Download section

All downloads are also available from ftp-directory : ftp directory or file server

Warning:
The following species have a disclaimer stating that the data is currently not available for bulk download. As such there will be no files available for the per-species data, and for mixed files (e.g. gene families) the information for the species with disclaimers will have been removed.

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 (1.88 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)
Apostasia shenzhenica annotation.all_transcripts.ash.csv.gz (8.16 MB) annotation.selected_transcript.ash.csv.gz (8.16 MB)
Arabidopsis thaliana annotation.all_transcripts.ath.csv.gz (28.76 MB) annotation.selected_transcript.ath.csv.gz (22.70 MB)
Asparagus officinalis annotation.all_transcripts.aof.csv.gz (9.69 MB) annotation.selected_transcript.aof.csv.gz (9.69 MB)
Brachypodium distachyon annotation.all_transcripts.bdi.csv.gz (17.90 MB) annotation.selected_transcript.bdi.csv.gz (13.13 MB)
Calamus simplicifolius annotation.all_transcripts.calsi.csv.gz (17.81 MB) annotation.selected_transcript.calsi.csv.gz (17.81 MB)
Cenchrus americanus annotation.all_transcripts.cam.csv.gz (13.16 MB) annotation.selected_transcript.cam.csv.gz (13.16 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 (10.95 MB) annotation.selected_transcript.egu.csv.gz (10.95 MB)
Hordeum vulgare annotation.all_transcripts.hvu.csv.gz (40.50 MB) annotation.selected_transcript.hvu.csv.gz (15.09 MB)
Lolium perenne annotation.all_transcripts.lpe.csv.gz (15.08 MB) annotation.selected_transcript.lpe.csv.gz (15.08 MB)
Marchantia polymorpha annotation.all_transcripts.mpo.csv.gz (9.88 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)
Miscanthus sinensis Not Available Not Available
Musa acuminata annotation.all_transcripts.mac.csv.gz (17.95 MB) annotation.selected_transcript.mac.csv.gz (14.27 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)
Physcomitrium 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)
Saccharum spontaneum annotation.all_transcripts.ssp.csv.gz (23.12 MB) annotation.selected_transcript.ssp.csv.gz (23.12 MB)
Selaginella moellendorffii annotation.all_transcripts.smo.csv.gz (21.53 MB) annotation.selected_transcript.smo.csv.gz (17.03 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 (54.06 MB) annotation.selected_transcript.tae.csv.gz (43.66 MB)
Triticum turgidum annotation.all_transcripts.ttu.csv.gz (48.07 MB) annotation.selected_transcript.ttu.csv.gz (25.63 MB)
Vitis vinifera annotation.all_transcripts.vvi.csv.gz (10.00 MB) annotation.selected_transcript.vvi.csv.gz (9.99 MB)
Zea mays B73 annotation.all_transcripts.zma.csv.gz (28.36 MB) annotation.selected_transcript.zma.csv.gz (16.45 MB)
Zea mays B104 Not Available Not Available
Zea mays PH207 annotation.all_transcripts.zma-ph207.csv.gz (14.95 MB) annotation.selected_transcript.zma-ph207.csv.gz (14.95 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)
Apostasia shenzhenica File 1 (2.63 MB) File 2 (2.04 MB) File 3 (2.63 MB) File 4 (2.04 MB)
Arabidopsis thaliana File 1 (9.79 MB) File 2 (6.85 MB) File 3 (6.97 MB) File 4 (5.30 MB)
Asparagus officinalis File 1 (3.66 MB) File 2 (2.72 MB) File 3 (3.66 MB) File 4 (2.72 MB)
Brachypodium distachyon File 1 (8.06 MB) File 2 (5.03 MB) File 3 (5.51 MB) File 4 (3.69 MB)
Calamus simplicifolius File 1 (5.71 MB) File 2 (4.14 MB) File 3 (5.71 MB) File 4 (4.14 MB)
Cenchrus americanus File 1 (4.00 MB) File 2 (2.92 MB) File 3 (4.00 MB) File 4 (2.92 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 (3.77 MB) File 2 (2.65 MB) File 3 (3.77 MB) File 4 (2.65 MB)
Hordeum vulgare File 1 (32.28 MB) File 2 (17.99 MB) File 3 (5.57 MB) File 4 (3.59 MB)
Lolium perenne File 1 (4.77 MB) File 2 (3.65 MB) File 3 (4.77 MB) File 4 (3.65 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 (881.48 KB) File 4 (656.38 KB)
Miscanthus sinensis Not Available Not Available Not Available Not Available
Musa acuminata File 1 (7.12 MB) File 2 (4.52 MB) File 3 (5.69 MB) File 4 (3.76 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)
Physcomitrium 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)
Saccharum spontaneum File 1 (12.02 MB) File 2 (8.35 MB) File 3 (12.02 MB) File 4 (8.35 MB)
Selaginella moellendorffii File 1 (7.30 MB) File 2 (4.59 MB) File 3 (5.54 MB) File 4 (3.63 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 (19.17 MB) File 2 (11.82 MB) File 3 (15.30 MB) File 4 (9.71 MB)
Triticum turgidum File 1 (21.82 MB) File 2 (14.38 MB) File 3 (8.18 MB) File 4 (6.16 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 B73 File 1 (22.70 MB) File 2 (13.19 MB) File 3 (6.57 MB) File 4 (4.44 MB)
Zea mays B104 Not Available Not Available Not Available Not Available
Zea mays PH207 File 1 (5.70 MB) File 2 (3.89 MB) File 3 (5.70 MB) File 4 (3.89 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 (129.40 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 (133.40 KB)
Apostasia shenzhenica transcript_mapping.all_transcripts.ash.csv.gz (104.08 KB) transcript_mapping.selected_transcript.ash.csv.gz (104.08 KB)
Arabidopsis thaliana transcript_mapping.all_transcripts.ath.csv.gz (432.26 KB) transcript_mapping.selected_transcript.ath.csv.gz (352.88 KB)
Asparagus officinalis transcript_mapping.all_transcripts.aof.csv.gz (139.90 KB) transcript_mapping.selected_transcript.aof.csv.gz (139.91 KB)
Brachypodium distachyon transcript_mapping.all_transcripts.bdi.csv.gz (237.92 KB) transcript_mapping.selected_transcript.bdi.csv.gz (173.48 KB)
Calamus simplicifolius transcript_mapping.all_transcripts.calsi.csv.gz (233.39 KB) transcript_mapping.selected_transcript.calsi.csv.gz (233.39 KB)
Cenchrus americanus transcript_mapping.all_transcripts.cam.csv.gz (164.73 KB) transcript_mapping.selected_transcript.cam.csv.gz (164.73 KB)
Chlamydomonas reinhardtii transcript_mapping.all_transcripts.cre.csv.gz (105.93 KB) transcript_mapping.selected_transcript.cre.csv.gz (96.18 KB)
Elaeis guineensis transcript_mapping.all_transcripts.egu.csv.gz (123.21 KB) transcript_mapping.selected_transcript.egu.csv.gz (123.21 KB)
Hordeum vulgare transcript_mapping.all_transcripts.hvu.csv.gz (853.14 KB) transcript_mapping.selected_transcript.hvu.csv.gz (237.81 KB)
Lolium perenne transcript_mapping.all_transcripts.lpe.csv.gz (194.02 KB) transcript_mapping.selected_transcript.lpe.csv.gz (194.02 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)
Miscanthus sinensis Not Available Not Available
Musa acuminata transcript_mapping.all_transcripts.mac.csv.gz (218.52 KB) transcript_mapping.selected_transcript.mac.csv.gz (175.38 KB)
Oropetium thomaeum transcript_mapping.all_transcripts.oth.csv.gz (134.69 KB) transcript_mapping.selected_transcript.oth.csv.gz (134.69 KB)
Oryza brachyantha transcript_mapping.all_transcripts.obr.csv.gz (161.34 KB) transcript_mapping.selected_transcript.obr.csv.gz (161.34 KB)
Oryza sativa ssp. indica transcript_mapping.all_transcripts.osaindica.csv.gz (412.60 KB) transcript_mapping.selected_transcript.osaindica.csv.gz (226.60 KB)
Oryza sativa ssp. japonica transcript_mapping.all_transcripts.osa.csv.gz (262.58 KB) transcript_mapping.selected_transcript.osa.csv.gz (219.77 KB)
Phalaenopsis equestris transcript_mapping.all_transcripts.peq.csv.gz (144.67 KB) transcript_mapping.selected_transcript.peq.csv.gz (144.68 KB)
Phyllostachys edulis transcript_mapping.all_transcripts.ped.csv.gz (179.00 KB) transcript_mapping.selected_transcript.ped.csv.gz (179.00 KB)
Physcomitrium patens transcript_mapping.all_transcripts.ppa.csv.gz (350.04 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 (333.36 KB)
Populus trichocarpa transcript_mapping.all_transcripts.ptr.csv.gz (304.14 KB) transcript_mapping.selected_transcript.ptr.csv.gz (217.91 KB)
Saccharum spontaneum transcript_mapping.all_transcripts.ssp.csv.gz (479.41 KB) transcript_mapping.selected_transcript.ssp.csv.gz (479.41 KB)
Selaginella moellendorffii transcript_mapping.all_transcripts.smo.csv.gz (225.19 KB) transcript_mapping.selected_transcript.smo.csv.gz (174.96 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 (179.24 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 (87.27 KB) transcript_mapping.selected_transcript.spo.csv.gz (87.27 KB)
Triticum aestivum transcript_mapping.all_transcripts.tae.csv.gz (652.02 KB) transcript_mapping.selected_transcript.tae.csv.gz (524.77 KB)
Triticum turgidum transcript_mapping.all_transcripts.ttu.csv.gz (769.93 KB) transcript_mapping.selected_transcript.ttu.csv.gz (356.87 KB)
Vitis vinifera transcript_mapping.all_transcripts.vvi.csv.gz (136.37 KB) transcript_mapping.selected_transcript.vvi.csv.gz (136.38 KB)
Zea mays B73 transcript_mapping.all_transcripts.zma.csv.gz (509.67 KB) transcript_mapping.selected_transcript.zma.csv.gz (247.09 KB)
Zea mays B104 Not Available Not Available
Zea mays PH207 transcript_mapping.all_transcripts.zma-ph207.csv.gz (180.25 KB) transcript_mapping.selected_transcript.zma-ph207.csv.gz (180.25 KB)
Zostera marina transcript_mapping.all_transcripts.zosmarina.csv.gz (89.24 KB) transcript_mapping.selected_transcript.zosmarina.csv.gz (89.24 KB)
Zoysia japonica ssp. nagirizaki transcript_mapping.all_transcripts.zjn.csv.gz (331.19 KB) transcript_mapping.selected_transcript.zjn.csv.gz (331.19 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 (303.00 B)
Ananas comosus id_conversion.aco.csv.gz (456.53 KB) gene_description.aco.csv.gz (258.99 KB)
Apostasia shenzhenica id_conversion.ash.csv.gz (387.71 KB) gene_description.ash.csv.gz (310.00 B)
Arabidopsis thaliana id_conversion.ath.csv.gz (1.82 MB) gene_description.ath.csv.gz (1.01 MB)
Asparagus officinalis id_conversion.aof.csv.gz (323.11 KB) gene_description.aof.csv.gz (305.00 B)
Brachypodium distachyon id_conversion.bdi.csv.gz (940.88 KB) gene_description.bdi.csv.gz (107.59 KB)
Calamus simplicifolius id_conversion.calsi.csv.gz (236.75 KB) gene_description.calsi.csv.gz (282.00 B)
Cenchrus americanus id_conversion.cam.csv.gz (292.00 B) gene_description.cam.csv.gz (296.00 B)
Chlamydomonas reinhardtii id_conversion.cre.csv.gz (445.18 KB) gene_description.cre.csv.gz (188.78 KB)
Elaeis guineensis id_conversion.egu.csv.gz (134.06 KB) gene_description.egu.csv.gz (272.00 B)
Hordeum vulgare id_conversion.hvu.csv.gz (240.61 KB) gene_description.hvu.csv.gz (280.00 B)
Lolium perenne id_conversion.lpe.csv.gz (378.79 KB) gene_description.lpe.csv.gz (253.00 B)
Marchantia polymorpha id_conversion.mpo.csv.gz (379.46 KB) gene_description.mpo.csv.gz (305.00 B)
Micromonas commoda id_conversion.mco.csv.gz (282.66 KB) gene_description.mco.csv.gz (308.00 B)
Miscanthus sinensis Not Available Not Available
Musa acuminata id_conversion.mac.csv.gz (461.57 KB) gene_description.mac.csv.gz (517.90 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 (276.59 KB) gene_description.obr.csv.gz (179.15 KB)
Oryza sativa ssp. indica id_conversion.osaindica.csv.gz (221.41 KB) gene_description.osaindica.csv.gz (130.50 KB)
Oryza sativa ssp. japonica id_conversion.osa.csv.gz (805.77 KB) gene_description.osa.csv.gz (364.96 KB)
Phalaenopsis equestris id_conversion.peq.csv.gz (148.39 KB) gene_description.peq.csv.gz (289.00 B)
Phyllostachys edulis id_conversion.ped.csv.gz (178.45 KB) gene_description.ped.csv.gz (340.24 KB)
Physcomitrium 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)
Saccharum spontaneum id_conversion.ssp.csv.gz (942.87 KB) gene_description.ssp.csv.gz (295.00 B)
Selaginella moellendorffii id_conversion.smo.csv.gz (173.29 KB) gene_description.smo.csv.gz (7.08 KB)
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 (541.64 KB) gene_description.tae.csv.gz (561.12 KB)
Triticum turgidum id_conversion.ttu.csv.gz (932.04 KB) gene_description.ttu.csv.gz (698.63 KB)
Vitis vinifera id_conversion.vvi.csv.gz (476.43 KB) gene_description.vvi.csv.gz (306.00 B)
Zea mays B73 id_conversion.zma.csv.gz (736.75 KB) gene_description.zma.csv.gz (429.29 KB)
Zea mays B104 Not Available Not Available
Zea mays PH207 id_conversion.zma-ph207.csv.gz (173.28 KB) gene_description.zma-ph207.csv.gz (311.00 B)
Zostera marina id_conversion.zosmarina.csv.gz (341.63 KB) gene_description.zosmarina.csv.gz (157.48 KB)
Zoysia japonica ssp. nagirizaki id_conversion.zjn.csv.gz (290.00 B) gene_description.zjn.csv.gz (293.00 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 (7.56 MB) interpro.atr.csv.gz (1.92 MB) Not Available
Ananas comosus go.aco.csv.gz (8.59 MB) interpro.aco.csv.gz (2.33 MB) Not Available
Apostasia shenzhenica go.ash.csv.gz (7.33 MB) interpro.ash.csv.gz (1.87 MB) Not Available
Arabidopsis thaliana go.ath.csv.gz (22.43 MB) interpro.ath.csv.gz (2.72 MB) Not Available
Asparagus officinalis go.aof.csv.gz (9.04 MB) interpro.aof.csv.gz (2.25 MB) Not Available
Brachypodium distachyon go.bdi.csv.gz (9.43 MB) interpro.bdi.csv.gz (2.75 MB) Not Available
Calamus simplicifolius go.calsi.csv.gz (14.89 MB) interpro.calsi.csv.gz (3.92 MB) Not Available
Cenchrus americanus go.cam.csv.gz (9.64 MB) interpro.cam.csv.gz (2.72 MB) Not Available
Chlamydomonas reinhardtii go.cre.csv.gz (4.33 MB) interpro.cre.csv.gz (1.29 MB) Not Available
Elaeis guineensis go.egu.csv.gz (10.01 MB) interpro.egu.csv.gz (2.47 MB) Not Available
Hordeum vulgare go.hvu.csv.gz (11.01 MB) interpro.hvu.csv.gz (2.87 MB) Not Available
Lolium perenne go.lpe.csv.gz (10.43 MB) interpro.lpe.csv.gz (3.12 MB) Not Available
Marchantia polymorpha go.mpo.csv.gz (6.12 MB) interpro.mpo.csv.gz (1.53 MB) Not Available
Micromonas commoda go.mco.csv.gz (3.22 MB) interpro.mco.csv.gz (947.30 KB) Not Available
Miscanthus sinensis Not Available Not Available Not Available
Musa acuminata go.mac.csv.gz (13.87 MB) interpro.mac.csv.gz (3.46 MB) Not Available
Oropetium thomaeum go.oth.csv.gz (8.68 MB) interpro.oth.csv.gz (2.09 MB) Not Available
Oryza brachyantha go.obr.csv.gz (8.80 MB) interpro.obr.csv.gz (2.45 MB) Not Available
Oryza sativa ssp. indica go.osaindica.csv.gz (9.59 MB) interpro.osaindica.csv.gz (2.81 MB) Not Available
Oryza sativa ssp. japonica go.osa.csv.gz (10.91 MB) interpro.osa.csv.gz (2.93 MB) Not Available
Phalaenopsis equestris go.peq.csv.gz (8.52 MB) interpro.peq.csv.gz (2.13 MB) Not Available
Phyllostachys edulis go.ped.csv.gz (11.81 MB) interpro.ped.csv.gz (2.97 MB) Not Available
Physcomitrium patens go.ppa.csv.gz (11.66 MB) interpro.ppa.csv.gz (2.42 MB) Not Available
Picea abies go.pab.csv.gz (15.09 MB) interpro.pab.csv.gz (3.43 MB) Not Available
Populus trichocarpa go.ptr.csv.gz (13.46 MB) interpro.ptr.csv.gz (3.67 MB) Not Available
Saccharum spontaneum go.ssp.csv.gz (20.99 MB) interpro.ssp.csv.gz (6.08 MB) Not Available
Selaginella moellendorffii go.smo.csv.gz (12.85 MB) interpro.smo.csv.gz (4.44 MB) Not Available
Setaria italica go.sit.csv.gz (10.01 MB) interpro.sit.csv.gz (2.98 MB) Not Available
Solanum lycopersicum go.sly.csv.gz (10.66 MB) interpro.sly.csv.gz (2.85 MB) Not Available
Sorghum bicolor go.sbi.csv.gz (9.65 MB) interpro.sbi.csv.gz (2.87 MB) Not Available
Spirodela polyrhiza go.spo.csv.gz (7.52 MB) interpro.spo.csv.gz (1.87 MB) Not Available
Triticum aestivum go.tae.csv.gz (30.07 MB) interpro.tae.csv.gz (10.11 MB) Not Available
Triticum turgidum go.ttu.csv.gz (18.34 MB) interpro.ttu.csv.gz (5.90 MB) Not Available
Vitis vinifera go.vvi.csv.gz (8.41 MB) interpro.vvi.csv.gz (2.38 MB) Not Available
Zea mays B73 go.zma.csv.gz (12.67 MB) interpro.zma.csv.gz (3.38 MB) Not Available
Zea mays B104 Not Available Not Available Not Available
Zea mays PH207 go.zma-ph207.csv.gz (12.76 MB) interpro.zma-ph207.csv.gz (3.34 MB) Not Available
Zostera marina go.zosmarina.csv.gz (8.33 MB) interpro.zosmarina.csv.gz (2.02 MB) Not Available
Zoysia japonica ssp. nagirizaki go.zjn.csv.gz (11.59 MB) interpro.zjn.csv.gz (2.54 MB) Not Available

These files contain the genomic sequences for each of the organisms present in this PLAZA instance.
SpeciesGenome
Amborella trichopoda atr.fasta.gz (192.53 MB)
Ananas comosus aco.fasta.gz (107.59 MB)
Apostasia shenzhenica ash.fasta.gz (92.35 MB)
Arabidopsis thaliana ath.fasta.gz (34.28 MB)
Asparagus officinalis aof.fasta.gz (323.41 MB)
Brachypodium distachyon bdi.fasta.gz (78.78 MB)
Calamus simplicifolius calsi.fasta.gz (538.73 MB)
Cenchrus americanus cam.fasta.gz (457.55 MB)
Chlamydomonas reinhardtii cre.fasta.gz (30.17 MB)
Elaeis guineensis egu.fasta.gz (316.51 MB)
Hordeum vulgare hvu.fasta.gz (1.28 GB)
Lolium perenne Not Available
Marchantia polymorpha mpo.fasta.gz (61.58 MB)
Micromonas commoda mco.fasta.gz (6.01 MB)
Miscanthus sinensis Not Available
Musa acuminata mac.fasta.gz (116.86 MB)
Oropetium thomaeum oth.fasta.gz (70.03 MB)
Oryza brachyantha obr.fasta.gz (71.45 MB)
Oryza sativa ssp. indica osaindica.fasta.gz (111.75 MB)
Oryza sativa ssp. japonica osa.fasta.gz (107.59 MB)
Phalaenopsis equestris peq.fasta.gz (290.71 MB)
Phyllostachys edulis ped.fasta.gz (539.39 MB)
Physcomitrium patens ppa.fasta.gz (133.32 MB)
Picea abies pab.fasta.gz (3.46 GB)
Populus trichocarpa ptr.fasta.gz (119.91 MB)
Saccharum spontaneum ssp.fasta.gz (883.56 MB)
Selaginella moellendorffii smo.fasta.gz (59.62 MB)
Setaria italica sit.fasta.gz (116.29 MB)
Solanum lycopersicum sly.fasta.gz (212.02 MB)
Sorghum bicolor sbi.fasta.gz (196.81 MB)
Spirodela polyrhiza spo.fasta.gz (37.83 MB)
Triticum aestivum tae.fasta.gz (3.93 GB)
Triticum turgidum ttu.fasta.gz (2.72 GB)
Vitis vinifera vvi.fasta.gz (133.18 MB)
Zea mays B73 zma.fasta.gz (590.81 MB)
Zea mays B104 Not Available
Zea mays PH207 zma-ph207.fasta.gz (502.81 MB)
Zostera marina zosmarina.fasta.gz (54.94 MB)
Zoysia japonica ssp. nagirizaki zjn.fasta.gz (94.77 MB)

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 (7.25 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)
Apostasia shenzhenica File 1 (6.77 MB) File 2 (6.77 MB) File 3 (6.78 MB) File 4 (6.78 MB) File 5 (4.58 MB) File 6 (4.58 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)
Asparagus officinalis File 1 (7.85 MB) File 2 (7.85 MB) File 3 (7.85 MB) File 4 (7.85 MB) File 5 (5.32 MB) File 6 (5.32 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)
Calamus simplicifolius File 1 (14.65 MB) File 2 (14.65 MB) File 3 (60.00 B) File 4 (64.00 B) File 5 (9.76 MB) File 6 (9.76 MB)
Cenchrus americanus File 1 (10.96 MB) File 2 (10.96 MB) File 3 (10.97 MB) File 4 (10.97 MB) File 5 (7.38 MB) File 6 (7.38 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 (9.00 MB) File 2 (9.00 MB) File 3 (9.87 MB) File 4 (9.87 MB) File 5 (6.04 MB) File 6 (6.04 MB)
Hordeum vulgare File 1 (23.46 MB) File 2 (9.85 MB) File 3 (43.69 MB) File 4 (17.61 MB) File 5 (15.54 MB) File 6 (6.63 MB)
Lolium perenne File 1 (12.41 MB) File 2 (12.41 MB) Not Available Not Available File 5 (8.41 MB) File 6 (8.41 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)
Miscanthus sinensis Not Available Not Available Not Available Not Available Not Available Not Available
Musa acuminata File 1 (14.58 MB) File 2 (11.64 MB) File 3 (18.85 MB) File 4 (14.91 MB) File 5 (9.84 MB) File 6 (7.87 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)
Physcomitrium 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)
Saccharum spontaneum File 1 (17.45 MB) File 2 (17.45 MB) File 3 (30.08 MB) File 4 (30.08 MB) File 5 (11.43 MB) File 6 (11.43 MB)
Selaginella moellendorffii File 1 (16.37 MB) File 2 (12.92 MB) File 3 (20.32 MB) File 4 (15.92 MB) File 5 (10.77 MB) File 6 (8.65 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 (44.58 MB) File 2 (36.26 MB) File 3 (57.14 MB) File 4 (46.43 MB) File 5 (29.65 MB) File 6 (24.05 MB)
Triticum turgidum File 1 (39.35 MB) File 2 (21.50 MB) File 3 (39.36 MB) File 4 (21.50 MB) File 5 (26.02 MB) File 6 (14.35 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 B73 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)
Zea mays B104 Not Available Not Available Not Available Not Available Not Available Not Available
Zea mays PH207 File 1 (12.11 MB) File 2 (12.11 MB) File 3 (14.75 MB) File 4 (14.75 MB) File 5 (8.14 MB) File 6 (8.14 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_intra_species.atr.csv.gz (1008.00 B)
Ananas comosus anchorpoints_intra_species.aco.csv.gz (30.99 KB)
Apostasia shenzhenica anchorpoints_intra_species.ash.csv.gz (7.44 KB)
Arabidopsis thaliana anchorpoints_intra_species.ath.csv.gz (41.80 KB)
Asparagus officinalis anchorpoints_intra_species.aof.csv.gz (12.78 KB)
Brachypodium distachyon anchorpoints_intra_species.bdi.csv.gz (30.14 KB)
Calamus simplicifolius anchorpoints_intra_species.calsi.csv.gz (9.78 KB)
Cenchrus americanus anchorpoints_intra_species.cam.csv.gz (27.17 KB)
Chlamydomonas reinhardtii anchorpoints_intra_species.cre.csv.gz (931.00 B)
Elaeis guineensis anchorpoints_intra_species.egu.csv.gz (80.06 KB)
Hordeum vulgare anchorpoints_intra_species.hvu.csv.gz (17.94 KB)
Lolium perenne anchorpoints_intra_species.lpe.csv.gz (465.00 B)
Marchantia polymorpha anchorpoints_intra_species.mpo.csv.gz (639.00 B)
Micromonas commoda anchorpoints_intra_species.mco.csv.gz (521.00 B)
Miscanthus sinensis Not Available
Musa acuminata anchorpoints_intra_species.mac.csv.gz (131.02 KB)
Oropetium thomaeum anchorpoints_intra_species.oth.csv.gz (32.22 KB)
Oryza brachyantha anchorpoints_intra_species.obr.csv.gz (35.83 KB)
Oryza sativa ssp. indica anchorpoints_intra_species.osaindica.csv.gz (44.59 KB)
Oryza sativa ssp. japonica anchorpoints_intra_species.osa.csv.gz (47.57 KB)
Phalaenopsis equestris anchorpoints_intra_species.peq.csv.gz (1.85 KB)
Phyllostachys edulis anchorpoints_intra_species.ped.csv.gz (25.04 KB)
Physcomitrium patens anchorpoints_intra_species.ppa.csv.gz (23.47 KB)
Picea abies anchorpoints_intra_species.pab.csv.gz (478.00 B)
Populus trichocarpa anchorpoints_intra_species.ptr.csv.gz (160.22 KB)
Saccharum spontaneum anchorpoints_intra_species.ssp.csv.gz (628.29 KB)
Selaginella moellendorffii anchorpoints_intra_species.smo.csv.gz (95.41 KB)
Setaria italica anchorpoints_intra_species.sit.csv.gz (43.20 KB)
Solanum lycopersicum anchorpoints_intra_species.sly.csv.gz (42.35 KB)
Sorghum bicolor anchorpoints_intra_species.sbi.csv.gz (38.28 KB)
Spirodela polyrhiza anchorpoints_intra_species.spo.csv.gz (11.07 KB)
Triticum aestivum anchorpoints_intra_species.tae.csv.gz (1.02 MB)
Triticum turgidum anchorpoints_intra_species.ttu.csv.gz (342.20 KB)
Vitis vinifera anchorpoints_intra_species.vvi.csv.gz (22.72 KB)
Zea mays B73 anchorpoints_intra_species.zma.csv.gz (96.56 KB)
Zea mays B104 Not Available
Zea mays PH207 anchorpoints_intra_species.zma-ph207.csv.gz (88.24 KB)
Zostera marina anchorpoints_intra_species.zosmarina.csv.gz (1.76 KB)
Zoysia japonica ssp. nagirizaki anchorpoints_intra_species.zjn.csv.gz (110.93 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 family genefamily_data.HOMFAM.csv.gz (8.86 MB) genefamily_enrichment.HOMFAM.csv.gz (3.32 MB)
Orthologous gene family genefamily_data.ORTHOFAM.csv.gz (8.39 MB) genefamily_enrichment.ORTHOFAM.csv.gz (5.17 MB)
Homoeologous gene family for Triticum Aestivum Not Available Not Available

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 (332.76 MB)
Orthologous gene family integrative_orthology.ORTHO.csv.gz (2.41 GB)
Anchor point integrative_orthology.anchor_point.csv.gz (74.88 MB)
Best-Hits-and-Inparalogs(BHI)family integrative_orthology.BHIF.csv.gz (436.87 MB)