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 (2.45 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
Actinidia chinensis annotation.all_transcripts.ach.csv.gz (14.32 MB) annotation.selected_transcript.ach.csv.gz (14.32 MB)
Amaranthus hypochondriacus Not Available Not Available
Amborella trichopoda annotation.all_transcripts.atr.csv.gz (8.86 MB) annotation.selected_transcript.atr.csv.gz (8.85 MB)
Arabidopsis lyrata annotation.all_transcripts.aly.csv.gz (13.21 MB) annotation.selected_transcript.aly.csv.gz (12.29 MB)
Arabidopsis thaliana annotation.all_transcripts.ath.csv.gz (28.76 MB) annotation.selected_transcript.ath.csv.gz (22.70 MB)
Arachis ipaensis annotation.all_transcripts.aip.csv.gz (15.92 MB) annotation.selected_transcript.aip.csv.gz (15.92 MB)
Beta vulgaris annotation.all_transcripts.bvu.csv.gz (11.06 MB) annotation.selected_transcript.bvu.csv.gz (10.12 MB)
Brassica oleracea annotation.all_transcripts.bol.csv.gz (20.80 MB) annotation.selected_transcript.bol.csv.gz (20.80 MB)
Brassica rapa annotation.all_transcripts.bra.csv.gz (17.21 MB) annotation.selected_transcript.bra.csv.gz (16.06 MB)
Cajanus cajan annotation.all_transcripts.ccaj.csv.gz (15.41 MB) annotation.selected_transcript.ccaj.csv.gz (15.41 MB)
Capsella rubella annotation.all_transcripts.cru.csv.gz (12.25 MB) annotation.selected_transcript.cru.csv.gz (11.42 MB)
Capsicum annuum annotation.all_transcripts.can.csv.gz (13.01 MB) annotation.selected_transcript.can.csv.gz (13.01 MB)
Carica papaya annotation.all_transcripts.cpa.csv.gz (8.58 MB) annotation.selected_transcript.cpa.csv.gz (8.58 MB)
Chenopodium quinoa annotation.all_transcripts.cqu.csv.gz (19.44 MB) annotation.selected_transcript.cqu.csv.gz (19.44 MB)
Chlamydomonas reinhardtii annotation.all_transcripts.cre.csv.gz (13.32 MB) annotation.selected_transcript.cre.csv.gz (12.15 MB)
Cicer arietinum annotation.all_transcripts.car.csv.gz (26.04 MB) annotation.selected_transcript.car.csv.gz (26.04 MB)
Citrullus lanatus annotation.all_transcripts.cla.csv.gz (71.75 MB) annotation.selected_transcript.cla.csv.gz (71.75 MB)
Citrus clementina annotation.all_transcripts.ccl.csv.gz (13.07 MB) annotation.selected_transcript.ccl.csv.gz (10.52 MB)
Coffea canephora annotation.all_transcripts.ccan.csv.gz (101.74 MB) annotation.selected_transcript.ccan.csv.gz (91.14 MB)
Corchorus olitorius annotation.all_transcripts.col.csv.gz (11.43 MB) annotation.selected_transcript.col.csv.gz (11.43 MB)
Cucumis melo annotation.all_transcripts.cme.csv.gz (11.09 MB) annotation.selected_transcript.cme.csv.gz (9.08 MB)
Cucumis sativus L. annotation.all_transcripts.csa.csv.gz (11.46 MB) annotation.selected_transcript.csa.csv.gz (8.85 MB)
Daucus carota annotation.all_transcripts.dca.csv.gz (12.65 MB) annotation.selected_transcript.dca.csv.gz (12.65 MB)
Erythranthe guttata annotation.all_transcripts.egut.csv.gz (13.32 MB) annotation.selected_transcript.egut.csv.gz (11.29 MB)
Eucalyptus grandis annotation.all_transcripts.egr.csv.gz (16.43 MB) annotation.selected_transcript.egr.csv.gz (13.40 MB)
Fragaria vesca annotation.all_transcripts.fve.csv.gz (13.02 MB) annotation.selected_transcript.fve.csv.gz (13.02 MB)
Glycine max annotation.all_transcripts.gma.csv.gz (30.93 MB) annotation.selected_transcript.gma.csv.gz (22.31 MB)
Gossypium raimondii annotation.all_transcripts.gra.csv.gz (24.06 MB) annotation.selected_transcript.gra.csv.gz (15.21 MB)
Hevea brasiliensis annotation.all_transcripts.hbr.csv.gz (38.30 MB) annotation.selected_transcript.hbr.csv.gz (26.68 MB)
Malus domestica annotation.all_transcripts.mdo.csv.gz (13.73 MB) annotation.selected_transcript.mdo.csv.gz (13.73 MB)
Manihot esculenta annotation.all_transcripts.mes.csv.gz (15.95 MB) annotation.selected_transcript.mes.csv.gz (13.04 MB)
Marchantia polymorpha annotation.all_transcripts.mpo.csv.gz (9.87 MB) annotation.selected_transcript.mpo.csv.gz (7.98 MB)
Medicago truncatula annotation.all_transcripts.mtr.csv.gz (19.97 MB) annotation.selected_transcript.mtr.csv.gz (16.57 MB)
Micromonas commoda annotation.all_transcripts.mco.csv.gz (4.40 MB) annotation.selected_transcript.mco.csv.gz (4.40 MB)
Nelumbo nucifera annotation.all_transcripts.nnu.csv.gz (10.45 MB) annotation.selected_transcript.nnu.csv.gz (10.45 MB)
Oryza sativa ssp. japonica annotation.all_transcripts.osa.csv.gz (18.65 MB) annotation.selected_transcript.osa.csv.gz (15.57 MB)
Petunia axillaris annotation.all_transcripts.pax.csv.gz (13.23 MB) annotation.selected_transcript.pax.csv.gz (13.23 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)
Prunus persica annotation.all_transcripts.ppe.csv.gz (15.87 MB) annotation.selected_transcript.ppe.csv.gz (10.94 MB)
Pyrus bretschneideri annotation.all_transcripts.pbr.csv.gz (16.23 MB) annotation.selected_transcript.pbr.csv.gz (16.23 MB)
Ricinus communis annotation.all_transcripts.rco.csv.gz (10.71 MB) annotation.selected_transcript.rco.csv.gz (10.71 MB)
Schrenkiella parvula annotation.all_transcripts.spa.csv.gz (10.72 MB) annotation.selected_transcript.spa.csv.gz (10.72 MB)
Selaginella moellendorffii annotation.all_transcripts.smo.csv.gz (8.79 MB) annotation.selected_transcript.smo.csv.gz (8.79 MB)
Solanum lycopersicum annotation.all_transcripts.sly.csv.gz (12.27 MB) annotation.selected_transcript.sly.csv.gz (12.27 MB)
Solanum tuberosum annotation.all_transcripts.stu.csv.gz (15.96 MB) annotation.selected_transcript.stu.csv.gz (12.24 MB)
Tarenaya hassleriana annotation.all_transcripts.tha.csv.gz (17.11 MB) annotation.selected_transcript.tha.csv.gz (12.88 MB)
Theobroma cacao annotation.all_transcripts.tca.csv.gz (16.47 MB) annotation.selected_transcript.tca.csv.gz (11.88 MB)
Trifolium pratense annotation.all_transcripts.tpr.csv.gz (14.78 MB) annotation.selected_transcript.tpr.csv.gz (14.23 MB)
Utricularia gibba annotation.all_transcripts.ugi.csv.gz (9.06 MB) annotation.selected_transcript.ugi.csv.gz (8.99 MB)
Vigna radiata var. radiata annotation.all_transcripts.vra.csv.gz (10.28 MB) annotation.selected_transcript.vra.csv.gz (9.82 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)
Ziziphus jujuba annotation.all_transcripts.zju.csv.gz (15.72 MB) annotation.selected_transcript.zju.csv.gz (12.98 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
Actinidia chinensis File 1 (4.36 MB) File 2 (3.29 MB) File 3 (4.36 MB) File 4 (3.29 MB)
Amaranthus hypochondriacus Not Available Not Available Not Available Not Available
Amborella trichopoda File 1 (3.47 MB) File 2 (2.74 MB) File 3 (3.47 MB) File 4 (2.74 MB)
Arabidopsis lyrata File 1 (5.61 MB) File 2 (3.54 MB) File 3 (5.33 MB) File 4 (3.40 MB)
Arabidopsis thaliana File 1 (8.49 MB) File 2 (5.61 MB) File 3 (5.73 MB) File 4 (4.11 MB)
Arachis ipaensis File 1 (6.22 MB) File 2 (4.17 MB) File 3 (6.22 MB) File 4 (4.17 MB)
Beta vulgaris File 1 (4.46 MB) File 2 (2.68 MB) File 3 (4.15 MB) File 4 (2.51 MB)
Brassica oleracea File 1 (7.53 MB) File 2 (5.95 MB) File 3 (7.53 MB) File 4 (5.95 MB)
Brassica rapa File 1 (6.79 MB) File 2 (4.42 MB) File 3 (6.42 MB) File 4 (4.23 MB)
Cajanus cajan File 1 (4.70 MB) File 2 (3.46 MB) File 3 (4.70 MB) File 4 (3.46 MB)
Capsella rubella File 1 (4.57 MB) File 2 (3.08 MB) File 3 (4.33 MB) File 4 (2.95 MB)
Capsicum annuum File 1 (4.19 MB) File 2 (3.21 MB) File 3 (4.19 MB) File 4 (3.21 MB)
Carica papaya File 1 (3.29 MB) File 2 (2.52 MB) File 3 (3.29 MB) File 4 (2.52 MB)
Chenopodium quinoa File 1 (7.06 MB) File 2 (4.91 MB) File 3 (7.06 MB) File 4 (4.91 MB)
Chlamydomonas reinhardtii File 1 (4.50 MB) File 2 (2.93 MB) File 3 (4.20 MB) File 4 (2.77 MB)
Cicer arietinum File 1 (6.49 MB) File 2 (5.73 MB) File 3 (6.49 MB) File 4 (5.73 MB)
Citrullus lanatus File 1 (15.76 MB) File 2 (14.99 MB) File 3 (15.76 MB) File 4 (14.99 MB)
Citrus clementina File 1 (5.33 MB) File 2 (3.40 MB) File 3 (4.06 MB) File 4 (2.73 MB)
Coffea canephora File 1 (17.99 MB) File 2 (16.50 MB) File 3 (17.99 MB) File 4 (16.50 MB)
Corchorus olitorius File 1 (4.42 MB) File 2 (3.44 MB) File 3 (4.42 MB) File 4 (3.44 MB)
Cucumis melo File 1 (4.38 MB) File 2 (2.76 MB) File 3 (3.54 MB) File 4 (2.32 MB)
Cucumis sativus L. File 1 (4.59 MB) File 2 (2.89 MB) File 3 (3.37 MB) File 4 (2.25 MB)
Daucus carota File 1 (4.03 MB) File 2 (3.12 MB) File 3 (4.03 MB) File 4 (3.12 MB)
Erythranthe guttata File 1 (5.43 MB) File 2 (3.49 MB) File 3 (4.69 MB) File 4 (3.10 MB)
Eucalyptus grandis File 1 (7.08 MB) File 2 (4.61 MB) File 3 (5.75 MB) File 4 (3.90 MB)
Fragaria vesca File 1 (4.37 MB) File 2 (3.44 MB) File 3 (4.37 MB) File 4 (3.44 MB)
Glycine max File 1 (14.60 MB) File 2 (9.17 MB) File 3 (10.06 MB) File 4 (6.74 MB)
Gossypium raimondii File 1 (11.73 MB) File 2 (6.89 MB) File 3 (6.26 MB) File 4 (4.00 MB)
Hevea brasiliensis File 1 (11.24 MB) File 2 (7.28 MB) File 3 (7.33 MB) File 4 (5.15 MB)
Malus domestica File 1 (6.18 MB) File 2 (4.61 MB) File 3 (6.18 MB) File 4 (4.61 MB)
Manihot esculenta File 1 (6.86 MB) File 2 (4.47 MB) File 3 (5.71 MB) File 4 (3.85 MB)
Marchantia polymorpha File 1 (4.02 MB) File 2 (2.48 MB) File 3 (3.22 MB) File 4 (2.05 MB)
Medicago truncatula File 1 (8.34 MB) File 2 (5.49 MB) File 3 (6.84 MB) File 4 (4.69 MB)
Micromonas commoda File 1 (885.98 KB) File 2 (660.36 KB) File 3 (885.98 KB) File 4 (660.36 KB)
Nelumbo nucifera File 1 (3.58 MB) File 2 (2.39 MB) File 3 (3.58 MB) File 4 (2.39 MB)
Oryza sativa ssp. japonica File 1 (7.49 MB) File 2 (4.90 MB) File 3 (6.22 MB) File 4 (4.24 MB)
Petunia axillaris File 1 (5.02 MB) File 2 (3.53 MB) File 3 (5.02 MB) File 4 (3.53 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 (9.97 MB) File 2 (6.22 MB) File 3 (7.20 MB) File 4 (4.76 MB)
Prunus persica File 1 (7.75 MB) File 2 (4.75 MB) File 3 (4.78 MB) File 4 (3.17 MB)
Pyrus bretschneideri File 1 (5.20 MB) File 2 (3.62 MB) File 3 (5.20 MB) File 4 (3.62 MB)
Ricinus communis File 1 (4.12 MB) File 2 (3.11 MB) File 3 (4.12 MB) File 4 (3.11 MB)
Schrenkiella parvula File 1 (3.57 MB) File 2 (2.37 MB) File 3 (3.57 MB) File 4 (2.37 MB)
Selaginella moellendorffii File 1 (3.50 MB) File 2 (2.64 MB) File 3 (3.50 MB) File 4 (2.64 MB)
Solanum lycopersicum File 1 (5.01 MB) File 2 (3.52 MB) File 3 (5.01 MB) File 4 (3.52 MB)
Solanum tuberosum File 1 (5.68 MB) File 2 (4.18 MB) File 3 (4.53 MB) File 4 (3.46 MB)
Tarenaya hassleriana File 1 (7.66 MB) File 2 (4.84 MB) File 3 (5.65 MB) File 4 (3.76 MB)
Theobroma cacao File 1 (7.93 MB) File 2 (4.88 MB) File 3 (5.58 MB) File 4 (3.61 MB)
Trifolium pratense File 1 (6.55 MB) File 2 (4.26 MB) File 3 (6.38 MB) File 4 (4.17 MB)
Utricularia gibba File 1 (3.18 MB) File 2 (2.39 MB) File 3 (3.16 MB) File 4 (2.38 MB)
Vigna radiata var. radiata File 1 (3.89 MB) File 2 (2.61 MB) File 3 (3.73 MB) File 4 (2.52 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)
Ziziphus jujuba File 1 (6.52 MB) File 2 (4.23 MB) File 3 (5.40 MB) File 4 (3.63 MB)

These files contain the mapping between genes and transcripts.
SpeciesAll transcriptsSelected transcript
Actinidia chinensis transcript_mapping.all_transcripts.ach.csv.gz (192.80 KB) transcript_mapping.selected_transcript.ach.csv.gz (192.81 KB)
Amaranthus hypochondriacus Not Available Not Available
Amborella trichopoda transcript_mapping.all_transcripts.atr.csv.gz (129.39 KB) transcript_mapping.selected_transcript.atr.csv.gz (129.39 KB)
Arabidopsis lyrata transcript_mapping.all_transcripts.aly.csv.gz (163.22 KB) transcript_mapping.selected_transcript.aly.csv.gz (151.63 KB)
Arabidopsis thaliana transcript_mapping.all_transcripts.ath.csv.gz (432.25 KB) transcript_mapping.selected_transcript.ath.csv.gz (352.87 KB)
Arachis ipaensis transcript_mapping.all_transcripts.aip.csv.gz (226.05 KB) transcript_mapping.selected_transcript.aip.csv.gz (226.06 KB)
Beta vulgaris transcript_mapping.all_transcripts.bvu.csv.gz (227.41 KB) transcript_mapping.selected_transcript.bvu.csv.gz (210.43 KB)
Brassica oleracea transcript_mapping.all_transcripts.bol.csv.gz (289.49 KB) transcript_mapping.selected_transcript.bol.csv.gz (289.49 KB)
Brassica rapa transcript_mapping.all_transcripts.bra.csv.gz (210.71 KB) transcript_mapping.selected_transcript.bra.csv.gz (195.95 KB)
Cajanus cajan transcript_mapping.all_transcripts.ccaj.csv.gz (247.25 KB) transcript_mapping.selected_transcript.ccaj.csv.gz (247.25 KB)
Capsella rubella transcript_mapping.all_transcripts.cru.csv.gz (144.49 KB) transcript_mapping.selected_transcript.cru.csv.gz (133.59 KB)
Capsicum annuum transcript_mapping.all_transcripts.can.csv.gz (156.19 KB) transcript_mapping.selected_transcript.can.csv.gz (156.19 KB)
Carica papaya transcript_mapping.all_transcripts.cpa.csv.gz (115.82 KB) transcript_mapping.selected_transcript.cpa.csv.gz (115.61 KB)
Chenopodium quinoa transcript_mapping.all_transcripts.cqu.csv.gz (223.81 KB) transcript_mapping.selected_transcript.cqu.csv.gz (223.82 KB)
Chlamydomonas reinhardtii transcript_mapping.all_transcripts.cre.csv.gz (105.91 KB) transcript_mapping.selected_transcript.cre.csv.gz (96.17 KB)
Cicer arietinum transcript_mapping.all_transcripts.car.csv.gz (873.05 KB) transcript_mapping.selected_transcript.car.csv.gz (873.05 KB)
Citrullus lanatus transcript_mapping.all_transcripts.cla.csv.gz (2.95 MB) transcript_mapping.selected_transcript.cla.csv.gz (2.95 MB)
Citrus clementina transcript_mapping.all_transcripts.ccl.csv.gz (173.53 KB) transcript_mapping.selected_transcript.ccl.csv.gz (129.73 KB)
Coffea canephora transcript_mapping.all_transcripts.ccan.csv.gz (2.66 MB) transcript_mapping.selected_transcript.ccan.csv.gz (2.34 MB)
Corchorus olitorius transcript_mapping.all_transcripts.col.csv.gz (191.26 KB) transcript_mapping.selected_transcript.col.csv.gz (191.27 KB)
Cucumis melo transcript_mapping.all_transcripts.cme.csv.gz (176.75 KB) transcript_mapping.selected_transcript.cme.csv.gz (145.31 KB)
Cucumis sativus L. transcript_mapping.all_transcripts.csa.csv.gz (146.63 KB) transcript_mapping.selected_transcript.csa.csv.gz (112.22 KB)
Daucus carota transcript_mapping.all_transcripts.dca.csv.gz (152.90 KB) transcript_mapping.selected_transcript.dca.csv.gz (152.87 KB)
Erythranthe guttata transcript_mapping.all_transcripts.egut.csv.gz (157.01 KB) transcript_mapping.selected_transcript.egut.csv.gz (132.42 KB)
Eucalyptus grandis transcript_mapping.all_transcripts.egr.csv.gz (221.40 KB) transcript_mapping.selected_transcript.egr.csv.gz (182.12 KB)
Fragaria vesca transcript_mapping.all_transcripts.fve.csv.gz (157.43 KB) transcript_mapping.selected_transcript.fve.csv.gz (157.43 KB)
Glycine max transcript_mapping.all_transcripts.gma.csv.gz (375.93 KB) transcript_mapping.selected_transcript.gma.csv.gz (249.40 KB)
Gossypium raimondii transcript_mapping.all_transcripts.gra.csv.gz (315.97 KB) transcript_mapping.selected_transcript.gra.csv.gz (169.00 KB)
Hevea brasiliensis transcript_mapping.all_transcripts.hbr.csv.gz (287.08 KB) transcript_mapping.selected_transcript.hbr.csv.gz (198.96 KB)
Malus domestica transcript_mapping.all_transcripts.mdo.csv.gz (278.02 KB) transcript_mapping.selected_transcript.mdo.csv.gz (278.02 KB)
Manihot esculenta transcript_mapping.all_transcripts.mes.csv.gz (184.70 KB) transcript_mapping.selected_transcript.mes.csv.gz (147.50 KB)
Marchantia polymorpha transcript_mapping.all_transcripts.mpo.csv.gz (108.64 KB) transcript_mapping.selected_transcript.mpo.csv.gz (86.50 KB)
Medicago truncatula transcript_mapping.all_transcripts.mtr.csv.gz (303.38 KB) transcript_mapping.selected_transcript.mtr.csv.gz (259.05 KB)
Micromonas commoda transcript_mapping.all_transcripts.mco.csv.gz (49.41 KB) transcript_mapping.selected_transcript.mco.csv.gz (49.42 KB)
Nelumbo nucifera transcript_mapping.all_transcripts.nnu.csv.gz (131.49 KB) transcript_mapping.selected_transcript.nnu.csv.gz (131.49 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)
Petunia axillaris transcript_mapping.all_transcripts.pax.csv.gz (198.47 KB) transcript_mapping.selected_transcript.pax.csv.gz (198.48 KB)
Physcomitrium patens transcript_mapping.all_transcripts.ppa.csv.gz (350.03 KB) transcript_mapping.selected_transcript.ppa.csv.gz (167.32 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)
Prunus persica transcript_mapping.all_transcripts.ppe.csv.gz (198.90 KB) transcript_mapping.selected_transcript.ppe.csv.gz (129.39 KB)
Pyrus bretschneideri transcript_mapping.all_transcripts.pbr.csv.gz (217.58 KB) transcript_mapping.selected_transcript.pbr.csv.gz (217.58 KB)
Ricinus communis transcript_mapping.all_transcripts.rco.csv.gz (142.54 KB) transcript_mapping.selected_transcript.rco.csv.gz (142.54 KB)
Schrenkiella parvula transcript_mapping.all_transcripts.spa.csv.gz (125.16 KB) transcript_mapping.selected_transcript.spa.csv.gz (125.16 KB)
Selaginella moellendorffii transcript_mapping.all_transcripts.smo.csv.gz (98.01 KB) transcript_mapping.selected_transcript.smo.csv.gz (98.02 KB)
Solanum lycopersicum transcript_mapping.all_transcripts.sly.csv.gz (179.22 KB) transcript_mapping.selected_transcript.sly.csv.gz (179.23 KB)
Solanum tuberosum transcript_mapping.all_transcripts.stu.csv.gz (292.70 KB) transcript_mapping.selected_transcript.stu.csv.gz (211.29 KB)
Tarenaya hassleriana transcript_mapping.all_transcripts.tha.csv.gz (230.58 KB) transcript_mapping.selected_transcript.tha.csv.gz (165.25 KB)
Theobroma cacao transcript_mapping.all_transcripts.tca.csv.gz (205.72 KB) transcript_mapping.selected_transcript.tca.csv.gz (146.09 KB)
Trifolium pratense transcript_mapping.all_transcripts.tpr.csv.gz (188.48 KB) transcript_mapping.selected_transcript.tpr.csv.gz (181.47 KB)
Utricularia gibba transcript_mapping.all_transcripts.ugi.csv.gz (119.87 KB) transcript_mapping.selected_transcript.ugi.csv.gz (118.26 KB)
Vigna radiata var. radiata transcript_mapping.all_transcripts.vra.csv.gz (111.87 KB) transcript_mapping.selected_transcript.vra.csv.gz (106.69 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)
Ziziphus jujuba transcript_mapping.all_transcripts.zju.csv.gz (202.49 KB) transcript_mapping.selected_transcript.zju.csv.gz (163.82 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
Actinidia chinensis id_conversion.ach.csv.gz (282.00 B) gene_description.ach.csv.gz (794.77 KB)
Amaranthus hypochondriacus Not Available Not Available
Amborella trichopoda id_conversion.atr.csv.gz (738.80 KB) gene_description.atr.csv.gz (301.00 B)
Arabidopsis lyrata id_conversion.aly.csv.gz (799.77 KB) gene_description.aly.csv.gz (301.00 B)
Arabidopsis thaliana id_conversion.ath.csv.gz (661.94 KB) gene_description.ath.csv.gz (1.01 MB)
Arachis ipaensis id_conversion.aip.csv.gz (286.00 B) gene_description.aip.csv.gz (642.07 KB)
Beta vulgaris id_conversion.bvu.csv.gz (284.00 B) gene_description.bvu.csv.gz (287.00 B)
Brassica oleracea id_conversion.bol.csv.gz (1.48 MB) gene_description.bol.csv.gz (201.12 KB)
Brassica rapa id_conversion.bra.csv.gz (818.05 KB) gene_description.bra.csv.gz (302.00 B)
Cajanus cajan id_conversion.ccaj.csv.gz (288.00 B) gene_description.ccaj.csv.gz (291.00 B)
Capsella rubella id_conversion.cru.csv.gz (426.98 KB) gene_description.cru.csv.gz (298.00 B)
Capsicum annuum id_conversion.can.csv.gz (281.42 KB) gene_description.can.csv.gz (282.00 B)
Carica papaya id_conversion.cpa.csv.gz (439.14 KB) gene_description.cpa.csv.gz (299.00 B)
Chenopodium quinoa id_conversion.cqu.csv.gz (650.67 KB) gene_description.cqu.csv.gz (588.33 KB)
Chlamydomonas reinhardtii id_conversion.cre.csv.gz (445.17 KB) gene_description.cre.csv.gz (188.78 KB)
Cicer arietinum id_conversion.car.csv.gz (1.49 MB) gene_description.car.csv.gz (5.57 KB)
Citrullus lanatus id_conversion.cla.csv.gz (5.64 MB) gene_description.cla.csv.gz (227.82 KB)
Citrus clementina id_conversion.ccl.csv.gz (412.38 KB) gene_description.ccl.csv.gz (299.00 B)
Coffea canephora id_conversion.ccan.csv.gz (7.25 MB) gene_description.ccan.csv.gz (283.91 KB)
Corchorus olitorius id_conversion.col.csv.gz (916.71 KB) gene_description.col.csv.gz (256.60 KB)
Cucumis melo id_conversion.cme.csv.gz (143.73 KB) gene_description.cme.csv.gz (298.00 B)
Cucumis sativus L. id_conversion.csa.csv.gz (317.44 KB) gene_description.csa.csv.gz (302.00 B)
Daucus carota id_conversion.dca.csv.gz (479.30 KB) gene_description.dca.csv.gz (86.21 KB)
Erythranthe guttata id_conversion.egut.csv.gz (710.59 KB) gene_description.egut.csv.gz (305.00 B)
Eucalyptus grandis id_conversion.egr.csv.gz (1.01 MB) gene_description.egr.csv.gz (301.00 B)
Fragaria vesca id_conversion.fve.csv.gz (771.53 KB) gene_description.fve.csv.gz (298.00 B)
Glycine max id_conversion.gma.csv.gz (1.89 MB) gene_description.gma.csv.gz (299.00 B)
Gossypium raimondii id_conversion.gra.csv.gz (610.25 KB) gene_description.gra.csv.gz (301.00 B)
Hevea brasiliensis id_conversion.hbr.csv.gz (1.26 MB) gene_description.hbr.csv.gz (492.96 KB)
Malus domestica id_conversion.mdo.csv.gz (622.91 KB) gene_description.mdo.csv.gz (7.27 KB)
Manihot esculenta id_conversion.mes.csv.gz (1.08 MB) gene_description.mes.csv.gz (300.00 B)
Marchantia polymorpha id_conversion.mpo.csv.gz (379.45 KB) gene_description.mpo.csv.gz (302.00 B)
Medicago truncatula id_conversion.mtr.csv.gz (856.55 KB) gene_description.mtr.csv.gz (450.71 KB)
Micromonas commoda id_conversion.mco.csv.gz (287.68 KB) gene_description.mco.csv.gz (306.00 B)
Nelumbo nucifera id_conversion.nnu.csv.gz (510.00 B) gene_description.nnu.csv.gz (305.80 KB)
Oryza sativa ssp. japonica id_conversion.osa.csv.gz (930.73 KB) gene_description.osa.csv.gz (364.96 KB)
Petunia axillaris id_conversion.pax.csv.gz (370.08 KB) gene_description.pax.csv.gz (364.62 KB)
Physcomitrium patens id_conversion.ppa.csv.gz (785.85 KB) gene_description.ppa.csv.gz (301.00 B)
Picea abies id_conversion.pab.csv.gz (350.66 KB) gene_description.pab.csv.gz (280.00 B)
Populus trichocarpa id_conversion.ptr.csv.gz (1.16 MB) gene_description.ptr.csv.gz (415.35 KB)
Prunus persica id_conversion.ppe.csv.gz (895.08 KB) gene_description.ppe.csv.gz (298.00 B)
Pyrus bretschneideri id_conversion.pbr.csv.gz (281.00 B) gene_description.pbr.csv.gz (284.00 B)
Ricinus communis id_conversion.rco.csv.gz (693.28 KB) gene_description.rco.csv.gz (240.04 KB)
Schrenkiella parvula id_conversion.spa.csv.gz (277.00 B) gene_description.spa.csv.gz (266.11 KB)
Selaginella moellendorffii id_conversion.smo.csv.gz (625.03 KB) gene_description.smo.csv.gz (306.00 B)
Solanum lycopersicum id_conversion.sly.csv.gz (667.15 KB) gene_description.sly.csv.gz (806.71 KB)
Solanum tuberosum id_conversion.stu.csv.gz (692.52 KB) gene_description.stu.csv.gz (340.07 KB)
Tarenaya hassleriana id_conversion.tha.csv.gz (849.97 KB) gene_description.tha.csv.gz (357.43 KB)
Theobroma cacao id_conversion.tca.csv.gz (901.57 KB) gene_description.tca.csv.gz (288.68 KB)
Trifolium pratense id_conversion.tpr.csv.gz (849.29 KB) gene_description.tpr.csv.gz (299.00 B)
Utricularia gibba id_conversion.ugi.csv.gz (532.30 KB) gene_description.ugi.csv.gz (290.00 B)
Vigna radiata var. radiata id_conversion.vra.csv.gz (232.98 KB) gene_description.vra.csv.gz (283.00 B)
Vitis vinifera id_conversion.vvi.csv.gz (477.43 KB) gene_description.vvi.csv.gz (304.00 B)
Zea mays id_conversion.zma.csv.gz (736.75 KB) gene_description.zma.csv.gz (429.28 KB)
Ziziphus jujuba id_conversion.zju.csv.gz (882.22 KB) gene_description.zju.csv.gz (352.10 KB)

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
Actinidia chinensis go.ach.csv.gz (14.63 MB) interpro.ach.csv.gz (3.39 MB) mapman.ach.csv.gz (280.00 B)
Amaranthus hypochondriacus Not Available Not Available Not Available
Amborella trichopoda go.atr.csv.gz (8.69 MB) interpro.atr.csv.gz (1.79 MB) mapman.atr.csv.gz (294.00 B)
Arabidopsis lyrata go.aly.csv.gz (11.80 MB) interpro.aly.csv.gz (3.12 MB) mapman.aly.csv.gz (294.00 B)
Arabidopsis thaliana go.ath.csv.gz (28.49 MB) interpro.ath.csv.gz (2.55 MB) mapman.ath.csv.gz (260.00 B)
Arachis ipaensis go.aip.csv.gz (13.02 MB) interpro.aip.csv.gz (3.54 MB) mapman.aip.csv.gz (282.00 B)
Beta vulgaris go.bvu.csv.gz (9.21 MB) interpro.bvu.csv.gz (2.43 MB) mapman.bvu.csv.gz (281.00 B)
Brassica oleracea go.bol.csv.gz (22.87 MB) interpro.bol.csv.gz (4.94 MB) mapman.bol.csv.gz (294.00 B)
Brassica rapa go.bra.csv.gz (16.74 MB) interpro.bra.csv.gz (4.32 MB) mapman.bra.csv.gz (294.00 B)
Cajanus cajan go.ccaj.csv.gz (12.60 MB) interpro.ccaj.csv.gz (3.68 MB) mapman.ccaj.csv.gz (285.00 B)
Capsella rubella go.cru.csv.gz (11.75 MB) interpro.cru.csv.gz (2.99 MB) mapman.cru.csv.gz (293.00 B)
Capsicum annuum go.can.csv.gz (13.30 MB) interpro.can.csv.gz (3.37 MB) mapman.can.csv.gz (275.00 B)
Carica papaya go.cpa.csv.gz (9.27 MB) interpro.cpa.csv.gz (2.09 MB) mapman.cpa.csv.gz (291.00 B)
Chenopodium quinoa go.cqu.csv.gz (17.48 MB) interpro.cqu.csv.gz (4.72 MB) mapman.cqu.csv.gz (299.00 B)
Chlamydomonas reinhardtii go.cre.csv.gz (5.24 MB) interpro.cre.csv.gz (1.26 MB) mapman.cre.csv.gz (297.00 B)
Cicer arietinum go.car.csv.gz (9.63 MB) interpro.car.csv.gz (2.43 MB) mapman.car.csv.gz (273.00 B)
Citrullus lanatus go.cla.csv.gz (9.24 MB) interpro.cla.csv.gz (2.23 MB) mapman.cla.csv.gz (280.00 B)
Citrus clementina go.ccl.csv.gz (10.38 MB) interpro.ccl.csv.gz (2.74 MB) mapman.ccl.csv.gz (294.00 B)
Coffea canephora go.ccan.csv.gz (9.93 MB) interpro.ccan.csv.gz (2.68 MB) mapman.ccan.csv.gz (271.00 B)
Corchorus olitorius go.col.csv.gz (12.25 MB) interpro.col.csv.gz (2.67 MB) mapman.col.csv.gz (306.00 B)
Cucumis melo go.cme.csv.gz (9.47 MB) interpro.cme.csv.gz (2.18 MB) mapman.cme.csv.gz (291.00 B)
Cucumis sativus L. go.csa.csv.gz (8.94 MB) interpro.csa.csv.gz (2.18 MB) mapman.csa.csv.gz (296.00 B)
Daucus carota go.dca.csv.gz (12.66 MB) interpro.dca.csv.gz (3.08 MB) mapman.dca.csv.gz (289.00 B)
Erythranthe guttata go.egut.csv.gz (12.90 MB) interpro.egut.csv.gz (2.58 MB) mapman.egut.csv.gz (299.00 B)
Eucalyptus grandis go.egr.csv.gz (12.97 MB) interpro.egr.csv.gz (3.51 MB) mapman.egr.csv.gz (295.00 B)
Fragaria vesca go.fve.csv.gz (9.78 MB) interpro.fve.csv.gz (2.72 MB) mapman.fve.csv.gz (291.00 B)
Glycine max go.gma.csv.gz (22.12 MB) interpro.gma.csv.gz (5.65 MB) mapman.gma.csv.gz (293.00 B)
Gossypium raimondii go.gra.csv.gz (15.59 MB) interpro.gra.csv.gz (4.03 MB) mapman.gra.csv.gz (295.00 B)
Hevea brasiliensis go.hbr.csv.gz (14.31 MB) interpro.hbr.csv.gz (3.93 MB) mapman.hbr.csv.gz (277.00 B)
Malus domestica go.mdo.csv.gz (14.08 MB) interpro.mdo.csv.gz (2.82 MB) mapman.mdo.csv.gz (284.00 B)
Manihot esculenta go.mes.csv.gz (12.88 MB) interpro.mes.csv.gz (3.42 MB) mapman.mes.csv.gz (293.00 B)
Marchantia polymorpha go.mpo.csv.gz (6.47 MB) interpro.mpo.csv.gz (1.45 MB) mapman.mpo.csv.gz (296.00 B)
Medicago truncatula go.mtr.csv.gz (14.11 MB) interpro.mtr.csv.gz (3.84 MB) mapman.mtr.csv.gz (296.00 B)
Micromonas commoda go.mco.csv.gz (3.57 MB) interpro.mco.csv.gz (898.19 KB) mapman.mco.csv.gz (299.00 B)
Nelumbo nucifera go.nnu.csv.gz (11.60 MB) interpro.nnu.csv.gz (2.66 MB) mapman.nnu.csv.gz (270.00 B)
Oryza sativa ssp. japonica go.osa.csv.gz (16.06 MB) interpro.osa.csv.gz (2.77 MB) mapman.osa.csv.gz (300.00 B)
Petunia axillaris go.pax.csv.gz (12.93 MB) interpro.pax.csv.gz (3.42 MB) mapman.pax.csv.gz (280.00 B)
Physcomitrium patens go.ppa.csv.gz (12.46 MB) interpro.ppa.csv.gz (2.27 MB) mapman.ppa.csv.gz (294.00 B)
Picea abies go.pab.csv.gz (16.15 MB) interpro.pab.csv.gz (3.21 MB) mapman.pab.csv.gz (273.00 B)
Populus trichocarpa go.ptr.csv.gz (15.94 MB) interpro.ptr.csv.gz (3.44 MB) mapman.ptr.csv.gz (298.00 B)
Prunus persica go.ppe.csv.gz (10.10 MB) interpro.ppe.csv.gz (2.80 MB) mapman.ppe.csv.gz (292.00 B)
Pyrus bretschneideri go.pbr.csv.gz (16.54 MB) interpro.pbr.csv.gz (4.14 MB) mapman.pbr.csv.gz (277.00 B)
Ricinus communis go.rco.csv.gz (9.96 MB) interpro.rco.csv.gz (2.71 MB) mapman.rco.csv.gz (292.00 B)
Schrenkiella parvula go.spa.csv.gz (10.45 MB) interpro.spa.csv.gz (2.63 MB) mapman.spa.csv.gz (273.00 B)
Selaginella moellendorffii go.smo.csv.gz (8.27 MB) interpro.smo.csv.gz (1.99 MB) mapman.smo.csv.gz (300.00 B)
Solanum lycopersicum go.sly.csv.gz (12.50 MB) interpro.sly.csv.gz (2.67 MB) mapman.sly.csv.gz (280.00 B)
Solanum tuberosum go.stu.csv.gz (11.75 MB) interpro.stu.csv.gz (3.02 MB) mapman.stu.csv.gz (294.00 B)
Tarenaya hassleriana go.tha.csv.gz (13.36 MB) interpro.tha.csv.gz (3.29 MB) mapman.tha.csv.gz (302.00 B)
Theobroma cacao go.tca.csv.gz (9.68 MB) interpro.tca.csv.gz (2.77 MB) mapman.tca.csv.gz (305.00 B)
Trifolium pratense go.tpr.csv.gz (13.23 MB) interpro.tpr.csv.gz (3.43 MB) mapman.tpr.csv.gz (293.00 B)
Utricularia gibba go.ugi.csv.gz (10.10 MB) interpro.ugi.csv.gz (2.16 MB) mapman.ugi.csv.gz (284.00 B)
Vigna radiata var. radiata go.vra.csv.gz (10.22 MB) interpro.vra.csv.gz (2.46 MB) mapman.vra.csv.gz (277.00 B)
Vitis vinifera go.vvi.csv.gz (10.09 MB) interpro.vvi.csv.gz (2.25 MB) mapman.vvi.csv.gz (297.00 B)
Zea mays go.zma.csv.gz (15.90 MB) interpro.zma.csv.gz (3.15 MB) mapman.zma.csv.gz (273.00 B)
Ziziphus jujuba go.zju.csv.gz (12.02 MB) interpro.zju.csv.gz (3.37 MB) mapman.zju.csv.gz (308.00 B)

These files contain the genomic sequences for each of the organisms present in this PLAZA instance.
SpeciesGenome
Actinidia chinensis ach.con.gz (173.18 MB)
Amaranthus hypochondriacus Not Available
Amborella trichopoda atr.con.gz (192.53 MB)
Arabidopsis lyrata aly.con.gz (52.55 MB)
Arabidopsis thaliana ath.con.gz (34.28 MB)
Arachis ipaensis aip.con.gz (356.29 MB)
Beta vulgaris bvu.con.gz (149.54 MB)
Brassica oleracea bol.con.gz (128.55 MB)
Brassica rapa bra.con.gz (74.03 MB)
Cajanus cajan ccaj.con.gz (162.57 MB)
Capsella rubella cru.con.gz (37.20 MB)
Capsicum annuum can.con.gz (1.61 GB)
Carica papaya cpa.con.gz (72.23 MB)
Chenopodium quinoa cqu.con.gz (361.77 MB)
Chlamydomonas reinhardtii cre.con.gz (30.17 MB)
Cicer arietinum car.con.gz (92.15 MB)
Citrullus lanatus cla.con.gz (93.31 MB)
Citrus clementina ccl.con.gz (83.32 MB)
Coffea canephora ccan.con.gz (135.68 MB)
Corchorus olitorius col.con.gz (94.97 MB)
Cucumis melo cme.con.gz (97.78 MB)
Cucumis sativus L. csa.con.gz (55.81 MB)
Daucus carota dca.con.gz (109.15 MB)
Erythranthe guttata egut.con.gz (79.88 MB)
Eucalyptus grandis egr.con.gz (185.33 MB)
Fragaria vesca fve.con.gz (56.15 MB)
Glycine max gma.con.gz (269.88 MB)
Gossypium raimondii gra.con.gz (214.00 MB)
Hevea brasiliensis hbr.con.gz (361.23 MB)
Malus domestica mdo.con.gz (182.74 MB)
Manihot esculenta mes.con.gz (142.37 MB)
Marchantia polymorpha mpo.con.gz (61.58 MB)
Medicago truncatula mtr.con.gz (110.93 MB)
Micromonas commoda mco.con.gz (6.01 MB)
Nelumbo nucifera nnu.con.gz (208.68 MB)
Oryza sativa ssp. japonica osa.con.gz (107.59 MB)
Petunia axillaris pax.con.gz (345.99 MB)
Physcomitrium patens ppa.con.gz (133.32 MB)
Picea abies pab.con.gz (3.46 GB)
Populus trichocarpa ptr.con.gz (119.91 MB)
Prunus persica ppe.con.gz (63.77 MB)
Pyrus bretschneideri pbr.con.gz (142.28 MB)
Ricinus communis rco.con.gz (93.96 MB)
Schrenkiella parvula spa.con.gz (35.52 MB)
Selaginella moellendorffii smo.con.gz (59.74 MB)
Solanum lycopersicum sly.con.gz (212.02 MB)
Solanum tuberosum stu.con.gz (193.35 MB)
Tarenaya hassleriana tha.con.gz (62.90 MB)
Theobroma cacao tca.con.gz (94.05 MB)
Trifolium pratense tpr.con.gz (89.81 MB)
Utricularia gibba ugi.con.gz (23.45 MB)
Vigna radiata var. radiata vra.con.gz (123.67 MB)
Vitis vinifera vvi.con.gz (133.18 MB)
Zea mays zma.con.gz (590.81 MB)
Ziziphus jujuba zju.con.gz (116.45 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
Actinidia chinensis File 1 (11.78 MB) File 2 (11.78 MB) File 3 (11.78 MB) File 4 (11.78 MB) File 5 (7.98 MB) File 6 (7.98 MB)
Amaranthus hypochondriacus Not Available Not Available Not Available Not Available Not Available Not Available
Amborella trichopoda File 1 (7.25 MB) File 2 (7.25 MB) File 3 (7.26 MB) File 4 (7.25 MB) File 5 (4.88 MB) File 6 (4.88 MB)
Arabidopsis lyrata File 1 (10.70 MB) File 2 (9.98 MB) File 3 (13.87 MB) File 4 (12.92 MB) File 5 (7.18 MB) File 6 (6.69 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)
Arachis ipaensis File 1 (12.57 MB) File 2 (12.57 MB) File 3 (16.21 MB) File 4 (16.21 MB) File 5 (8.46 MB) File 6 (8.46 MB)
Beta vulgaris File 1 (8.91 MB) File 2 (8.19 MB) File 3 (12.39 MB) File 4 (11.51 MB) File 5 (5.90 MB) File 6 (5.41 MB)
Brassica oleracea File 1 (17.26 MB) File 2 (17.26 MB) File 3 (17.27 MB) File 4 (17.27 MB) File 5 (11.55 MB) File 6 (11.55 MB)
Brassica rapa File 1 (14.12 MB) File 2 (13.21 MB) File 3 (17.32 MB) File 4 (16.07 MB) File 5 (9.51 MB) File 6 (8.89 MB)
Cajanus cajan File 1 (12.92 MB) File 2 (12.92 MB) File 3 (12.94 MB) File 4 (12.94 MB) File 5 (8.61 MB) File 6 (8.61 MB)
Capsella rubella File 1 (10.10 MB) File 2 (9.44 MB) File 3 (12.79 MB) File 4 (11.78 MB) File 5 (6.80 MB) File 6 (6.35 MB)
Capsicum annuum File 1 (10.76 MB) File 2 (10.76 MB) File 3 (10.76 MB) File 4 (10.77 MB) File 5 (7.20 MB) File 6 (7.20 MB)
Carica papaya File 1 (7.03 MB) File 2 (7.03 MB) File 3 (7.05 MB) File 4 (7.04 MB) File 5 (4.75 MB) File 6 (4.75 MB)
Chenopodium quinoa File 1 (15.90 MB) File 2 (15.90 MB) File 3 (18.98 MB) File 4 (18.98 MB) File 5 (10.60 MB) File 6 (10.60 MB)
Chlamydomonas reinhardtii File 1 (11.14 MB) File 2 (10.19 MB) File 3 (16.89 MB) File 4 (15.44 MB) File 5 (7.34 MB) File 6 (6.71 MB)
Cicer arietinum File 1 (7.91 MB) File 2 (7.91 MB) File 3 (21.54 MB) File 4 (21.54 MB) File 5 (5.29 MB) File 6 (5.29 MB)
Citrullus lanatus File 1 (7.33 MB) File 2 (7.33 MB) File 3 (59.18 MB) File 4 (59.18 MB) File 5 (4.93 MB) File 6 (4.93 MB)
Citrus clementina File 1 (10.66 MB) File 2 (8.67 MB) File 3 (14.07 MB) File 4 (10.85 MB) File 5 (7.10 MB) File 6 (5.77 MB)
Coffea canephora File 1 (8.50 MB) File 2 (8.50 MB) File 3 (91.52 MB) File 4 (82.46 MB) File 5 (5.68 MB) File 6 (5.68 MB)
Corchorus olitorius File 1 (9.42 MB) File 2 (9.42 MB) File 3 (9.59 MB) File 4 (9.59 MB) File 5 (6.32 MB) File 6 (6.32 MB)
Cucumis melo File 1 (8.88 MB) File 2 (7.35 MB) File 3 (11.51 MB) File 4 (9.25 MB) File 5 (5.90 MB) File 6 (4.87 MB)
Cucumis sativus L. File 1 (9.25 MB) File 2 (7.24 MB) File 3 (11.79 MB) File 4 (8.95 MB) File 5 (5.99 MB) File 6 (4.64 MB)
Daucus carota File 1 (10.53 MB) File 2 (10.53 MB) File 3 (10.54 MB) File 4 (10.53 MB) File 5 (7.07 MB) File 6 (7.07 MB)
Erythranthe guttata File 1 (10.84 MB) File 2 (9.25 MB) File 3 (13.94 MB) File 4 (11.74 MB) File 5 (7.21 MB) File 6 (6.14 MB)
Eucalyptus grandis File 1 (13.28 MB) File 2 (10.94 MB) File 3 (17.63 MB) File 4 (14.08 MB) File 5 (8.66 MB) File 6 (7.11 MB)
Fragaria vesca File 1 (10.83 MB) File 2 (10.83 MB) File 3 (10.82 MB) File 4 (10.82 MB) File 5 (7.10 MB) File 6 (7.10 MB)
Glycine max File 1 (24.88 MB) File 2 (18.13 MB) File 3 (35.66 MB) File 4 (25.49 MB) File 5 (16.72 MB) File 6 (12.21 MB)
Gossypium raimondii File 1 (19.29 MB) File 2 (12.40 MB) File 3 (27.54 MB) File 4 (17.04 MB) File 5 (12.93 MB) File 6 (8.34 MB)
Hevea brasiliensis File 1 (23.66 MB) File 2 (14.66 MB) File 3 (26.47 MB) File 4 (19.95 MB) File 5 (15.64 MB) File 6 (9.68 MB)
Malus domestica File 1 (10.74 MB) File 2 (10.74 MB) File 3 (10.84 MB) File 4 (10.84 MB) File 5 (7.01 MB) File 6 (7.01 MB)
Manihot esculenta File 1 (12.98 MB) File 2 (10.68 MB) File 3 (17.44 MB) File 4 (14.08 MB) File 5 (8.73 MB) File 6 (7.19 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)
Medicago truncatula File 1 (16.25 MB) File 2 (13.57 MB) File 3 (20.64 MB) File 4 (16.55 MB) File 5 (10.82 MB) File 6 (9.02 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)
Nelumbo nucifera File 1 (8.54 MB) File 2 (8.54 MB) File 3 (11.03 MB) File 4 (11.03 MB) File 5 (5.74 MB) File 6 (5.74 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)
Petunia axillaris File 1 (10.73 MB) File 2 (10.73 MB) File 3 (11.58 MB) File 4 (11.58 MB) File 5 (7.23 MB) File 6 (7.23 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)
Prunus persica File 1 (12.84 MB) File 2 (8.98 MB) File 3 (19.07 MB) File 4 (13.12 MB) File 5 (8.54 MB) File 6 (5.99 MB)
Pyrus bretschneideri File 1 (13.41 MB) File 2 (13.41 MB) File 3 (15.48 MB) File 4 (15.48 MB) File 5 (8.91 MB) File 6 (8.91 MB)
Ricinus communis File 1 (8.92 MB) File 2 (8.92 MB) File 3 (9.38 MB) File 4 (9.38 MB) File 5 (5.87 MB) File 6 (5.87 MB)
Schrenkiella parvula File 1 (8.84 MB) File 2 (8.84 MB) File 3 (10.16 MB) File 4 (10.16 MB) File 5 (5.82 MB) File 6 (5.82 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)
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)
Solanum tuberosum File 1 (13.23 MB) File 2 (10.21 MB) File 3 (13.26 MB) File 4 (10.23 MB) File 5 (8.92 MB) File 6 (6.87 MB)
Tarenaya hassleriana File 1 (13.41 MB) File 2 (10.05 MB) File 3 (17.86 MB) File 4 (13.43 MB) File 5 (8.91 MB) File 6 (6.66 MB)
Theobroma cacao File 1 (13.21 MB) File 2 (9.61 MB) File 3 (20.15 MB) File 4 (14.83 MB) File 5 (8.84 MB) File 6 (6.42 MB)
Trifolium pratense File 1 (11.94 MB) File 2 (11.51 MB) File 3 (16.00 MB) File 4 (15.47 MB) File 5 (8.02 MB) File 6 (7.73 MB)
Utricularia gibba File 1 (7.61 MB) File 2 (7.55 MB) File 3 (7.62 MB) File 4 (7.59 MB) File 5 (5.02 MB) File 6 (4.99 MB)
Vigna radiata var. radiata File 1 (8.35 MB) File 2 (8.00 MB) File 3 (10.20 MB) File 4 (9.76 MB) File 5 (5.60 MB) File 6 (5.36 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)
Ziziphus jujuba File 1 (12.55 MB) File 2 (10.37 MB) File 3 (16.30 MB) File 4 (13.66 MB) File 5 (8.08 MB) File 6 (6.64 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
Actinidia chinensis anchorpoints_intra_species.ach.csv.gz (82.75 KB)
Amaranthus hypochondriacus Not Available
Amborella trichopoda anchorpoints_intra_species.atr.csv.gz (931.00 B)
Arabidopsis lyrata anchorpoints_intra_species.aly.csv.gz (49.97 KB)
Arabidopsis thaliana anchorpoints_intra_species.ath.csv.gz (50.62 KB)
Arachis ipaensis anchorpoints_intra_species.aip.csv.gz (46.53 KB)
Beta vulgaris anchorpoints_intra_species.bvu.csv.gz (7.61 KB)
Brassica oleracea anchorpoints_intra_species.bol.csv.gz (189.18 KB)
Brassica rapa anchorpoints_intra_species.bra.csv.gz (185.07 KB)
Cajanus cajan anchorpoints_intra_species.ccaj.csv.gz (22.31 KB)
Capsella rubella anchorpoints_intra_species.cru.csv.gz (58.40 KB)
Capsicum annuum anchorpoints_intra_species.can.csv.gz (5.16 KB)
Carica papaya anchorpoints_intra_species.cpa.csv.gz (4.33 KB)
Chenopodium quinoa anchorpoints_intra_species.cqu.csv.gz (110.25 KB)
Chlamydomonas reinhardtii anchorpoints_intra_species.cre.csv.gz (722.00 B)
Cicer arietinum anchorpoints_intra_species.car.csv.gz (30.23 KB)
Citrullus lanatus anchorpoints_intra_species.cla.csv.gz (15.91 KB)
Citrus clementina anchorpoints_intra_species.ccl.csv.gz (22.53 KB)
Coffea canephora anchorpoints_intra_species.ccan.csv.gz (14.34 KB)
Corchorus olitorius anchorpoints_intra_species.col.csv.gz (913.00 B)
Cucumis melo anchorpoints_intra_species.cme.csv.gz (12.95 KB)
Cucumis sativus L. anchorpoints_intra_species.csa.csv.gz (9.10 KB)
Daucus carota anchorpoints_intra_species.dca.csv.gz (39.53 KB)
Erythranthe guttata anchorpoints_intra_species.egut.csv.gz (32.70 KB)
Eucalyptus grandis anchorpoints_intra_species.egr.csv.gz (25.00 KB)
Fragaria vesca anchorpoints_intra_species.fve.csv.gz (8.72 KB)
Glycine max anchorpoints_intra_species.gma.csv.gz (289.49 KB)
Gossypium raimondii anchorpoints_intra_species.gra.csv.gz (102.67 KB)
Hevea brasiliensis anchorpoints_intra_species.hbr.csv.gz (24.60 KB)
Malus domestica anchorpoints_intra_species.mdo.csv.gz (29.42 KB)
Manihot esculenta anchorpoints_intra_species.mes.csv.gz (74.52 KB)
Marchantia polymorpha anchorpoints_intra_species.mpo.csv.gz (659.00 B)
Medicago truncatula anchorpoints_intra_species.mtr.csv.gz (28.65 KB)
Micromonas commoda anchorpoints_intra_species.mco.csv.gz (543.00 B)
Nelumbo nucifera anchorpoints_intra_species.nnu.csv.gz (34.64 KB)
Oryza sativa ssp. japonica anchorpoints_intra_species.osa.csv.gz (30.38 KB)
Petunia axillaris anchorpoints_intra_species.pax.csv.gz (15.69 KB)
Physcomitrium patens anchorpoints_intra_species.ppa.csv.gz (16.83 KB)
Picea abies anchorpoints_intra_species.pab.csv.gz (515.00 B)
Populus trichocarpa anchorpoints_intra_species.ptr.csv.gz (119.26 KB)
Prunus persica anchorpoints_intra_species.ppe.csv.gz (21.74 KB)
Pyrus bretschneideri anchorpoints_intra_species.pbr.csv.gz (101.31 KB)
Ricinus communis anchorpoints_intra_species.rco.csv.gz (10.21 KB)
Schrenkiella parvula anchorpoints_intra_species.spa.csv.gz (43.82 KB)
Selaginella moellendorffii anchorpoints_intra_species.smo.csv.gz (9.03 KB)
Solanum lycopersicum anchorpoints_intra_species.sly.csv.gz (31.39 KB)
Solanum tuberosum anchorpoints_intra_species.stu.csv.gz (79.46 KB)
Tarenaya hassleriana anchorpoints_intra_species.tha.csv.gz (69.18 KB)
Theobroma cacao anchorpoints_intra_species.tca.csv.gz (24.42 KB)
Trifolium pratense anchorpoints_intra_species.tpr.csv.gz (6.97 KB)
Utricularia gibba anchorpoints_intra_species.ugi.csv.gz (7.52 KB)
Vigna radiata var. radiata anchorpoints_intra_species.vra.csv.gz (24.26 KB)
Vitis vinifera anchorpoints_intra_species.vvi.csv.gz (17.42 KB)
Zea mays anchorpoints_intra_species.zma.csv.gz (65.70 KB)
Ziziphus jujuba anchorpoints_intra_species.zju.csv.gz (14.67 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 (10.34 MB) genefamily_enrichment.HOMFAM.csv.gz (3.15 MB)
Orthologous gene family genefamily_data.ORTHOFAM.csv.gz (10.50 MB) genefamily_enrichment.ORTHOFAM.csv.gz (5.29 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 (521.62 MB)
Orthologous gene family integrative_orthology.ORTHO.csv.gz (3.10 GB)
Anchor point integrative_orthology.anchor_point.csv.gz (189.22 MB)
Best-Hits-and-Inparalogs(BHI)family integrative_orthology.BHIF.csv.gz (729.28 MB)