Ensembl

Identifier

ensembl

License

No restrictions on use

Citation

Harrison, P.W., Amode, M.R., Austine-Orimoloye, O. et al. Ensembl 2024. Nucleic Acids Research 2024;52:D891-D899. doi:10.1093/nar/gkad1049

Overview

Ensembl provides reference genome annotation across many species.

This namespace contains selected Ensembl and Ensembl Genomes species and assemblies, plus regions, genes, transcripts, exons, coding features, and cross-references.

species identifies the assembly and taxon for Ensembl annotations. genes resolves gene symbols; gene_id links genes to transcripts, and transcript_id links transcripts to exons, coding sequences, and untranslated regions.

Sequence tables are queried by identifier and interval. xrefs connects Ensembl identifiers to resources such as UniProt, RefSeq, Entrez, and ENA.

Coordinates are 1-based; is_ensembl_canonical or, for human transcripts, is_mane_select identifies a representative transcript.

Tables

• ensembl.cdna_sequences — Individual nucleotide positions in Ensembl cDNA transcript sequences.
• ensembl.cds — Coding sequence (CDS) annotation — translated exon segments and their Ensembl protein IDs.
• ensembl.cds_sequences — Individual nucleotide positions in Ensembl coding sequences.
• ensembl.chromosomes — Reference chromosome intervals and their Ensembl GFF3 aliases.
• ensembl.dna_sequences — Individual nucleotide positions in Ensembl’s soft-masked top-level genomic DNA FASTA.
• ensembl.exons — Exon annotation (one row per exon within a transcript).
• ensembl.gene_segments — Immunoglobulin and T-cell receptor gene-segment annotation.
• ensembl.genes — Gene-level annotation (one row per Ensembl gene).
• ensembl.ncrna_sequences — Individual nucleotide positions in Ensembl non-coding RNA transcript sequences.
• ensembl.protein_sequences — Individual amino-acid positions in Ensembl protein translations.
• ensembl.regions — Assembly and biologically annotated regions from Ensembl GFF3.
• ensembl.species — Selected Ensembl and Ensembl Genomes species and genome assemblies.
• ensembl.transcripts — Transcript-level annotation (one row per Ensembl transcript).
• ensembl.transposable_elements — Annotated transposable-element loci.
• ensembl.utrs — Untranslated region (UTR) annotation — 5’ and 3’ UTR segments of coding transcripts.
• ensembl.xrefs — Cross-references from Ensembl gene/transcript/protein IDs to external databases (UniProt, RefSeq, Entrez, ENA).