Gene: AT5G39550 (Arabidopsis thaliana)

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Gene Identifier
AT5G39550
Transcript Identifier
AT5G39550.1
Gene Type
Coding gene
Location
5 : 15837408-15840503 : negative

Family

Gene family
HOM03D001750
(94 genes in 30 species)
specific family
Subfamily
ORTHO03D000897
(63 genes in 28 species)
specific family
Duplication type
Block duplicate

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Descriptions

Description
Zinc finger (C3HC4-type RING finger) family protein
Curated Summary
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.
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Identifiers

Identifier Name
aliasVIM3
aliasORTH1
aliasVARIANT IN METHYLATION 3
aliasORTHRUS 1
uniprotQ9FKA7

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Biological Process

GO termEvidence(s)ProviderDescriptionSource
GO:0032776IMPGene OntologyDNA methylation on cytosine1
GO:0010228IMPUniProtvegetative to reproductive phase transition of meristem1 2 3 4 5 6 7
GO:0016567IDAGene Ontologyprotein ubiquitination1
GO:0010424IMPUniProtDNA methylation on cytosine within a CG sequence1 2 3 4 5 6 7
GO:0090309IMPUniProtpositive regulation of methylation-dependent chromatin silencing1 2 3 4 5 6 7
GO:0016568IEAUniProtchromatin modification1 2 3 4 5 6
GO:0051301ISOPLAZA Tree-based Orthologycell divisionAT1G57820
GO:0031508ISOPLAZA Tree-based Orthologycentromeric heterochromatin assemblyAT1G57820

Molecular Function

GO termEvidence(s)ProviderDescriptionSource
GO:0008270IEA, ISSUniProtzinc ion binding1 2 3 4 5 6 7
GO:0008327IDAUniProtmethyl-CpG binding1 2 3 4 5 6 7
GO:0010428IDAUniProtmethyl-CpNpG binding1 2 3 4 5 6 7
GO:0010429IDAUniProtmethyl-CpNpN binding1 2 3 4 5 6 7
GO:0004842IDAUniProtubiquitin-protein ligase activity1 2 3 4 5 6 7
GO:0005515IEAInterProprotein binding
GO:0042393ISS, IEAUniProthistone binding1 2 3 4 5 6
GO:0046872IEAInterPrometal ion binding
GO:0010385ISOPLAZA Tree-based Orthologydouble-stranded methylated DNA bindingAT1G57820
GO:0003682ISOPLAZA Tree-based Orthologychromatin bindingAT1G57820

Cellular Component

GO termEvidence(s)ProviderDescriptionSource
GO:0005634IDA, ISM, UniProtnucleus1 2 3 4 5 6 7 8
GO:0005737ISOPLAZA Tree-based OrthologycytoplasmAT4G08590
GO:0010369ISOPLAZA Tree-based OrthologychromocenterAT1G57820

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Experimental Evidence
Electronic Evidence
Computational Reviewed Evidence
GO Sources:   Primary     Orthology     Homology  
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InterPro Description
IPR001965Zinc finger, PHD-type
IPR013083Zinc finger, RING/FYVE/PHD-type
IPR017907Zinc finger, RING-type, conserved site
IPR011011Zinc finger, FYVE/PHD-type
IPR003105SRA-YDG
IPR019786Zinc finger, PHD-type, conserved site
IPR001841Zinc finger, RING-type
IPR018957Zinc finger, C3HC4 RING-type
IPR015947PUA-like domain

Mapman id Description
27.3.11RNA.regulation of transcription.C2H2 zinc finger family
No SignalP domains detected for this gene.