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EHMT1 euchromatic histone lysine methyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 79813, updated on 8-Dec-2022

Summary

Official Symbol
EHMT1provided by HGNC
Official Full Name
euchromatic histone lysine methyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:24650
See related
Ensembl:ENSG00000181090 MIM:607001; AllianceGenome:HGNC:24650
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
GLP; GLP1; KMT1D; KLEFS1; FP13812; EHMT1-IT1; EUHMTASE1; Eu-HMTase1
Summary
The protein encoded by this gene is a histone methyltransferase that methylates the lysine-9 position of histone H3. This action marks the genomic region packaged with these methylated histones for transcriptional repression. This protein may be involved in the silencing of MYC- and E2F-responsive genes and therefore could play a role in the G0/G1 cell cycle transition. Defects in this gene are a cause of chromosome 9q subtelomeric deletion syndrome (9q-syndrome, also known as Kleefstra syndrome). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2017]
Expression
Ubiquitous expression in testis (RPKM 9.7), spleen (RPKM 7.2) and 25 other tissues See more
Orthologs
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Genomic context

See EHMT1 in Genome Data Viewer
Location:
9q34.3
Exon count:
38
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137619005..137836127)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149870687..150093989)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140513457..140730579)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902318 Neighboring gene ARRDC1 antisense RNA 1 Neighboring gene arrestin domain containing 1 Neighboring gene Sharpr-MPRA regulatory region 6441 Neighboring gene SET pseudogene 5 Neighboring gene uncharacterized LOC124902319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140575207-140575806 Neighboring gene forkhead box H1 pseudogene Neighboring gene uncharacterized LOC651337 Neighboring gene 9q34.3 EHMT1 distal recombination region Neighboring gene microRNA 602

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

Associated conditions

Description Tests
Kleefstra syndrome 1
MedGen: C0795833 OMIM: 610253 GeneReviews: Kleefstra Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

Little evidence for dosage pathogenicity (Last evaluated 2012-07-06)

ClinGen Genome Curation PagePubMed
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2012-07-06)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ12879, FLJ40292, FLJ46107, KIAA1876, DKFZp667M072

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables C2H2 zinc finger domain binding IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K27 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables histone H3K9 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3K9 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables histone H3K9me2 methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables p53 binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription corepressor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in DNA methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in DNA methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in chromatin organization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in facultative heterochromatin formation IEA
Inferred from Electronic Annotation
more info
 
involved_in histone H3-K9 methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in peptidyl-lysine dimethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in peptidyl-lysine dimethylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in peptidyl-lysine monomethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in regulation of embryonic development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of histone H3-K9 methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
is_active_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IC
Inferred by Curator
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
histone-lysine N-methyltransferase EHMT1
Names
EHMT1 intronic transcript 1
G9a-like protein 1
H3-K9-HMTase 5
euchromatic histone-lysine N-methyltransferase 1
histone H3-K9 methyltransferase 5
histone-lysine N-methyltransferase, H3 lysine-9 specific 5
lysine N-methyltransferase 1D
NP_001138999.1
NP_001341188.1
NP_001341192.1
NP_001341540.1
NP_001341541.1
NP_079033.4
XP_005266167.1
XP_011517323.1
XP_011517324.1
XP_011517325.1
XP_011517331.1
XP_011517332.1
XP_011517333.1
XP_016870623.1
XP_016870627.1
XP_024303445.1
XP_024303446.2
XP_047279828.1
XP_047279829.1
XP_047279830.1
XP_047279831.1
XP_047279832.1
XP_047279833.1
XP_047279834.1
XP_047279835.1
XP_047279836.1
XP_047279837.1
XP_047279838.1
XP_047279839.1
XP_047279840.1
XP_047279841.1
XP_047279842.1
XP_047279843.1
XP_047279844.1
XP_047279845.1
XP_047279846.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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.

Genomic

  1. NG_011776.1 RefSeqGene

    Range
    5014..222136
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145527.2NP_001138999.1  histone-lysine N-methyltransferase EHMT1 isoform 2

    See identical proteins and their annotated locations for NP_001138999.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AB028932, BC047504, BM681619
    Consensus CDS
    CCDS56595.1
    UniProtKB/Swiss-Prot
    Q9H9B1
    Related
    ENSP00000417328.1, ENST00000462484.5
    Conserved Domains (3) summary
    cd00204
    Location:742796
    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 ...
    pfam13637
    Location:742793
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:742768
    ANK; ANK repeat [structural motif]
  2. NM_001354259.2NP_001341188.1  histone-lysine N-methyltransferase EHMT1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' region and differs in the 3' exon structure compared to variant 1. It initiates translation at a downstream start codon. The encoded isoform (3) has a shorter N-terminus and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AK022941, AL590627, AL611925, BC047504
    Conserved Domains (2) summary
    cd00204
    Location:711802
    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:743772
    ANK; ANK repeat [structural motif]
  3. NM_001354263.2NP_001341192.1  histone-lysine N-methyltransferase EHMT1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AL365502, AL590627, AL611925
    Conserved Domains (5) summary
    smart00317
    Location:11191241
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:793919
    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:798829
    ANK; ANK repeat [structural motif]
    pfam05033
    Location:10071111
    Pre-SET; Pre-SET motif
    cl26073
    Location:740999
    Ank_2; Ankyrin repeats (3 copies)
  4. NM_001354611.2NP_001341540.1  histone-lysine N-methyltransferase EHMT1 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks multiple 3' exons and contains an alternate 3' coding region and 3' UTR compared to variant 1. The encoded isoform (5) has a shorter, distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL365502, AL590627
    Consensus CDS
    CCDS87721.1
    UniProtKB/TrEMBL
    A0A1B0GUD1
    Related
    ENSP00000490056.1, ENST00000629335.2
  5. NM_001354612.2NP_001341541.1  histone-lysine N-methyltransferase EHMT1 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an exon in the 5' region, initiates translation at a downstream start codon and differs in the 3' coding region and 3' UTR compared to variant 1. The encoded isoform (6) has a shorter N-terminus and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL365502, AL590627
    Related
    ENSP00000485900.1, ENST00000626066.2
  6. NM_024757.5NP_079033.4  histone-lysine N-methyltransferase EHMT1 isoform 1

    See identical proteins and their annotated locations for NP_079033.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB028932, BC011608, BC047504, CA426038
    Consensus CDS
    CCDS7050.2
    UniProtKB/Swiss-Prot
    Q96KH4, Q9H9B1
    Related
    ENSP00000417980.1, ENST00000460843.6
    Conserved Domains (4) summary
    sd00045
    Location:805836
    ANK; ANK repeat [structural motif]
    cd10535
    Location:10361266
    SET_EHMT1; SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins
    cd20905
    Location:514644
    EHMT_ZBD; Zinc-binding domain of euchromatic histone lysine methyltransferases EHMT1 and EHTM2
    pfam12796
    Location:810903
    Ank_2; Ankyrin repeats (3 copies)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    137619005..137836127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423872.1XP_047279828.1  histone-lysine N-methyltransferase EHMT1 isoform X3

  2. XM_047423875.1XP_047279831.1  histone-lysine N-methyltransferase EHMT1 isoform X8

  3. XM_047423878.1XP_047279834.1  histone-lysine N-methyltransferase EHMT1 isoform X10

    UniProtKB/TrEMBL
    A0A1B0GV09
  4. XM_005266110.2XP_005266167.1  histone-lysine N-methyltransferase EHMT1 isoform X10

    See identical proteins and their annotated locations for XP_005266167.1

    UniProtKB/TrEMBL
    A0A1B0GV09
    Conserved Domains (6) summary
    smart00248
    Location:741769
    ANK; ankyrin repeats
    smart00317
    Location:10951217
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:769895
    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 ...
    pfam05033
    Location:9831087
    Pre-SET; Pre-SET motif
    pfam12796
    Location:779872
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:774805
    ANK; ANK repeat [structural motif]
  5. XM_047423883.1XP_047279839.1  histone-lysine N-methyltransferase EHMT1 isoform X15

  6. XM_047423881.1XP_047279837.1  histone-lysine N-methyltransferase EHMT1 isoform X13

  7. XM_017015138.2XP_016870627.1  histone-lysine N-methyltransferase EHMT1 isoform X11

  8. XM_047423884.1XP_047279840.1  histone-lysine N-methyltransferase EHMT1 isoform X16

  9. XM_047423882.1XP_047279838.1  histone-lysine N-methyltransferase EHMT1 isoform X14

  10. XM_047423885.1XP_047279841.1  histone-lysine N-methyltransferase EHMT1 isoform X17

  11. XM_024447678.2XP_024303446.2  histone-lysine N-methyltransferase EHMT1 isoform X19

  12. XM_047423886.1XP_047279842.1  histone-lysine N-methyltransferase EHMT1 isoform X20

  13. XM_047423888.1XP_047279844.1  histone-lysine N-methyltransferase EHMT1 isoform X22

  14. XM_047423887.1XP_047279843.1  histone-lysine N-methyltransferase EHMT1 isoform X21

    Related
    ENSP00000489961.1, ENST00000636027.1
  15. XM_047423889.1XP_047279845.1  histone-lysine N-methyltransferase EHMT1 isoform X23

  16. XM_011519022.4XP_011517324.1  histone-lysine N-methyltransferase EHMT1 isoform X2

    Conserved Domains (6) summary
    smart00248
    Location:774802
    ANK; ankyrin repeats
    smart00317
    Location:11281250
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:802928
    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 ...
    pfam05033
    Location:10161120
    Pre-SET; Pre-SET motif
    pfam12796
    Location:812905
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:807838
    ANK; ANK repeat [structural motif]
  17. XM_017015134.2XP_016870623.1  histone-lysine N-methyltransferase EHMT1 isoform X5

  18. XM_047423873.1XP_047279829.1  histone-lysine N-methyltransferase EHMT1 isoform X6

  19. XM_047423879.1XP_047279835.1  histone-lysine N-methyltransferase EHMT1 isoform X11

  20. XM_011519021.4XP_011517323.1  histone-lysine N-methyltransferase EHMT1 isoform X1

    Conserved Domains (4) summary
    COG0666
    Location:765932
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:808839
    ANK; ANK repeat [structural motif]
    pfam13637
    Location:912962
    Ank_4; Ankyrin repeats (many copies)
    cd10535
    Location:10391269
    SET_EHMT1; SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins
  21. XM_047423880.1XP_047279836.1  histone-lysine N-methyltransferase EHMT1 isoform X12

  22. XM_047423874.1XP_047279830.1  histone-lysine N-methyltransferase EHMT1 isoform X7

  23. XM_011519023.4XP_011517325.1  histone-lysine N-methyltransferase EHMT1 isoform X4

    Conserved Domains (6) summary
    smart00248
    Location:768796
    ANK; ankyrin repeats
    smart00317
    Location:11221244
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:796922
    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 ...
    pfam05033
    Location:10101114
    Pre-SET; Pre-SET motif
    pfam12796
    Location:806899
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:801832
    ANK; ANK repeat [structural motif]
  24. XM_047423876.1XP_047279832.1  histone-lysine N-methyltransferase EHMT1 isoform X9

  25. XM_047423877.1XP_047279833.1  histone-lysine N-methyltransferase EHMT1 isoform X10

    UniProtKB/TrEMBL
    A0A1B0GV09
    Related
    ENSP00000490328.1, ENST00000637161.1
  26. XM_024447677.2XP_024303445.1  histone-lysine N-methyltransferase EHMT1 isoform X18

    Conserved Domains (5) summary
    smart00317
    Location:834956
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:508634
    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:513544
    ANK; ANK repeat [structural motif]
    pfam05033
    Location:722826
    Pre-SET; Pre-SET motif
    pfam12796
    Location:450544
    Ank_2; Ankyrin repeats (3 copies)
  27. XM_011519029.4XP_011517331.1  histone-lysine N-methyltransferase EHMT1 isoform X24

    Conserved Domains (6) summary
    smart00248
    Location:249277
    ANK; ankyrin repeats
    smart00317
    Location:603725
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:277403
    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 ...
    pfam05033
    Location:491595
    Pre-SET; Pre-SET motif
    pfam12796
    Location:287380
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:282313
    ANK; ANK repeat [structural motif]
  28. XM_011519030.4XP_011517332.1  histone-lysine N-methyltransferase EHMT1 isoform X25

    Conserved Domains (7) summary
    smart00248
    Location:199228
    ANK; ankyrin repeats
    smart00317
    Location:387509
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:61187
    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 ...
    pfam05033
    Location:275379
    Pre-SET; Pre-SET motif
    pfam12796
    Location:71164
    Ank_2; Ankyrin repeats (3 copies)
    pfam13637
    Location:5487
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:6697
    ANK; ANK repeat [structural motif]
  29. XM_047423890.1XP_047279846.1  histone-lysine N-methyltransferase EHMT1 isoform X26

  30. XM_011519031.2XP_011517333.1  histone-lysine N-methyltransferase EHMT1 isoform X26

    See identical proteins and their annotated locations for XP_011517333.1

    Conserved Domains (5) summary
    smart00317
    Location:316438
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd00204
    Location:23149
    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 ...
    pfam05033
    Location:204308
    Pre-SET; Pre-SET motif
    pfam12796
    Location:193
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:2860
    ANK; ANK repeat [structural motif]

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149870687..150093989
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001039765.1: Suppressed sequence

    Description
    NM_001039765.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.