Dicots PLAZA 4.5 gene overview : AT5G04560

Gene: AT5G04560 (Arabidopsis thaliana)

Overview

Gene Identifier: AT5G04560
Transcript Identifier: AT5G04560.3
Gene Type: Coding gene
Location: Chr5 : 1310671-1318091 : positive

Family Information

Homologous gene family: HOM04D001046
(277 genes in 55 species)
specific family
Orthologous gene family: ORTHO04D000949
(261 genes in 55 species)
specific family

Descriptions

Description: HhH-GPD base excision DNA repair family protein

Curated Summary: Encodes a DNA glycosylase DEMETER (DME). Responsible for endosperm maternal-allele-specific hypomethylation at the MEDEA (MEA) gene. DME can excise 5-methylcytosine in vitro and when expressed in E. coli. DME establishes MEA imprinting by removing 5-methylcytosine to activate the maternal allele.

Identifiers

Type	Value
full_name	DEMETER
symbol	DME
tid	AT5G04560.3

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Biological Process

GO term	Evidence(s)	Provider(s)	Description	Source(s)
GO:0006284	IEA	UniProt	base-excision repair
GO:0006284	IEA	Gene Ontology	base-excision repair	1
GO:0006284	IEA	InterPro	base-excision repair
GO:0006351	IEA	UniProt	transcription, DNA-templated
GO:0006351	IEA	Gene Ontology	transcription, DNA-templated	2
GO:0006355	IEA	UniProt	regulation of transcription, DNA-templated
GO:0006355	IEA	Gene Ontology	regulation of transcription, DNA-templated	2
GO:0009793	IMP	UniProt	embryo development ending in seed dormancy
GO:0009793	IMP	Gene Ontology	embryo development ending in seed dormancy	3
GO:0006349	IMP	UniProt	regulation of gene expression by genetic imprinting
GO:0006349	IMP	Gene Ontology	regulation of gene expression by genetic imprinting	4
GO:0006306	IDA	UniProt	DNA methylation
GO:0006306	IDA	Gene Ontology	DNA methylation	5
GO:0006281	IEA	InterPro	DNA repair

Molecular Function

GO term	Evidence(s)	Provider(s)	Description	Source(s)
GO:0003677	IEA	UniProt	DNA binding
GO:0003677	IEA	Gene Ontology	DNA binding	2
GO:0046872	IEA	UniProt	metal ion binding
GO:0046872	IEA	Gene Ontology	metal ion binding	2
GO:0051539	IEA	UniProt	4 iron, 4 sulfur cluster binding
GO:0051539	IEA	Gene Ontology	4 iron, 4 sulfur cluster binding	2
GO:0051539	IEA	InterPro	4 iron, 4 sulfur cluster binding
GO:0019104	IDA	UniProt	DNA N-glycosylase activity
GO:0019104	IDA ISS	Gene Ontology	DNA N-glycosylase activity	3 5
GO:0003906	IDA	UniProt	DNA-(apurinic or apyrimidinic site) lyase activity
GO:0003906	IDA	Gene Ontology	DNA-(apurinic or apyrimidinic site) lyase activity	5
GO:0003824	IEA	InterPro	catalytic activity

Cellular Component

GO term	Evidence(s)	Provider(s)	Description	Source(s)
GO:0005634	ISS	UniProt	nucleus
GO:0005634	ISS, ISM	Gene Ontology	nucleus	3 6
GO:0043078	IDA	UniProt	polar nucleus
GO:0043078	IDA	Gene Ontology	polar nucleus	3

Color Legend

Experimental Evidence

Computational Reviewed Evidence

Electronic Evidence

InterPro	Description
IPR003265	HhH-GPD domain
IPR023170	Helix-turn-helix, base-excision DNA repair, C-terminal
IPR028925	Demeter, RRM-fold domain
IPR028924	Permuted single zf-CXXC unit
IPR003651	Endonuclease III-like, iron-sulphur cluster loop motif
IPR011257	DNA glycosylase

Mapman id	Description
12.5.3.1	.Chromatin organisation.DNA methylation.ROS1-mediated DNA demethylation.methylcytosine-specific DNA glycosylase (ROS1)
14.5.4	.DNA damage response.base excision repair (BER).bifunctional DNA glycosylase/lyase (ROS1)