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

Gene ID: 84505, updated on 11-Apr-2024

Summary

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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

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See Setdb1 in Genome Data Viewer
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_000069.7Genomic Context describing neighboring genes Neighboring gene prune exopolyphosphatase Neighboring gene STARR-positive B cell enhancer ABC_E2672 Neighboring gene MINDY lysine 48 deubiquitinase 1 Neighboring gene annexin A9 Neighboring gene STARR-positive B cell enhancer ABC_E9560 Neighboring gene predicted gene, 53243 Neighboring gene ceramide synthase 2 Neighboring gene STARR-seq mESC enhancer starr_08380 Neighboring gene STARR-positive B cell enhancer mm9_chr3:95161130-95161430 Neighboring gene predicted gene, 37500 Neighboring gene cortexin domain containing 2 Neighboring gene STARR-seq mESC enhancer starr_08381 Neighboring gene ribosomal protein S2 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Active DNA damage response signaling initiates and maintains meiotic sex chromosome inactivation. Abe H, et al. Nat Commun, 2022 Nov 28. PMID 36443288, Free PMC Article
  2. Histone Methyltransferase SETDB1 Regulates the Development of Cortical Htr3a-Positive Interneurons and Mood Behaviors. Li J, et al. Biol Psychiatry, 2023 Feb 1. PMID 36335068
  3. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Warrier T, et al. Nucleic Acids Res, 2022 Jul 22. PMID 35776115, Free PMC Article
  4. SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers. Barral A, et al. Mol Cell, 2022 Feb 17. PMID 35081363, Free PMC Article
  5. Histone methyltransferase SET domain bifurcated 1 negatively regulates parathyroid hormone/parathyroid hormone-related peptide receptor to control chondrocyte proliferation in Meckel's cartilage. Thiha P, et al. Arch Oral Biol, 2021 Nov. PMID 34521010

See all (130) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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†.
  4. 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.
  5. Alcoholic Setdb1 suppression promotes hepatosteatosis in mice by strengthening Plin2.
    Title: Alcoholic Setdb1 suppression promotes hepatosteatosis in mice by strengthening Plin2.
  6. NF-kappaB p65 and SETDB1 expedite lipopolysaccharide-induced intestinal inflammation in mice by inducing IRF7/NLR-dependent macrophage M1 polarization.
    Title: NF-ÎşB p65 and SETDB1 expedite lipopolysaccharide-induced intestinal inflammation in mice by inducing IRF7/NLR-dependent macrophage M1 polarization.
  7. 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.
  8. 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.
  9. 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.
  10. 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

Homology

Clone Names

  • MGC90670

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
NP_001157114.1
NP_061365.3
XP_036019318.1

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)

  1. 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

  2. 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

  3. 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

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    95230836..95264513 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O88974.1 GenPept UniProtKB/Swiss-Prot:O88974

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