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Gene : VIM3 A. thaliana

DB identifier	AT5G39550	Secondary Identifier	locus:2164835
Name	VARIANT IN METHYLATION 3	Brief Description	Zinc finger (C3HC4-type RING finger) family protein

TAIR Computational Description	Zinc finger (C3HC4-type RING finger) family protein;(source:Araport11)
TAIR Curator 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.
TAIR Short Description	Zinc finger (C3HC4-type RING finger) family protein
TAIR Aliases	ORTH1, VIM3

3 Gene Rifs

1 Organism

19 Publications

0 Synonyms

Genomics

Genome feature

Region:	gene	Length:	3501
Location:	Chr5:15837178-15840678 reverse strand

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10 Child Features

0 Cross References

1 Downstream Intergenic Region

0 Located Features

1 Upstream Intergenic Region

Proteins

Show proteins
Curated comments from UniProt

Type	Comment	Proteins
ORTH1_ARATH	function	E3 ubiquitin-protein ligase. Participates in CpG methylation-dependent transcriptional regulation and epigenetic transcriptional silencing. Mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. Promotes methylation-mediated gene silencing leading, for example, to early flowering. Can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrate.
ORTH1_ARATH	pathway	Protein modification; protein ubiquitination.
ORTH1_ARATH	subcellular location	Broadly distributed in the nucleus and enriched in the heterochromatic chromocenters.
ORTH1_ARATH	tissue specificity	Expressed in inflorescences and leaves.

1 Proteins

Function

Gene Ontology

cellular component
nucleus	ECO
molecular function
methyl-CpNpG binding	ECO
histone binding	ECO
methyl-CpNpN binding	ECO
ubiquitin-protein transferase activity	ECO
methyl-CpG binding	ECO
metal ion binding	ECO
biological process
protein ubiquitination	ECO
vegetative to reproductive phase transition of meristem	ECO
negative regulation of gene expression via chromosomal CpG island methylation	ECO

Interactions

Interaction Network

Expression

Data Source:

BAR Webservices

Querying ATTED Service... Data Source: ATTED-II

Homology

0 Homologues

Other

7 Data Sets

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