General references and annotations

Arabidopsis thaliana (TAIR10.52)

Common name Thale cress
Assembly TAIR10
Ensembl release 52
Reference sequence http://ftp.ensemblgenomes.org/pub/plants/release-52/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
Ensembl annotations http://ftp.ensemblgenomes.org/pub/plants/release-52/gff3/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.52.gff3.gz

Bos taurus (ARS-UCD1.2.105)

Common name Cow
Assembly ARS-UCD1.2
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/bos_taurus/dna/Bos_taurus.ARS-UCD1.2.dna.primary_assembly.*.fa.gz (*: 1-29, X, MT)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/bos_taurus/Bos_taurus.ARS-UCD1.2.105.chr.gff3.gz

Caenorhabditis elegans (WBcel235.105)

Common name Roundworm
Assembly WBcel235
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa.gz
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.105.gff3.gz

Canis lupus familiaris (ROS_Cfam_1.0.105)

Common name Dog (labrador retriever breed)
Assembly ROS_Cfam_1.0
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/canis_lupus_familiaris/dna/Canis_lupus_familiaris.ROS_Cfam_1.0.dna.primary_assembly.*.fa.gz (*: 1-38, X, Y)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/canis_lupus_familiaris/Canis_lupus_familiaris.ROS_Cfam_1.0.105.chr.gff3.gz

Danio rerio (GRCz11.10.105)

Common name Zebra fish
Assembly GRCz11.10
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.chromosome.*.fa.gz (*: 1-25, MT)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/danio_rerio/Danio_rerio.GRCz11.105.chr.gff3.gz

Drosophila melanogaster (BDGP6.32.105)

Common name Fruit fly
Assembly BDGP6.32
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.32.dna.primary_assembly.*.fa.gz (*: 2L, 2R, 3L, 3R, 4, X, Y, mitochondrion_genome)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.32.105.chr.gff3.gz

Equus caballus (EquCab3.0.105)

Common name Horse
Assembly EquCab3.0
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/equus_caballus/dna/Equus_caballus.EquCab3.0.dna.primary_assembly.*.fa.gz (*: 1-31, X)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/equus_caballus/Equus_caballus.EquCab3.0.105.chr.gff3.gz

Gallus gallus (GRCg6a.105) (legacy)

Common name Chicken
Assembly GRCg6a
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/gallus_gallus/dna/Gallus_gallus.GRCg6a.dna.chromosome.*.fa.gz (*: 1-33, W, Z, MT)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/gallus_gallus/Gallus_gallus.GRCg6a.105.chr.gff3.gz

Gallus gallus (GRCg7b.110)

Common name Chicken
Assembly GRCg7b
Ensembl release 110
Reference sequence http://ftp.ensembl.org/pub/release-110/fasta/gallus_gallus/dna/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna.primary_assembly.*.fa.gz (*: 1-33, W, Z, MT)
Ensembl annotations http://ftp.ensembl.org/pub/release-110/gff3/gallus_gallus/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.110.gff3.gz

Gasterosteus aculeatus (GAculeatus_UGA_version5.112)

Common name Three-spined stickleback
Assembly GAculeatus_UGA_version5
Ensembl release 112
Reference sequence https://ftp.ensembl.org/pub/release-112/fasta/gasterosteus_aculeatus/dna/Gasterosteus_aculeatus.GAculeatus_UGA_version5.dna.primary_assembly.*.fa.gz (*: I, II, III, IV, IX, V, VI, VII, VIII, X, XI, XII, XIII, XIV, XIX, XV, XVI, XVII, XVIII, XX, XXI, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-112/gff3/gasterosteus_aculeatus/Gasterosteus_aculeatus.GAculeatus_UGA_version5.112.gff3.gz

Gasterosteus aculeatus (GAculeatus_UGA_version5.112)

Homo sapiens (GRCh38.103)

Common name Human
Assembly GRCh38.p13
Ensembl release 103
Reference sequence http://ftp.ensembl.org/pub/release-103/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.*.fa.gz (*: 1-22, MT, X, Y)
Ensembl annotations http://ftp.ensembl.org/pub/release-103/gff3/homo_sapiens/Homo_sapiens.GRCh38.103.chr.gff3.gz

Homo sapiens (GRCh38.noalt.106)

Reference sequence includes unlocalized scaffolds and unplaced scaffolds.

Common name Human
Assembly GRCh38
Ensembl release 106
Reference sequence https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
Ensembl annotations http://ftp.ensembl.org/pub/release-106/gff3/homo_sapiens/Homo_sapiens.GRCh38.106.chr.gff3.gz

Macaca fascicularis (Macaca_fascicularis_6.0.105)

Common name Crab-eating macaque
Assembly Macaca_fascicularis_6.0
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/macaca_fascicularis/dna/Macaca_fascicularis.Macaca_fascicularis_6.0.dna.primary_assembly.*.fa.gz (*: 1-20, X)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/macaca_fascicularis/Macaca_fascicularis.Macaca_fascicularis_6.0.105.chr.gff3.gz

Macaca mulatta (Mmul_10.105)

Common name Rhesus macaque
Assembly Macaca_mulatta.Mmul_10
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/macaca_mulatta/dna/Macaca_mulatta.Mmul_10.dna.primary_assembly.*.fa.gz (*: 1-20, X, Y, MT)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/macaca_mulatta/Macaca_mulatta.Mmul_10.105.chr.gff3.gz

Mus musculus (GRCm38.101)

Common name Mouse
Assembly GRCm38.p6
Ensembl release 101
Reference sequence http://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.chromosome.*.fa.gz (*: 1-19, MT, X, Y)
Ensembl annotations http://ftp.ensembl.org/pub/release-101/gff3/mus_musculus/Mus_musculus.GRCm38.101.chr.gff3.gz

Oncorhynchus mykiss (Omyk_1.0.105)

Common name Rainbow trout
Assembly Omyk_1.0
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/oncorhynchus_mykiss/dna/Oncorhynchus_mykiss.Omyk_1.0.dna.primary_assembly.*.fa.gz (*: 1-29)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/oncorhynchus_mykiss/Oncorhynchus_mykiss.Omyk_1.0.105.chr.gff3.gz

Oryctolagus cuniculus (OryCun2.0.105)

Common name Rabbit
Assembly OryCun2.0
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/oncorhynchus_mykiss/dna/Oncorhynchus_mykiss.Omyk_1.0.dna.primary_assembly.*.fa.gz (*: 1-21, X, MT)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/oryctolagus_cuniculus/Oryctolagus_cuniculus.OryCun2.0.105.chr.gff3.gz

Rattus norvegicus (Rnor6.0.103) (legacy)

Common name Rat
Assembly Rnor_6.0
Ensembl release 103
Reference sequence http://ftp.ensembl.org/pub/release-103/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.chromosome.*.fa.gz (*: 1-20, MT, X, Y)
Ensembl annotations http://ftp.ensembl.org/pub/release-103/gff3/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.103.chr.gff3.gz

Rattus norvegicus (mRatBN7.2.110)

Common name Rat
Assembly mRatBN_7.2
Ensembl release 110
Reference sequence https://ftp.ensembl.org/pub/release-110/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.primary_assembly.*.fa.gz (*: 1-20, MT, X, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-110/gff3/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.110.chr.gff3.gz

Saccharomyces cerevisiae (R64-1-1.105)

Common name Baker's yeast, brewer's yeast, budding yeast
Assembly R64-1-1
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.chromosome.*.fa.gz (*: I, II, III, IV, IX, V, VI, VII, VIII, X, XI, XII, XIII, XIV, XV, XVI, Mito)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.105.gff3.gz

Schizosaccharomyces pombe (ASM294v2.52)

Common name Fission yeast
Assembly ASM294v2
Ensembl release 52
Reference sequence http://ftp.ensemblgenomes.org/pub/fungi/release-52/fasta/schizosaccharomyces_pombe/dna/Schizosaccharomyces_pombe.ASM294v2.dna.chromosome.*.fa.gz (*: I, II, III, MT)
Ensembl annotations http://ftp.ensemblgenomes.org/pub/fungi/release-52/gff3/schizosaccharomyces_pombe/Schizosaccharomyces_pombe.ASM294v2.52.chr.gff3.gz

Sus scrofa (Sscrofa11.1.105)

Common name Pig
Assembly Sscrofa11.1
Ensembl release 105
Reference sequence http://ftp.ensembl.org/pub/release-105/fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa11.1.dna.chromosome.*.fa.gz (*: 1-18, X, Y, MT)
Ensembl annotations http://ftp.ensembl.org/pub/release-105/gff3/sus_scrofa/Sus_scrofa.Sscrofa11.1.105.chr.gff3.gz

Zea mays (Zm-B73-REFERENCE-NAM-5.0.57)

Common name Maize
Assembly Zm-B73-REFERENCE-NAM-5.0
Ensembl release 57
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-57/fasta/zea_mays/dna/Zea_mays.Zm-B73-REFERENCE-NAM-5.0.dna.chromosome.*.fa.gz (*: 1-10, nonchromosomal)
Ensembl annotations https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-57/plants/gff3/zea_mays/Zea_mays.Zm-B73-REFERENCE-NAM-5.0.57.chr.gff3.gz