Nsd3 nuclear receptor binding SET domain protein 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nsd3provided by MGI
Official Full Name: nuclear receptor binding SET domain protein 3provided by MGI
Primary source: MGI:MGI:2142581
See related: Ensembl:ENSMUSG00000054823 AllianceGenome:MGI:2142581
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: WHISTLE; Whsc1l1; 6720429E03; A530023P05
Summary: This gene encodes a member of the SET domain family of histone lysine N-methyltransferase proteins. This protein methylates histone H3 at lysine residues 4 and 27, which represses gene transcription. It acts in opposition to the histone demethylase Jmjd1c. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2015]
Expression: Ubiquitous expression in placenta adult (RPKM 8.2), CNS E18 (RPKM 5.3) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 8 A2; 8 14.17 cM

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	8	NC_000074.7 (26091617..26209694)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	8	NC_000074.6 (25601601..25719667)

Chromosome 8 - NC_000074.7 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?

WHSC1L1-mediated epigenetic downregulation of VMP1 participates in herpes simplex virus 1 infection-induced mitophagy impairment and neuroinflammation.
Title: WHSC1L1-mediated epigenetic downregulation of VMP1 participates in herpes simplex virus 1 infection-induced mitophagy impairment and neuroinflammation.
This study reveals a critical role of NSD3-mediated IRF3 methylation in enhancing antiviral innate immunity.
Title: The methyltransferase NSD3 promotes antiviral innate immunity via direct lysine methylation of IRF3.
WHSC1L1-L acts as a histone methyltransferase in podocytes and regulates nephrin gene expression, which may in turn contribute to the integrity of the slit diaphragm of the glomerular filtration barrier.
Title: Wolf-Hirschhorn syndrome candidate 1-like 1 epigenetically regulates nephrin gene expression.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Targeted (3) 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

NoName (e-PCR)
- UniSTS:235854

AU015590 (e-PCR)
- UniSTS:208255

RH136180 (e-PCR)
- UniSTS:210175

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables histone H3K27 dimethyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K27 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K27 trimethyltransferase activity	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	ISO Inferred from Sequence Orthology more info
enables histone H3K4 dimethyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K4 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
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 transcription regulator activator activity	ISO Inferred from Sequence Orthology more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in chromosome	IEA Inferred from Electronic Annotation 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 NSD3

Names: WHSC1-like protein 1; nuclear SET domain-containing protein 3; wolf-Hirschhorn syndrome candidate 1-like protein 1 homolog

NP_001001735.1

EC 2.1.1.370

EC 2.1.1.371

NP_001074738.1

EC 2.1.1.370

EC 2.1.1.371

NP_001295410.1

EC 2.1.1.370

EC 2.1.1.371

NP_001295411.1

EC 2.1.1.370

EC 2.1.1.371

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_001001735.2 → NP_001001735.1 histone-lysine N-methyltransferase NSD3 isoform 1

See identical proteins and their annotated locations for NP_001001735.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 3 encode the same isoform (1).

Source sequence(s)

AC156990, AC162367, BC064447

Consensus CDS

CCDS40305.1

UniProtKB/TrEMBL

A0A1B0GSG3

Related

ENSMUSP00000115470.2, ENSMUST00000146919.8

Conserved Domains (1) summary

cd05837
Location:277 → 393

MSH6_like; The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been ...
NM_001081269.2 → NP_001074738.1 histone-lysine N-methyltransferase NSD3 isoform 2

See identical proteins and their annotated locations for NP_001074738.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has a shorter 5' UTR, lacks the 3' terminal exon, and contains multiple alternate 3' exons, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is longer than isoform 1.

Source sequence(s)

AC156990, AC162367

Consensus CDS

CCDS52528.1

UniProtKB/Swiss-Prot

Q3TDS4, Q3U0L8, Q3V131, Q6P2L6, Q8BJT3

UniProtKB/TrEMBL

D3Z357

Related

ENSMUSP00000117778.2, ENSMUST00000142395.8

Conserved Domains (8) summary

cd05837
Location:277 → 393

MSH6_like; The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been ...

cd05838
Location:968 → 1061

WHSC1_related; The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as ...

smart00570
Location:1104 → 1154

AWS; associated with SET domains

smart00317
Location:1155 → 1278

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

cd15652
Location:761 → 807

PHD2_NSD3; PHD finger 2 found in nuclear SET domain-containing protein 3 (NSD3)

cd15658
Location:927 → 962

PHD4_NSD3; PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3)

cd15661
Location:1332 → 1374

PHD5_NSD3; PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3)

cl22851
Location:808 → 860

PHD_SF; PHD finger superfamily
NM_001308481.1 → NP_001295410.1 histone-lysine N-methyltransferase NSD3 isoform 1

See identical proteins and their annotated locations for NP_001295410.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same isoform (1).

Source sequence(s)

AC156990, AC162367, BB618167, BC064447

Consensus CDS

CCDS40305.1

UniProtKB/TrEMBL

A0A1B0GSG3

Related

ENSMUSP00000117596.2, ENSMUST00000155861.8

Conserved Domains (1) summary

cd05837
Location:277 → 393

MSH6_like; The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been ...
NM_001308482.1 → NP_001295411.1 histone-lysine N-methyltransferase NSD3 isoform 3

See identical proteins and their annotated locations for NP_001295411.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two 3' exons and its transcription extends past a splice site used in variant 1, resulting in a distinct 3' coding region and 3' UTR. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AC156990, BC064447, BP766225

Consensus CDS

CCDS85518.1

UniProtKB/TrEMBL

A0A1B0GSG3

Related

ENSMUSP00000147840.2, ENSMUST00000136107.9

Conserved Domains (1) summary

cd05837
Location:277 → 393

MSH6_like; The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been ...