Setd2 SET domain containing 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Setd2provided by MGI
Official Full Name: SET domain containing 2provided by MGI
Primary source: MGI:MGI:1918177
See related: Ensembl:ENSMUSG00000044791 AllianceGenome:MGI:1918177
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: KMT3A; 4921524K10Rik
Summary: Enables histone H3K36 methyltransferase activity. Involved in endodermal cell differentiation and stem cell differentiation. Acts upstream of or within several processes, including chordate embryonic development; peptidyl-lysine trimethylation; and tube morphogenesis. Located in chromosome and nucleus. Is expressed in cerebral cortex; early embryo; and inner cell mass. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder; clear cell renal cell carcinoma; gastrointestinal system cancer (multiple); lung disease (multiple); and malignant mesothelioma (multiple). Orthologous to human SETD2 (SET domain containing 2, histone lysine methyltransferase). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 11.9), CNS E14 (RPKM 11.1) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 F2; 9 60.0 cM

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (110361368..110447703)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (110532500..110618633)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Catalytic activity of Setd2 is essential for embryonic development in mice: establishment of a mouse model harboring patient-derived Setd2 mutation.
Title: Catalytic activity of Setd2 is essential for embryonic development in mice: establishment of a mouse model harboring patient-derived Setd2 mutation.
SETD2 regulates SLC family transporter-mediated sodium and glucose reabsorptions in renal tubule.
Title: SETD2 regulates SLC family transporter-mediated sodium and glucose reabsorptions in renal tubule.
Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation.
Title: Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation.
SET domain containing 2 promotes megakaryocyte polyploidization and platelet generation through methylation of alpha-tubulin.
Title: SET domain containing 2 promotes megakaryocyte polyploidization and platelet generation through methylation of α-tubulin.
SETD2 deficiency accelerates sphingomyelin accumulation and promotes the development of renal cancer.
Title: SETD2 deficiency accelerates sphingomyelin accumulation and promotes the development of renal cancer.
Spatiotemporal role of SETD2-H3K36me3 in murine pancreatic organogenesis.
Title: Spatiotemporal role of SETD2-H3K36me3 in murine pancreatic organogenesis.
Tumor cell-intrinsic SETD2 inactivation sensitizes cancer cells to immune checkpoint blockade through the NR2F1-STAT1 pathway.
Title: Tumor cell-intrinsic SETD2 inactivation sensitizes cancer cells to immune checkpoint blockade through the NR2F1-STAT1 pathway.
Setd2 deficiency promotes gastric tumorigenesis through inhibiting the SIRT1/FOXO pathway.
Title: Setd2 deficiency promotes gastric tumorigenesis through inhibiting the SIRT1/FOXO pathway.
SETD2 deficiency promotes renal fibrosis through the TGF-beta/Smad signalling pathway in the absence of VHL.
Title: SETD2 deficiency promotes renal fibrosis through the TGF-β/Smad signalling pathway in the absence of VHL.
Loss of SETD2 aggravates colorectal cancer progression caused by SMAD4 deletion through the RAS/ERK signalling pathway.
Title: Loss of SETD2 aggravates colorectal cancer progression caused by SMAD4 deletion through the RAS/ERK signalling pathway.

Submit: New GeneRIF Correction See all GeneRIFs (43)

Variation

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Alleles

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

Endonuclease-mediated (5) 1 citation
Targeted (8) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:236260

UniSTS:236262 (e-PCR)
- UniSTS:236262

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables alpha-tubulin binding	IEA Inferred from Electronic Annotation more info
enables alpha-tubulin binding	ISO Inferred from Sequence Orthology more info
enables histone H3K36 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K36 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K36 methyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K36 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein-lysine N-methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables protein-lysine N-methyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell migration involved in vasculogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within coronary vasculature morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in defense response to virus	ISO Inferred from Sequence Orthology more info
involved_in defense response to virus	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic organ development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic placenta morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endodermal cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mesoderm morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in microtubule cytoskeleton organization involved in mitosis	ISO Inferred from Sequence Orthology more info
involved_in microtubule cytoskeleton organization involved in mitosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in mismatch repair	ISO Inferred from Sequence Orthology more info
involved_in mismatch repair	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within morphogenesis of a branching structure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural tube closure	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleosome organization	ISO Inferred from Sequence Orthology more info
involved_in nucleosome organization	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within peptidyl-lysine trimethylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in peptidyl-lysine trimethylation	ISO Inferred from Sequence Orthology more info
involved_in peptidyl-lysine trimethylation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within pericardium development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of autophagy	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interferon-alpha production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interferon-alpha production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of ossification	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ossification	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of cytokinesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of cytokinesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
involved_in regulation of double-strand break repair via homologous recombination	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mRNA export from nucleus	IEA Inferred from Electronic Annotation more info
involved_in regulation of mRNA export from nucleus	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization to chromatin	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization to chromatin	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to alkaloid	IEA Inferred from Electronic Annotation more info
involved_in response to metal ion	IEA Inferred from Electronic Annotation more info
involved_in response to organic cyclic compound	IEA Inferred from Electronic Annotation more info
involved_in response to type I interferon	ISO Inferred from Sequence Orthology more info
involved_in response to type I interferon	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within stem cell development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transcription elongation by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within vasculogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in chromosome	IBA Inferred from Biological aspect of Ancestor more info
located_in chromosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETD2

Names: SET domain-containing protein 2; lysine N-methyltransferase 3A; protein-lysine N-methyltransferase SETD2

NP_001074809.2

EC 2.1.1.359

XP_006512151.1

EC 2.1.1.359

XP_006512154.1

EC 2.1.1.359

XP_006512155.1

EC 2.1.1.359

XP_036010808.1

EC 2.1.1.359

XP_036010809.1

EC 2.1.1.359

XP_036010810.1

EC 2.1.1.359

XP_036010811.1

EC 2.1.1.359

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_001081340.3 → NP_001074809.2 histone-lysine N-methyltransferase SETD2

See identical proteins and their annotated locations for NP_001074809.2

Status: VALIDATED

Source sequence(s)

AC132103

Consensus CDS

CCDS40781.2

UniProtKB/Swiss-Prot

E9Q5F9, Q69ZC0, Q6PCY9, Q8K0F3

Related

ENSMUSP00000116313.3, ENSMUST00000153838.8

Conserved Domains (6) summary

pfam05279
Location:1914 → 2096

Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region

smart00570
Location:1469 → 1523

AWS; associated with SET domains

smart00317
Location:1524 → 1647

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

smart00508
Location:1648 → 1664

PostSET; Cysteine-rich motif following a subset of SET domains

pfam00397
Location:2364 → 2393

WW; WW domain

pfam08236
Location:2442 → 2521

SRI; SRI (Set2 Rpb1 interacting) domain

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_000075.7 Reference GRCm39 C57BL/6J

Range

110361368..110447703

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036154915.1 → XP_036010808.1 histone-lysine N-methyltransferase SETD2 isoform X1
XM_036154916.1 → XP_036010809.1 histone-lysine N-methyltransferase SETD2 isoform X3

Conserved Domains (4) summary

smart00570
Location:1483 → 1537

AWS; associated with SET domains

cd19172
Location:1537 → 1678

SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins

pfam00397
Location:2377 → 2406

WW; WW domain

pfam08236
Location:2453 → 2541

SRI; SRI (Set2 Rpb1 interacting) domain
XM_036154917.1 → XP_036010810.1 histone-lysine N-methyltransferase SETD2 isoform X4

Conserved Domains (4) summary

smart00570
Location:1478 → 1532

AWS; associated with SET domains

cd19172
Location:1532 → 1673

SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins

pfam00397
Location:2373 → 2402

WW; WW domain

pfam08236
Location:2449 → 2537

SRI; SRI (Set2 Rpb1 interacting) domain
XM_006512088.5 → XP_006512151.1 histone-lysine N-methyltransferase SETD2 isoform X2

Conserved Domains (5) summary

pfam05279
Location:1927 → 2109

Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region

smart00570
Location:1482 → 1536

AWS; associated with SET domains

pfam00397
Location:2377 → 2406

WW; WW domain

pfam08236
Location:2455 → 2542

SRI; SRI (Set2 Rpb1 interacting) domain

cd19172
Location:1536 → 1677

SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins
XM_006512091.5 → XP_006512154.1 histone-lysine N-methyltransferase SETD2 isoform X5

Conserved Domains (5) summary

pfam05279
Location:1922 → 2104

Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region

smart00570
Location:1477 → 1531

AWS; associated with SET domains

pfam00397
Location:2372 → 2401

WW; WW domain

pfam08236
Location:2450 → 2537

SRI; SRI (Set2 Rpb1 interacting) domain

cd19172
Location:1531 → 1672

SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins
XM_006512092.5 → XP_006512155.1 histone-lysine N-methyltransferase SETD2 isoform X6

Conserved Domains (5) summary

pfam05279
Location:1919 → 2101

Asp-B-Hydro_N; Aspartyl beta-hydroxylase N-terminal region

smart00570
Location:1474 → 1528

AWS; associated with SET domains

pfam00397
Location:2369 → 2398

WW; WW domain

pfam08236
Location:2447 → 2534

SRI; SRI (Set2 Rpb1 interacting) domain

cd19172
Location:1528 → 1669

SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins
XM_036154918.1 → XP_036010811.1 histone-lysine N-methyltransferase SETD2 isoform X7