| Species | Release | Last updated |
| Anopheles gambiae | AgamP3 | 11-03-2006 |
| Apis mellifera | Amel v4.0 | 08-09-2006 |
| Arabidopsis thaliana | NCBI Build TAIR7.0 | 18-07-2007 |
| Aspergillus fumigatus | NCBI Build 1.1 | 15-09-2005 |
| Bos taurus | NCBI Build 3.1, Btau_3.1 | 26-01-2007 |
| Caenorhabditis elegans | NCBI Build WS170 | 27-04-2007 |
| Candida glabrata | NCBI Build 1.1 | 12-07-2006 |
| Canis familiaris | NCBI Build 2.1, CanFam2.0 | 12-07-2006 |
| Cryptococcus neoformans B-3501A | | 31-05-2005 |
| Cryptococcus neoformans JEC21 | NCBI Build 1.1 | 12-08-2005 |
| Debaryomyces hansenii | NCBI Build 1.1 | 12-08-2005 |
| Danio rerio | NCBI Build Zv6 | 12-07-2006 |
| Drosophila melanogaster | NCBI Build 5.1 (euchromatin v5.1, heterochromatin v3.2) | 06-12-2006 |
| Encephalitozoon cuniculi | NCBI Build 1.1 | 12-08-2005 |
| Equus caballus | NCBI Build 1.1, EquCab1 | 18-07-2007 |
| Eremothecium gossypii (Ashbya gossypii) | NCBI Build 1.1 | 12-08-2005 |
| Gallus gallus | NCBI Build 2.1, WASHUC2 | 05-12-2006 |
| Homo sapiens | NCBI Build 36.2 | 26-10-2006 |
| Kluyveromyces lactis | NCBI Build 1.1 | 12-08-2005 |
| Macaca mulatta | NCBI Build 1.1 | 12-07-2006 |
| Monodelphis domestica | NCBI Build MonDom5 | 28-03-2007 |
| Mus musculus | NCBI Build 37.1 | 18-07-2007 |
| Oryza sativa ssp japonica | Genome assembly v5 | 27-04-2007 |
| Ostreococcus lucimarinus | NCBI Build 1 | 09-05-2007 |
| Pan troglodytes | NCBI Build 2.1, PanTro2.1 | 26-10-2006 |
| Plasmodium falciparum | NCBI Build 1.1 | 13-05-2004 |
| Rattus norvegicus | NCBI Build 3.1, RGSC v3.4 | 12-07-2006 |
| Saccharomyces cerevisiae | NCBI Build 2.1 | 12-07-2006 |
| Schizosaccharomyces pombe | NCBI Build 1.1 | 12-08-2005 |
| Tetraodon nigroviridis | Tetraodon 7 | 16-06-2005 |
| Tribolium_castaneum | NCBI Build 1.1, Tcas_2.0 | 12-07-2006 |
| Yarrowia lipolytica | NCBI Build 1.1 | 12-07-2006 |
| Species | Release | Last updated |
| Aedes aegypti | AaegL1 (Oct 2005), Ensembl release 49.1b | 04-28-2008 |
| Aspergillus nidulans | release 4 | 31-05-2005 |
| Aspergillus terreus | release 1 | 12-07-2006 |
| Botrytis cinerea | release 1 | 12-07-2006 |
| Caenorhabditis briggsae | cb25.agp8 | 29-06-2005 |
| Candida albicans | release 1 | 12-07-2006 |
| Candida guilliermondii | v1.0 | 31-05-2005 |
| Candida lusitaniae | v1.0 | 31-05-2005 |
| Candida tropicalis | release 3 | 12-07-2006 |
| Canis familiaris | canFam1 | 21-10-2004 |
| Cavia porcellus | cavPor2 (Jun 2006), Ensembl release 49.1c | 04-28-2008 |
| Chaetomium globosum | release 1 | 12-07-2006 |
| Chlamydomonas reinhardtii | v3.1 | weekly |
| Ciona intestinalis | JGI2 (Mar 2005), Ensembl release 49.2i | 04-28-2008 |
| Ciona savignyi | CSAV 2.0 (Oct 2005), Ensembl release 49.2f | 04-28-2008 |
| Coccidioides immitis | release 2 | 12-07-2006 |
| Coprinus cinereus | v1.0 | 31-05-2005 |
| Cryptococcus neoformans H99 | release 1 | 12-07-2006 |
| Cryptococcus neoformans R265 | release 1 | 12-07-2006 |
| Dasypus novemcinctus | ARMA (May 2005), Ensembl release 49.1f | 04-28-2008 |
| Drosophila ananassae | August 1 2002 draft genome assembly | 12-07-2006 |
| Drosophila erecta | August 1 2002 draft genome assembly | 12-07-2006 |
| Drosophila grimshawi | August 1 2002 draft genome assembly | 12-07-2006 |
| Drosophila mojavensis | August 1 2005 draft genome assembly | 12-07-2006 |
| Drosophila persimilis | October 28 2005 draft genome assembly | 12-07-2006 |
| Drosophila pseudoobscura | release 1 | 31-05-2005 |
| Drosophila sechellia | August 1 2005 draft genome assembly | 12-07-2006 |
| Drosophila simulans | Aug 2005 draft genome assembly | 12-08-2005 |
| Drosophila virilis | August 1 2005 draft genome assembly | 12-07-2006 |
| Drosophila yakuba | November 2005 draft genome assembly | 12-07-2006 |
| Echinops telfairi | TENREC (July 2005), Ensembl release 49.1e | 04-28-2008 |
| Entamoeba histolytica | | 24-05-2007 |
| Erinaceus europaeus | eriEur1 (Jun 2006), Ensembl release 49.1c | 04-28-2008 |
| Felis catus | CAT (Mar 2006), Ensembl release 49.1c | 04-28-2008 |
| Fusarium graminearum | release 2 | 12-07-2006 |
| Gasterosteus aculeatus | BROAD S1 (Feb 2006), Ensembl release 49.1f | 04-28-2008 |
| Gibberella moniliformis | assembly 2 | 12-07-2006 |
| Histoplasma capsulatum | assembly 1 | 12-07-2006 |
| Leishmania major | v5.0 | 15-09-2005 |
| Lodderomyces elongisporus | assembly 1 | 12-07-2006 |
| Loxodonta africana | BROAD E1 (May 2005), Ensembl release 49.1d | 04-28-2008 |
| Magnaporthe grisea | release 5.0 | 12-07-2006 |
| Microcebus murinus | micMur1 (Jun 2007), Ensembl release 49.1 | 04-28-2008 |
| Myotis lucifugus | myoLuc1 (mar 2006), Ensembl release 49.1e | 04-28-2008 |
| Neurospora crassa | release 7 | 12-07-2006 |
| Ochotona princeps | OchPri2.0 (Jun 2007), Ensembl release 49.1 | 04-28-2008 |
| Ornithorhynchus anatinus | Oana-5.0 (Dec 2005), Ensembl release 49.1f | 04-28-2008 |
| Oryctolagus cuniculus | RABBIT (May 2005), Ensembl release 49.1f | 04-28-2008 |
| Oryza sativa ssp indica | | 31-05-2005 |
| Oryzias latipes | HdrR (Oct 2005), Ensembl release 49.1e | 04-28-2008 |
| Otolemur garnettii | otoGar1 (May 2006), Ensembl release 49.1c | 04-28-2008 |
| Phaeosphaeria nodorum | assembly 1 | 12-07-2006 |
| Populus trichocarpa | v1.0 | 23-09-2004 |
| Pongo pygmaeus | PPYG2 (Sep 2007), Ensembl release 49.1 | 04-28-2008 |
| Rhizopus oryzae | release 3 | 12-07-2006 |
| Sclerotina sclerotiorum | release 1 | 12-07-2006 |
| Sorex araneus | sorAra1 (Oct 2005), Ensembl release 49.1c | 04-28-2008 |
| Spermophilus tridecemlineatus | speTri1 (Jun 2006), Ensembl release 49.1e | 04-28-2008 |
| Takifugu rubripes | FUGU 4.0 (Jun 2005), Ensembl release 49.4i | 04-28-2008 |
| Thalassiosira pseudonana | v1.0 | 01-10-2004 |
| Tupaia belangeri | tupBel1 (Jun 2006), Ensembl release 49.1d | 04-28-2008 |
| Uncinocarpus reesii | release 2 | 12-07-2006 |
| Ustilago maydis | v1.0 | 31-05-2005 |
| Xenopus tropicalis | JGI 4.1 (Aug 2005), Ensembl release 49.41i | 04-28-2008 |
