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Orthologues View

Example page

Orthologues inferred from gene trees are determined using all species in that particular database, i.e. all the (mostly) chordates in Ensembl, all the fungi in Ensembl Fungi, all the plants in Ensembl plants, all the metazoa in Ensembl Metazoa, all the protists in Ensembl Protists, or all the species in the Pan-Compara set for Pan-Compara orthologues in Ensembl Genomes. A detailed description of the method is provided here.

Unaligned sequences (nucleotide and/or amino acids) of orthologous genes can be exported in FASTA format by clicking on Sequence export. The Compara API and BioMart can also be used to export orthologues.

List of selected orthologues

The list of orthologues underneath the top table shows the species, the orthologue type, the dN/dS value (if calculated), the Ensembl gene ID and name, links to other views, the Target %ID and the Query %ID, the Gene Order Conservation (GOC) score, the Whole Genome Alignment (WGA) coverage, and an indication of confidence of orthology.

The Query %ID refers to the percentage of the query sequence (human) that matches to the homologue (the mouse protein). Target %ID refers to the percentage of the target sequence (mouse) that matches to the query sequence (human).

Protein and cDNA alignments can be found using links in the Orthologue column. Links are also provided to a graphical display of the alignment (Region Comparison view), and the gene tree.

IDs, orthology types, and dn/ds values can also be obtained using the compara API or with BioMart.