Ensembl
Identifier
Section titled “Identifier”License
Section titled “License”Open — no restrictions on use (Ensembl / EMBL-EBI terms of use).
Citation
Section titled “Citation”Overview
Section titled “Overview”Reference gene, transcript, exon, and protein-coding annotation from the Ensembl genome annotation project, harmonised across species and keyed by NCBI taxonomy ID.
Domain: genomics.
Source: https://www.ensembl.org.
Reference genome annotation.
Every table except taxonomies is partitioned by taxonomy_id (NCBI taxonomy ID; 9606 = human) — always filter on it. taxonomies is a small unpartitioned lookup of the species and assemblies covered.
Genes, transcripts, exons, cds, utrs, codons, and selenocysteines form a hierarchy joined by gene_id → transcript_id; mappings provides cross-references from Ensembl IDs to external databases (UniProt, RefSeq, Entrez, ENA).
Positions are 1-based and strand is forward/reverse.
To translate a gene symbol to an Ensembl gene ID, look it up in genes by symbol; for the single representative transcript per gene, filter transcripts to is_ensembl_canonical = True (or in_mane_select = True for human).
Tables
Section titled “Tables”ensembl.cds— Coding sequence (CDS) annotation — translated exon segments and their Ensembl protein IDs.ensembl.codons— Start and stop codon annotation for coding transcripts.ensembl.exons— Exon annotation (one row per exon within a transcript).ensembl.genes— Gene-level annotation (one row per Ensembl gene).ensembl.mappings— Cross-references from Ensembl gene/transcript/protein IDs to external databases (UniProt, RefSeq, Entrez, ENA).ensembl.selenocysteines— Selenocysteine (U) residue annotation for transcripts that recode a UGA stop codon as selenocysteine.ensembl.taxonomies— Species and genome assemblies covered by the Ensembl annotation in this catalogue.ensembl.transcripts— Transcript-level annotation (one row per Ensembl transcript).ensembl.utrs— Untranslated region (UTR) annotation — 5’ and 3’ UTR segments of coding transcripts.