Documentation

Data sources

Genome sequences

Organism Genomes Sources and releases Number of sequences
Oryza sativa ORYSA_IR8_v1.0 v1.0
(Stein et al, 2018)
35495
Oryza sativa ORYSA_Kitaake_v3.1 v3.1
35594
Oryza sativa ORYSA_MH63_v1.0 v1.0
(Zhang et al, 2017)
60123
Oryza sativa ORYSA_N22_v1.0 v1.0
(Stein et al, 2018)
36140
Oryza sativa ORYSA_Nipponbare_v7.0 v7.0
(Goff et al, 2002)
55986
Oryza sativa ORYSA_R498_IGDB_v3.0 v3.0
(Du et al, 2017)
37549
Oryza sativa ORYSA_ZS97_v1.0 v1.0
(Zhang et al, 2017)
60897
Oryza sativa ORYSA n/a 56785
Arabidopsis thaliana ARATH_Araport11 vAraport11
(AGI, 2000)
27655
Medicago truncatula MEDTR_A17_r5.0 v5.0
(Pecrix et al, 2018)
44623
Medicago truncatula MEDTR_Mt4.0v2 v4.0.2
(Tang et al, 2014)
50444
Medicago truncatula MEDTR n/a 43859
Sorghum bicolor SORBI_BTx623_v3.1.1 v3.1.1
(McCormick RF, 2017)
34129
Sorghum bicolor SORBI_Tx430_v1.0 v1.0
(Deschamp et al, 2018)
36110
Sorghum bicolor SORBI n/a 31074
Vitis vinifera VITVI_12X.2 v2.0
(Canaguier et al, 2017)
41733
Vitis vinifera VITVI_CabernetSauvignon_v1.0 v1.0
(Minio et al, 2018)
96331
Vitis vinifera VITVI_Carmenere_v1.0 v1.0
(Minio et al, 2019)
73109
Vitis vinifera VITVI n/a 43766
Brachypodium distachyon BRADI_ABR2_337_v1.ABR2 v1.ABR2
(Gordon et al, 2026)
46637
Brachypodium distachyon BRADI_ABR3_343_v1.ABR3 v1.ABR3
(Gordon et al, 2034)
46370
Brachypodium distachyon BRADI_ABR4_364_v1.ABR4 v1.ABR4
(Gordon et al, 2030)
46109
Brachypodium distachyon BRADI_ABR5_379_v1.ABR5 v1.ABR5
(Gordon et al, 2046)
46591
Brachypodium distachyon BRADI_ABR6_336_v1.ABR6_r v1.ABR6_r
(Gordon et al, 2021)
46043
Brachypodium distachyon BRADI_ABR7_369_v1.ABR7 v1.ABR7
(Gordon et al, 2020)
46293
Brachypodium distachyon BRADI_ABR8_356_v1.ABR8 v1.ABR8
(Gordon et al, 2065)
44257
Brachypodium distachyon BRADI_ABR9_333_v1.ABR9_r v1.ABR9_r
(Gordon et al, 2029)
35015
Brachypodium distachyon BRADI_Adi_10_381_v1.Adi-10 v1.Adi-10
(Gordon et al, 2067)
41786
Brachypodium distachyon BRADI_Adi_12_359_v1.Adi-12 v1.Adi-12
(Gordon et al, 2055)
45370
Brachypodium distachyon BRADI_Adi_2_372_v1.Adi-2 v1.Adi-2
(Gordon et al, 2023)
46560
Brachypodium distachyon BRADI_Arn1_355_v1.Arn1 v1.Arn1
(Gordon et al, 2024)
45851
Brachypodium distachyon BRADI_Bd18_1_362_v1.Bd18-1 v1.Bd18-1
(Gordon et al, 2019)
46621
Brachypodium distachyon BRADI_Bd1_1_349_v1.Bd1-1 v1.Bd1-1
(Gordon et al, 2053)
42227
Brachypodium distachyon BRADI_Bd21_3_378_v1.Bd21-3_r v1.Bd21-3_r
(Gordon et al, 2045)
44011
Brachypodium distachyon BRADI_Bd21v2_1_283_Bd21v2 v2.0
(Gordon et al, 2017)
42868
Brachypodium distachyon BRADI_Bd29_1_346_v1.Bd29-1 v1.Bd29-1
(Gordon et al, 2064)
44278
Brachypodium distachyon BRADI_Bd2_3_353_v1.Bd2-3 v1.Bd2-3
(Gordon et al, 2057)
45459
Brachypodium distachyon BRADI_Bd30_1_344_v1.Bd30-1 v1.Bd30-1
(Gordon et al, 2048)
42026
Brachypodium distachyon BRADI_Bd3_1_328_v1.Bd3-1_r v1.Bd3-1_r
(Gordon et al, 2066)
37234
Brachypodium distachyon BRADI_BdTR10c_374_v1.BdTR10C v1.BdTR10C
(Gordon et al, 2062)
44299
Brachypodium distachyon BRADI_BdTR11a_380_v1.BdTR11A v1.BdTR11A
(Gordon et al, 2056)
49561
Brachypodium distachyon BRADI_BdTR11g_357_v1.BdTR11G v1.BdTR11G
(Gordon et al, 2035)
46726
Brachypodium distachyon BRADI_BdTR11i_363_v1.BdTR11I v1.BdTR11I
(Gordon et al, 2043)
46207
Brachypodium distachyon BRADI_BdTR12c_352_v1.BdTR12c v1.BdTR12c
(Gordon et al, 2058)
44583
Brachypodium distachyon BRADI_BdTR13a_334_v1.BdTR13a v1.BdTR13a
(Gordon et al, 2025)
47194
Brachypodium distachyon BRADI_BdTR13c_365_v1.BdTR13C v1.BdTR13C
(Gordon et al, 2059)
45083
Brachypodium distachyon BRADI_BdTR1i_345_v1.BdTR1i v1.BdTR1i
(Gordon et al, 2027)
46722
Brachypodium distachyon BRADI_BdTR2b_376_v1.BdTR2B v1.BdTR2B
(Gordon et al, 2050)
45974
Brachypodium distachyon BRADI_BdTR2g_367_v1.BdTR2G v1.BdTR2G
(Gordon et al, 2060)
45130
Brachypodium distachyon BRADI_BdTR3c_354_v1.BdTR3C v1.BdTR3C
(Gordon et al, 2018)
43389
Brachypodium distachyon BRADI_BdTR5i_370_v1.BdTR5I v1.BdTR5I
(Gordon et al, 2063)
44350
Brachypodium distachyon BRADI_BdTR7a_329_v1.BdTR7a v1.BdTR7a
(Gordon et al, 2047)
45440
Brachypodium distachyon BRADI_BdTR8i_348_v1.BdTR8i v1.BdTR8i
(Gordon et al, 2037)
44427
Brachypodium distachyon BRADI_BdTR9k_358_v1.BdTR9K v1.BdTR9K
(Gordon et al, 2061)
44670
Brachypodium distachyon BRADI_Bis_1_338_v1.Bis-1 v1.Bis-1
(Gordon et al, 2044)
45734
Brachypodium distachyon BRADI_Foz1_366_v1.Foz1 v1.Foz1
(Gordon et al, 2042)
46457
Brachypodium distachyon BRADI_Gaz_8_339_v1.Gaz-8 v1.Gaz-8
(Gordon et al, 2069)
36875
Brachypodium distachyon BRADI_Jer1_375_v1.Jer1 v1.Jer1
(Gordon et al, 2049)
46047
Brachypodium distachyon BRADI_Kah_1_351_v1.Kah-1 v1.Kah-1
(Gordon et al, 2068)
44606
Brachypodium distachyon BRADI_Kah_5_342_v1.Kah-5 v1.Kah-5
(Gordon et al, 2036)
46744
Brachypodium distachyon BRADI_Koz_1_330_v1.Koz-1 v1.Koz-1
(Gordon et al, 2028)
46872
Brachypodium distachyon BRADI_Koz_3_368_v1.Koz-3 v1.Koz-3
(Gordon et al, 2051)
41884
Brachypodium distachyon BRADI_Luc1_347_v1.Luc1 v1.Luc1
(Gordon et al, 2022)
46198
Brachypodium distachyon BRADI_Mig3_377_v1.Mig3 v1.Mig3
(Gordon et al, 2039)
46077
Brachypodium distachyon BRADI_Mon3_350_v1.Mon3 v1.Mon3
(Gordon et al, 2033)
44757
Brachypodium distachyon BRADI_Mur1_373_v1.Mur1 v1.Mur1
(Gordon et al, 2054)
45912
Brachypodium distachyon BRADI_Per1_326_v1.Per1 v1.Per1
(Gordon et al, 2031)
46229
Brachypodium distachyon BRADI_Ron2_360_v1.RON2 v1.RON2
(Gordon et al, 2032)
46068
Brachypodium distachyon BRADI_S8iiC_340_v1.S8iiC v1.S8iiC
(Gordon et al, 2040)
46088
Brachypodium distachyon BRADI_Sig2_371_v1.Sig2 v1.Sig2
(Gordon et al, 2041)
46526
Brachypodium distachyon BRADI_Tek_2_341_v1.Tek-2 v1.Tek-2
(Gordon et al, 2052)
44903
Brachypodium distachyon BRADI_Tek_4_332_v1.Tek-4 v1.Tek-4
(Gordon et al, 2070)
43220
Brachypodium distachyon BRADI_Uni2_327_v1.Uni2 v1.Uni2
(Gordon et al, 2038)
45793
Brachypodium distachyon BRADI n/a 61622
Musa balbisiana MUSBA_Mba1.1 v1.1
(Wang et al, 2019)
33021
Musa acuminata MUSAC_Macba2 v2.0
(Rouard et al, 2018)
32692
Musa acuminata MUSAC_Macbu1 v1.0
(Rouard et al, 2018)
45069
Musa acuminata MUSAC_Macma2 v2.0
(Martin et al, 2016)
35276
Musa acuminata MUSAC_Macze1 v1.0
(Rouard et al, 2018)
44702
Musa acuminata MUSAC n/a 45905
Theobroma cacao THECC_Criollo_v2.0 v2.0
(Argout et al, 2018)
21330
Theobroma cacao THECC_Matina1_6_v1.1 v1.1
(Motamayor et al, 2013)
44607
Theobroma cacao THECC n/a 32917
Manihot esculenta MANES_AM560_2_v6.1 v6.1
(Bredeson et al, 2016)
33033
Malus domestica MALDO_Borkh_v3.0.a1 v3.0.a1
(Velasco et al, 2010; Li et al, 2016)
95232
Malus domestica MALDO_GDDH13_v1.1 v1.1
(Daccord et al, 2017)
45116
Malus domestica MALDO_HFTH1 vHFTH1
(Zhang et al, 2019)
44677
Malus domestica MALDO n/a 54987
Cucumis sativus CUCSA_ASM407_v2.0 v2.0
(Huang et al, 2009)
23780
Cucumis sativus CUCSA_Gy14_v2.0 v2.0
(unpublished)
22324
Cucumis sativus CUCSA_PI183967 vPI183967
(Qi et al, 2013)
22935
Cucumis sativus CUCSA n/a 23446
Cajanus cajan CAJCA_Asha_v1.0 v1.0
(Varshney et al, 2012)
40071
Hordeum vulgare HORVU_IBSC_v2.0 v2.0
(IBGC, 2012)
37705
Phaseolus vulgaris PHAVU_v2.0 v2.0
(Schmutz et al. 2014)
27433
Citrus sinensis CITSI_v2.0 v2.0
(Xu et al, 2013)
29406
Solanum tuberosum SOLTU_PGSC_v4.03 v4.03
(PGSC)
39031
Amborella trichopoda AMBTC_v1.0 v1.0
(Albert et al, 2013)
26846
Elaeis guineensis ELAGV_RefSeq_v1.0 v1.0
(Singh et al, 2013)
41887
Cicer arietinum CICAR_CDC_Frontier_kabuli vKabuli
(Varshney et al, 2013)
28269
Cicer arietinum CICAR_ICC_4958_desi vDesi
(Parween et al, 2015)
30257
Cicer arietinum CICAR n/a 25013
Coffea canephora COFCA_v1.0 v1.0
(Denoeud et al, 2014)
25574
Citrus maxima CITMA_v1.0 v1.0
(Wang et al, 2017)
30123
Cucumis melo CUCME_DHL92_v3.6.1 v3.6.1
(Garcia-Mas et al. 2012)
29980
Coffea arabica COFAR_RB_v1.0 v1.0
(unpublished)
78311
Brassica napus BRANA_Darmor_v8.1 v8.1
(Bayer et al. (2017))
80382
Brassica napus BRANA_Tapidor_v6.3 v6.3
(Bayer et al. (2017))
70162
Brassica napus BRANA_v5.0 v5.0
(Chalhoub et al. 2014. Science)
101040
Brassica napus BRANA n/a 77456
Daucus carota DAUCA_JGI_v2.0 v2.0
(Iorizzo et al, 2016)
32118
Ipomoea trifida IPOTF_NSP306 vNSP306
(Wu et al, 2018)
32301
Ipomoea trifida IPOTF_Y22 vY22
(Li et al, 2019)
30227
Ipomoea trifida IPOTF n/a 31276
Fragaria vesca FRAVE_v4.0a1 v4.0a1
(Shulaev et al, 2011)
28588
Cocos nucifera COCNU_C3B02_v2.0 v2.0
52931
Cocos nucifera COCNU_CATD vCatigan Green Dwarf
(Lantican et al, 2019)
34953
Cocos nucifera COCNU n/a 38584
Capsicum annuum CAPAN_CM334_v2.0 v2.0
(Kim et al, 2014)
35884
Capsicum annuum CAPAN_Glabriusculum_Chiltepin_v2.0 v2.0
(Qin et al, 2014)
34476
Capsicum annuum CAPAN_Zunla_1_v2.0 v2.0
(Qin et al, 2014)
35336
Capsicum annuum CAPAN n/a 41828
Phoenix dactylifera PHODC_v3.0 v3.0
(Al-Mssallem et al, 2013)
40634
Oryza glaberrima ORYGL_v1.0 v1.0
(Wang et al, 2014 ;stein et al, 2018)
33164
Olea europaea OLEEU_v1.0 v1.0
(Unver et al, 2017)
50684
Ipomoea triloba IPOTR_NSP323 vNSP323
(Wu et al, 2018)
31426
Beta vulgaris BETVU_RefBeet_v1.2 v1.2
(Minoche et al. 2015)
29088
Glycine max SOYBN_Wm82_a2_v1.0 v1.0
(Schmutz et al, 2010)
54175
Glycine max SOYBN_ZH13 vZH13
(Shen et al, 2018)
52130
Glycine max SOYBN n/a 45055
Solanum lycopersicum SOLLC_ITAG3.2 v3.2
34727
Helianthus annuus HELAN_XRQ_v1.2 v1.2
(Badouin et al, 2017)
52243
Chenopodium quinoa CHEQI_JGI_v1.0 v1.0
(Jarvis et al, 2017)
44776
Citrus medica CITME_v1.0 v1.0
(Wang et al, 2017)
46851
Brassica oleracea BRAOL_A2_v1.0 v1.0
(Liu et al. (2014))
35400
Brassica oleracea BRAOL_HDEM vHDEM
(Belsner et al, 2018)
61279
Brassica oleracea BRAOL_TO1000 vTO1000
(Parkin et al. (2014) )
56687
Brassica oleracea BRAOL n/a 60869
Triticum turgidum TRITU_Svevo_v2.0 v2.0
(Maccaferri et al, 2019)
67182
Triticum turgidum TRITU_Zavitan_v1.1 v1.1
(IWGSC)
107891
Triticum turgidum TRITU n/a 54687
Zea mays MAIZE_B73_v4.0 v4.0
(Schnable et al, 2009?)
39591
Zea mays MAIZE_CML247_v1.0 v1.0
(Lu et al, 2015)
36509
Zea mays MAIZE_Mo17_v1.0 v1.0
(Yang et al, 2017)
40003
Zea mays MAIZE_PH207_v1.0 v1.0
(Hirsch et al, 2016)
40557
Zea mays MAIZE n/a 45300
Saccharum spontaneum SACSP_AP85_441_v1.0 v1.0
(Zhang et al, 2018)
83826
Brassica rapa subsp. rapa BRARR_Z1 vZ1
(Belsner et al, 2018)
46721
Brassica rapa subsp. rapa BRARR_v3.0 v3.0
(Wang et al. (2011); Zhang et al,2018)
46250
Brassica rapa subsp. rapa BRARR n/a 49916
Dioscorea rotundata DIORT_TDr96_F1_v1.0 v1.0
(Tamiru et al, 2017)
26198

Sequence identifiers
Sequences are uniquely identifed by a the locus tags defined by the consortia responsible of the annotation (e.g. At5g20240.1). Only sequences with of the pangenes are greated by us and start with the _pan as a prefix (e.g. orysa_pan_)

Here are some random example of valid gene sequence identifiers for each species of the database:
Organism Example of sequence identifiers
Oryza sativa OsIR8_01T0018700, OsKitaake01g071500.1, OsMH_01T0087200, A2J10_01T0065600, LOC_Os01g03400.1, OsR498G0100469700.01.T01, OsZS_01T0012700, orysa_pan_p000485
Arabidopsis thaliana AT1G04170.1
Medicago truncatula MtrunA17_Chr1g0172711, Medtr0030s0360.1, medtr_pan_p000928
Sorghum bicolor Sobic.001G043700.3, 3381.casb001g003860.635.1, sorbi_pan_p000188
Vitis vinifera Vitvi10g02190.t01, VvCabSauv08_H0000F_025.ver1.0.g002820.m01, VvCarFPS02VCR702_v1_Hc0000F_125.ver1_0.g415740.m01, vitvi_pan_p000025
Brachypodium distachyon Brdisv1ABR21029042m_1, Brdisv1ABR31032892m_1, Brdisv1ABR41027540m_1, Brdisv1ABR51023099m_1, Brdisv1ABR6_r1025533m_1, Brdisv1ABR71030675m_1, Brdisv1ABR81037180m_1, Brdisv1ABR9_r1023631m_1, Brdisv1Adi-101016272m_1, Brdisv1Adi-121022322m_1, Brdisv1Adi-21025660m_1, Brdisv1Arn11029840m_1, Brdisv1Bd18-11030350m_1, Brdisv1Bd1-11021694m_1, Brdisv1Bd21-3_r1025796m_1, Bradi2g49550.3_1, Brdisv1Bd29-11022219m_1, Brdisv1Bd2-31024074m_1, Brdisv1Bd30-11024593m_1, Brdisv1Bd3-1_r1022667m_1, Brdisv1BdTR10C1021452m_1, Brdisv1BdTR11A1022972m_1, Brdisv1BdTR11G1027144m_1, Brdisv1BdTR11I1028935m_1, Brdisv1BdTR12c1027327m_1, Brdisv1BdTR13a1028719m_1, Brdisv1BdTR13C1025478m_1, Brdisv1BdTR1i1028713m_1, Brdisv1BdTR2B1027276m_1, Brdisv1BdTR2G1026260m_1, Brdisv1BdTR3C1025457m_1, Brdisv1BdTR5I1020809m_1, Brdisv1BdTR7a1029701m_1, Brdisv1BdTR8i1025896m_1, Brdisv1BdTR9K1021781m_1, Brdisv1Bis-11024154m_1, Brdisv1Foz11025324m_1, Brdisv1Gaz-81012222m_1, Brdisv1Jer11025024m_1, Brdisv1Kah-11020767m_1, Brdisv1Kah-51027252m_1, Brdisv1Koz-11024846m_1, Brdisv1Koz-31024580m_1, Brdisv1Luc11025463m_1, Brdisv1Mig31024153m_1, Brdisv1Mon31027340m_1, Brdisv1Mur11025009m_1, Brdisv1Per11028270m_1, Brdisv1RON21027771m_1, Brdisv1S8iiC1032123m_1, Brdisv1Sig21022475m_1, Brdisv1Tek-21026334m_1, Brdisv1Tek-41015868m_1, Brdisv1Uni21022572m_1, bradi_pan_p000667
Musa balbisiana Mba00_g04260.1
Musa acuminata Maban_Contig101_t003710, Mabur_Contig10429_t000010, Ma00_t05370.1, Mazeb_scaffold1034_t000040, musac_pan_p000001
Theobroma cacao Tc01v2_t003350.1, Thecc1EG005117t1, thecc_pan_p000739
Manihot esculenta Manes.01G034100.1
Malus domestica MDP0000190809, MD00G1047200, HF10210-RA, maldo_pan_p000645
Cucumis sativus KGN43854, CsGy1G001460.1, evm.model.Chr1.1273, cucsa_pan_p000537
Cajanus cajan cajca.ICPL87119.gnm1.ann1.C.cajan_00853.1
Hordeum vulgare HORVU0Hr1G006890.2
Phaseolus vulgaris phavu.G19833.gnm2.ann1.Phvul.001G066550.1
Citrus sinensis Cs1g08250.2
Solanum tuberosum PGSC0003DMP400038432
Amborella trichopoda evm_27.model.AmTr_v1.0_scaffold00001.461
Elaeis guineensis XP_010905108.1
Cicer arietinum cicar.CDCFrontier.gnm1.ann1.Ca_00002.1, cicar.ICC4958.gnm2.ann1.Ca_00284.1, cicar_pan_p000446
Coffea canephora Cc01_g08310
Citrus maxima Cg1g007800.1
Cucumis melo MELO3C001795.2.1
Coffea arabica Ca_10_339.1
Brassica napus BnaA01g04470.1D2, BnaA01g01290.1T, GSBRNA2T00000666001, brana_pan_p000662
Daucus carota DCAR_000360
Ipomoea trifida itf00g04500.t1, Itr.Sc0000089.28, ipotf_pan_p000098
Fragaria vesca FvH4_1g00350.1
Cocos nucifera COCNU_HT001RO02_U03PF15240.1, Cnu_16201-RA, cocnu_pan_p000135
Capsicum annuum CA.PGAv.1.6.scaffold1013.37, Capang12g000011, Capana00g000880, capan_pan_p000142
Phoenix dactylifera XP_008775916.1
Oryza glaberrima ORGLA01G0055600.1
Olea europaea Oeu000825.1
Ipomoea triloba itb01g04050.t1
Beta vulgaris Bv1_000460_rcun.t1
Glycine max Glyma01g09160.1, SoyZH13_01G058200.m1, soybn_pan_p000598
Solanum lycopersicum Solyc00g009790.1.1
Helianthus annuus HanXRQChr00c0434g0574701
Chenopodium quinoa AUR62000608-RA
Citrus medica Cm002500.1
Brassica oleracea Bol004922, BolC1p00925H, NC_016118.1_cds_YP_004927491.1_56658, braol_pan_p000782
Triticum turgidum TRIDC1Av2G037550.1, TraesCS1A02G095800.1, tritu_pan_p000371
Zea mays Zm00001d000216, Zm00006a000069, ZmMO1701t000126, Zm00008a040527_T01, maize_pan_p000314
Saccharum spontaneum Sspon.01G0006580-1A
Brassica rapa subsp. rapa BraA05t22163Z, BraA01g006650.3C, brarr_pan_p000583
Dioscorea rotundata Dr00829


Data associated to genomes

Protein domain: Each sequence was analysed using InterProScan to identify InterPro domain (release ).

UniProt: Correspondance between UniProtKB-Swissprot ( last updated: January 2020) was made based on the ordered locus when available (in 'Gene names' section). Otherwise, mapping was done by using blast with UniProtKB-Swissprot against a specific whole genome. We transfered UniProtKB-Swissprot for the first hit with an identity score > 90%.

Gene Ontology (GO): GO terms were obtained from the interpro (InterPro to GO mapping version: 2019/09/07 14:18:45) and UniProt (UniProt to GO mapping version: n/a).

Pubmed: Gene families were mapped by selected pubmed id referenced in UniProt entries. GreenPhyl Curators can also add additional publications manually.