Comparison of the current RefSeq, Ensembl and EST databases for counting genes and gene discovery

FEBS Lett. 2005 Jan 31;579(3):690-8. doi: 10.1016/j.febslet.2004.12.046.


Large amounts of refined sequence material in the form of predicted, curated and annotated genes and expressed sequences tags (ESTs) have recently been added to the NCBI databases. We matched the transcript-sequences of RefSeq, Ensembl and dbEST in an attempt to provide an updated overview of how many unique human genes can be found. The results indicate that there are about 25000 unique genes in the union of RefSeq and Ensembl with 12-18% and 8-13% of the genes in each set unique to the other set, respectively. About 20% of all genes had splice variants. There are a considerable number of ESTs (2200000) that do not match the identified genes and we used an in-house pipeline to identify 22 novel genes from Genscan predictions that have considerable EST coverage. The study provides an insight into the current status of human gene catalogues and shows that considerable refinement of methods and datasets is needed to come to a conclusive gene count.

Publication types

  • Comparative Study

MeSH terms

  • Alternative Splicing
  • Expressed Sequence Tags*
  • Genome, Human
  • Humans
  • RNA, Messenger / genetics


  • RNA, Messenger