Microarray experiments to specifically-expressed genes

GSM ID GSM245919
Assay name csn3-1 mutant dark replicate 1
GSE experiment GSE9728: COP9 signalosome (csn) mutant analysis

Click Gene ID to show a list of GSM assays in which the gene are specifically expressed.

Std2 GX %ile Std GX Gene ID Repr. ID Gene name Functional description O.I. C.G. H.G. Other DB
283.7100.099.0At1g17960838375threonyl-tRNA synthetase, putative / threonine--tRNA ligase, putativeF:nucleotide binding, aminoacyl-tRNA ligase activity, threonine-tRNA ligase activity, ATP binding;P:threonyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:cytoplasm;BOMFAPO.I.C.G.H.G.
173.4100.047.0At1g67180843038zinc finger (C3HC4-type RING finger) family protein / BRCT domain-containing proteinF:protein binding, zinc ion binding;P:unknown;C:intracellular;MOFPVO.I.C.G.H.G.
118.599.966.4At4g21070827854ATBRCA1Encodes AtBRCA1, an ortholog of the human breast cancer susceptibility gene 1. Contains one N-terminal RING finger, two C-terminal BRCT and the p300/CBP interacting domain. Strongly induced by gamma rays, consistent with a putative role in DNA repair and in cell cycle control.O.I.C.G.H.G.
95.899.932.6At4g19130827651DNA binding / nucleic acid binding / zinc ion bindingF:DNA binding, zinc ion binding, nucleic acid binding;P:DNA replication;C:nucleus;MPOFAO.I.C.G.H.G.
90.899.9236.7At1g76930844028ATEXT4 (EXTENSIN 4)Encodes an Arabidopsis extensin gene that belongs to cell-wall hydroxyproline-rich glycoproteins. The cross-link of extensins enforces cell wall strength. Transgenic plants overexpressing this gene show an increase in stem thickness.O.I.C.G.H.G.
71.399.975.9At4g02390828049APP (ARABIDOPSIS POLY(ADP-RIBOSE) POLYMERASE)Encodes a DNA dependent nuclear poly (ADP-ribose) polymerase (E.C.2.4.2.30), thought to be involved in post-translational modification .O.I.C.G.H.G.
69.099.920.6At1g20750838665helicase-relatedF:in 6 functions;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;C:chloroplast;MOFBPAO.I.C.G.H.G.
63.399.8107.7At5g49160834975MET1 (METHYLTRANSFERASE 1)Encodes a cytosine methyltransferase MET1. Required for silencing of FWA paternal allele in endosperm. Two lines with RNAi constructs directed against DMT1 have reduced agrobacterium-mediated tumor formation.O.I.C.G.H.G.
59.099.831.3At5g38780833869S-adenosyl-L-methionine:carboxyl methyltransferase family proteinF:S-adenosylmethionine-dependent methyltransferase activity, methyltransferase activity;P:biological_process unknown;C:cellular_component unknown;POBMFO.I.C.G.H.G.
57.099.8464.4At4g15910827273ATDI21 (ARABIDOPSIS THALIANA DROUGHT-INDUCED 21)encodes a gene whose transcript level in root and leaves increases to progressive drought stress. The transcript level is also affected by changes of endogenous or exogenous abscisic acid level. It appears to be a member of plant-specific gene family that includes late embryo-abundant and zinc- IAA-induced proteins in other plants.O.I.C.G.H.G.
50.599.8151.8At2g07722815395unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
47.299.8185.8At3g07800819971thymidine kinase, putativeF:thymidine kinase activity, ATP binding;P:pyrimidine deoxyribonucleoside interconversion, anaerobic respiration;C:cellular_component unknown;BOVMPAFO.I.C.G.H.G.
44.399.8107.2At3g54750824640unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.C.G.H.G.
43.099.815.7At4g00010--O.I.C.G.H.G.
41.599.871.0At2g07739815412-F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.C.G.H.G.
41.499.8143.6At1g14720838037XTR2 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE RELATED 2)member of Glycoside Hydrolase Family 16O.I.C.G.H.G.
40.599.899.5At1g57820842157VIM1 (VARIANT IN METHYLATION 1)Encodes a 645-amino acid methylcytosine-binding protein with a PHD domain, two RING finger domains, and an SRA domain that is involved in centromere heterochromatinization. This protein functions as an E3 ubiquitin ligase in vitro. The protein has been shown to bind to methylated cytosines of CG, CNG and CNN motifs via its SRA domain but has a preference for the former. It plays a role in the establishment/maintenance of chromatin structure during cell division and is localized in the nucleus. Plants over-expressing VIM1/ORTH2 show an inhibition in root growth and a delay in flowering. Both over-expression of GFP:ORTH2 and loss of ORTH2/VIM1 lead to decreased levels of DNA methylation. GFP:ORTH2 over-expressers also have increased levels of FWA transcripts.O.I.C.G.H.G.
39.599.8168.2At2g076993768015-F:unknown;P:unknown;C:unknownO.I.C.G.H.G.
39.499.8375.3At4g12490826861protease inhibitor/seed storage/lipid transfer protein (LTP) family proteinF:lipid binding;P:defense response to fungus, lipid transport;C:unknown;PBOMVFAO.I.C.G.H.G.
36.899.724.7At1g203903766766transposable element geneF:unknown;P:unknown;C:unknownO.I.C.G.H.G.
34.799.788.5At3g61960825369protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOFBVAO.I.C.G.H.G.
30.199.7789.1At3g22120821775CWLP (CELL WALL-PLASMA MEMBRANE LINKER PROTEIN)cell wall-plasma membrane linker protein homolog (CWLP)O.I.C.G.H.G.
28.699.7340.7At4g14690827119ELIP2 (EARLY LIGHT-INDUCIBLE PROTEIN 2)Encodes an early light-induced protein. ELIPs are thought not to be directly involved in the synthesis and assembly of specific photosynthetic complexes, but rather affect the biogenesis of all chlorophyll-binding complexes. A study (PMID 17553115) has shown that the chlorophyll synthesis pathway was downregulated as a result of constitutive ELIP2 expression, leading to decreased chlorophyll availability for the assembly of pigment-binding proteins for photosynthesis.O.I.C.G.H.G.
28.199.750.4At1g15660838135CENP-C (CENTROMERE PROTEIN C)Encodes a homologue of the human centromeric protein C (CENP-C). CENP-C co-localizes with the 180 bp centromeric regions of chromosomes throughout the cell cycle, but does not completely cover the 180 bp regions.O.I.C.G.H.G.
27.899.7600.1At3g16770820929ATEBP (ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN)Encodes a member of the ERF (ethylene response factor) subfamily B-2 of the plant specific ERF/AP2 transcription factor family (RAP2.3). The protein contains one AP2 domain. There are 5 members in this subfamily including RAP2.2 AND RAP2.12.It is localized to the nucleus and acts as a transcriptional activator through the GCC-box. It has been identified as a suppressor of Bax-induced cell death by functional screening in yeast and can also suppress Bax-induced cell death in tobacco plants. Overexpression of this gene in tobacco BY-2 cells confers resistance to H2O2 and heat stresses. Overexpression in Arabidopsis causes upregulation of PDF1.2 and GST6. It is part of the ethylene signaling pathway and is predicted to act downstream of EIN2 and CTR1, but not under EIN3.O.I.C.G.H.G.
26.799.751.0At1g57770842152amine oxidase familyF:oxidoreductase activity;P:unknown;C:chloroplast;OBMPAFO.I.C.G.H.G.
25.599.7334.2At3g27060822324TSO2 (TSO meaning 'ugly' in Chinese)Encodes one of the 3 ribonucleotide reductase (RNR) small subunit genes. TSO2 transcription occurs predominantly at the S-phase of the cell cycle and its expression pattern is consistent with its role in dNDP biosynthesis during DNA replication in actively dividing cells. Critical for cell cycle progression, DNA damage repair and plant development.O.I.C.G.H.G.
25.599.774.3At1g73990843737SPPAEncodes a putative protease SppA (SppA).O.I.C.G.H.G.
25.099.632.5At3g59100825079ATGSL11 (glucan synthase-like 11)encodes a protein similar to callose synthaseO.I.C.G.H.G.
24.599.685.5At5g14250831275COP13 (CONSTITUTIVE PHOTOMORPHOGENIC 13)Encodes subunit 3 of the COP9 signalosome.O.I.C.G.H.G.
24.599.624.4At5g38690833859-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPBFAVO.I.C.G.H.G.
23.299.620.8At3g27640822386transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAO.I.C.G.H.G.
23.199.6275.9At4g12480826860pEARLI 1a putative lipid transfer protein, vernalization-responsive and cold-inducedO.I.C.G.H.G.
23.099.657.0At3g28540822484AAA-type ATPase family proteinF:nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;P:unknown;C:unknown;BOMFPAVO.I.C.G.H.G.
22.799.622.6At5g02220831792unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
22.399.632.9At2g07721815394unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
21.599.6114.3At2g21790816715RNR1 (RIBONUCLEOTIDE REDUCTASE 1)encodes large subunit of ribonucleotide reductase involved in the production of deoxyribonucleoside triphosphates (dNTPs) for DNA replication and repairO.I.C.G.H.G.
21.199.656.0At2g33250817887unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO.I.C.G.H.G.
21.199.653.6At5g61000836221replication protein, putativeF:DNA binding, nucleic acid binding;P:DNA replication;C:nucleus;PMOFAO.I.C.G.H.G.
21.099.6614.2At3g49110824072PRXCA (PEROXIDASE CA)Class III peroxidase Perx33. Expressed in roots. Located in the cell wall. Involved in cell elongation. Expression activated by light. May play a role in generating H2O2 during defense response.O.I.C.G.H.G.
21.099.617.4At4g35740829727RecQl3F:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:DNA recombination;C:cellular_component unknown;BOMFPAVO.I.C.G.H.G.
20.899.629.8At2g32590817819-F:unknown;P:mitosis, mitotic cell cycle;C:nucleus, chloroplast;MFOPVO.I.C.G.H.G.
20.399.678.3At2g41230818722unknown proteinF:unknown;P:biological_process unknown;C:unknown;PMO.I.C.G.H.G.
19.599.6100.1At2g07751815347NADH-ubiquinone oxidoreductase chain 3, putativeF:NADH dehydrogenase (ubiquinone) activity;P:mitochondrial electron transport, NADH to ubiquinone;C:endomembrane system;MOBPFAO.I.C.G.H.G.
19.499.63.3At2g05270815075unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
19.099.522.8At3g25740822165MAP1B (METHIONINE AMINOPEPTIDASE 1C)Encodes a plastid localized methionine aminopeptidase. Formerly called MAP1C, now called MAP1B.O.I.C.G.H.G.
18.899.5163.8At2g36910818265ABCB1 (ATP BINDING CASSETTE SUBFAMILY B1)Belongs to the family of ATP-binding cassette (ABC) transporters. Also known as AtMDR1.Possibly regulates auxin-dependent responses by influencing basipetal auxin transport in the root. Exerts nonredundant, partially overlapping functions with the ABC transporter encoded by AT3G28860. PGP1 mediates cellular efflux of IAA and interacts with PIN genes that may confer an accelerated vectoral component to PGP-mediated transport. The non-polar localization of PGP1 at root and shoot apices, where IAA gradient-driven transport is impaired, may be required to confer directionality to auxin transport in those tissues.O.I.C.G.H.G.
18.899.524.4At1g33720840263CYP76C6member of CYP76CO.I.C.G.H.G.
18.499.522.3At5g43080834324CYCA3F:cyclin-dependent protein kinase regulator activity;P:regulation of cell cycle;C:nucleus;MPOFVO.I.C.G.H.G.
18.199.5283.6At3g22840821855ELIP1 (EARLY LIGHT-INDUCABLE PROTEIN)Encodes an early light-inducible protein.O.I.C.G.H.G.
18.099.543.0At4g12760826888unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.C.G.H.G.
17.599.533.9At2g45920819200U-box domain-containing proteinF:ubiquitin-protein ligase activity;P:protein ubiquitination;C:ubiquitin ligase complex;POMFBAVO.I.C.G.H.G.
17.399.520.2At4g12020826810WRKY19member of MEKK subfamilyO.I.C.G.H.G.
17.099.525.0At1g68240843153transcription factorF:transcription factor activity;P:regulation of transcription;C:nucleus;PMO.I.C.G.H.G.
17.099.522.2At3g25100822101CDC45 (cell division cycle 45)Required for normal meiosis, may act in the last round of DNA replication prior to meiosis, sequence similar to yeast CDC45O.I.C.G.H.G.
16.799.533.4At1g66040842917VIM4 (VARIANT IN METHYLATION 4)predicted to encode a protein with an N-terminal PHD domain and two RING domains surrounding an SRA domain. Attempts to isolate ORTH4/VIM4 cDNA through RT-PCR were unsuccessful and analysis of the expression of this gene is difficult since it shares 99% nucleotide identity with ORTH5/VIM2.O.I.C.G.H.G.
16.499.533.4At3g50380824202-F:unknown;P:protein localization;C:mitochondrion;MFPOO.I.C.G.H.G.
16.499.530.4At4g37490829904CYCB1Cyclin-dependent protein kinase CYCB1;1. Functions as an effector of growth control at G2/M. Regulated by TCP20.O.I.C.G.H.G.
16.399.538.9At1g24340839050emb2421 (embryo defective 2421)F:oxidoreductase activity, monooxygenase activity;P:embryonic development ending in seed dormancy;C:unknown;BOFPMO.I.C.G.H.G.
16.299.517.0At3g47460823900ATSMC2member of SMC subfamilyO.I.C.G.H.G.
16.199.59.6At3g61090825281unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
16.099.523.5At1g10570837598OTS2 (OVERLY TOLERANT TO SALT 2)Encodes a deSUMOylating enzyme. In vitro it has both peptidase activity and isopeptidase activity: it can cleave the C-terminal residues from SUMO to activate it for attachment to a target protein and it can also act on the isopeptide bond between SUMO and another protein. sYFP:OTS2 protein accumulates in nuclei in a punctate pattern. Double mutant analysis with ULP1D/OTS1 indicates that these genes are involved in salt stress responses and flowering time regulation.O.I.C.G.H.G.
15.899.522.3At1g67500843071ATREV3 (ARABIDOPSIS THALIANA RECOVERY PROTEIN 3)Encodes the catalytic subunit of DNA polymerase zeta.Mutants are sensitive to UV-B radiation. Gene is involved in damage-tolerance mechanisms through translesion synthesis(TLS).O.I.C.G.H.G.
15.799.592.2At1g63980842701D111/G-patch domain-containing proteinF:nucleic acid binding;P:biological_process unknown;C:intracellular;OMFBPVAO.I.C.G.H.G.
15.599.538.8At5g48720834930XRI1 (X-RAY INDUCED TRANSCRIPT 1)Encodes XRI1 (X-ray induced 1). Required for post-meiotic stages of pollen development and male and female meiosis. Maybe required for meiotic DNA repair. Inducible by X-ray. Homozygous xri1 mutants are sterile due to extensive chromosome fragmentation.O.I.C.G.H.G.
15.399.41.6At4g03990825711transposable element geneF:unknown;P:unknown;C:unknownO.I.C.G.H.G.
15.199.412.2At3g20710821619F-box protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
14.899.416.8At4g39500830104CYP96A11member of CYP96AO.I.C.G.H.G.
14.799.430.5At3g20430821588unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOBO.I.C.G.H.G.
14.599.412.4At2g07674815346unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PVMOBO.I.C.G.H.G.
14.299.414.9At1g08260837346TIL1 (TILTED 1)Similar to POL2A, DNA polymerase epsilon catalytic subunit. Essential for Arabidopsis growth. Null homozygotes are embryo lethal, partial loss of function alleles show embryo patterning defects such as root pole displacement. Delayed progression through cell cycle results in embryos with smaller numbers of larger cells.O.I.C.G.H.G.
14.199.416.4At1g66540842972cytochrome P450, putativeF:electron carrier activity, monooxygenase activity, iron ion binding, oxygen binding, heme binding;P:unknown;C:unknown;MPFBOAVO.I.C.G.H.G.
14.199.411.7At5g03780831726TRFL10 (TRF-LIKE 10)Encodes a protein whose sequence is similar to human telomere proteins. This belongs to TRFL family 2, which do not show DNA binding in vitro.O.I.C.G.H.G.
13.899.418.0At2g18600816375RUB1-conjugating enzyme, putativeF:ubiquitin-protein ligase activity, small conjugating protein ligase activity, acid-amino acid ligase activity, ATP binding;P:regulation of protein metabolic process, protein modification process, post-translational protein modification;C:cellular_component unknown;MFOPVO.I.C.G.H.G.
13.799.475.2At1g60830842376U2 snRNP auxiliary factor large subunit, putativeF:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MOFPO.I.C.G.H.G.
13.699.45.6At4g25330828636unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
13.599.425.0At3g45730823715unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.C.G.H.G.
13.399.469.7At5g59440836063ZEU1 (ZEUS1)Encodes thymidylate kinase which exists in two isoforms in plants. The longer variant of 263 amino acids with a N-terminal extension that is required for localization to the mitochondrion. The second isoform of 224 residues is localized to the cytoplasm and nucleoplasm. Peak of expression occurs during G1/S phase transition.O.I.C.G.H.G.
13.299.418.7At5g66130836745ATRAD17 (ARABIDOPSIS THALIANA RADIATION SENSITIVE)Encodes a homolog to yeast RAD17. Involved in the regulation of DNA damage repair and homologous recombination. Mutant has increased sensitivity to MMS and increased telomere lengths.O.I.C.G.H.G.
13.199.422.7At5g50110835075-F:molecular_function unknown;P:cell cycle;C:cellular_component unknown;BOPMO.I.C.G.H.G.
13.199.417.2At1g52710841704cytochrome c oxidase-relatedF:cytochrome-c oxidase activity;P:biological_process unknown;C:mitochondrial envelope;MPOFO.I.C.G.H.G.
13.099.411.8At4g39380830093-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
12.999.329.1At2g46180819225GC4 (golgin candidate 4)This gene is predicted to encode a protein that functions as a Golgi apparatus structural component known as a golgin in mammals and yeast. A fluorescently-tagged version of GC4 co-localizes with Golgi markers, and this localization appears to be replicated using the C-terminal (169 aa) portion of the protein.O.I.C.G.H.G.
12.999.326.2At5g24970832567ABC1 family proteinF:protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;OBPMFAVO.I.C.G.H.G.
12.899.350.8At4g01660828127ATABC1 (ARABIDOPSIS THALIANA ABC TRANSPORTER 1)Encodes an ABC1-like protein, member of the ATH subfamily; putative ABC transporter; isolated by functional complementation of a yeast abc1 mutantO.I.C.G.H.G.
12.699.318.8At5g01970830706unknown proteinF:unknown;P:unknown;C:unknown;PMOFBO.I.C.G.H.G.
12.599.378.2At1g04080839314PRP39F:binding;P:regulation of timing of transition from vegetative to reproductive phase;C:intracellular;MFBOPVO.I.C.G.H.G.
12.599.337.5At1g07500837264unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
12.599.324.2At1g04020839329BARD1 (BREAST CANCER ASSOCIATED RING 1)Encodes a protein containing two tandem BRCA1 C-Terminal (BRCT) domains, which function in phosphorylation-dependent protein–protein interactions.Loss of function mutations cause defects in meristem organization due to failure to repress WUS. BARD1 binds to WUS promoter and over expression of BARD reduces the extent of WUS expression.O.I.C.G.H.G.
12.399.313.5At1g21160838712GTP binding / GTPase/ translation initiation factorF:GTP binding, GTPase activity, translation initiation factor activity;P:biological_process unknown;C:cellular_component unknown;OBMFPAVO.I.C.G.H.G.
12.299.334.9At1g50240841446--O.I.C.G.H.G.
12.299.329.9At1g60890842381phosphatidylinositol-4-phosphate 5-kinase family proteinF:1-phosphatidylinositol-4-phosphate 5-kinase activity, phosphatidylinositol phosphate kinase activity, ATP binding;P:phosphatidylinositol metabolic process;C:plasma membrane;OMBPFO.I.C.G.H.G.
12.199.346.5At1g69770843313CMT3 (chromomethylase 3)Encodes a chromomethylase involved in methylating cytosine residues at non-CG sites. Involved in preferentially methylating transposon-related sequences, reducing their mobility. CMT3 interacts with an Arabidopsis homologue of HP1 (heterochromatin protein 1), which in turn interacts with methylated histones. Involved in gene silencing.O.I.C.G.H.G.
12.099.333.3At1g20120838601family II extracellular lipase, putativeF:lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBOFMAVO.I.C.G.H.G.
12.099.323.0At5g24280832495-F:unknown;P:unknown;C:unknown;PMOBFO.I.C.G.H.G.
12.099.322.1At2g43540818956unknown proteinF:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;PO.I.C.G.H.G.
11.899.37.6At3g63480825523kinesin heavy chain, putativeF:microtubule motor activity, ATP binding;P:microtubule-based movement;C:microtubule associated complex;MOFPO.I.C.G.H.G.
11.799.327.6At5g18270831945ANAC087F:transcription factor activity;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;PO.I.C.G.H.G.
11.799.36.0At1g27720839665TAF4B (TBP-ASSOCIATED FACTOR 4B)F:transcription initiation factor activity;P:transcription initiation;C:transcription factor TFIID complex;OMFPBVO.I.C.G.H.G.
11.499.320.9At5g20220832144zinc knuckle (CCHC-type) family proteinF:unfolded protein binding, heat shock protein binding, zinc ion binding, nucleic acid binding;P:protein folding;C:unknown;VMFOPBO.I.C.G.H.G.



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