NCBI to Retire the UniGene Database

In July 2019, we will retire the UniGene database and take down the web interface.

UniGene was originally implemented as a gene-oriented grouping of transcript sequences in the absence of a reference genome for a broad range of organisms. We added genome-based grouping later.

UniGene has since been used as a source of approximate expression profiles, an index of available cDNA clones, and as a guide to transcript-oriented resource design. However, with the advent of short read sequencing, fewer and fewer ESTs are submitted to NCBI every year, and reference genomes are available for most organisms with a sizable research community. Consequently, the usage of and need for UniGene has dropped significantly.

Although we will retire the web interfaces, we will continue to have the most recent UniGene builds available on NCBI’s FTP site.  Web traffic to UniGene entries will redirect to relevant gene entries when those are available. When that’s not possible, web requests will be routed to either a representative nucleotide sequence entry or a helpful Entrez query against nucleotide records.

Please contact us at with any comments, concerns, or if you need help with the use of UniGene data.