| Incomplete vertebrate orthologue sequence download files for Mouse and Pig from 114 live site (RESOLVED) | |
| Affected: Ensembl 114 live site | Fix version: Ensembl 115, 114 archive |
| Orthologue sequence download files may be obtained from an orthologue view by clicking the button to “Download orthologues”. In the 114 live site, such files were incomplete when exported for the Pig and Mouse reference genomes in FASTA or other sequence alignment formats. OrthoXML and PhyloXML downloads were unaffected by this issue. This issue no longer affects either the Mouse or Pig reference genomes on the e114 archive. | |
| Workaround: We recommend users who generated orthologue sequence files for Pig or Mouse reference genomes from the 114 live site to regenerate these using the e114 archive. | |
| Mismatching initial residues in Compara protein member sequences | |
| Affects: Ensembl 114 | Fix Version: Ensembl 115 |
| Following improvements to the behaviour of Transcript::translate in the Ensembl core Perl API taking effect in release 114, an initial CTG codon may be translated under the standard genetic code to methionine (M), where previously it would have been translated to a leucine (L). As a result, some protein member sequences input to comparative analyses before this change in translation behaviour start with a leucine, while the corresponding translation obtained via the Ensembl core API starts with a methionine. The resulting sequence mismatches affect 43,991 proteins in Ensembl Vertebrates, 15,747 in Ensembl Plants, 8,879 in Ensembl Metazoa, and 3,258 in Pan-taxonomic Compara. We will correct 67% (revised on 30-05-2025) of these mismatching sequences in release 115. Following this, correction of mismatching sequences will be applied to comparative datasets as and when they are updated. | |
| Workaround: There is currently no workaround. | |
| Anopheles gambiae transcript de-sync between CoreDB and Variation DB | |
| Affects: Ensembl 114 | Fix version: Ensembl 115 |
| There is a known issue between the core and variation DB of Anopheles gambiae (production_name -> anopheles_gambiae). The Automation team discovered the issue when running the full suite of DCsThis issue is seemingly due to the submitted update to the core itself and handed over as part of Ensembl 114. Whereby community annotation update to the gene set resulted in some genes being dropped\altered. This change in gene set was not reflected in an appropriate update to the variation DB. Intentions will be to rerun the transcript variation pipeline and correct this bug for Ensembl 115. | |
| Workaround: No work around, except using most up to date datasets. | |
| Large number of ancient paralogies for Triticum aestivum Kariega in a Wheat cultivar supertree | |
| Affects: Ensembl 113, Ensembl 114 | Fix versions: Ensembl 115 |
| During preparation of Wheat cultivar protein trees for Ensembl release 113, it became apparent that supertree PTHR11439_SF127 has approximately 40,000 genes in Triticum aestivum cultivar Kariega. Generation of the 261 million ancient paralogies between these genes took two weeks, and it would not have been possible to include them in Ensembl Plants 113 without delaying the release. | |
| Workaround: A cross-section of the relevant ancient paralogies was loaded during production, involving genes with stable IDs TraesKAR6A01G0279700, TraesKAR7B01G0056390, TraesKAR7B01G0463280 and TraesKAR1D01G0304830. Due to the large number of paralogies involved, these may fail to load correctly on the Ensembl Plants website, though it should be possible to access them via the Ensembl REST API and Compara Perl API.A file containing data on these 40,000 genes is available for download at the following location on the Ensembl Genomes FTP site:http://ftp.ensemblgenomes.org/pub/release-60/plants/emf/ensembl-compara/homologies/Compara.113.protein_wheat_cultivars.other_paralogies.cds.fasta.gz | |
| Drop in Cebus imitator ncRNA paralogs from 110 to 111 | |
| Affects: Ensembl 111, Ensembl 112, Ensembl 113, Ensembl 114 | Fix version: Ensembl 115 |
| In Ensembl 111, there was a significant drop (relative to release 110) in the number of ncRNA paralogues for Cebus imitator.This was due to the application in this species of a paralogue filter that was intended for use with low-coverage 2X genomes. | |
| Workaround: Both species are in 110. We recommend that the users interested in ncRNA paralogues for this species to check out the 110 archive. | |
| Avena sativa cv. Sang homoeologues misclassified as paralogues | |
| Affects: Ensembl 109, Ensembl 110, Ensembl 111, Ensembl 112, Ensembl 113, Ensembl 114 | Fix version: Ensembl 115 |
| Due to a data synchronisation issue, Avena sativa cultivar Sang was loaded into Plants Compara databases without subgenome component information.As a result, homologues that would otherwise be classified as homoeologues will have been annotated as paralogues. | |
| Workaround: There is currently no workaround. | |
| Funcgen database is missing for Medicago truncatula, Oryza sativa and Vitis vinifera | |
| Affects: Ensembl 114 | Fix version: None |
| Due to change in the assemblies for Medicago truncatula and Vitis vinifera as well as the upgrade in the Oryza sativa annotation, their funcgen databases have been dropped. | |
| Workaround: This database can be accessed from the latest archive. | |
| Barke is missing from cultivar list of Barley Pangenome | |
| Affects: Ensembl 114 | Fix version: Ensembl 115 |
| Due to a missing meta key in the database, the cultivar Barke is missing from the cultivar list of the barley pangenome. | |
| Workaround: This data can still be accessed through the species list. | |
| Variation database is missing for Vitis vinifera | |
| Affects: Ensembl 114 | Fix version: TBC |
| A new assembly is available for Vitis vinifera (GCA_030704535.1); however, its variation db has not been updated. Due to this, this variation db has been removed for this release. | |
| Workaround: This database can be accessed from the latest archive. | |
| Otherfeatures database is missing for Medicago truncatula | |
| Affects: Ensembl 113, Ensembl 114 | Fix version: TBC |
| The new assembly is available for Medicago truncatula (GCA_003473485.2) however the otherfeatures database has not been updated. Due to this, its otherfeatures database has been removed. | |
| Workaround: This database can be accessed from the latest archive. | |
| Trypanosoma brucei GCA_003072535.3 displays the wrong GCA accession in its URL | |
| Affects: Ensembl 114 | Fix version: Ensembl 115 |
| The URL for Trypanosoma brucei displays the wrong GCA accession. The correct GCA accession is: GCA000002445.1. This doesn’t affect any other data shown in the browser page of this genome. | |
| Workaround: There is currently no workaround. | |
| Missing Gene Ontology pages on Gene-based displays | |
| Affects: Ensembl 114, Ensembl Genomes, BioMart | Fix version: Ensembl 115 |
| Gene Ontology (GO) related pages on the Gene-based display tabs are unavailable. The following pages are unavailable on the live site: GO: Cellular component GO: Biological Process GO: Molecular function Please make use of the Ensembl archive sites to access these gene-based display pages. This also affects Ensembl Genome sites and Biomart, please use the latest archive where possible | |
| Workaround: Please use the latest Ensembl archive site to access these pages. | |
| Amino-acid substitution model used with cDNA alignment in 59 Rice cultivar gene trees | |
| Affects: Ensembl 112, Ensembl 113, Ensembl 114, Ensembl 115, Ensembl Genomes | Fix version: Ensembl 116 |
| Due to a software bug, the WAG amino-acid substitution model was used with a cDNA alignment to infer 59 Rice cultivar gene trees in Ensembl Plants release 112. The 59 affected gene trees are listed below. We urge users to exercise caution when interpreting these gene trees or their associated homologies. | |
| Workaround: There is currently no workaround. | |