DML3 demeter-like protein 3 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: DML3
Official Full Name: demeter-like protein 3
Primary source: TAIR:AT4G34060
Locus tag: AT4G34060
See related: Araport:AT4G34060
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: demeter-like protein 3; F28A23.180; F28A23_180
Summary: Encodes a protein with 5-meC and thymine-DNA glycosylase activity with a preference for CpG and CpHpG sequences. Involved in maintaining methylation marks.
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Genomic context

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See DML3 in Genome Data Viewer

Location:: chromosome: 4

Exon count:: 21

Sequence:: Chromosome: 4; NC_003075.7 (16313366..16319426)

Chromosome 4 - NC_003075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ROS1, DML2, and DML3 play a role in fungal disease resistance in Arabidopsis
Title: DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis.
Results suggest that DML3 is required not only for removing DNA methylation marks from improperly-methylated cytosines, but also for maintenance of high methylation levels in properly targeted sites.
Title: Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks.
DML3 excises 5-methylcytosine in vitro.
Title: DNA demethylation in the Arabidopsis genome.

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General gene information

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NM_001125640.1

Supported by ESTs:

NM_001342251.1

Supported by ESTs:

NM_001342252.1

Supported by ESTs:

NM_119567.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA N-glycosylase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA N-glycosylase activity	IEA Inferred from Electronic Annotation more info
enables DNA demethylase activity	IEA Inferred from Electronic Annotation more info
enables cytosine C-5 DNA demethylase activity	IMP Inferred from Mutant Phenotype more info

Process	Evidence Code	Pubs
involved_in base-excision repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within leaf senescence	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in mitochondrion	ISM Inferred from Sequence Model more info
located_in nucleus	IDA Inferred from Direct Assay more info
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: demeter-like protein 3

NP_001119112.1

demeter-like protein 3 (DML3); CONTAINS InterPro DOMAIN/s: DNA glycosylase (InterPro:IPR011257), Endonuclease III-like, iron-sulphur cluster loop motif (InterPro:IPR003651), HhH-GPD domain (InterPro:IPR003265); BEST Arabidopsis thaliana protein match is: HhH-GPD base excision DNA repair family protein (TAIR:AT5G04560.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).

NP_195132.3

demeter-like protein 3 (DML3); CONTAINS InterPro DOMAIN/s: DNA glycosylase (InterPro:IPR011257), HhH-GPD domain (InterPro:IPR003265); BEST Arabidopsis thaliana protein match is: demeter-like 1 (TAIR:AT2G36490.1); Has 3859 Blast hits to 3748 proteins in 1288 species: Archae - 200; Bacteria - 2252; Metazoa - 138; Fungi - 63; Plants - 258; Viruses - 0; Other Eukaryotes - 948 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003075.7 Reference assembly

Range

16313366..16319426

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001342250.1 → NP_001329149.1 demeter-like protein 3 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B6V3, A0A5S9XYF7
NM_119567.4 → NP_195132.3 demeter-like protein 3 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_195132.3

Status: REVIEWED

UniProtKB/Swiss-Prot

O49498, Q5XV59

UniProtKB/TrEMBL

A0A178V2G2

Conserved Domains (3) summary

smart00478
Location:570 → 675

ENDO3c; endonuclease III

pfam15628
Location:929 → 1030

RRM_DME; RRM in Demeter

pfam15629
Location:896 → 926

Perm-CXXC; Permuted single zf-CXXC unit
NM_001125640.1 → NP_001119112.1 demeter-like protein 3 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001119112.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A178V2G2, B3H5X5

Conserved Domains (3) summary

smart00478
Location:570 → 675

ENDO3c; endonuclease III

pfam15628
Location:929 → 954

RRM_DME; RRM in Demeter

pfam15629
Location:896 → 926

Perm-CXXC; Permuted single zf-CXXC unit
NM_001342251.1 → NP_001329150.1 demeter-like protein 3 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A178V2G2, A0A1P8B6U7
NM_001342252.1 → NP_001329148.1 demeter-like protein 3 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A178V2G2, A0A1P8B6V0