Ensembl Genome Database

Overview

Ensembl is a comprehensive genome annotation database covering 300+ vertebrate and non-vertebrate species. The Ensembl REST API provides programmatic access to gene models, transcript/protein sequences, variant annotations, cross-references, regulatory features, and comparative genomics without requiring any login or API key.

When to Use

• Retrieving official gene and transcript annotations (stable IDs, biotype, genomic coordinates) for human or model organism genes
• Converting between gene identifier namespaces (HGNC symbol ↔ Ensembl ID ↔ RefSeq ↔ UniProt)
• Fetching genomic or cDNA/CDS/protein sequences for a gene or transcript
• Looking up variant consequences and functional impact (VEP) for a list of SNPs
• Querying regulatory features (promoters, enhancers, CTCF sites) in a genomic region
• Performing comparative genomics queries (orthologs, paralogs, gene trees) across species
• For local offline access to large genomic annotations, use pyensembl instead
• For pathway and metabolic annotations, use kegg-database or reactome-database instead

Prerequisites