Setdb1 SET domain, bifurcated 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Setdb1provided by MGI
Official Full Name: SET domain, bifurcated 1provided by MGI
Primary source: MGI:MGI:1934229
See related: Ensembl:ENSMUSG00000015697 AllianceGenome:MGI:1934229
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: ESET; KMT1E; mKIAA0067
Summary: Enables DNA binding activity; histone methyltransferase activity (H3-K9 specific); and promoter-specific chromatin binding activity. Involved in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate and positive regulation of DNA methylation-dependent heterochromatin assembly. Acts upstream of or within several processes, including histone H3-K9 trimethylation; inner cell mass cell proliferation; and negative regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including 1-cell stage embryo; central nervous system; long bone; oocyte; and white fat. Human ortholog(s) of this gene implicated in autistic disorder and lung cancer. Orthologous to human SETDB1 (SET domain bifurcated histone lysine methyltransferase 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 22.1), limb E14.5 (RPKM 18.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 F2.1; 3 40.74 cM

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (95230836..95264513, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (95323525..95357202, complement)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The crucial role of SETDB1 in structural and functional transformation of epithelial cells during regeneration after intestinal ischemia reperfusion injury.
Title: The crucial role of SETDB1 in structural and functional transformation of epithelial cells during regeneration after intestinal ischemia reperfusion injury.
Hyperglycaemia aggravates periodontal inflamm-aging by promoting SETDB1-mediated LINE-1 de-repression in macrophages.
Title: Hyperglycaemia aggravates periodontal inflamm-aging by promoting SETDB1-mediated LINE-1 de-repression in macrophages.
YTHDF2 promotes DNA damage repair by positively regulating the histone methyltransferase SETDB1 in spermatogoniadagger.
Title: YTHDF2 promotes DNA damage repair by positively regulating the histone methyltransferase SETDB1 in spermatogonia†.
Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions.
Title: Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions.
Alcoholic Setdb1 suppression promotes hepatosteatosis in mice by strengthening Plin2.
Title: Alcoholic Setdb1 suppression promotes hepatosteatosis in mice by strengthening Plin2.
NF-kappaB p65 and SETDB1 expedite lipopolysaccharide-induced intestinal inflammation in mice by inducing IRF7/NLR-dependent macrophage M1 polarization.
Title: NF-κB p65 and SETDB1 expedite lipopolysaccharide-induced intestinal inflammation in mice by inducing IRF7/NLR-dependent macrophage M1 polarization.
Histone Methyltransferase SETDB1 Regulates the Development of Cortical Htr3a-Positive Interneurons and Mood Behaviors.
Title: Histone Methyltransferase SETDB1 Regulates the Development of Cortical Htr3a-Positive Interneurons and Mood Behaviors.
SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates.
Title: SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates.
Expression of the histone lysine methyltransferases SETD1B, SETDB1, SETD2, and CFP1 exhibits significant changes in the oocytes and granulosa cells of aged mouse ovaries.
Title: Expression of the histone lysine methyltransferases SETD1B, SETDB1, SETD2, and CFP1 exhibits significant changes in the oocytes and granulosa cells of aged mouse ovaries.
Histone H3K9 methyltransferase SETDB1 augments invadopodia formation to promote tumor metastasis.
Title: Histone H3K9 methyltransferase SETDB1 augments invadopodia formation to promote tumor metastasis.

Submit: New GeneRIF Correction See all GeneRIFs (75)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (9) 1 citation
Chemically induced (ENU) (2) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

UniSTS:234764 (e-PCR)
- UniSTS:234764

NoName (e-PCR)
- UniSTS:234765

PMC355869P1 (e-PCR)
- UniSTS:273262

AU022152 (e-PCR)
- UniSTS:207535

RH126094 (e-PCR)
- UniSTS:162806

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables histone H3K9 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K9 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9 trimethyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9me2 methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within bone development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within inner cell mass cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA methylation-dependent heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA methylation-dependent heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA methylation-dependent heterochromatin formation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETDB1

Names: ERG-associated protein with SET domain; SET domain ERG-associated histone methyltransferase

NP_001157113.1

EC 2.1.1.366

NP_001157114.1

EC 2.1.1.366

NP_061365.3

EC 2.1.1.366

XP_036019318.1

EC 2.1.1.366

NCBI Reference Sequences (RefSeq)

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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)

NM_001163641.1 → NP_001157113.1 histone-lysine N-methyltransferase SETDB1 isoform a

See identical proteins and their annotated locations for NP_001157113.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AK132202, BC060173, BY074856

Consensus CDS

CCDS17613.1

UniProtKB/Swiss-Prot

O88974, Q6AXH8, Q78N64, Q78N65, Q80U84, Q8BTV6, Q8CIX7, Q922K1

UniProtKB/TrEMBL

D3YYC3

Related

ENSMUSP00000015841.6, ENSMUST00000015841.12

Conserved Domains (5) summary

smart00391
Location:615 → 690

MBD; Methyl-CpG binding domain

smart00468
Location:697 → 804

PreSET; N-terminal to some SET domains

smart00333
Location:348 → 400

TUDOR; Tudor domain

smart00317
Location:1223 → 1285

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

pfam11068
Location:24 → 98

YlqD; YlqD protein
NM_001163642.1 → NP_001157114.1 histone-lysine N-methyltransferase SETDB1 isoform b

See identical proteins and their annotated locations for NP_001157114.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is 1 aa shorter compared to isoform a.

Source sequence(s)

AK132202, BC060173, BY074856, CN461297

Consensus CDS

CCDS50991.1

UniProtKB/Swiss-Prot

O88974, Q6AXH8, Q78N64, Q78N65, Q80U84, Q8BTV6, Q8CIX7, Q922K1

UniProtKB/TrEMBL

G5E8N3

Related

ENSMUSP00000102789.4, ENSMUST00000107171.10

Conserved Domains (6) summary

smart00391
Location:614 → 689

MBD; Methyl-CpG binding domain

cd10517
Location:691 → 911

SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins

cl40432
Location:1218 → 1307

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

pfam18300
Location:193 → 250

DUF5604; Domain of unknown function (DUF5604)

cd20382
Location:260 → 341

Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins

cd21181
Location:348 → 401

Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
NM_018877.3 → NP_061365.3 histone-lysine N-methyltransferase SETDB1 isoform a

See identical proteins and their annotated locations for NP_061365.3

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AK132202, BC060173, BY074856

Consensus CDS

CCDS17613.1

UniProtKB/Swiss-Prot

O88974, Q6AXH8, Q78N64, Q78N65, Q80U84, Q8BTV6, Q8CIX7, Q922K1

UniProtKB/TrEMBL

D3YYC3

Related

ENSMUSP00000102788.3, ENSMUST00000107170.3

Conserved Domains (5) summary

smart00391
Location:615 → 690

MBD; Methyl-CpG binding domain

smart00468
Location:697 → 804

PreSET; N-terminal to some SET domains

smart00333
Location:348 → 400

TUDOR; Tudor domain

smart00317
Location:1223 → 1285

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

pfam11068
Location:24 → 98

YlqD; YlqD protein

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

95230836..95264513 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036163425.1 → XP_036019318.1 histone-lysine N-methyltransferase SETDB1 isoform X1

UniProtKB/Swiss-Prot

O88974, Q6AXH8, Q78N64, Q78N65, Q80U84, Q8BTV6, Q8CIX7, Q922K1

UniProtKB/TrEMBL

G5E8N3

Conserved Domains (6) summary

smart00391
Location:614 → 689

MBD; Methyl-CpG binding domain

cd10517
Location:691 → 911

SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins

cl40432
Location:1218 → 1307

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

pfam18300
Location:193 → 250

DUF5604; Domain of unknown function (DUF5604)

cd20382
Location:260 → 341

Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins

cd21181
Location:348 → 401

Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins