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SUV39H1 suppressor of variegation 3-9 homolog 1 [ Homo sapiens (human) ]

Gene ID: 6839, updated on 15-Jun-2019

Summary

Official Symbol
SUV39H1provided by HGNC
Official Full Name
suppressor of variegation 3-9 homolog 1provided by HGNC
Primary source
HGNC:HGNC:11479
See related
Ensembl:ENSG00000101945 MIM:300254
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
MG44; KMT1A; SUV39H; H3-K9-HMTase 1
Summary
This gene encodes an evolutionarily-conserved protein containing an N-terminal chromodomain and a C-terminal SET domain. The encoded protein is a histone methyltransferase that trimethylates lysine 9 of histone H3, which results in transcriptional gene silencing. Loss of function of this gene disrupts heterochromatin formation and may cause chromosome instability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Expression
Ubiquitous expression in bone marrow (RPKM 4.9), lymph node (RPKM 3.6) and 24 other tissues See more
Orthologs

Genomic context

See SUV39H1 in Genome Data Viewer
Location:
Xp11.23
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (48695554..48709016)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (48553945..48567407)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985695 Neighboring gene vomeronasal 1 receptor 110 pseudogene Neighboring gene WASP actin nucleation promoting factor Neighboring gene RNA, U6 small nuclear 1056, pseudogene Neighboring gene glyoxalase domain containing 5

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 FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr COUP-TF-interacting protein 2 (CTIP2) abolishes Vpr-mediated stimulation of p21 by cooperating with SUV39H1 and HDAC1/HDAC2 to silence the p21 gene transcription PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
S-adenosylmethionine-dependent methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding TAS
Traceable Author Statement
more info
PubMed 
histone methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone methyltransferase activity (H3-K9 specific) EXP
Inferred from Experiment
more info
PubMed 
histone methyltransferase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase activity (H3-K9 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein N-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
cellular response to DNA damage stimulus IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to hypoxia IDA
Inferred from Direct Assay
more info
PubMed 
chromatin organization TAS
Traceable Author Statement
more info
PubMed 
chromatin silencing at rDNA IDA
Inferred from Direct Assay
more info
PubMed 
chromatin silencing at rDNA TAS
Traceable Author Statement
more info
 
histone H3-K9 dimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K9 trimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone lysine methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
rRNA processing IEA
Inferred from Electronic Annotation
more info
 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chromatin silencing complex IDA
Inferred from Direct Assay
more info
PubMed 
chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
condensed nuclear chromosome TAS
Traceable Author Statement
more info
PubMed 
heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear lamina IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
rDNA heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase SUV39H1
Names
Su(var)3-9 homolog 1
histone H3-K9 methyltransferase 1
histone-lysine N-methyltransferase, H3 lysine-9 specific 1
lysine N-methyltransferase 1A
position-effect variegation 3-9 homolog
NP_001269095.1
NP_003164.1

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.

Genomic

  1. NG_012530.2 RefSeqGene

    Range
    4994..17277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001282166.1NP_001269095.1  histone-lysine N-methyltransferase SUV39H1 isoform 1

    See identical proteins and their annotated locations for NP_001269095.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AF019968, AK299900, AW327567, BC006238
    Consensus CDS
    CCDS65252.1
    UniProtKB/Swiss-Prot
    O43463
    Related
    ENSP00000337976.6, ENST00000337852.10
    Conserved Domains (3) summary
    smart00317
    Location:254377
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:54102
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam05033
    Location:147246
    Pre-SET; Pre-SET motif
  2. NM_003173.4NP_003164.1  histone-lysine N-methyltransferase SUV39H1 isoform 2

    See identical proteins and their annotated locations for NP_003164.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC231533, AF019968, AW327567, BC006238
    Consensus CDS
    CCDS14304.1
    UniProtKB/Swiss-Prot
    O43463
    Related
    ENSP00000365877.3, ENST00000376687.3
    Conserved Domains (3) summary
    smart00317
    Location:243366
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:4391
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam05033
    Location:136235
    Pre-SET; Pre-SET motif

RefSeqs of Annotated Genomes: Homo sapiens 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_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    48695554..48709016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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