Microarray experiments to specifically-expressed genes

GSM ID GSM245913
Assay name csn5 (csn5a-2 csn5b) mutant light 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
155.899.976.1At4g21070827854ATBRCA1Encodes 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.
109.099.9624.1At4g12490826861protease 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.
90.399.9215.0At1g65500842862unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.C.G.H.G.
54.199.8115.0At1g57820842157VIM1 (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.
53.299.824.3At4g19130827651DNA 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.
49.699.895.3At5g49160834975MET1 (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.
43.499.8345.9At2g43510818952ATTI1Member of the defensin-like (DEFL) family. Encodes putative trypsin inhibitor protein which may function in defense against herbivory.O.I.C.G.H.G.
36.499.7150.0At1g76930844028ATEXT4 (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.
32.599.719.7At4g29170829038ATMND1A homolog of yeast, mouse and human mnd1delta protein. Null mutants exhibit normal vegetative and flower development; however, during prophase I, chromosomes become fragmented resulting in random distribution of the fragments between polyads. Both male and female meiosis are defective and strong accumulation of AtRAD51 was observed in the inflorescence nuclei of mutant plants. Similarly to its yeast and animal homologues, AtMnd1 might play a role in DSB repair during meiosis.O.I.C.G.H.G.
29.199.786.9At3g54750824640unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.C.G.H.G.
28.199.7351.0At3g27060822324TSO2 (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.
27.099.7140.6At3g07800819971thymidine kinase, putativeF:thymidine kinase activity, ATP binding;P:pyrimidine deoxyribonucleoside interconversion, anaerobic respiration;C:cellular_component unknown;BOVMPAFO.I.C.G.H.G.
26.799.7172.8At4g12500826862protease inhibitor/seed storage/lipid transfer protein (LTP) family proteinF:lipid binding;P:lipid transport;C:unknown;POBMVFAO.I.C.G.H.G.
24.399.6273.1At3g18280821356protease inhibitor/seed storage/lipid transfer protein (LTP) family proteinF:lipid binding;P:lipid transport;C:endomembrane system;PO.I.C.G.H.G.
22.599.6272.1At4g12480826860pEARLI 1a putative lipid transfer protein, vernalization-responsive and cold-inducedO.I.C.G.H.G.
21.999.645.4At1g33560840250ADR1 (ACTIVATED DISEASE RESISTANCE 1)Encodes a NBS-LRR disease resistance protein that possesses N-terminal kinase subdomains. Activation tagged mutant of ADR1 showed elevated levels of SA and reactive oxygen species in addition to number of defense gene transcripts. Exhibits resistance to number of microbial pathogens.O.I.C.G.H.G.
21.799.6104.0At1g14720838037XTR2 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE RELATED 2)member of Glycoside Hydrolase Family 16O.I.C.G.H.G.
21.299.6292.8At4g14690827119ELIP2 (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.
20.499.616.1At1g67180843038zinc 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.
19.099.539.2At4g02390828049APP (ARABIDOPSIS POLY(ADP-RIBOSE) POLYMERASE)Encodes a DNA dependent nuclear poly (ADP-ribose) polymerase (E.C., thought to be involved in post-translational modification .O.I.C.G.H.G.
18.699.525.4At1g17960838375threonyl-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.
17.999.5567.7At3g49110824072PRXCA (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.
17.999.535.8At5g42200834225zinc finger (C3HC4-type RING finger) family proteinF:ubiquitin-protein ligase activity, protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVO.I.C.G.H.G.
17.399.548.6At4g33560829495unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.C.G.H.G.
17.299.5255.1At4g15910827273ATDI21 (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.
17.099.533.8At1g66040842917VIM4 (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.
15.799.521.0At1g63530842658-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVO.I.C.G.H.G.
15.799.512.0At4g26460828752-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
15.699.517.2At3g20490821595unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBPO.I.C.G.H.G.
15.299.496.1At2g21790816715RNR1 (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.
15.299.418.9At2g18600816375RUB1-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.
15.199.4243.8At5g19550832075ASP2 (ASPARTATE AMINOTRANSFERASE 2)Nitrogen metabolism. Major cytosolic isoenzyme controlling aspartate biosynthesis in the light.O.I.C.G.H.G.
14.999.420.9At3g25100822101CDC45 (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.
14.299.444.0At5g61000836221replication protein, putativeF:DNA binding, nucleic acid binding;P:DNA replication;C:nucleus;PMOFAO.I.C.G.H.G.
13.999.47.9At1g13330837893-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBFAPVO.I.C.G.H.G.
13.899.4325.5At2g38870818471protease inhibitor, putativePredicted to encode a PR (pathogenesis-related) peptide that belongs to the PR-6 proteinase inhibitor family. Six putative PR-6-type protein encoding genes are found in Arabidopsis: At2g38900, At2g38870, At5g43570, At5g43580, At3g50020 and At3g46860.O.I.C.G.H.G.
13.399.4241.1At2g16060816103AHB1 (ARABIDOPSIS HEMOGLOBIN 1)Encodes a class 1 nonsymbiotic hemoglobin induced by low oxygen levels with very high oxygen affinity. It is not likely to be a hemoglobin transporter because of its extremely high affinity for oxygen.O.I.C.G.H.G.
13.299.432.7At4g23260828425ATP binding / protein kinase/ protein serine/threonine kinase/ protein tyrosine kinaseF:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:response to abscisic acid stimulus;C:endomembrane system;MPOBFVAO.I.C.G.H.G.
13.299.413.7At2g37060818282NF-YB8 (NUCLEAR FACTOR Y, SUBUNIT B8)F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus, intracellular;MPFOO.I.C.G.H.G.
12.899.3172.3At4g33070829444pyruvate decarboxylase, putativeF:in 6 functions;P:unknown;C:membrane;BOFPAMVO.I.C.G.H.G.
12.899.373.4At5g39890833986unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.C.G.H.G.
12.799.313.8At5g17890831657DAR4 (DA1-RELATED PROTEIN 4)F:protein binding, zinc ion binding, ATP binding;P:defense response, apoptosis;C:unknown;PMOFBVAO.I.C.G.H.G.
12.699.343.3At5g10040830868unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
12.599.3133.7At2g36910818265ABCB1 (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.
12.499.3360.3At4g37870829943PCK1 (PHOSPHOENOLPYRUVATE CARBOXYKINASE 1)Encodes a putative phosphoenolpyruvate carboxykinase (ATP-dependent).O.I.C.G.H.G.
11.499.326.2At3g23150821891ETR2 (ethylene response 2)Involved in ethylene perception in ArabidopsisO.I.C.G.H.G.
11.499.314.3At1g02970839453WEE1 (ARABIDOPSIS WEE1 KINASE HOMOLOG)Protein kinase that negatively regulates the entry into mitosis.O.I.C.G.H.G.
11.399.333.2At1g57770842152amine oxidase familyF:oxidoreductase activity;P:unknown;C:chloroplast;OBMPAFO.I.C.G.H.G.
11.299.2344.8At2g254508170832-oxoglutarate-dependent dioxygenase, putativeencodes a protein whose sequence is similar to ACC oxidaseO.I.C.G.H.G. factor activity;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;PO.I.C.G.H.G.
11.199.2106.2At4g10270826619wound-responsive family proteinF:molecular_function unknown;P:response to wounding;C:unknown;PO.I.C.G.H.G. unknown;P:aging;C:endomembrane system;BOPAMFO.I.C.G.H.G. proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPBOFVAO.I.C.G.H.G.
10.799.2345.8At3g10860820256ubiquinol-cytochrome C reductase complex ubiquinone-binding protein, putative / ubiquinol-cytochrome C reductase complex 8.2 kDa protein, putativeF:ubiquinol-cytochrome-c reductase activity;P:unknown;C:mitochondrion, mitochondrial respiratory chain complex III, membrane;PO.I.C.G.H.G.
10.799.212.0At3g01330821221DEL3 (DP-E2F-LIKE PROTEIN 3)Member of the E2F transcription factors, (cell cycle genes), key components of the cyclin D/retinoblastoma/E2F pathway.O.I.C.G.H.G.
10.699.224.3At2g47680819381zinc finger (CCCH type) helicase family proteinF:helicase activity, zinc ion binding, nucleic acid binding, ATP binding;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;C:chloroplast;MBOFPVO.I.C.G.H.G.
10.599.220.6At1g59660842256nucleoporin family proteinF:transporter activity;P:transport;C:chloroplast, nuclear pore;MBOFPVAO.I.C.G.H.G.
10.499.233.7At5g60250836147zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding, nucleic acid binding;P:unknown;C:unknown;MFPOBO.I.C.G.H.G.
10.499.222.0At1g04020839329BARD1 (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.
10.299.2107.8At4g10040826595CYTC-2 (cytochrome c-2)Encodes cytochrome c. Promoter directs preferential expression in vascular tissues of cotyledons, leaves, roots, and hypocotyls, and in anthers.O.I.C.G.H.G. (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. bindingF:protein binding;P:signal transduction;C:cellular_component unknown;PMOBFAVO.I.C.G.H.G.;P:biological_process unknown;C:cellular_component unknown;MFOPVO.I.C.G.H.G. (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.
9.999.1622.1At2g38530818435LTP2 (LIPID TRANSFER PROTEIN 2)Involved in lipid transfer between membranes. Belongs to a family of Lipid transfer proteins. Sequence similarity to other plant/Arabidopsis LPT genes but highest similarity to LPT1. Stress and pathogen-inducible motifs found in the upstream region. Expressed in flower, leaves and siliques but absent in roots. Predicted to be a member of PR-14 pathogenesis-related protein family with the following members: At2g38540/LTP1, At2g38530/LTP2, At5g59320/LTP3, At5g59310/LTP4, At3g51600/LTP5, At3g08770/LTP6, At2g15050/LTP7, At2g18370/LTP8, At2g15325/LTP9, At5g01870/LTP10, At4g33355/LTP11, At3g51590/LTP12, At5g44265/LTP13, At5g62065/LTP14, At4g08530/LTP15.O.I.C.G.H.G.
9.999.1180.9At2g43620818964chitinase, putativeF:chitin binding, chitinase activity;P:response to salt stress;C:apoplast;PBFOVMO.I.C.G.H.G.
9.999.194.2At5g57330835838aldose 1-epimerase family proteinF:isomerase activity, carbohydrate binding, aldose 1-epimerase activity, catalytic activity;P:galactose metabolic process, carbohydrate metabolic process;C:cellular_component unknown;BOPFMO.I.C.G.H.G.
9.999.118.4At3g06030819774ANP3 (ARABIDOPSIS NPK1-RELATED PROTEIN KINASE 3)NPK1-related protein kinase 3O.I.C.G.H.G.
9.799.115.3At5g38690833859-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPBFAVO.I.C.G.H.G.
9.599.19.7At1g67370843058ASY1 (ASYNAPTIC 1)meiotic asynaptic mutant 1 (ASY1). ASY1 protein is initially distributed as numerous foci throughout the chromatin. During early G2, the foci are juxtaposed to the nascent chromosome axes to form a continuous axis associated signal.O.I.C.G.H.G.
9.399.1191.4At3g085908200062,3-biphosphoglycerate-independent phosphoglycerate mutase, putative / phosphoglyceromutase, putativeF:manganese ion binding, phosphoglycerate mutase activity, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity, catalytic activity, metal ion binding;P:response to cadmium ion;C:cytosol, apoplast;BOPFAMO.I.C.G.H.G. (ARABIDOPSIS HOMOLOG OF SEPARASE)Putative separase gene, homologous to human and mouse separase protein. It contains a predicted 2Fe2S-ferredoxin domain that is not present in the proteins of other organisms. Also contains a putative EF-hand calcium binding domain. Mutant seeds exhibited embryo arrest at the globular stage. The endosperm also exhibited a weak titan-like phenotype. Transgenic plants expressing AESP RNA interference (RNAi) from the meiosis-specific DMC1 promoter exhibited alterations in chromosome segregation during meiosis I and II that resulted in polyads containing from one to eight microspores. AESP plays an essential role in embryo development and is required for the removal of cohesin from meiotic chromosomes.O.I.C.G.H.G. (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. (COP9-SIGNALOSOME 5B)Encodes a subunit of the COP9 complex, similar to JAB1, a specific mammalian coactivator of AP-1 transcription. Involved in protein deneddylation. Double mutants with CSN5A are constitutively photomorphogenic (de-etiolated) and have abnormal auxin responses.O.I.C.G.H.G.
8.999.0110.8At3g02550821112LBD41 (LOB DOMAIN-CONTAINING PROTEIN 41)F:unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
8.899.020.4At4g23300828429protein kinase family proteinF:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.C.G.H.G.
8.699.019.9At3g45730823715unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.C.G.H.G.

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