Suv39h1 MGI Mouse Gene Detail - MGI:1099440 - suppressor of variegation 3-9 1

Symbol

Suv39h1
Name

suppressor of variegation 3-9 1
Synonyms

DXHXS7466e, KMT1A, mIS6, Suv39h histone methyltransferase

Feature Type

protein coding gene
IDs

MGI:1099440
NCBI Gene: 20937
Alliance

genome feature page
Transcription Start Sites

2 TSS

Sequence Map

ChrX:7927410-7940999 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome X, 3.64 cM, cytoband A1-A2
Mapping Data

7 experiments

SNPs within 2kb

214 from dbSNP Build 142
Strain Annotations

19
PCR

1
RFLP

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1099440	protein coding gene	ChrX:7927401-7940999 (-)
129S1/SvImJ	ENSMUSG00200030903	protein coding gene	ChrX:2627883-2641473 (-)
A/J	ENSMUSG00195040233	protein coding gene	ChrX:2651058-2664647 (-)
AKR/J	ENSMUSG00220033366	protein coding gene	ChrX:2638501-2652090 (-)
BALB/cJ	ENSMUSG00180025174	protein coding gene	ChrX:2648767-2662358 (-)
C3H/HeJ	ENSMUSG00175030152	protein coding gene	ChrX:2662709-2676298 (-)
C57BL/6NJ	ENSMUSG00215039781	protein coding gene	ChrX:3326583-3340172 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032911	protein coding gene	ChrX:2207926-2221219 (-)
CAST/EiJ	ENSTCUG00005030569	protein coding gene	ChrX:2597057-2610668 (-)
CBA/J	ENSMUSG00210035636	protein coding gene	ChrX:2679602-2693191 (-)
DBA/2J	ENSMUSG00185028428	protein coding gene	ChrX:9296725-9310314 (-)
FVB/NJ	ENSMUSG00205027151	protein coding gene	ChrX:2673364-2686955 (-)
JF1/MsJ	ENSUMUG00000037242	protein coding gene	ChrX:23184131-23197720 (-)
LP/J	ENSMUSG00230030107	protein coding gene	ChrX:13816722-13830312 (-)
NOD/ShiLtJ	ENSMUSG00190028466	protein coding gene	ChrX:2653348-2666937 (-)
NZO/HlLtJ	ENSMUSG00225044535	protein coding gene	ChrX:19082449-19096038 (-)
PWK/PhJ	ENSLUMG00010033921	protein coding gene	ChrX:2645893-2659479 (-)
SPRET/EiJ	ENSMSPG00010021013	protein coding gene	ChrX:2682769-2696325 (-)
WSB/EiJ	ENSIUOG00005030623	protein coding gene	ChrX:15860972-15874560 (+)

Human Ortholog

SUV39H1, SUV39H1 histone lysine methyltransferase

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SUV39H1, SUV39H1 histone lysine methyltransferase
Synonyms

H3-K9-HMTase 1, KMT1A, MG44, SUV39H
Links

HGNC:11479

NCBI Gene ID: 6839

UniProt: O43463
Chr Location

Xp11.23; chrX:48695554-48709016 (+) GRCh38

MGI Vertebrate Homology

Suv39h1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SUV39H1
Protein SuperFamily

SUV39_SET
Gene Tree

Suv39h1

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Phenotype Summary

3 phenotypes from 1 allele in 2 genetic backgrounds
7 phenotypes from multigenic genotypes
26 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

18
Chemically induced (ENU)

1
Endonuclease-mediated

6
Gene trapped

8
Targeted

3
Find Mice (IMSR)

14 strains or lines available

About one third of mice either heterozygous or homozygous for a reporter/null allele develop late-onset B cell lymphomas.

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All GO Annotations

108
GO References

25

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

867
Tissues

201
cDNA Data

21
Literature Summary

26

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

Xenbase suv39h1

ZFIN suv39h1a

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All Sequences

64
RefSeq

12
UniProt

2
CCDS

CCDS40846.1, CCDS72337.1

Ensembl

ENSMUSG00000039231 (Evidence)
NCBI Gene

20937

			Length	Strain/Species	Flank
genomic	ENSMUSG00000039231	Ensembl Gene Model \| MGI Sequence Detail	13590	C57BL/6J	± kb
transcript	ENSMUST00000115637	Ensembl \| MGI Sequence Detail	2778	Not Applicable
polypeptide	ENSMUSP00000111300	Ensembl \| MGI Sequence Detail	413	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000015844 histone-lysine N-methyltransferase SUV39H1

(term hierarchy)
EC

2.1.1.-
InterPro Domains

IPR000953 Chromo/chromo shadow domain

IPR023780 Chromo domain

IPR023779 Chromo domain, conserved site

IPR016197 Chromo-like domain superfamily

IPR050973 Histone-lysine N-methyltransferase, H3 Lys-9 specific

IPR011381 Histone-lysine N-methyltransferase SUV39H1/2-like

IPR003616 Post-SET domain

IPR007728 Pre-SET domain

IPR001214 SET domain

IPR046341 SET domain superfamily

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All nucleic 32

Genomic 3

cDNA 23

Primer pair 5

Other 1

Antibodies 4

Microarray probesets 5

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MGI:2147928, MGI:2147944

Summaries

All 137

Developmental Gene Expression 26

Gene Ontology 25

Phenotypes 26
Earliest

J:54310 Aagaard L, et al., Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J. 1999 Apr 1;18(7):1923-38
Latest

J:364427 Belenki D, et al., Senescence-associated lineage-aberrant plasticity evokes T-cell-mediated tumor control. Nat Commun. 2025 Mar 31;16(1):3079

TSS for Suv39h1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr162847	ChrX:7940959-7940975 (-)	32 bp
Tssr162846	ChrX:7940809-7940865 (-)	162 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/08/2026 MGI 6.24