Setdb2 SET domain, bifurcated 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Setdb2provided by MGI
Official Full Name: SET domain, bifurcated 2provided by MGI
Primary source: MGI:MGI:2685139
See related: Ensembl:ENSMUSG00000071350 AllianceGenome:MGI:2685139
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: Clld8; Gm293; KMT1F
Summary: Predicted to enable histone methyltransferase activity (H3-K9 specific). Predicted to be involved in several processes, including heterochromatin organization; histone H3-K9 methylation; and regulation of gene expression. Predicted to act upstream of or within cell division; chromatin organization; and methylation. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including gonad; nervous system; and nose. Orthologous to human SETDB2 (SET domain bifurcated histone lysine methyltransferase 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in liver E14 (RPKM 2.7), liver E18 (RPKM 2.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 14 C3; 14 31.48 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	14	NC_000080.7 (59639458..59678329, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	14	NC_000080.6 (59402009..59440880, complement)

Chromosome 14 - NC_000080.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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 Histone Methyltransferase SETDB2 Modulates Tissue Inhibitors of Metalloproteinase-Matrix Metalloproteinase Activity During Abdominal Aortic Aneurysm Development.
Title: The Histone Methyltransferase SETDB2 Modulates Tissue Inhibitors of Metalloproteinase-Matrix Metalloproteinase Activity During Abdominal Aortic Aneurysm Development.
Deficiency of histone lysine methyltransferase SETDB2 in hematopoietic cells promotes vascular inflammation and accelerates atherosclerosis.
Title: Deficiency of histone lysine methyltransferase SETDB2 in hematopoietic cells promotes vascular inflammation and accelerates atherosclerosis.
Coronavirus induces diabetic macrophage-mediated inflammation via SETDB2.
Title: Coronavirus induces diabetic macrophage-mediated inflammation via SETDB2.
identify Caveolin-1 as a key regulator of BBB permeability in influenza-associated encephalopathy and reveal that it acts through histone modification induced by Setdb2.
Title: Abrogated Caveolin-1 expression via histone modification enzyme Setdb2 regulates brain edema in a mouse model of influenza-associated encephalopathy.
Setdb2 regulates macrophage plasticity during normal and pathologic wound repair
Title: The Histone Methyltransferase Setdb2 Modulates Macrophage Phenotype and Uric Acid Production in Diabetic Wound Repair.
Lentivirus-mediated Setdb2-knockout and overexpression experiments verified that Setdb2 levels in monocytes correlated negatively with antifungal gene expression and survival rates.
Title: Bacteria-induced susceptibility to Candida albicans super-infection in mice via monocyte methyltransferase Setdb2.
INSIG2 is a negative regulator of SREBP, and acute glucocorticoid treatment decreased active SREBP during refeeding or in livers of Ob/Ob mice, both systems of elevated SREBP-1c-driven lipogenesis.
Title: SETDB2 Links Glucocorticoid to Lipid Metabolism through Insig2a Regulation.
these findings identify Setdb2 as a novel regulator of the immune system in acute respiratory viral infection.
Title: Type I Interferon Induced Epigenetic Regulation of Macrophages Suppresses Innate and Adaptive Immunity in Acute Respiratory Viral Infection.
Results suggest that a Setdb2-mediated regulatory crosstalk between the type I interferons and NF-kappaB pathways is a mechanism for virus-induced susceptibility to bacterial superinfection.
Title: The methyltransferase Setdb2 mediates virus-induced susceptibility to bacterial superinfection.

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Variation

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Alleles

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

Endonuclease-mediated (3)
Targeted (3) 1 citation

General gene information

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Markers

Setdb2 (e-PCR), detects polymorphism
- UniSTS:546984

Setdb2 (e-PCR), detects polymorphism
- UniSTS:548026

Readthrough Gm45935

Readthrough gene: Gm45935, Included gene: Phf11d, Included gene: Phf11c

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables histone H3K9 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 methyltransferase 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 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 cell cycle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell division	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromosome segregation	ISO Inferred from Sequence Orthology more info
involved_in heterochromatin organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info
involved_in mitotic cell cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism development	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 positive regulation of DNA methylation-dependent heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytosol	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	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETDB2

NP_001307649.1

EC 2.1.1.366

NP_001307650.1

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_001320720.1 → NP_001307649.1 histone-lysine N-methyltransferase SETDB2 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).

Source sequence(s)

AC114007, AI428348, BC172021

Consensus CDS

CCDS84142.1

UniProtKB/TrEMBL

B2RXP3, B4XVN8, B4XVN9

Related

ENSMUSP00000124696.2, ENSMUST00000161459.8

Conserved Domains (3) summary

smart00317
Location:612 → 674

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

cd01395
Location:152 → 212

HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...

pfam05033
Location:234 → 346

Pre-SET; Pre-SET motif
NM_001320721.1 → NP_001307650.1 histone-lysine N-methyltransferase SETDB2 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC114007, AI428348, BC172021

UniProtKB/TrEMBL

B4XVP0

Conserved Domains (3) summary

smart00317
Location:590 → 652

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

cd01395
Location:130 → 190

HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...

pfam05033
Location:212 → 324

Pre-SET; Pre-SET motif

RNA

NR_135463.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC114007, AI428348, BC172021

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_000080.7 Reference GRCm39 C57BL/6J

Range

59639458..59678329 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001081024.1: Suppressed sequence

Description

NM_001081024.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.