Gene omics information

Query gene ID At1g57820
Gene name VIM1 (VARIANT IN METHYLATION 1)
Organism Arabidopsis thaliana


Co-expressed genes



As this page just shows up to 10 genes to the query, if you wish to have the complete list of co-expressed genes, click Gene/Probe ID.

VF%ileGene/Probe IDRepr.IDGene NameFunctional DescriptionS.X.H.G.Other DB
0.6982.9At1g57820842157VIM1 (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.S.X.H.G.
0.5673.0At1g18370838418HIK (HINKEL)Mutant has cytokinesis defects; seedling lethalS.X.H.G.
0.5570.6At4g33260829462CDC20.2putative cdc20 protein (CDC20.2)S.X.H.G.
0.5368.6At1g76310843964CYCB2core cell cycle genesS.X.H.G.
0.5368.6At5g44560834483VPS2.2F:unknown;P:vesicle-mediated transport;C:ESCRT III complex;MPFOBS.X.H.G.
0.5267.4At4g21270827876ATK1 (ARABIDOPSIS THALIANA KINESIN 1)Encodes a kinesin-like motor protein heavy chain. Loss of function mutations have reduced fertility and are defective in spindle formation in male meiosis.S.X.H.G.
0.5065.3At3g53190824485pectate lyase family proteinF:lyase activity, pectate lyase activity;P:biological_process unknown;C:anchored to membrane;BPFOS.X.H.G.
0.5065.3At4g15830827264bindingF:binding;P:biological_process unknown;C:cellular_component unknown;MPOFS.X.H.G.
0.4963.5At1g72670843599iqd8 (IQ-domain 8)F:calmodulin binding;P:biological_process unknown;C:cellular_component unknown;PMFOS.X.H.G.
0.4862.5At1g59540842245ZCF125Encodes a kinesin-like protein.S.X.H.G.
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Specifically expressed experiments



As this page just shows up to 10 assays to the query, if you wish to have the complete list of assays that the query gene/probe was specifically expressed, click here.
Std2 GX%ileGSM IDAssay NameGSE IDExperiment Title
54.199.8GSM245913csn5 (csn5a-2 csn5b) mutant light replicate 1GSE9728COP9 signalosome (csn) mutant analysis
52.699.8GSM270870Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3GSE10719Response of Arabidopsis cell culture to phytoprostane A1
52.099.8GSM245914csn5 (csn5a-2 csn5b) mutant light replicate 2GSE9728COP9 signalosome (csn) mutant analysis
50.799.8GSM270868Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2GSE10719Response of Arabidopsis cell culture to phytoprostane A1
46.699.8GSM245915csn5 (csn5a-2 csn5b) mutant light replicate 3GSE9728COP9 signalosome (csn) mutant analysis
44.899.8GSM245910csn3-1 mutant light replicate 1GSE9728COP9 signalosome (csn) mutant analysis
41.499.8GSM270866Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep1GSE10719Response of Arabidopsis cell culture to phytoprostane A1
41.199.8GSM245912csn3-1 mutant light replicate 3GSE9728COP9 signalosome (csn) mutant analysis
40.599.8GSM245919csn3-1 mutant dark replicate 1GSE9728COP9 signalosome (csn) mutant analysis
40.399.8GSM311274Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stage
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Homologous genes



Paralogous genes



Click Gene ID to show a list of homologous genes.

HFEvBSGene IDRepr. IDGene NameFunctional descriptionC.G.S.X.Other DB
0.692e-171603At1g57800842155VIM5 (VARIANT IN METHYLATION 5)predicted to encode a protein with an N-terminal PHD domain and two RING domains surrounding an SRA domain. Attempts to isolate ORTH3/VIM5 cDNA through RT-PCR were unsuccessful and only one Arabidopsis EST is associated with this locus.C.G.S.X.
0.422e-134480At1g66050842919VIM2 (VARIANT IN METHYLATION 2)Encodes a protein that is similar to VIM1 but is not involved in cytosine methylation. This protein has an N-terminal PHD domain and two RING domains surrounding an SRA domain. ORTH5/VIM2 has E3 ubiquitin ligase activity in vitro.C.G.S.X.
0.422e-134480At1g66040842917VIM4 (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.C.G.S.X.
0.362e-97357At4g08590826420ORTHL (ORTHRUS-LIKE)F:ubiquitin-protein ligase activity, zinc ion binding;P:protein ubiquitination;C:cytoplasm;MPOFBVC.G.S.X.
0.468e-94345At5g39550833951VIM3 (VARIANT IN METHYLATION 3)Encodes the VIM3/ORTH1 protein that is similar to VIM1. This protein has an N-terminal PHD domain and two RING domains surrounding an SRA domain. 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. This protein functions as an E3 ubiquitin ligase in vitro with members of the UBC8 family E2s. Either of the two RING domains present in the protein can promote ubiquitylation in vitro, but, not the PHD domain. Over-expression of ORTH1/VIM3 leads to decreased levels of FWA methylation, increased levels of FWA transcripts, and delayed flowering. Cen180 repeats are also hypomethylated in plants overexpressing this protein.C.G.S.X.
0.024e-344At5g48350834888nucleic acid bindingF:nucleic acid binding;P:biological_process unknown;C:unknown;PMFBOC.G.S.X.
0.016e-240At3g17170820974RFC3 (REGULATOR OF FATTY-ACID COMPOSITION 3)F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, intracellular, chloroplast;MOBFPVAC.G.S.X.
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Orthologous genes



Click Gene ID to show a list of orthologous genes.

HFEvBSSpeciesGene IDRepr. IDGene NameFunctional descriptionEvAGI codeArabidopsis gene nameC.G.S.X.Other DB
0.023e-138Glycine maxGmaAffx.82822.1.S1_atAI460612--2e-32At1g20920DEAD box RNA helicase, putativeC.G.S.X.
0.011e-138Hordeum vulgareContig10845_atContig10845--6e-2At4g20850TPP2 (TRIPEPTIDYL PEPTIDASE II)C.G.S.X.
0.144e-26121Oryza sativaOs05g0102600AK101136.1-Zn-finger, RING domain containing protein3e-26At1g57820VIM1 (VARIANT IN METHYLATION 1)C.G.S.X.
0.155e-28127Populus trichocarpaPtp.6811.1.S1_atBU830393hypothetical protein-7e-19At1g57820VIM1 (VARIANT IN METHYLATION 1)C.G.S.X.
0.091e-656Triticum aestivumTa.9515.1.S1_atBJ239628--9e-7At1g57820VIM1 (VARIANT IN METHYLATION 1)C.G.S.X.
0.031e-344Vitis vinifera1621501_atCB342916hypothetical protein LOC100243553-1e-3At1g57820VIM1 (VARIANT IN METHYLATION 1)C.G.S.X.
0.135e-1995Zea maysZm.13093.1.S1_atCD437312--2e-12At5g39550VIM3 (VARIANT IN METHYLATION 3)C.G.S.X.
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Biological processes



Click GO ID to show a list of genes that are associated with the GO ID.

ECCGO IDProcess Name
XGO:0016567The process by which one or more ubiquitin moieties are added to a protein.
XGO:0006325Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
XGO:0051301The process resulting in the physical partitioning and separation of a cell into daughter cells.
XGO:0031508The assembly of chromatin into heterochromatin near the centromere.
XGO:0032776The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule.
CGO:0006355Any process that modulates the frequency, rate or extent of DNA-dependent transcription.
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Metabolic pathways



Click KaPPA-View ID to show a list of genes that are assigned to the KaPPA-View ID.

KaPPA-View IDLink to Kappa-ViewPathway Name



Click KEGG PATHWAY ID to show a list of genes that are assigned to the KEGG PATHWAY ID.

KEGG PATHWAY IDLink to KEGG PATHWAYPathway Name
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