Setdb1 MGI Mouse Gene Detail - MGI:1934229

Symbol

Setdb1
Name

SET domain, bifurcated 1
Synonyms

ESET, KMT1E, mKIAA0067

Feature Type

protein coding gene
IDs

MGI:1934229
NCBI Gene: 84505
Alliance

genome feature page
Transcription Start Sites

4 TSS

Sequence Map

Chr3:95230836-95264513 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 40.74 cM, cytoband F2
Mapping Data

2 experiments

SNPs within 2kb

690 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1934229	protein coding gene	Chr3:95230836-95264513 (-)
129S1/SvImJ	ENSMUSG00200043340	protein coding gene	Chr3:91894180-91929495 (-)
A/J	ENSMUSG00195047309	protein coding gene	Chr3:92211364-92246554 (-)
AKR/J	ENSMUSG00220049719	protein coding gene	Chr3:90598423-90633614 (-)
BALB/cJ	ENSMUSG00180032720	protein coding gene	Chr3:92211151-92246353 (-)
C3H/HeJ	ENSMUSG00175025097	protein coding gene	Chr3:91855053-91890241 (-)
C57BL/6NJ	ENSMUSG00215028450	protein coding gene	Chr3:92573880-92609069 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025342	protein coding gene	Chr3:89429994-89463912 (-)
CAST/EiJ	ENSTCUG00005043657	protein coding gene	Chr3:92419782-92455094 (-)
CBA/J	ENSMUSG00210051072	protein coding gene	Chr3:92392512-92427700 (-)
DBA/2J	ENSMUSG00185040395	protein coding gene	Chr3:92809171-92844360 (-)
FVB/NJ	ENSMUSG00205032671	protein coding gene	Chr3:91508874-91544064 (-)
JF1/MsJ	ENSUMUG00000043859	protein coding gene	Chr3:91712584-91747056 (-)
LP/J	ENSMUSG00230044631	protein coding gene	Chr3:94757637-94792949 (-)
NOD/ShiLtJ	ENSMUSG00190041909	protein coding gene	Chr3:92903457-92938995 (-)
NZO/HlLtJ	ENSMUSG00225012201	protein coding gene	Chr3:97172611-97207800 (-)
PWK/PhJ	ENSLUMG00010049421	protein coding gene	Chr3:91692516-91727824 (-)
SPRET/EiJ	ENSMSPG00010043012	protein coding gene	Chr3:91995490-92031837 (-)
WSB/EiJ	ENSIUOG00005025552	protein coding gene	Chr3:92331702-92366938 (-)

Human Ortholog

SETDB1, SET domain bifurcated histone lysine methyltransferase 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SETDB1, SET domain bifurcated histone lysine methyltransferase 1
Synonyms

ESET, H3-K9-HMTase4, KG1T, KMT1E, TDRD21
Links

HGNC:10761

NCBI Gene ID: 9869

UniProt: Q15047
Chr Location

1q21.3; chr1:150926263-150964744 (+) GRCh38

MGI Vertebrate Homology

Setdb1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SETDB1
Gene Tree

Setdb1

Diseases

2 with human SETDB1 associations

				Human Disease	Mouse Models
				autistic disorder IDs autistic disorder DOID:12849 EFO:0003758 ICD10CM:F84.0 ICD9CM:299.0 MESH:D001321 NCI:C97161 OMIM:209850 ORDO:106 UMLS_CUI:C0004352
				lung cancer IDs lung cancer DOID:1324 DOID:13075 DOID:1322 DOID:9881 ICD10CM:C34.1 ICD10CM:C34.2 ICD10CM:C34.3 ICD9CM:162.3 ICD9CM:162.4 ICD9CM:162.5 ICD9CM:162.8 NCI:C194105 OMIM:211980 OMIM:608935 OMIM:612571 OMIM:612593 OMIM:614210 UMLS_CUI:C0024624 UMLS_CUI:C0153491 UMLS_CUI:C0153492 UMLS_CUI:C0153493

Click on a disease name to see all genes associated with that disease.

References

1 with disease annotations

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Phenotype Summary

33 phenotypes from 6 alleles in 7 genetic backgrounds
4 phenotypes from multigenic genotypes
65 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

55
Chemically induced (ENU)

2
Chemically induced (other)

1
Endonuclease-mediated

6
Gene trapped

34
Radiation induced

1
Targeted

10
Transgenic

1
Genomic Mutations

2 involving Setdb1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

60 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous inactivation of this locus results in peri-implantation lethality. Inner cell mass growth is impaired in null blastocysts.

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All GO Annotations

69
GO References

18

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

764
Tissues

139
cDNA Data

12
Literature Summary

24

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA MLLT11

Xenbase setdb1

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All Sequences

60
RefSeq

8
UniProt

3
CCDS

CCDS17613.1, CCDS50991.1

Ensembl

ENSMUSG00000015697 (Evidence)
NCBI Gene

84505

			Length	Strain/Species	Flank
genomic	84505	NCBI Gene Model \| MGI Sequence Detail	33678	C57BL/6J	± kb
transcript	NM_001163641	RefSeq \| MGI Sequence Detail	4682	C57BL/6
polypeptide	O88974	UniProt \| EBI \| MGI Sequence Detail	1307	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000014724 histone-lysine N-methyltransferase SETDB1

(term hierarchy)
EC

2.1.1.366
InterPro Domains

IPR016177 DNA-binding domain superfamily

IPR040880 Domain of unknown function DUF5604

IPR051516 Histone-lysine N-methyltransferase SETDB

IPR025796 Histone-lysine N-methyltransferase SETDB1

IPR047232 Histone-lysine N-methyltransferase SETDB1/2-like, methyl-CpG binding domains

IPR041291 Histone methyltransferase, Tudor domain 1

IPR041292 Histone methyltransferase, Tudor domain 2

IPR001739 Methyl-CpG DNA binding

IPR003616 Post-SET domain

IPR007728 Pre-SET domain

IPR001214 SET domain

IPR046341 SET domain superfamily

IPR002999 Tudor domain
GlyGen

O88974 3 sites, 1 O-linked glycan (2 sites)

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All nucleic 14

cDNA 13

Primer pair 1

Antibodies 4

Microarray probesets 4

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MGI:2139889

Summaries

All 151

Developmental Gene Expression 24

Diseases 1

Gene Ontology 18

Phenotypes 65
Earliest

J:60984 Ko MS, et al., Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Development. 2000 Apr;127(8):1737-49
Latest

J:388190 Chen S, et al., Endogenous retrovirus-derived RNA-DNA hybrids induce microglial synaptic pruning in autism models. Neuron. 2026 Feb 24;

TSS for Setdb1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr34477	Chr3:95264528-95264555 (-)	-29 bp
Tssr34476	Chr3:95264497-95264522 (-)	3 bp
Tssr34475	Chr3:95247280-95247301 (-)	17,222 bp
Tssr34474	Chr3:95238997-95239001 (-)	25,514 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