Database cross-references

ENA provides cross-references to external data resources deemed to be important to the user. External resources include services operated by colleagues at the EBI (such as UniProt and Ensembl) and those operated outside the EBI (including SILVA and RFAM). In most cases, we operate a close collaboration with the resources to which we cross-refer, in order to maximise the quality and appropriateness of the cross-references. Typically, reciprocal cross-references are shown in the external resources and we are able to provide support to developers at external resources to take advantage of the most appropriate mechanisms for cross-referencing.

We welcome those responsible for external resources to contact us to express interest in developing cross-referencing collaborations.

ENA currently shows cross-references to the external resources listed below. A list of url addresses to identifiers issued by these external data resources can be found here.

Cross-references are available from the individual records within the ENA browser, and can also be accessed directly via our REST service.


GOA (Gene Ontology Annotation Database)

HGNC (Human Gene Nomenclature Database)

IMGT/HLA (Immunogenetics/Human Leucocyte Antigens)

IMGT/LIGM (Immunogenetics/Immunoglobulins and T-cell Receptors)

IPD/KIR (IPD-Killer-cell Immunoglobulin-like Receptor Database)

IPD/MHC (IPD-Non-Human Major Histocompatibility Complex Database)

EPD (Eukaryotic Promoter Database)

InterPro (Database of Protein families, domains and functional sites)

PDB (Protein Data Bank)

UniProtKB/Swiss-Prot (manually annotated Protein Knowledgebase)

UniProtKB/TrEMBL (automatically annotated Protein Knowledgebase)

VBASE2 (Integrative Database of germ-line Variable genes)


ArrayExpress (Database of functional genomics experiments)

GtRNAdb (Genomic tRNA Database)

lncRNAdb (Long Non-Coding RNA Database)

miRBase (Database of published miRNA sequences and annotation)

PR2 (Protist Ribosomal Reference Database)

Silva-LSU (Database of large subunit (23S/28S) ribosomal RNA)

Silva-SSU (Database of small subunit (16S/18S) ribosomal RNA)

SRPDB (Signal Recognition Particle Database)

RFAM (Database of RNA Families)

tmRNA-Website (The tmRNA Website)

PLncDB (Plant Long noncoding RNA Database)

snOPY (snoRNA Orthological Gene Database)

Sample origin-related

CABRI (Common Access to Biological Resources and Information)

CCAP (Culture Collection of Algae and Protozoa)

BCCM/LMBP (BCCM/LMBP Plasmid Collection)

NCBI-Taxonomy (Taxonomic information of all organisms represented in the genetic databases with at least one nucleotide or protein sequence)

StrainInfo (Microbial Strain Information Source)

WoRMS (World Register of Marine Species)

Genome browsers

Ensembl (Genome Database of eukaryotic species)

Ensembl Genomes (Genome Database of bacteria, protists, fungi, plants and invertebrate metazoa)



H-InvDB (Integrated Database of Human genes and transcripts)

MGI (Mouse Genome Informatics Database)

VEGA (The Vertebrate Genome Annotation Database)

ZFIN (Zebrafish model organism Database)


FlyBase (Database of Drosophila sp. genes and genomes)

VectorBase (Genome Database of invertebrate Vectors of human pathogens)

WormBase (Database on genetics of C. elegans and related nematodes)

DictyBase (Central resource for Dictyostelid genomics)


GeneDB (Genome Database of Pathogens)

SubtiList (Genome Database of Bacillus subtilis 168)


GrainGenes (Database for Triticeae and Avena)

SGD (Saccharomyces Genome Database)

PomBase (A comprehensive database for the fission yeast Schizosaccharomyces pombe)

Unite (Fungal rDNA ITS sequence Database)

TAIR (The Arabidopsis Information Resource)


AGRICOLA (National Agricultural Library)

DOI (Resolver of Digital Object Identifiers)

Europe PMC (Europe PubMed Central)

PubMed (Biomedical Library)