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These files contains the overview of all species in this PLAZA instance.
Additionally, extra information such as naming conventions, source information, version information, publication information, etc. are also provided.
SpeciesData File
All Species species_information.csv.gz (1.38 KB)
These files contain, per species, the structural annotation for each gene in this PLAZA instance in CSV format.
This includes gene identifier information, coordinate information, strand information, etc.
SpeciesAll transcriptsSelected transcript
Amborella trichopoda annotation.all_transcripts.atr.csv.gz (8.86 MB) annotation.selected_transcript.atr.csv.gz (8.85 MB)
Ananas comosus annotation.all_transcripts.aco.csv.gz (10.98 MB) annotation.selected_transcript.aco.csv.gz (10.98 MB)
Arabidopsis thaliana annotation.all_transcripts.ath.csv.gz (28.76 MB) annotation.selected_transcript.ath.csv.gz (22.70 MB)
Brachypodium distachyon annotation.all_transcripts.bdi.csv.gz (17.90 MB) annotation.selected_transcript.bdi.csv.gz (13.13 MB)
Chlamydomonas reinhardtii annotation.all_transcripts.cre.csv.gz (13.32 MB) annotation.selected_transcript.cre.csv.gz (12.15 MB)
Elaeis guineensis annotation.all_transcripts.egu.csv.gz (25.04 MB) annotation.selected_transcript.egu.csv.gz (18.51 MB)
Hordeum vulgare annotation.all_transcripts.hvu.csv.gz (16.01 MB) annotation.selected_transcript.hvu.csv.gz (8.98 MB)
Marchantia polymorpha annotation.all_transcripts.mpo.csv.gz (9.87 MB) annotation.selected_transcript.mpo.csv.gz (7.98 MB)
Micromonas commoda annotation.all_transcripts.mco.csv.gz (4.40 MB) annotation.selected_transcript.mco.csv.gz (4.40 MB)
Musa acuminata annotation.all_transcripts.mac.csv.gz (13.65 MB) annotation.selected_transcript.mac.csv.gz (13.65 MB)
Oropetium thomaeum annotation.all_transcripts.oth.csv.gz (9.55 MB) annotation.selected_transcript.oth.csv.gz (9.55 MB)
Oryza brachyantha annotation.all_transcripts.obr.csv.gz (11.65 MB) annotation.selected_transcript.obr.csv.gz (11.65 MB)
Oryza sativa ssp. indica annotation.all_transcripts.osaindica.csv.gz (22.15 MB) annotation.selected_transcript.osaindica.csv.gz (12.89 MB)
Oryza sativa ssp. japonica annotation.all_transcripts.osa.csv.gz (18.65 MB) annotation.selected_transcript.osa.csv.gz (15.57 MB)
Phalaenopsis equestris annotation.all_transcripts.peq.csv.gz (9.12 MB) annotation.selected_transcript.peq.csv.gz (9.12 MB)
Phyllostachys edulis annotation.all_transcripts.ped.csv.gz (13.50 MB) annotation.selected_transcript.ped.csv.gz (13.50 MB)
Physcomitrella patens annotation.all_transcripts.ppa.csv.gz (24.70 MB) annotation.selected_transcript.ppa.csv.gz (12.47 MB)
Picea abies annotation.all_transcripts.pab.csv.gz (16.09 MB) annotation.selected_transcript.pab.csv.gz (16.09 MB)
Populus trichocarpa annotation.all_transcripts.ptr.csv.gz (21.45 MB) annotation.selected_transcript.ptr.csv.gz (15.66 MB)
Selaginella moellendorffii annotation.all_transcripts.smo.csv.gz (8.79 MB) annotation.selected_transcript.smo.csv.gz (8.79 MB)
Setaria italica annotation.all_transcripts.sit.csv.gz (16.59 MB) annotation.selected_transcript.sit.csv.gz (13.71 MB)
Solanum lycopersicum annotation.all_transcripts.sly.csv.gz (12.27 MB) annotation.selected_transcript.sly.csv.gz (12.27 MB)
Sorghum bicolor annotation.all_transcripts.sbi.csv.gz (17.14 MB) annotation.selected_transcript.sbi.csv.gz (13.32 MB)
Spirodela polyrhiza annotation.all_transcripts.spo.csv.gz (7.42 MB) annotation.selected_transcript.spo.csv.gz (7.42 MB)
Triticum aestivum annotation.all_transcripts.tae.csv.gz (69.67 MB) annotation.selected_transcript.tae.csv.gz (52.40 MB)
Vitis vinifera annotation.all_transcripts.vvi.csv.gz (9.99 MB) annotation.selected_transcript.vvi.csv.gz (9.99 MB)
Zea mays annotation.all_transcripts.zma.csv.gz (28.36 MB) annotation.selected_transcript.zma.csv.gz (16.45 MB)
Zostera marina annotation.all_transcripts.zosmarina.csv.gz (8.30 MB) annotation.selected_transcript.zosmarina.csv.gz (8.30 MB)
Zoysia japonica ssp. nagirizaki annotation.all_transcripts.zjn.csv.gz (17.50 MB) annotation.selected_transcript.zjn.csv.gz (17.50 MB)
These files contain, per species, the structural annotation for each gene in this PLAZA instance in GFF format.
This includes gene identifier information, coordinate information, strand information, etc.
SpeciesAll transcriptsSelected transcript
All featuresExon features onlyAll featuresExon features only
Amborella trichopoda File 1 (3.47 MB) File 2 (2.74 MB) File 3 (3.47 MB) File 4 (2.74 MB)
Ananas comosus File 1 (4.25 MB) File 2 (2.98 MB) File 3 (4.25 MB) File 4 (2.98 MB)
Arabidopsis thaliana File 1 (9.81 MB) File 2 (6.86 MB) File 3 (6.98 MB) File 4 (5.31 MB)
Brachypodium distachyon File 1 (8.06 MB) File 2 (5.03 MB) File 3 (5.51 MB) File 4 (3.69 MB)
Chlamydomonas reinhardtii File 1 (4.50 MB) File 2 (2.93 MB) File 3 (4.20 MB) File 4 (2.77 MB)
Elaeis guineensis File 1 (8.30 MB) File 2 (5.47 MB) File 3 (5.72 MB) File 4 (4.04 MB)
Hordeum vulgare File 1 (8.39 MB) File 2 (4.79 MB) File 3 (3.85 MB) File 4 (2.43 MB)
Marchantia polymorpha File 1 (4.02 MB) File 2 (2.48 MB) File 3 (3.22 MB) File 4 (2.05 MB)
Micromonas commoda File 1 (881.47 KB) File 2 (656.38 KB) File 3 (881.47 KB) File 4 (656.38 KB)
Musa acuminata File 1 (5.52 MB) File 2 (3.98 MB) File 3 (5.52 MB) File 4 (3.98 MB)
Oropetium thomaeum File 1 (3.98 MB) File 2 (2.84 MB) File 3 (3.98 MB) File 4 (2.84 MB)
Oryza brachyantha File 1 (4.23 MB) File 2 (3.17 MB) File 3 (4.23 MB) File 4 (3.17 MB)
Oryza sativa ssp. indica File 1 (11.69 MB) File 2 (6.48 MB) File 3 (5.59 MB) File 4 (3.38 MB)
Oryza sativa ssp. japonica File 1 (7.34 MB) File 2 (4.76 MB) File 3 (6.07 MB) File 4 (4.11 MB)
Phalaenopsis equestris File 1 (3.12 MB) File 2 (2.36 MB) File 3 (3.12 MB) File 4 (2.36 MB)
Phyllostachys edulis File 1 (5.23 MB) File 2 (3.18 MB) File 3 (5.23 MB) File 4 (3.18 MB)
Physcomitrella patens File 1 (12.63 MB) File 2 (7.49 MB) File 3 (5.57 MB) File 4 (3.70 MB)
Picea abies File 1 (5.38 MB) File 2 (4.08 MB) File 3 (5.38 MB) File 4 (4.08 MB)
Populus trichocarpa File 1 (9.96 MB) File 2 (6.21 MB) File 3 (7.20 MB) File 4 (4.76 MB)
Selaginella moellendorffii File 1 (3.49 MB) File 2 (2.62 MB) File 3 (3.49 MB) File 4 (2.62 MB)
Setaria italica File 1 (6.85 MB) File 2 (4.45 MB) File 3 (5.71 MB) File 4 (3.85 MB)
Solanum lycopersicum File 1 (5.00 MB) File 2 (3.51 MB) File 3 (5.00 MB) File 4 (3.51 MB)
Sorghum bicolor File 1 (7.48 MB) File 2 (4.73 MB) File 3 (5.81 MB) File 4 (3.85 MB)
Spirodela polyrhiza File 1 (2.62 MB) File 2 (1.97 MB) File 3 (2.62 MB) File 4 (1.97 MB)
Triticum aestivum File 1 (24.11 MB) File 2 (14.44 MB) File 3 (17.50 MB) File 4 (11.04 MB)
Vitis vinifera File 1 (4.66 MB) File 2 (3.13 MB) File 3 (4.66 MB) File 4 (3.13 MB)
Zea mays File 1 (22.70 MB) File 2 (13.19 MB) File 3 (6.57 MB) File 4 (4.44 MB)
Zostera marina File 1 (3.20 MB) File 2 (2.16 MB) File 3 (3.20 MB) File 4 (2.16 MB)
Zoysia japonica ssp. nagirizaki File 1 (6.42 MB) File 2 (4.34 MB) File 3 (6.42 MB) File 4 (4.34 MB)
These files contain the mapping between genes and transcripts.
SpeciesAll transcriptsSelected transcript
Amborella trichopoda transcript_mapping.all_transcripts.atr.csv.gz (129.39 KB) transcript_mapping.selected_transcript.atr.csv.gz (129.40 KB)
Ananas comosus transcript_mapping.all_transcripts.aco.csv.gz (133.39 KB) transcript_mapping.selected_transcript.aco.csv.gz (133.39 KB)
Arabidopsis thaliana transcript_mapping.all_transcripts.ath.csv.gz (432.25 KB) transcript_mapping.selected_transcript.ath.csv.gz (352.87 KB)
Brachypodium distachyon transcript_mapping.all_transcripts.bdi.csv.gz (237.91 KB) transcript_mapping.selected_transcript.bdi.csv.gz (173.47 KB)
Chlamydomonas reinhardtii transcript_mapping.all_transcripts.cre.csv.gz (105.92 KB) transcript_mapping.selected_transcript.cre.csv.gz (96.17 KB)
Elaeis guineensis transcript_mapping.all_transcripts.egu.csv.gz (209.76 KB) transcript_mapping.selected_transcript.egu.csv.gz (145.49 KB)
Hordeum vulgare transcript_mapping.all_transcripts.hvu.csv.gz (252.38 KB) transcript_mapping.selected_transcript.hvu.csv.gz (133.16 KB)
Marchantia polymorpha transcript_mapping.all_transcripts.mpo.csv.gz (108.65 KB) transcript_mapping.selected_transcript.mpo.csv.gz (86.51 KB)
Micromonas commoda transcript_mapping.all_transcripts.mco.csv.gz (49.42 KB) transcript_mapping.selected_transcript.mco.csv.gz (49.42 KB)
Musa acuminata transcript_mapping.all_transcripts.mac.csv.gz (176.32 KB) transcript_mapping.selected_transcript.mac.csv.gz (176.33 KB)
Oropetium thomaeum transcript_mapping.all_transcripts.oth.csv.gz (134.68 KB) transcript_mapping.selected_transcript.oth.csv.gz (134.69 KB)
Oryza brachyantha transcript_mapping.all_transcripts.obr.csv.gz (161.33 KB) transcript_mapping.selected_transcript.obr.csv.gz (161.33 KB)
Oryza sativa ssp. indica transcript_mapping.all_transcripts.osaindica.csv.gz (412.59 KB) transcript_mapping.selected_transcript.osaindica.csv.gz (226.59 KB)
Oryza sativa ssp. japonica transcript_mapping.all_transcripts.osa.csv.gz (262.57 KB) transcript_mapping.selected_transcript.osa.csv.gz (219.76 KB)
Phalaenopsis equestris transcript_mapping.all_transcripts.peq.csv.gz (144.67 KB) transcript_mapping.selected_transcript.peq.csv.gz (144.67 KB)
Phyllostachys edulis transcript_mapping.all_transcripts.ped.csv.gz (178.99 KB) transcript_mapping.selected_transcript.ped.csv.gz (179.00 KB)
Physcomitrella patens transcript_mapping.all_transcripts.ppa.csv.gz (350.03 KB) transcript_mapping.selected_transcript.ppa.csv.gz (167.33 KB)
Picea abies transcript_mapping.all_transcripts.pab.csv.gz (333.35 KB) transcript_mapping.selected_transcript.pab.csv.gz (333.35 KB)
Populus trichocarpa transcript_mapping.all_transcripts.ptr.csv.gz (304.13 KB) transcript_mapping.selected_transcript.ptr.csv.gz (217.90 KB)
Selaginella moellendorffii transcript_mapping.all_transcripts.smo.csv.gz (98.02 KB) transcript_mapping.selected_transcript.smo.csv.gz (98.02 KB)
Setaria italica transcript_mapping.all_transcripts.sit.csv.gz (206.44 KB) transcript_mapping.selected_transcript.sit.csv.gz (171.76 KB)
Solanum lycopersicum transcript_mapping.all_transcripts.sly.csv.gz (179.23 KB) transcript_mapping.selected_transcript.sly.csv.gz (179.23 KB)
Sorghum bicolor transcript_mapping.all_transcripts.sbi.csv.gz (228.47 KB) transcript_mapping.selected_transcript.sbi.csv.gz (173.63 KB)
Spirodela polyrhiza transcript_mapping.all_transcripts.spo.csv.gz (87.26 KB) transcript_mapping.selected_transcript.spo.csv.gz (87.27 KB)
Triticum aestivum transcript_mapping.all_transcripts.tae.csv.gz (777.71 KB) transcript_mapping.selected_transcript.tae.csv.gz (568.29 KB)
Vitis vinifera transcript_mapping.all_transcripts.vvi.csv.gz (136.37 KB) transcript_mapping.selected_transcript.vvi.csv.gz (136.37 KB)
Zea mays transcript_mapping.all_transcripts.zma.csv.gz (509.66 KB) transcript_mapping.selected_transcript.zma.csv.gz (247.08 KB)
Zostera marina transcript_mapping.all_transcripts.zosmarina.csv.gz (89.23 KB) transcript_mapping.selected_transcript.zosmarina.csv.gz (89.23 KB)
Zoysia japonica ssp. nagirizaki transcript_mapping.all_transcripts.zjn.csv.gz (331.18 KB) transcript_mapping.selected_transcript.zjn.csv.gz (331.18 KB)
These files contain, per species, the gene identifiers and descriptions available for each gene in this PLAZA instance.
Many genes are known by their aliases (e.g. E2F3 for AT2G36010). These files contain this kind of identifier mappings.
SpeciesIdentifiersDescriptions
Amborella trichopoda id_conversion.atr.csv.gz (738.81 KB) gene_description.atr.csv.gz (302.00 B)
Ananas comosus id_conversion.aco.csv.gz (456.52 KB) gene_description.aco.csv.gz (258.98 KB)
Arabidopsis thaliana id_conversion.ath.csv.gz (1.82 MB) gene_description.ath.csv.gz (1.00 MB)
Brachypodium distachyon id_conversion.bdi.csv.gz (940.87 KB) gene_description.bdi.csv.gz (107.59 KB)
Chlamydomonas reinhardtii id_conversion.cre.csv.gz (445.17 KB) gene_description.cre.csv.gz (188.78 KB)
Elaeis guineensis id_conversion.egu.csv.gz (1.17 MB) gene_description.egu.csv.gz (24.32 KB)
Hordeum vulgare id_conversion.hvu.csv.gz (289.86 KB) gene_description.hvu.csv.gz (144.45 KB)
Marchantia polymorpha id_conversion.mpo.csv.gz (379.45 KB) gene_description.mpo.csv.gz (304.00 B)
Micromonas commoda id_conversion.mco.csv.gz (282.66 KB) gene_description.mco.csv.gz (307.00 B)
Musa acuminata id_conversion.mac.csv.gz (326.42 KB) gene_description.mac.csv.gz (180.90 KB)
Oropetium thomaeum id_conversion.oth.csv.gz (530.84 KB) gene_description.oth.csv.gz (409.31 KB)
Oryza brachyantha id_conversion.obr.csv.gz (276.58 KB) gene_description.obr.csv.gz (179.14 KB)
Oryza sativa ssp. indica id_conversion.osaindica.csv.gz (221.40 KB) gene_description.osaindica.csv.gz (130.49 KB)
Oryza sativa ssp. japonica id_conversion.osa.csv.gz (805.76 KB) gene_description.osa.csv.gz (364.96 KB)
Phalaenopsis equestris id_conversion.peq.csv.gz (148.38 KB) gene_description.peq.csv.gz (287.00 B)
Phyllostachys edulis id_conversion.ped.csv.gz (178.44 KB) gene_description.ped.csv.gz (340.24 KB)
Physcomitrella patens id_conversion.ppa.csv.gz (785.85 KB) gene_description.ppa.csv.gz (303.00 B)
Picea abies id_conversion.pab.csv.gz (350.65 KB) gene_description.pab.csv.gz (267.00 B)
Populus trichocarpa id_conversion.ptr.csv.gz (1.16 MB) gene_description.ptr.csv.gz (415.35 KB)
Selaginella moellendorffii id_conversion.smo.csv.gz (607.67 KB) gene_description.smo.csv.gz (308.00 B)
Setaria italica id_conversion.sit.csv.gz (1.02 MB) gene_description.sit.csv.gz (299.00 B)
Solanum lycopersicum id_conversion.sly.csv.gz (664.46 KB) gene_description.sly.csv.gz (806.71 KB)
Sorghum bicolor id_conversion.sbi.csv.gz (1.04 MB) gene_description.sbi.csv.gz (193.53 KB)
Spirodela polyrhiza id_conversion.spo.csv.gz (292.60 KB) gene_description.spo.csv.gz (182.50 KB)
Triticum aestivum id_conversion.tae.csv.gz (1.68 MB) gene_description.tae.csv.gz (156.92 KB)
Vitis vinifera id_conversion.vvi.csv.gz (476.43 KB) gene_description.vvi.csv.gz (305.00 B)
Zea mays id_conversion.zma.csv.gz (736.75 KB) gene_description.zma.csv.gz (429.29 KB)
Zostera marina id_conversion.zosmarina.csv.gz (341.62 KB) gene_description.zosmarina.csv.gz (157.48 KB)
Zoysia japonica ssp. nagirizaki id_conversion.zjn.csv.gz (288.00 B) gene_description.zjn.csv.gz (291.00 B)
These files contain, per species, the functional annotation of the genes within this PLAZA instance.

This information is limited to the annotation of the genes.
For the associated ontologies (such as parent-child relationships between the various terms), you can find the necessary information here:
SpeciesGene OntologyInterProMapMan
Amborella trichopoda go.atr.csv.gz (9.17 MB) interpro.atr.csv.gz (1.79 MB) mapman.atr.csv.gz (296.00 B)
Ananas comosus go.aco.csv.gz (10.66 MB) interpro.aco.csv.gz (2.19 MB) mapman.aco.csv.gz (291.00 B)
Arabidopsis thaliana go.ath.csv.gz (31.00 MB) interpro.ath.csv.gz (2.55 MB) mapman.ath.csv.gz (261.00 B)
Brachypodium distachyon go.bdi.csv.gz (12.13 MB) interpro.bdi.csv.gz (2.59 MB) mapman.bdi.csv.gz (300.00 B)
Chlamydomonas reinhardtii go.cre.csv.gz (5.45 MB) interpro.cre.csv.gz (1.26 MB) mapman.cre.csv.gz (298.00 B)
Elaeis guineensis go.egu.csv.gz (13.07 MB) interpro.egu.csv.gz (2.66 MB) mapman.egu.csv.gz (280.00 B)
Hordeum vulgare go.hvu.csv.gz (10.26 MB) interpro.hvu.csv.gz (1.97 MB) mapman.hvu.csv.gz (289.00 B)
Marchantia polymorpha go.mpo.csv.gz (6.91 MB) interpro.mpo.csv.gz (1.45 MB) mapman.mpo.csv.gz (297.00 B)
Micromonas commoda go.mco.csv.gz (3.63 MB) interpro.mco.csv.gz (898.19 KB) mapman.mco.csv.gz (300.00 B)
Musa acuminata go.mac.csv.gz (17.33 MB) interpro.mac.csv.gz (3.06 MB) mapman.mac.csv.gz (268.00 B)
Oropetium thomaeum go.oth.csv.gz (10.89 MB) interpro.oth.csv.gz (1.93 MB) mapman.oth.csv.gz (297.00 B)
Oryza brachyantha go.obr.csv.gz (11.25 MB) interpro.obr.csv.gz (2.30 MB) mapman.obr.csv.gz (283.00 B)
Oryza sativa ssp. indica go.osaindica.csv.gz (12.28 MB) interpro.osaindica.csv.gz (2.65 MB) mapman.osaindica.csv.gz (285.00 B)
Oryza sativa ssp. japonica go.osa.csv.gz (16.69 MB) interpro.osa.csv.gz (2.77 MB) mapman.osa.csv.gz (302.00 B)
Phalaenopsis equestris go.peq.csv.gz (10.49 MB) interpro.peq.csv.gz (1.98 MB) mapman.peq.csv.gz (282.00 B)
Phyllostachys edulis go.ped.csv.gz (14.82 MB) interpro.ped.csv.gz (2.77 MB) mapman.ped.csv.gz (273.00 B)
Physcomitrella patens go.ppa.csv.gz (13.01 MB) interpro.ppa.csv.gz (2.27 MB) mapman.ppa.csv.gz (296.00 B)
Picea abies go.pab.csv.gz (17.78 MB) interpro.pab.csv.gz (3.21 MB) mapman.pab.csv.gz (261.00 B)
Populus trichocarpa go.ptr.csv.gz (17.31 MB) interpro.ptr.csv.gz (3.46 MB) mapman.ptr.csv.gz (300.00 B)
Selaginella moellendorffii go.smo.csv.gz (8.75 MB) interpro.smo.csv.gz (1.99 MB) mapman.smo.csv.gz (302.00 B)
Setaria italica go.sit.csv.gz (13.03 MB) interpro.sit.csv.gz (2.82 MB) mapman.sit.csv.gz (292.00 B)
Solanum lycopersicum go.sly.csv.gz (13.81 MB) interpro.sly.csv.gz (2.68 MB) mapman.sly.csv.gz (280.00 B)
Sorghum bicolor go.sbi.csv.gz (12.66 MB) interpro.sbi.csv.gz (2.71 MB) mapman.sbi.csv.gz (295.00 B)
Spirodela polyrhiza go.spo.csv.gz (9.12 MB) interpro.spo.csv.gz (1.75 MB) mapman.spo.csv.gz (298.00 B)
Triticum aestivum go.tae.csv.gz (39.37 MB) interpro.tae.csv.gz (9.10 MB) mapman.tae.csv.gz (282.00 B)
Vitis vinifera go.vvi.csv.gz (10.77 MB) interpro.vvi.csv.gz (2.25 MB) mapman.vvi.csv.gz (298.00 B)
Zea mays go.zma.csv.gz (16.61 MB) interpro.zma.csv.gz (3.15 MB) mapman.zma.csv.gz (274.00 B)
Zostera marina go.zosmarina.csv.gz (10.07 MB) interpro.zosmarina.csv.gz (1.89 MB) mapman.zosmarina.csv.gz (299.00 B)
Zoysia japonica ssp. nagirizaki go.zjn.csv.gz (14.78 MB) interpro.zjn.csv.gz (2.33 MB) mapman.zjn.csv.gz (284.00 B)
These files contain sequences for each locus/transcript for each of the organisms in this PLAZA instance.

  • CDS: Coding Sequences. The concatenated exonic DNA sequence per locus/transcript (coding genes only), from start codon to stop codon.
  • Transcript: Transcript sequences. The spliced transcribed DNA sequence per locus/transcript (all gene types). Contains UTR regions.
  • Protein: Amino Acid Sequences. The translated coding sequence per gene, using the appropriate translation table
SpeciesCDS filesTranscript filesProtein files
All transcriptsSelected transcriptAll transcriptsSelected transcriptAll transcriptsSelected transcript
Amborella trichopoda File 1 (7.25 MB) File 2 (7.25 MB) File 3 (7.25 MB) File 4 (7.26 MB) File 5 (4.88 MB) File 6 (4.88 MB)
Ananas comosus File 1 (8.84 MB) File 2 (8.84 MB) File 3 (11.12 MB) File 4 (11.12 MB) File 5 (5.96 MB) File 6 (5.96 MB)
Arabidopsis thaliana File 1 (13.87 MB) File 2 (9.29 MB) File 3 (29.02 MB) File 4 (22.43 MB) File 5 (9.27 MB) File 6 (6.22 MB)
Brachypodium distachyon File 1 (14.55 MB) File 2 (10.77 MB) File 3 (22.79 MB) File 4 (16.70 MB) File 5 (9.73 MB) File 6 (7.23 MB)
Chlamydomonas reinhardtii File 1 (11.14 MB) File 2 (10.19 MB) File 3 (16.89 MB) File 4 (15.45 MB) File 5 (7.34 MB) File 6 (6.71 MB)
Elaeis guineensis File 1 (13.39 MB) File 2 (9.55 MB) File 3 (19.99 MB) File 4 (14.48 MB) File 5 (8.31 MB) File 6 (6.03 MB)
Hordeum vulgare File 1 (12.56 MB) File 2 (7.20 MB) File 3 (21.40 MB) File 4 (12.15 MB) File 5 (8.49 MB) File 6 (4.89 MB)
Marchantia polymorpha File 1 (8.05 MB) File 2 (6.52 MB) File 3 (14.62 MB) File 4 (11.98 MB) File 5 (5.38 MB) File 6 (4.37 MB)
Micromonas commoda File 1 (4.04 MB) File 2 (4.04 MB) File 3 (4.25 MB) File 4 (4.25 MB) File 5 (2.76 MB) File 6 (2.76 MB)
Musa acuminata File 1 (10.81 MB) File 2 (10.81 MB) File 3 (12.56 MB) File 4 (12.56 MB) File 5 (7.35 MB) File 6 (7.35 MB)
Oropetium thomaeum File 1 (7.74 MB) File 2 (7.74 MB) File 3 (8.94 MB) File 4 (8.94 MB) File 5 (5.25 MB) File 6 (5.25 MB)
Oryza brachyantha File 1 (9.41 MB) File 2 (9.41 MB) File 3 (11.23 MB) File 4 (11.23 MB) File 5 (6.36 MB) File 6 (6.36 MB)
Oryza sativa ssp. indica File 1 (17.47 MB) File 2 (10.40 MB) File 3 (28.42 MB) File 4 (16.33 MB) File 5 (11.84 MB) File 6 (7.04 MB)
Oryza sativa ssp. japonica File 1 (15.30 MB) File 2 (12.88 MB) File 3 (21.10 MB) File 4 (17.08 MB) File 5 (10.16 MB) File 6 (8.54 MB)
Phalaenopsis equestris File 1 (7.43 MB) File 2 (7.43 MB) File 3 (10.25 MB) File 4 (10.25 MB) File 5 (5.01 MB) File 6 (5.01 MB)
Phyllostachys edulis File 1 (10.97 MB) File 2 (10.97 MB) File 3 (20.71 MB) File 4 (20.71 MB) File 5 (7.45 MB) File 6 (7.45 MB)
Physcomitrella patens File 1 (19.83 MB) File 2 (10.08 MB) File 3 (35.09 MB) File 4 (18.40 MB) File 5 (13.17 MB) File 6 (6.79 MB)
Picea abies File 1 (13.41 MB) File 2 (13.41 MB) File 3 (13.61 MB) File 4 (13.61 MB) File 5 (9.19 MB) File 6 (9.19 MB)
Populus trichocarpa File 1 (17.29 MB) File 2 (12.69 MB) File 3 (25.84 MB) File 4 (18.70 MB) File 5 (11.57 MB) File 6 (8.50 MB)
Selaginella moellendorffii File 1 (7.16 MB) File 2 (7.16 MB) File 3 (7.47 MB) File 4 (7.47 MB) File 5 (4.76 MB) File 6 (4.76 MB)
Setaria italica File 1 (13.61 MB) File 2 (11.29 MB) File 3 (19.88 MB) File 4 (16.26 MB) File 5 (9.11 MB) File 6 (7.56 MB)
Solanum lycopersicum File 1 (10.04 MB) File 2 (10.04 MB) File 3 (11.55 MB) File 4 (11.55 MB) File 5 (6.79 MB) File 6 (6.79 MB)
Sorghum bicolor File 1 (13.97 MB) File 2 (10.92 MB) File 3 (22.38 MB) File 4 (17.36 MB) File 5 (9.36 MB) File 6 (7.32 MB)
Spirodela polyrhiza File 1 (6.10 MB) File 2 (6.10 MB) File 3 (6.10 MB) File 4 (6.10 MB) File 5 (4.11 MB) File 6 (4.11 MB)
Triticum aestivum File 1 (49.59 MB) File 2 (36.58 MB) File 3 (32.89 MB) File 4 (60.01 MB) File 5 (33.43 MB) File 6 (24.71 MB)
Vitis vinifera File 1 (7.87 MB) File 2 (7.87 MB) File 3 (10.32 MB) File 4 (10.32 MB) File 5 (5.29 MB) File 6 (5.29 MB)
Zea mays File 1 (21.01 MB) File 2 (12.39 MB) File 3 (36.14 MB) File 4 (18.28 MB) File 5 (13.84 MB) File 6 (8.33 MB)
Zostera marina File 1 (6.79 MB) File 2 (6.79 MB) File 3 (8.14 MB) File 4 (8.14 MB) File 5 (4.60 MB) File 6 (4.60 MB)
Zoysia japonica ssp. nagirizaki File 1 (12.64 MB) File 2 (12.64 MB) File 3 (17.22 MB) File 4 (17.22 MB) File 5 (8.59 MB) File 6 (8.59 MB)
These files contain the information about genes that are detected as being duplicates due to a segmental duplication event or a whole genome duplication event, for all the species within this PLAZA instance.

The files contain gene-pairs (i.e. the duplicates), as well as the associated Ks value (#of synonymous substitutions per synonymous site).
SpeciesAnchorpoints
Amborella trichopoda anchorpoints.atr.csv.gz (763.00 B)
Ananas comosus anchorpoints.aco.csv.gz (24.87 KB)
Arabidopsis thaliana anchorpoints.ath.csv.gz (27.23 KB)
Brachypodium distachyon anchorpoints.bdi.csv.gz (25.63 KB)
Chlamydomonas reinhardtii anchorpoints.cre.csv.gz (761.00 B)
Elaeis guineensis anchorpoints.egu.csv.gz (57.36 KB)
Hordeum vulgare anchorpoints.hvu.csv.gz (1.53 KB)
Marchantia polymorpha anchorpoints.mpo.csv.gz (570.00 B)
Micromonas commoda anchorpoints.mco.csv.gz (473.00 B)
Musa acuminata anchorpoints.mac.csv.gz (77.50 KB)
Oropetium thomaeum anchorpoints.oth.csv.gz (25.39 KB)
Oryza brachyantha anchorpoints.obr.csv.gz (28.85 KB)
Oryza sativa ssp. indica anchorpoints.osaindica.csv.gz (41.65 KB)
Oryza sativa ssp. japonica anchorpoints.osa.csv.gz (45.13 KB)
Phalaenopsis equestris anchorpoints.peq.csv.gz (1.16 KB)
Phyllostachys edulis anchorpoints.ped.csv.gz (20.28 KB)
Physcomitrella patens anchorpoints.ppa.csv.gz (15.06 KB)
Picea abies anchorpoints.pab.csv.gz (430.00 B)
Populus trichocarpa anchorpoints.ptr.csv.gz (115.38 KB)
Selaginella moellendorffii anchorpoints.smo.csv.gz (8.47 KB)
Setaria italica anchorpoints.sit.csv.gz (36.50 KB)
Solanum lycopersicum anchorpoints.sly.csv.gz (29.27 KB)
Sorghum bicolor anchorpoints.sbi.csv.gz (34.42 KB)
Spirodela polyrhiza anchorpoints.spo.csv.gz (7.27 KB)
Triticum aestivum anchorpoints.tae.csv.gz (6.03 KB)
Vitis vinifera anchorpoints.vvi.csv.gz (15.99 KB)
Zea mays anchorpoints.zma.csv.gz (73.62 KB)
Zostera marina anchorpoints.zosmarina.csv.gz (1.19 KB)
Zoysia japonica ssp. nagirizaki anchorpoints.zjn.csv.gz (98.98 KB)
These files contain the gene family information for the (coding) genes within this PLAZA instance, separated per gene family type

The following data files are available:
  • Gene family - gene mapping: mapping between the gene families and their constituent genes. Each gene can be part of only 1 gene family (per family type).
  • Gene family functional annotation: the functional annotation per gene family (GO/InterPro), which is based on enrichment analysis of the constituent genes in the family.Also included is a global score which reflects both the enrichment score and the associated p-value.See the documentation for more information.
Data TypeGene Family ClustersGene Family Enrichments
Homologous gene families genefamily_data.hom.csv.gz (5.56 MB) genefamily_enrichment.hom.csv.gz (2.96 MB)
Orthologous gene families genefamily_data.orth.csv.gz (5.75 MB) genefamily_enrichment.orth.csv.gz (4.30 MB)
These files contain the orthologous relationships between genes, as detected by the various methods within the Integrative Orthology approach.

For more information about the integrative orthology, see the documentation
Orthology TypeData File
Tree-based ortholog integrative_orthology.TROG.csv.gz (173.30 MB)
Orthologous gene family integrative_orthology.ORTHO.csv.gz (1.00 GB)
Anchor point integrative_orthology.anchor_point.csv.gz (26.98 MB)
Best-Hits-and-Inparalogs(BHI)family integrative_orthology.BHIF.csv.gz (208.64 MB)