the main UniProt ID only. Furthermore, the dbprimary_acc field in the xref table contains the UniProt entry without the version.
This problem is caused due to an incorrect entry in the display_label field of the xref table. The field is suopposed to contain the UniProt entry (i.e. P35579), but it contains the UniProt entry including its version (i.e. P35579.240) instead.
Workaround: Please remove the offending UniProt version from the original URL. See an example below:

Original URL:
Modified URL (the UniProt ID version has been removed):

No Pairwise Genomic Alignment for Human versus Chicken

Affects: Live site Expected Versions: Ensembl 107, Ensembl 108
Description: With the introduction of new chicken assemblies in Ensembl release 107, the chicken (maternal Broiler) assembly ‘bGalGal1.mat.broiler.GRCg7b’ was included in place of Chicken assembly ‘GRCg6a’ in comparative genomics processing, but a new human-versus-chicken LastZ alignment was not included in release 107 or in release 108.
We are generating a new LastZ alignment between human ‘GRCh38’ and chicken (Maternal Broiler) assembly ‘bGalGal1.mat.broiler.GRCg7b’, which will be available in Ensembl release 109.
Workaround: A pairwise genomic alignment between chicken assembly ‘GRCg6a’ and human can be accessed from the Ensembl 106 archive site.

Gene Synonym Name Issue

Affects: Live site, Mirrors Expected Versions: Ensembl 106, Ensembl 107, Ensembl 108
Description: The human gene AKT2 has the synonym PKBβ. However, it is being displayed as PKBβ on the website and the API.
The problem is caused by the character encoding in the core DB latin1, which cannot recognise greek characters. To fix this, the character encoding (and related collation) in the core DBs needs to be changed. To keep the impact at the minimum, we may consider to apply changes to character encoding/collation to the external_synonym table only. In this case though, character encoding/collation would be inconsistent across the tables in core schema.
Workaround: None.

Missing Mitochondrial sequence_location Attribute

Affects: Live site Expected Versions: Ensembl 105, Ensembl 106, Ensembl 107, Ensembl 108
Description: Mitochondrial DNA sequences from 12 species were mistakenly processed as nuclear DNA sequences. This affected pairwise and multiple genome alignments, and consequently syntenies for vertebrate and metazoan genomes involved. The species affected are:
    Anolis carolinensis (Green anole)
    Anopheles coluzzii (Ngousso)
    Ficedula albicollis (Collared flycatcher)
    Macaca fascicularis (Crab-eating macaque)
    Mastacembelus armatus (Zig-zag eel)
    Meleagris gallopavo
    Nannizzia gypsea CBS 118893
    Papio anubis (Olive baboon)
    Pongo abelii (Sumatran orangutan)
    Rattus norvegicus (Rat)
    Scophthalmus maximus (Turbot)
    Ustilago bromivora str. UB2112
Workaround: None.

Missing APPRIS Annotation for New Chromosomes for Chicken

Affects: Live site Expected Versions: Ensembl 108, Ensembl 109
Description: Some “new” chromosomes (chr34 to ch39) were not annotated during our APRIS annotation load of our data analysis for chicken. Those data will be re-introduced in the next release.
Workaround: None.

Missing Protein Features for Human and Mouse

Affects: Live site, Mirrors Expected Versions: Ensembl 108
Description: There are missing protein features for both human and mouse datasets, which impacts GeneMart where some data is not returned.    
Workaround: Please use one of our archive sites instead.

Mismatching species name in comparative genomics data for Cebus imitator (Panamanian white-faced capuchin)

Affects: Live site Expected Versions: Ensembl 108, Ensembl 109
Description: As its species name was updated from Cebus capucinus to Cebus imitator, the Panamanian white-faced capuchin (or Capuchin) was inadvertently included under its old name in comparative genomics processing for Ensembl 108. As a result, though Ensembl 108 has comparative genomics data for this species, some elements of the data are missing.
  • In the gene-tree view image, Capuchin genes are shown with the correct gene display name, but the species name is shown as “Ancestral sequence”. The menu shows the updated species name “Panamanian white-faced capuchin (C. imitator)”, while files downloaded via the “Export” button refer to it by the old species name (i.e. “cebus_capucinus” or its abbreviated form “Ccap”).
  • The orthologue table view of a Capuchin gene shows its orthologues in other species, and the “Download orthologues” button enables download of alignment files including the Capuchin gene itself. However, for genes of other species, Capuchin orthologues are missing from both the orthologue table view and downloadable orthologue alignment files.
  • In gene gain/loss tree views, gene-tree stats and species tree pages, Capuchin may be omitted or have missing elements (e.g. thumbnail image).
  • Genomic alignments of Capuchin are not available via the Ensembl 108 website. This will be fixed in Ensembl 110 with the inclusion of the Panamanian white-faced capuchin in comparative genomics processing under its updated species name, C. imitator.
Workaround: Genomic alignments involving Capuchin were not updated in the Ensembl 108 website, so it is recommended to access these via the Ensembl 107 archive site. We also recommend to use comparative genomics resources from the Ensembl 107 archive site for use cases that are negatively affected by the missing elements of Capuchin gene tree and homology data.