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EHMT2 euchromatic histone lysine methyltransferase 2 [ Homo sapiens (human) ]

Gene ID: 10919, updated on 1-Jun-2020

Summary

Official Symbol
EHMT2provided by HGNC
Official Full Name
euchromatic histone lysine methyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:14129
See related
Ensembl:ENSG00000204371 MIM:604599
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
G9A; BAT8; GAT8; NG36; KMT1C; C6orf30
Summary
This gene encodes a methyltransferase that methylates lysine residues of histone H3. Methylation of H3 at lysine 9 by this protein results in recruitment of additional epigenetic regulators and repression of transcription. This gene was initially thought to be two different genes, NG36 and G9a, adjacent to each other in the HLA locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in ovary (RPKM 14.8), testis (RPKM 14.4) and 25 other tissues See more
Orthologs

Genomic context

See EHMT2 in Genome Data Viewer
Location:
6p21.33
Exon count:
29
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (31879759..31897698, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31847536..31865464, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene neuraminidase 1 Neighboring gene solute carrier family 44 member 4 Neighboring gene uncharacterized LOC107986588 Neighboring gene zinc finger and BTB domain containing 12 Neighboring gene complement C2 Neighboring gene C2 antisense RNA 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study identified new variants associated with the risk of chronic hepatitis B.
NHGRI GWA Catalog
A genome-wide integrative genomic study localizes genetic factors influencing antibodies against Epstein-Barr virus nuclear antigen 1 (EBNA-1).
NHGRI GWA Catalog
Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.
NHGRI GWA Catalog
The genetic architecture of economic and political preferences.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat Histone H3 Lysine9 (H3K9) methyltransferase G9a significantly inhibits basal and the TNF-alpha- or HIV-1 Tat- induced HIV-1 gene expression for the maintenance of HIV-1 latency PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ35547, DKFZp686H08213

Gene Ontology Provided by GOA

Function Evidence Code Pubs
C2H2 zinc finger domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone methyltransferase activity (H3-K27 specific) ISS
Inferred from Sequence or Structural Similarity
more info
 
histone methyltransferase activity (H3-K9 specific) ISS
Inferred from Sequence or Structural Similarity
more info
 
histone-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone-lysine N-methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
p53 binding IPI
Inferred from Physical Interaction
more info
PubMed 
promoter-specific chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to starvation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K27 methylation IEA
Inferred from Electronic Annotation
more info
 
histone H3-K9 methylation IEA
Inferred from Electronic Annotation
more info
 
histone lysine methylation IDA
Inferred from Direct Assay
more info
PubMed 
histone methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of G0 to G1 transition TAS
Traceable Author Statement
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
peptidyl-lysine dimethylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of DNA replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
histone-lysine N-methyltransferase EHMT2
Names
G9A histone methyltransferase
H3-K9-HMTase 3
HLA-B associated transcript 8
ankyrin repeat-containing protein
euchromatic histone-lysine N-methyltransferase 2
histone H3-K9 methyltransferase 3
histone-lysine N-methyltransferase, H3 lysine-9 specific 3
lysine N-methyltransferase 1C
NP_001276342.1
NP_001305762.1
NP_001350618.1
NP_006700.3
NP_079532.5
XP_006715037.1
XP_006715038.1
XP_006715039.1
XP_016865691.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001289413.1NP_001276342.1  histone-lysine N-methyltransferase EHMT2 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 5. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform e.
    Source sequence(s)
    AK302904, BC009351, CN397400, X69838
    Consensus CDS
    CCDS75425.1
    UniProtKB/Swiss-Prot
    Q96KQ7
    UniProtKB/TrEMBL
    A2ABF8, B7Z852
    Related
    ENSP00000364678.4, ENST00000375528.8
    Conserved Domains (7) summary
    smart00468
    Location:9461045
    PreSET; N-terminal to some SET domains
    smart00317
    Location:10611183
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:709828
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:745838
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:808838
    ANK; ANK repeat [structural motif]
    cl02529
    Location:677728
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cl09938
    Location:46139
    cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
  2. NM_001318833.1NP_001305762.1  histone-lysine N-methyltransferase EHMT2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains multiple differences in the 5' region, initiates translation at a downstream start codon, and lacks an alternate in-frame exon compared to variant 1. The encoded isoform (d) is shorter than isoform c.
    Source sequence(s)
    AB209433, AL671762, HY067184, X69838
    UniProtKB/Swiss-Prot
    Q96KQ7
    UniProtKB/TrEMBL
    Q59FM7
    Related
    ENST00000480912.5
    Conserved Domains (7) summary
    smart00468
    Location:721820
    PreSET; N-terminal to some SET domains
    smart00317
    Location:836958
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:477596
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:513606
    Ank_2; Ankyrin repeats (3 copies)
    pfam13857
    Location:635688
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:477506
    ANK; ANK repeat [structural motif]
    cl02529
    Location:445496
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
  3. NM_001363689.1NP_001350618.1  histone-lysine N-methyltransferase EHMT2 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) encodes the longest isoform (e).
    Source sequence(s)
    AL671762
    Consensus CDS
    CCDS87384.1
    Related
    ENSP00000379078.3, ENST00000395728.7
    Conserved Domains (7) summary
    smart00468
    Location:9801079
    PreSET; N-terminal to some SET domains
    smart00317
    Location:10951217
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:743862
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    sd00045
    Location:842872
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:711772
    Ank_2; Ankyrin repeats (3 copies)
    cl26464
    Location:5261
    Atrophin-1; Atrophin-1 family
    cl27511
    Location:275383
    Na_Ca_ex; Sodium/calcium exchanger protein
  4. NM_006709.5NP_006700.3  histone-lysine N-methyltransferase EHMT2 isoform a

    See identical proteins and their annotated locations for NP_006700.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as NG36/G9a) uses an alternate 5' UTR and 5' coding region, contains an alternate in-frame exon in the 5' coding region, and lacks an alternate in-frame exon compared to variant 3. It encodes isoform a, which is shorter and has a distinct N-terminus, compared to isoform c.
    Source sequence(s)
    BC009351, CN397400, HY067184, X69838
    Consensus CDS
    CCDS4725.1
    UniProtKB/Swiss-Prot
    Q96KQ7
    UniProtKB/TrEMBL
    A0A024RCN9
    Related
    ENSP00000364687.4, ENST00000375537.8
    Conserved Domains (7) summary
    smart00468
    Location:9231022
    PreSET; N-terminal to some SET domains
    smart00317
    Location:10381160
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:686805
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    sd00045
    Location:785815
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:654715
    Ank_2; Ankyrin repeats (3 copies)
    cl26464
    Location:42204
    Atrophin-1; Atrophin-1 family
    cl27511
    Location:218326
    Na_Ca_ex; Sodium/calcium exchanger protein
  5. NM_025256.7NP_079532.5  histone-lysine N-methyltransferase EHMT2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3, also known as NG36/G9a-SPI) uses an alternate 5' UTR and 5' coding region and lacks an alternate in-frame exon compared to variant 3. It encodes isoform b, which has a shorter and distinct N-terminus and is shorter compared to isoform c.
    Source sequence(s)
    BC009351, CN397400, HY067184, X69838
    Consensus CDS
    CCDS4726.1
    UniProtKB/Swiss-Prot
    Q96KQ7
    Related
    ENSP00000364680.4, ENST00000375530.8
    Conserved Domains (6) summary
    smart00468
    Location:889988
    PreSET; N-terminal to some SET domains
    smart00317
    Location:10041126
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:652771
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:688781
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:751781
    ANK; ANK repeat [structural motif]
    cl02529
    Location:620671
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    31879759..31897698 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010202.1XP_016865691.1  histone-lysine N-methyltransferase EHMT2 isoform X5

  2. XM_006714976.1XP_006715039.1  histone-lysine N-methyltransferase EHMT2 isoform X4

    See identical proteins and their annotated locations for XP_006715039.1

    Conserved Domains (7) summary
    smart00468
    Location:9301029
    PreSET; N-terminal to some SET domains
    smart00317
    Location:10451167
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:686805
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:722815
    Ank_2; Ankyrin repeats (3 copies)
    pfam13857
    Location:844897
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:686715
    ANK; ANK repeat [structural motif]
    cl02529
    Location:654705
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
  3. XM_006714975.1XP_006715038.1  histone-lysine N-methyltransferase EHMT2 isoform X3

    See identical proteins and their annotated locations for XP_006715038.1

    Conserved Domains (8) summary
    smart00468
    Location:9531052
    PreSET; N-terminal to some SET domains
    smart00317
    Location:10681190
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:709828
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:745838
    Ank_2; Ankyrin repeats (3 copies)
    pfam13857
    Location:867920
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:709738
    ANK; ANK repeat [structural motif]
    cl02529
    Location:677728
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cl09938
    Location:46139
    cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
  4. XM_006714974.1XP_006715037.1  histone-lysine N-methyltransferase EHMT2 isoform X1

    See identical proteins and their annotated locations for XP_006715037.1

    Conserved Domains (8) summary
    smart00468
    Location:9871086
    PreSET; N-terminal to some SET domains
    smart00317
    Location:11021224
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:743862
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:779872
    Ank_2; Ankyrin repeats (3 copies)
    pfam13857
    Location:901954
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:743772
    ANK; ANK repeat [structural motif]
    cl02529
    Location:711762
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cl09938
    Location:46139
    cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    3212374..3230320 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    3357184..3375123 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    3127533..3145472 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    3221824..3239770 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    3135732..3153670 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    3180981..3190908 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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