Species & Dataset

  • Populus trichocarpa

  • Common name: Poplar cottonwood

  • Family: Salicaceae

Foliar Ozone Injury

Experiment

  • Genotype: An inbred F2 mapping population (Family 331), formed from a cross between Populus trichocarpa and P. deltoides

  • Tissue: Shoot leaves

  • Ozone concentration: 16.7 nL L-1 (Control)

  • 93.1 nL L-1 (Treatment)

  • Ozone exposure: Whole experimental period

  • Sampling time: End of exposure period

  • Platform: Microarray

  • Year of study: 2010

  • Location: UK

Title: The physiological, transcriptional and genetic responses of an ozone- sensitive and an ozone tolerant poplar and selected extremes of their F2 progeny

 

Summary: Relatively little is known about the transcriptional response or genetic control of response and adaptation of trees to tropospheric ozone exposure. Such understanding is needed as up to 50% of forests, globally, may be subjected to phytotoxic concentrations of ozone. The physiological, transcriptional and genetic response to ozone was examined in Populus trichocarpa and P. deltoides, which show extreme sensitivity and tolerance to ozone, respectively. Using an inbred F2 mapping population derived from these two species, we mapped quantitative trait loci (QTL) for traits associated with ozone response, examined segregation of the transcriptional response to ozone and co-located genes showing divergent responses between tolerant and sensitive genotypes with QTL. QTL were identified linking detrimental effects of ozone with leaf and biomass traits and differential responses were found for key genes involved in ethylene production and response.

Reference: Street, N.R., James, T.M., James, T., Mikael, B., Jaakko, K., Mark, B. and Taylor, G., 2011. The physiological, transcriptional and genetic responses of an ozone-sensitive and an ozone tolerant poplar and selected extremes of their F2 progeny. Environmental Pollution, 159(1), pp.45-54

Gene Id
AGI code
Protein_ID
logFC
P.Value
Gene description
Summary
estExt_fgenesh4_kg.C_LG_I0088
AT2G14880.1
813615
-1.216494995
0.004183637
SWIB complex BAF60b domain-containing protein
eugene3.00120058
AT3G17760.1
569405
-0.895077679
0.004184581
glutamate decarboxylase, putative
estExt_Genewise1_v1.C_LG_II2093
AT4G09720.1
710660
-1.105828186
0.004185608
AtRABG3a; GTP binding
estExt_Genewise1_v1.C_LG_XIV0850
AT3G60900.1
730906
-1.31521213
0.004197384
FLA10 (fasciclin-like arabinogalactan-protein 10)
gw1.VI.2059.1
AT4G32272.1
417686
-0.63993361
0.004200701
gw1.XI.359.1
AT1G51100.1
232379
-0.673989369
0.00420511
estExt_fgenesh4_pm.C_290079
AT5G46630.1
836330
-1.334920196
0.004227773
clathrin adaptor complexes medium subunit family protein
clathrin adaptor complexes medium subunit family protein, contains Pfam profile: PF00928 adaptor complexes medium subunit family; similar to micro-adaptins of clathrin coated vesicle adaptor complexes
grail3.0025023802
AT5G01650.1
668121
-0.752543494
0.004233836
macrophage migration inhibitory factor family protein / MIF family protein
gw1.I.5773.1
AT2G17420.1
177173
0.739294637
0.004248294
NTRA (NADPH-dependent thioredoxin reductase 2)
NADPH-dependent thioredoxin reductase, major cytosolic isoform
estExt_fgenesh4_pm.C_LG_XVIII0041
AT4G26210.1
835756
0.713842943
0.004241989
mitochondrial ATP synthase g subunit family protein
eugene3.00050506
AT5G67210.1
558891
-0.903634343
0.004238435
nucleic acid binding / pancreatic ribonuclease
gw1.XV.2690.1
AT1G31260.1
NA
-1.236184108
0.004257964
ZIP10 (ZINC TRANSPORTER 10 PRECURSOR); cation transporter
member of Fe(II) transporter isolog family
grail3.0023002901
AT2G26580.1
652803
-1.075403937
0.004258658
plant-specific transcription factor YABBY family protein
estExt_fgenesh4_pg.C_LG_III0677
AT4G10770.1
817209
0.754948002
0.003676495
ATOPT7 (oligopeptide transporter 7); oligopeptide transporter
oligopeptide transporter
grail3.0082000101
AT1G69230.1
680830
-1.167890628
0.00363505
SP1L2
SPIRAL1-LIKE2 belongs to a six-member gene family in Arabidopsis; all members share a high sequence similarity in amino- and carboxy-terminal regions. Regulates cortical microtubule organization. Mutant plants exhibit altered patterns of root and organ growth as a result of defective anisotropic cell expansion.
estExt_Genewise1_v1.C_LG_III0271
AT1G01620.1
711735
-1.060450382
0.003708258
PIP1C (PLASMA MEMBRANE INTRINSIC PROTEIN 1;3); water channel
a member of the plasma membrane intrinsic protein subfamily PIP1. localizes to the plasma membrane and exhibits water transport activity in Xenopus oocyte. expressed ubiquitously and protein level decreases slightly during leaf development.
estExt_fgenesh4_pg.C_LG_I1918
AT3G08580.1
815411
0.979587054
0.003709255
AAC1 (ADP/ATP CARRIER 1); ATP:ADP antiporter/ binding
mitochondrial ADP/ATP carrier
grail3.0025015101
AT5G01530.1
668020
-1.399356617
0.00371849
chlorophyll A-B binding protein CP29 (LHCB4)
estExt_fgenesh4_pm.C_LG_II0453
AT1G22410.1
830232
0.96690875
0.003725376
2-dehydro-3-deoxyphosphoheptonate aldolase, putative / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, putative / DAHP synthetase, putative
estExt_Genewise1_v1.C_LG_V4766
AT4G31700.1
716478
0.924915524
0.003736795
RPS6 (RIBOSOMAL PROTEIN S6); structural constituent of ribosome
Encodes a putative ribosomal protein S6 (rps6).
eugene3.00130661
AT5G17710.2
571297
-1.400750145
0.003715672
EMB1241 (EMBRYO DEFECTIVE 1241); adenyl-nucleotide exchange factor/ chaperone binding / protein binding / protein homodimerization
estExt_fgenesh4_pg.C_LG_I1718
AT1G76440.1
815335
0.708335285
0.003751181
gw1.XII.1231.1
AT5G24470.1
422771
-1.02719151
0.003773923
APRR5 (PSEUDO-RESPONSE REGULATOR 5); transcription regulator
Encodes a pseudo-response regulator whose mutation affects various circadian-associated biological events such as flowering time in the long-day photoperiod conditions, red light sensitivity of seedlings during early photomorphogenesis, and the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light.
eugene3.00010913
AT1G63460.1
548472
0.774521623
0.003793172
glutathione peroxidase, putative
grail3.0035028601
AT1G01360.1
664102
-0.699870617
0.003820852
estExt_fgenesh4_pg.C_LG_I0594
AT3G61110.1
814939
0.873811005
0.003825464
ARS27A (ARABIDOPSIS RIBOSOMAL PROTEIN S27); structural constituent of ribosome
Arabidopsis ribosomal protein
estExt_Genewise1_v1.C_LG_II1134
AT4G08685.1
710229
-1.163036401
0.003820316
SAH7
Encodes a protein, expressed in leaves, with similarity to pollen allergens.
eugene3.00021350
AT2G45300.1
552035
0.922969474
0.003828877
3-phosphoshikimate 1-carboxyvinyltransferase / 5-enolpyruvylshikimate-3-phosphate / EPSP synthase
grail3.0013041501
AT2G45180.1
654168
-1.734874249
0.00383458
protease inhibitor/seed storage/lipid transfer protein (LTP) family protein
estExt_Genewise1_v1.C_LG_V4944
AT4G30100.1
716529
-1.142325479
0.003841825
tRNA-splicing endonuclease positive effector-related
eugene3.00190136
AT1G58440.1
573662
-0.924309035
0.00384798
XF1; oxidoreductase
Encodes a putative protein that has been speculated, based on sequence similarities, to have squalene monooxygenase activity.
estExt_fgenesh4_pg.C_LG_I2092
AT5G62680.1
815481
-0.88420142
0.003860153
proton-dependent oligopeptide transport (POT) family protein
gw1.IX.2337.1
AT4G34200.1
201872
0.992104853
0.003880839
EDA9 (embryo sac development arrest 9); NAD binding / amino acid binding / cofactor binding / oxidoreductase, acting on the CH-OH group of donors, NAD or NADP as acceptor / phosphoglycerate dehydrogenase
grail3.0026021301
AT5G09920.1
650821
-1.256675335
0.003883562
RPB15.9 (RNA polymerase II 15.9)
15.9 kDa subunit of RNA polymerase II
eugene3.00090180
AT2G27180.1
556920
-0.799781805
0.00391112
estExt_fgenesh4_pm.C_LG_VI0635
AT2G05830.1
832064
-1.117313561
0.003925048
eukaryotic translation initiation factor 2B family protein / eIF-2B family protein
estExt_fgenesh4_pg.C_LG_V1618
AT4G35190.1
818852
0.772830198
0.003938614
gw1.XII.577.1
AT5G61640.1
422117
0.76597794
0.003941195
PMSR1 (PEPTIDEMETHIONINE SULFOXIDE REDUCTASE 1); protein-methionine-S-oxide reductase
ubiquitous enzyme that repairs oxidatively damaged proteins
eugene3.00081422
AT4G02770.1
564827
-1.514727701
0.003952965
PSAD-1 (photosystem I subunit D-1)
Encodes a protein predicted by sequence similarity with spinach PsaD to be photosystem I reaction center subunit II (PsaD1)
estExt_Genewise1_v1.C_LG_XIV2782
AT3G63010.1
731943
1.675410238
0.003971384
ATGID1B/GID1B (GA INSENSITIVE DWARF1B)
Encodes a gibberellin (GA) receptor ortholog of the rice GA receptor gene (OsGID1). Has GA-binding activity, showing higher affinity to GA4. Interacts with DELLA proteins in vivo in the presence of GA4.
estExt_fgenesh4_pg.C_1580005
AT5G07990.1
828416
-1.463777806
0.003980266
TT7 (TRANSPARENT TESTA 7); flavonoid 3-monooxygenase/ oxygen binding
Required for flavonoid 3 hydroxylase activity.
estExt_fgenesh4_pg.C_LG_II2554
AT5G43970.1
816979
0.657451606
0.003985091
TOM22-V (TRANSLOCASE OUTER MITOCHONDRIAL MEMBRANE 22-V)
Subunit of the TOM complex, a translocase in the outer mitochondrial membrane that selectively allows proteins with a mitochondrial targeting sequence to enter the mitochondrion.
estExt_fgenesh4_pg.C_LG_III0079
AT1G25290.1
817004
-0.774450522
0.004009396
rhomboid family protein
estExt_fgenesh4_pg.C_LG_X0791
AT2G32090.1
821968
-0.95074895
0.004007583
lactoylglutathione lyase family protein / glyoxalase I family protein
estExt_Genewise1_v1.C_LG_II4045
AT3G07220.1
711559
2.118279366
0.004011266
transcriptional activator, putative
gw1.XI.904.1
AT1G64720.1
232924
-1.282748063
0.004024331
CP5
membrane related protein CP5
estExt_fgenesh4_pg.C_LG_XVI0885
AT2G36870.1
825278
-0.818369902
0.004024608
xyloglucan:xyloglucosyl transferase, putative / xyloglucan endotransglycosylase, putative / endo-xyloglucan transferase, putative
estExt_fgenesh4_pg.C_14770002
AT4G23700.1
829032
-0.645020105
0.004041193
ATCHX17 (CATION/H+ EXCHANGER 17); monovalent cation:proton antiporter
member of Putative Na+/H+ antiporter family
gw1.21115.1.1
AT1G69523.1
278829
-1.236717846
0.004062921
UbiE/COQ5 methyltransferase family protein
eugene3.00970009
AT3G15900.1
597614
-1.293670777
0.004073509
eugene3.00040363
AT4G18780.1
555650
-1.080673106
0.004070904
CESA8 (CELLULASE SYNTHASE 8); cellulose synthase/ transferase, transferring glycosyl groups
Encodes a member of the cellulose synthase family involved in secondary cell wall biosynthesis. Mutants have abnormal xylem formation, reduced cellulose content, and enhanced drought and osmotic stress tolerance.
eugene3.02630001
AT5G51190.1
588763
0.995397822
0.004070322
AP2 domain-containing transcription factor, putative
encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5.
gw1.IX.3861.1
AT2G29630.2
203396
-1.650155848
0.004102098
thiamine biosynthesis family protein / thiC family protein
estExt_fgenesh4_pm.C_LG_XII0286
AT4G22220.1
834330
-0.863019753
0.004122598
ISU1 (Iron-sulfur cluster assembly complex protein)
Encodes a mitochondrial protein similar to E.coli IscU. In bacteria, IscU is a scaffold protein accepting sulfur and iron to build a transient Fe-S cluster,which is subsequently transferred to a target apoprotein.
estExt_fgenesh4_pg.C_LG_XIX0692
AT1G09645.1
826232
0.778352266
0.0041231
eugene3.00080078
AT1G16880.1
563483
-1.368581316
0.00414833
uridylyltransferase-related
estExt_Genewise1_v1.C_LG_XIV3377
AT2G32520.1
732264
-0.639621337
0.004143425
dienelactone hydrolase family protein
grail3.0039014201
AT2G46370.1
644556
1.221119925
0.004137066
JAR1 (JASMONATE RESISTANT 1)
An auxin-induced gene encoding a cytoplasmic localized phytochrome A signaling component protein similar to the GH3 family of proteins Loss of function mutants are defective in a variety of responses to jasmonic acid.
estExt_Genewise1_v1.C_LG_XI1809
AT4G05320.2
727584
1.08196861
0.004135403
UBQ10 (POLYUBIQUITIN 10); protein binding
One of five polyubiquitin genes in A. thaliana. These genes encode the highly conserved 76-amino acid protein ubiquitin that is covalently attached to substrate proteins targeting most for degradation. Polyubiquitin genes are characterized by the presence of tandem repeats of the 228 bp that encode a ubiquitin monomer. Induced by salicylic acid. Independent of NPR1 for their induction by salicylic acid.
estExt_Genewise1_v1.C_LG_I9848
AT5G24690.1
709698
-0.701497425
0.004145839
estExt_Genewise1_v1.C_660785
AT1G06890.1
741937
-1.035473972
0.004172496
transporter-related
estExt_Genewise1_v1.C_LG_VI1108
AT2G29150.1
717182
-0.719415679
0.004171272
tropinone reductase, putative / tropine dehydrogenase, putative
grail3.0007002601
AT4G29340.1
668776
-0.654812631
0.004163179
PRF4 (PROFILIN 4); actin binding
Profilin is a low-molecular weight, actin monomer-binding protein that regulates the organization of actin cytoskeleton in eukaryotes, including higher plants. PRF4 and PRF5 are late pollen-specific and are not detectable in other cell types of the plant body including microspores and root hairs. Immunocytochemical studies at the subcellular level reveal that both the constitutive and pollen-specific profilins are abundant in the cytoplasm. In vegetative cell types, such as root apical cells, profilins showed localization to nuclei in addition to the cytoplasmic staining.
estExt_Genewise1_v1.C_290420
AT5G46800.1
740022
-1.700153003
0.003338435
BOU (A BOUT DE SOUFFLE); binding
Seedling lethal mutation; Mitochondrial Carnitine Acyl Carrier-Like Protein
fgenesh4_pg.C_LG_VIII000845
AT5G61040.1
765831
-0.864023998
0.003347572
fgenesh4_pg.C_LG_III000072
AT1G71220.1
756530
0.68761352
0.003373669
UDP-glucose:glycoprotein glucosyltransferase/ transferase, transferring glycosyl groups / transferase, transferring hexosyl groups
estExt_fgenesh4_pm.C_LG_VIII0258
AT2G40100.1
832587
-1.018989685
0.003372131
LHCB4.3 (LIGHT HARVESTING COMPLEX PSII); chlorophyll binding
Lhcb4:3 protein (Lhcb4.3, light harvesting complex of photosystem II
grail3.0019029901
AT1G07660.1
655445
-0.894165882
0.003399572
histone H4
estExt_Genewise1_v1.C_LG_I1289
AT2G28900.1
706161
-1.521697622
0.003404473
OEP16 (OUTER ENVELOPE PROTEIN 16); protein translocase
Encodes AtOEP16, a 16-KDa plastid outer membrane protein involved in plastid import of protochlorophyllide oxidoreductase A. Predominantly expressed in leaves and is also inducible by cold treatment.
estExt_Genewise1_v1.C_LG_XIV2179
AT2G47110.1
731624
0.79768478
0.003394703
UBQ6 (ubiquitin 6); protein binding
polyubiquitin gene
estExt_fgenesh4_pm.C_LG_XIV0257
AT4G01850.1
834837
-1.052794668
0.003402455
MAT2/SAM-2 (S-adenosylmethionine synthetase 2); methionine adenosyltransferase
estExt_Genewise1_v1.C_1240101
AT4G27470.1
743801
0.838256591
0.003386745
zinc finger (C3HC4-type RING finger) family protein
eugene3.00080332
AT5G42300.1
563737
0.760425762
0.003389319
ubiquitin family protein
gw1.VI.1016.1
AT5G57035.1
416643
-1.047952022
0.003388069
protein kinase family protein
gw1.131.249.1
AT1G56560.1
268247
-1.304770123
0.003408987
beta-fructofuranosidase, putative / invertase, putative / saccharase, putative / beta-fructosidase, putative
fgenesh4_pg.C_LG_IX000393
AT4G34760.1
767342
-1.428737635
0.003423805
auxin-responsive family protein
gw1.1574.2.1
AT5G47220.1
273372
1.381652974
0.003412573
ATERF-2/ATERF2/ERF2 (ETHYLENE RESPONSE FACTOR 2); DNA binding / transcription factor/ transcriptional activator
Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-2). The protein contains one AP2 domain. Functions as activator of GCC box?dependent transcription. Positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation.
estExt_fgenesh4_pg.C_LG_I0621
AT5G47870.1
814951
0.863455539
0.003420063
eugene3.00130695
AT5G45350.1
571331
-0.67317148
0.003435773
proline-rich family protein
grail3.0071006401
AT2G42610.1
660778
0.717979751
0.003445365
grail3.0210000501
AT4G15830.1
674954
-1.457657131
0.003454577
binding
fgenesh4_pg.C_LG_X001297
AT3G57270.1
769807
2.819907996
0.00336622
BG1 (BETA-1,3-GLUCANASE 1); hydrolase, hydrolyzing O-glycosyl compounds
encodes a member of glycosyl hydrolase family 17
gw1.XI.1745.1
AT4G16340.1
233765
1.02151375
0.003473612
SPK1 (SPIKE1); GTP binding / GTPase binding / guanyl-nucleotide exchange factor
mutant has Seedling lethal; Cotyledon, leaf-shape, trichome defects; Putative Cytoskeletal Protein
eugene3.00012665
AT4G26620.1
550224
-1.262362516
0.003475943
sucrase-related
gw1.VII.1749.1
AT4G39970.1
217444
-1.400865352
0.003476825
haloacid dehalogenase-like hydrolase family protein
eugene3.00060040
AT5G47770.1
560081
1.247988113
0.00346525
FPS1 (FARNESYL DIPHOSPHATE SYNTHASE 1); dimethylallyltranstransferase/ geranyltranstransferase
Encodes a protein with farnesyl diphosphate synthase activity.
eugene3.00012691
AT1G30475.1
550250
-1.51466401
0.003493294
estExt_Genewise1_v1.C_LG_IX1362
AT2G21170.1
721810
-1.069281349
0.003491279
TIM (TRIOSEPHOSPHATE ISOMERASE); triose-phosphate isomerase
Encodes a nuclear triosephosphate isomerase.
gw1.XII.444.1
AT3G48050.1
421984
0.934990162
0.003496368
bromo-adjacent homology (BAH) domain-containing protein
grail3.0064002701
AT4G05320.2
679519
-0.794067922
0.003509863
UBQ10 (POLYUBIQUITIN 10); protein binding
One of five polyubiquitin genes in A. thaliana. These genes encode the highly conserved 76-amino acid protein ubiquitin that is covalently attached to substrate proteins targeting most for degradation. Polyubiquitin genes are characterized by the presence of tandem repeats of the 228 bp that encode a ubiquitin monomer. Induced by salicylic acid. Independent of NPR1 for their induction by salicylic acid.
gw1.148.129.1
AT2G44300.1
271871
-1.163926221
0.003517054
lipid transfer protein-related
eugene3.00141000
AT1G05190.1
572955
-1.285565927
0.003531393
EMB2394 (EMBRYO DEFECTIVE 2394); structural constituent of ribosome
gw1.VIII.591.1
AT3G26340.1
419163
0.649632243
0.003529187
20S proteasome beta subunit E, putative
gw1.VI.639.1
AT5G03880.1
416266
-1.237637195
0.00353861
estExt_fgenesh4_pm.C_LG_I1023
AT4G34050.1
829835
1.832029745
0.00354435
caffeoyl-CoA 3-O-methyltransferase, putative
gw1.140.324.1
AT1G30760.1
270279
-0.930021976
0.003556933
FAD-binding domain-containing protein
estExt_fgenesh4_pg.C_LG_IV0751
AT1G65890.1
817932
-1.093686407
0.003559473
acyl-activating enzyme 12 (AAE12)
estExt_fgenesh4_pg.C_1180067
AT5G47040.1
827676
-1.449677815
0.003564233
Lon protease homolog 1, mitochondrial (LON)
gw1.IV.950.1
AT4G34830.1
195861
-0.87649596
0.003567949
binding
gw1.70.171.1
AT1G04250.1
294718
-1.05220064
0.003588651
AXR3 (AUXIN RESISTANT 3); transcription factor
Transcription regulator acting as repressor of auxin-inducible gene expression. Auxin-inducible AUX/IAA gene. Short-lived nuclear protein with four conserved domains. Domain III has homology to beta alpha alpha dimerization and DNA binding domains. Involved in auxin signaling. Auxin induces the degradation of the protein in a dosage-dependent manner in a process mediated by AtRac1. Auxin induced the relocalization of the protein within the nucleus from a diffused nucleoplasmic pattern to a discrete particulated pattern named nuclear protein bodies or NPB in a process also mediated by Rac1. Colocalizes with SCF, CSN and 26S proteasome components.
estExt_fgenesh4_pg.C_LG_II2454
AT2G21660.1
816925
0.762027884
0.003579037
ATGRP7 (COLD, CIRCADIAN RHYTHM, AND RNA BINDING 2); RNA binding / double-stranded DNA binding / single-stranded DNA binding
Encodes a small glycine-rich RNA binding protein that is part of a negative-feedback loop through which AtGRP7 regulates the circadian oscillations of its own transcript. Gene expression is induced by cold.
estExt_fgenesh4_pm.C_LG_VIII0291
AT2G40370.1
832603
-0.855061174
0.003589656
LAC5 (laccase 5); copper ion binding / oxidoreductase
putative laccase, a member of laccase family of genes (17 members in Arabidopsis).
gw1.I.9073.1
AT4G11650.1
180473
2.219216184
0.003573415
ATOSM34 (OSMOTIN 34)
osmotin-like protein
grail3.0106016302
AT5G04600.1
660197
1.010477084
0.00358471
RNA recognition motif (RRM)-containing protein
gw1.VIII.9.1
AT5G19990.1
418581
0.825522139
0.003595489
ATSUG1; ATPase
member of conserved Sug1 CAD family
eugene3.00660043
AT5G22770.1
594849
0.737267385
0.003593151
ALPHA-ADR (ALPHA-ADAPTIN); binding / structural molecule
estExt_fgenesh4_pg.C_LG_I0880
AT4G23496.1
815072
-1.168681538
0.003485947
SP1L5 (SPIRAL1-LIKE5)
Belongs to a six-member gene family in Arabidopsis; all members share high sequence similarity in amino- and carboxy-terminal regions. Regulates cortical microtubule organization. Mutant plants exhibit altered patterns of root, leaf and petal growth as a result of defective anisotropic cell expansion.
estExt_fgenesh4_pg.C_LG_II1494
AT5G12370.1
816613
-0.746600173
0.003633068
SEC10 (EXOCYST COMPLEX COMPONENT SEC10)
estExt_Genewise1_v1.C_LG_IV1055
AT4G38690.1
713245
-0.684871867
0.003641285
1-phosphatidylinositol phosphodiesterase-related
grail3.0008019901
AT1G09590.1
640151
0.809646862
0.003663608
60S ribosomal protein L21 (RPL21A)
estExt_fgenesh4_pm.C_LG_III0216
AT3G49910.1
830744
0.81485295
0.00362046
60S ribosomal protein L26 (RPL26A)
gw1.XIII.1138.1
AT3G49010.1
240889
0.897308441
0.003669661
ATBBC1 (breast basic conserved 1); structural constituent of ribosome
Encodes 60S ribosomal protein L13. Homolog of human breast basic conserved 1 (BBC1).
eugene3.00120808
AT5G03340.1
570155
-1.395055559
0.003673235
(Cell division control protein 48 homolog E); ATPase
gw1.I.7425.1
AT2G32060.1
178825
0.926813468
0.003081287
40S ribosomal protein S12 (RPS12C)
estExt_fgenesh4_pg.C_LG_V1127
AT1G34000.1
818603
-0.837660896
0.003090623
OHP2 (ONE-HELIX PROTEIN 2)
Encodes a novel member of the Lhc family from Arabidopsis with one predicted transmembrane alpha-helix closely related to helix I of Lhc protein from PSI (Lhca4). Gene expression is triggered by light stress and both transcript and protein accumulate in a light intensity-dependent manner. Ohp2 is associated with PSI under low- or high-light conditions.
estExt_fgenesh4_pg.C_LG_XIX0984
AT1G73325.1
826324
1.659406821
0.003099456
trypsin and protease inhibitor family protein / Kunitz family protein
estExt_Genewise1_v1.C_LG_II4011
AT1G04480.1
711541
1.057803489
0.003097982
60S ribosomal protein L23 (RPL23A)
estExt_fgenesh4_pm.C_1210019
AT2G36460.1
836979
1.072890368
0.003099703
fructose-bisphosphate aldolase, putative
estExt_fgenesh4_pg.C_LG_XIV0805
AT3G26650.1
824231
-1.562120185
0.0030979
GAPA (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE A SUBUNIT); glyceraldehyde-3-phosphate dehydrogenase
Encodes one of the two subunits forming the photosynthetic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and as such a constituent of the supramolecular complex with phosphoribulokinase (PRK) thought to be linked by a small peptide encoded by CP12-2. GapA-1 is coordinately expressed by light with PRK and CP12-2. The enzyme activity, tested in leaf protein extracts dropped significantly after external sucrose treatment for the photosynthetic GAPDH (NADPH-dependent) but not for the cytosolic GAPDH (NADH-dependent).
estExt_Genewise1_v1.C_LG_I0230
AT1G79850.1
705737
-1.329795181
0.003082822
RPS17 (ribosomal protein S17); structural constituent of ribosome
nuclear-encoded 30S chloroplast ribosomal protein S17
gw1.X.4789.1
AT1G67430.1
230092
0.781706431
0.003126853
60S ribosomal protein L17 (RPL17B)
estExt_fgenesh4_kg.C_LG_XIV0024
AT2G47640.2
814376
0.810758556
0.003127541
small nuclear ribonucleoprotein D2, putative / snRNP core protein D2, putative / Sm protein D2, putative
estExt_Genewise1_v1.C_LG_I7944
AT5G13430.1
708849
0.758678517
0.003126864
ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial, putative / Rieske iron-sulfur protein, putative
estExt_Genewise1_v1.C_LG_VIII2173
AT1G68710.1
720837
1.04757598
0.003137513
haloacid dehalogenase-like hydrolase family protein
grail3.0005049701
AT4G00100.1
666912
0.74082215
0.003132666
ATRPS13A (RIBOSOMAL PROTEIN S13A); structural constituent of ribosome
Encodes a cytoplasmic ribosomal protein S13 homologue involved in early leaf development
gw1.XV.2932.1
AT4G22680.1
253496
0.677268113
0.003147488
MYB85 (myb domain protein 85); DNA binding / transcription factor
Encodes a putative transcription factor (MYB85).
grail3.0007003501
AT5G57040.1
668789
-0.820073132
0.003145403
lactoylglutathione lyase family protein / glyoxalase I family protein
estExt_Genewise1_v1.C_LG_VII0556
AT3G15210.1
718207
1.42123979
0.003152452
ATERF-4/ATERF4/ERF4/RAP2.5 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 4); DNA binding / protein binding / transcription factor/ transcriptional repressor
Encodes a member of the ERF (ethylene response factor) subfamily B-1 of ERF/AP2 transcription factor family (ATERF-4). The protein contains one AP2 domain. Acts as a negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation.
estExt_fgenesh4_pg.C_LG_I1883
AT4G05320.2
815396
1.30217614
0.003162497
UBQ10 (POLYUBIQUITIN 10); protein binding
One of five polyubiquitin genes in A. thaliana. These genes encode the highly conserved 76-amino acid protein ubiquitin that is covalently attached to substrate proteins targeting most for degradation. Polyubiquitin genes are characterized by the presence of tandem repeats of the 228 bp that encode a ubiquitin monomer. Induced by salicylic acid. Independent of NPR1 for their induction by salicylic acid.
gw1.VII.769.1
AT1G30890.1
216464
0.739206637
0.003172588
integral membrane HRF1 family protein
estExt_Genewise1_v1.C_LG_VIII1306
AT5G08670.1
720428
-1.177148072
0.003174944
ATP synthase beta chain 1, mitochondrial
estExt_Genewise1_v1.C_1290095
AT5G61410.1
744163
-1.273815257
0.003133407
RPE (EMBRYO DEFECTIVE 2728); ribulose-phosphate 3-epimerase
Arabidopsis thaliana ribulose-5-phosphate-3-epimerase mRNA
grail3.0202001702
AT1G79040.1
674736
-1.572120639
0.00321575
PSBR (photosystem II subunit R)
Encodes for the 10 kDa PsbR subunit of photosystem II (PSII). This subunit appears to be involved in the stable assembly of PSII, particularly that of the oxygen-evolving complex subunit PsbP. Mutants defective in this gene have reduced amounts of subunits PsbP and PsbQ in PSII. In turn, assembly of PsbR is dependent on the presence of PsbJ.
estExt_Genewise1_v1.C_LG_X3287
AT5G64140.1
725361
0.892493346
0.003101001
RPS28 (RIBOSOMAL PROTEIN S28); structural constituent of ribosome
Encodes a putative ribosomal protein S28.
estExt_Genewise1_v1.C_LG_XIV3195
AT2G43050.1
732175
-1.088296467
0.003193454
pectinesterase family protein
eugene3.00070145
AT2G43460.1
562207
0.86213593
0.003199697
60S ribosomal protein L38 (RPL38A)
eugene3.00130566
AT1G55340.1
571202
-0.683981126
0.003202293
eugene3.00161069
AT5G01210.1
576934
0.952770258
0.003215626
transferase family protein
eugene3.00061117
AT1G70600.1
561158
1.031978305
0.00324456
60S ribosomal protein L27A (RPL27aC)
estExt_fgenesh4_pg.C_LG_VIII0948
AT3G06700.1
820575
0.738710248
0.003233183
60S ribosomal protein L29 (RPL29A)
grail3.0022028404
AT1G07770.1
659725
0.893655435
0.003240298
RPS15A (RIBOSOMAL PROTEIN S15A); structural constituent of ribosome
Encodes cytoplasmic ribosomal protein S15a.
grail3.0019011103
AT2G27530.1
655205
0.767316553
0.003240616
60S ribosomal protein L10A (RPL10aB)
gw1.VI.2058.1
AT4G32260.1
417685
-1.34941726
0.003236185
ATP synthase family
gw1.X.1601.1
AT2G40320.1
226904
-1.243106411
0.003245735
eugene3.00140120
AT4G00050.1
572075
-1.117499668
0.003258238
UNE10 (unfertilized embryo sac 10); DNA binding / transcription factor
estExt_Genewise1_v1.C_LG_III1770
AT1G31970.1
712352
0.780209412
0.003263801
DEAD/DEAH box helicase, putative
gw1.IX.4167.1
AT2G29060.1
203702
0.965829053
0.003268686
scarecrow transcription factor family protein
eugene3.00180672
AT5G24105.1
578448
1.855190001
0.003317554
AGP41
Encodes a putative arabinogalactan-protein (AGP41).
estExt_fgenesh4_pg.C_LG_IV1320
AT1G75390.1
818112
-0.726378551
0.003283235
bZIP transcription factor family protein
estExt_Genewise1_v1.C_LG_X2037
AT1G07070.1
724644
0.906650241
0.003292911
60S ribosomal protein L35a (RPL35aA)
eugene3.00082008
AT1G27100.1
565413
0.931475748
0.00329272
eugene3.00090586
AT2G15890.1
557326
-1.358168041
0.003304483
MEE14 (maternal effect embryo arrest 14)
eugene3.00010810
AT3G61640.1
548369
-0.980654978
0.003307698
AGP20 (ARABINOGALACTAN PROTEIN 20)
estExt_fgenesh4_pm.C_LG_II0962
AT2G05070.1
830495
-1.514693268
0.00333839
LHCB2.2 (Photosystem II light harvesting complex gene 2.2); chlorophyll binding
Encodes Lhcb2.2. Belongs to the Lhc super-gene family encodes the light-harvesting chlorophyll a/b-binding (LHC) proteins that constitute the antenna system of the photosynthetic apparatus.
eugene3.00070973
AT2G23620.1
563035
2.836263836
0.003333474
esterase, putative
estExt_fgenesh4_pm.C_LG_IX0111
AT2G27720.1
832971
1.049454957
0.003329855
60S acidic ribosomal protein P2 (RPP2A)
estExt_Genewise1_v1.C_280751
AT2G36880.1
739535
-1.189340692
0.003345429
MAT3 (METHIONINE ADENOSYLTRANSFERASE 3); methionine adenosyltransferase
gw1.XIII.1268.1
AT3G05060.1
241019
1.002521547
0.003356714
SAR DNA-binding protein, putative
SAR DNA-binding protein, putative, strong similarity to SAR DNA-binding protein-1 (Pisum sativum) GI:3132696; contains Pfam profile PF01798: Putative snoRNA binding domain; encodes NOP58-like protein
estExt_fgenesh4_pg.C_640120
AT3G13720.1
827148
0.712692121
0.003350442
prenylated rab acceptor (PRA1) family protein
estExt_Genewise1_v1.C_LG_I1353
AT3G46440.1
706198
0.812946902
0.003319982
UXS5 (UDP-Xyl synthase 5); catalytic
encodes a protein similar to UDP-glucuronic acid decarboxylase. UDP-glucuronic acid decarboxylase produces UDP-xylose, which is a substrate for many cell wall carbohydrates including hemicellulose and pectin. UDP-xylose is also known to feedback regulate several cell wall biosynthetic enzymes.
estExt_fgenesh4_pm.C_LG_I0800
AT3G47340.1
829702
0.72136284
0.00333596
ASN1 (DARK INDUCIBLE 6)
encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the genes expression pattern is responding to the level of sugar in the cell.
estExt_Genewise1_v1.C_LG_X1818
AT4G00430.1
724520
0.989642247
0.003329864
TMP-C (plasma membrane intrinsic protein 1;4); water channel
a member of the plasma membrane intrinsic protein subfamily PIP1.
grail3.0054016801
AT5G40690.1
641734
0.87696667
0.003327559
estExt_fgenesh4_kg.C_LG_VI0025
AT5G60670.1
813911
1.006570063
0.002774689
60S ribosomal protein L12 (RPL12C)
eugene3.00041306
AT2G21160.1
556593
0.961853797
0.002697347
translocon-associated protein alpha (TRAP alpha) family protein
estExt_fgenesh4_kg.C_LG_X0057
AT5G46020.1
814174
0.81224867
0.002595674
estExt_fgenesh4_pm.C_LG_V0048
AT4G31700.1
831359
1.097123556
0.002812057
RPS6 (RIBOSOMAL PROTEIN S6); structural constituent of ribosome
Encodes a putative ribosomal protein S6 (rps6).
estExt_fgenesh4_pg.C_LG_VI1428
AT1G53750.1
819430
0.93516828
0.002830084
RPT1A (regulatory particle triple-A 1A); ATPase
26S proteasome AAA-ATPase subunit RPT1a (RPT1a) mRNA,
grail3.0043013701
AT1G67920.1
666345
-1.042069136
0.002825124
eugene3.00180824
AT1G07660.1
578600
-0.74471611
0.00286594
histone H4
estExt_fgenesh4_pg.C_8990003
AT1G17180.1
828962
1.349725832
0.002850339
ATGSTU25 (Arabidopsis thaliana Glutathione S-transferase (class tau) 25); glutathione transferase
Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002).
eugene3.00081703
AT1G24510.1
565108
0.722695673
0.00287392
T-complex protein 1 epsilon subunit, putative / TCP-1-epsilon, putative / chaperonin, putative
estExt_Genewise1_v1.C_LG_XI3607
AT1G53310.1
728315
1.430902153
0.002863472
ATPPC1 (PHOSPHOENOLPYRUVATE CARBOXYLASE 1); phosphoenolpyruvate carboxylase
Encodes one of four Arabidopsis phosphoenolpyruvate carboxylase proteins.
grail3.0021029701
AT1G62480.1
645492
-0.794460929
0.002876788
vacuolar calcium-binding protein-related
estExt_fgenesh4_pg.C_LG_III1155
AT2G04620.1
817407
1.175443799
0.002875749
cation efflux family protein
eugene3.01230072
AT3G02520.1
580782
0.962112199
0.002866994
GRF7 (General regulatory factor 7); protein phosphorylated amino acid binding
Encodes GF14 &957;, a 14-3-3 protein isoform (14-3-3&957;).
grail3.0015017401
AT3G03430.1
662039
-1.029452754
0.002858621
polcalcin, putative / calcium-binding pollen allergen, putative
estExt_fgenesh4_pg.C_LG_XIX0927
AT3G10860.1
826300
0.812811678
0.002891934
ubiquinol-cytochrome C reductase complex ubiquinone-binding protein, putative / ubiquinol-cytochrome C reductase complex 8.2 kDa protein, putative
gw1.V.3269.1
AT3G19950.1
207868
-1.475309521
0.002881004
zinc finger (C3HC4-type RING finger) family protein
fgenesh4_pm.C_LG_VIII000713
AT5G43310.1
803758
0.791335205
0.002891437
COP1-interacting protein-related
estExt_Genewise1_v1.C_2730019
AT5G43330.1
747123
0.722577761
0.002878445
malate dehydrogenase, cytosolic, putative
estExt_fgenesh4_pg.C_LG_VII1013
AT5G66680.1
820006
-1.912049674
0.002887409
DGL1 (defective glycosylation 1); dolichyl-diphosphooligosaccharide-protein glycotransferase
Encodes a protein ortholog of human SOT48 or yeast WBP1, an essential protein subunit of the oligosaccharyltransferase (OST) complex, which is responsible for the transfer in the ER of the N-linked glycan precursor onto Asn residues of candidate proteins.
gw1.III.2689.1
AT1G72640.1
415586
-0.738523145
0.002900608
estExt_Genewise1_v1.C_280409
AT3G09630.1
739311
-0.052033894
0.002729915
60S ribosomal protein L4/L1 (RPL4A)
grail3.0036009801
AT2G29420.1
658124
1.724551335
0.002865151
ATGSTU7 (GLUTATHIONE S-TRANSFERASE 25); glutathione transferase
Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002). Induced by Salicylic acid. Independent of NPR1 for their induction by salicylic acid.
estExt_fgenesh4_pm.C_LG_II0164
AT1G75280.1
830063
-1.109873268
0.002884299
isoflavone reductase, putative
isoflavone reductase, putative, identical to SP:P52577 Isoflavone reductase homolog P3 (EC 1.3.1.-) {Arabidopsis thaliana}; contains Pfam profile PF02716: isoflavone reductase. Involved in response to oxidative stress.
fgenesh4_pm.C_LG_XIII000297
AT2G43030.1
806997
-1.209187694
0.002913346
ribosomal protein L3 family protein
grail3.0049017902
AT1G07770.1
656057
1.020084568
0.002908933
RPS15A (RIBOSOMAL PROTEIN S15A); structural constituent of ribosome
Encodes cytoplasmic ribosomal protein S15a.
fgenesh4_pg.C_LG_VIII001084
AT3G25920.1
766070
-1.429884468
0.002930625
RPL15 (ribosomal protein L15)
encodes a plastid ribosomal protein CL15, a constituent of the large subunit of the ribosomal complex
estExt_fgenesh4_pm.C_280146
AT3G52880.1
836268
0.707867088
0.002929227
ATMDAR1 (MONODEHYDROASCORBATE REDUCTASE 1); monodehydroascorbate reductase (NADH)
Encodes a peroxisomal monodehydroascorbate reductase, involved in the ascorbate-glutathione cycle which removes toxic H2O2
estExt_fgenesh4_pm.C_LG_XVI0204
AT5G64140.1
835446
0.814255466
0.002938362
RPS28 (RIBOSOMAL PROTEIN S28); structural constituent of ribosome
Encodes a putative ribosomal protein S28.
eugene3.00012291
AT5G64260.1
549850
1.272126751
0.002951559
phosphate-responsive protein, putative
gw1.IX.2512.1
AT2G14830.1
202047
-1.301560386
0.00296012
grail3.0072001304
AT4G18100.1
665064
0.814518509
0.002963399
60S ribosomal protein L32 (RPL32A)
estExt_Genewise1_v1.C_400481
AT1G74970.1
740274
-1.288708636
0.002977928
RPS9 (RIBOSOMAL PROTEIN S9); structural constituent of ribosome
ribosomal protein S9, nuclear encoded component of the chloroplast ribosome
grail3.0003061401
AT5G41470.1
643510
0.718126032
0.002976526
estExt_Genewise1_v1.C_LG_XII0064
AT3G17980.1
728460
1.027609819
0.002991353
C2 domain-containing protein
gw1.I.8918.1
AT4G11650.1
180318
2.470862344
0.003022215
ATOSM34 (OSMOTIN 34)
osmotin-like protein
estExt_Genewise1_v1.C_1330112
AT1G09150.1
744559
0.761331425
0.003015981
pseudouridine synthase and archaeosine transglycosylase (PUA) domain-containing protein
grail3.0130005601
AT2G15560.1
671445
-1.068143663
0.003012185