Setd3 SET domain containing 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Setd3provided by MGI
Official Full Name: SET domain containing 3provided by MGI
Primary source: MGI:MGI:1289184
See related: Ensembl:ENSMUSG00000056770 AllianceGenome:MGI:1289184
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: D12Ertd771e; 2610102I01Rik; 2610305M23Rik; 6030490B17Rik
Summary: Enables RNA polymerase II-specific DNA-binding transcription factor binding activity and protein methyltransferase activity. Involved in actin modification; peptidyl-histidine methylation; and regulation of uterine smooth muscle contraction. Acts upstream of or within positive regulation of muscle cell differentiation and positive regulation of transcription by RNA polymerase II. Located in chromatin. Orthologous to human SETD3 (SET domain containing 3, actin N3(tau)-histidine methyltransferase). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in cerebellum adult (RPKM 15.5), bladder adult (RPKM 14.4) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 12 F1; 12 59.23 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	12	NC_000078.7 (108072690..108145616, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	12	NC_000078.6 (108106431..108179345, complement)

Chromosome 12 - NC_000078.7 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?

SETD3 regulates endoderm differentiation of mouse embryonic stem cells through canonical Wnt signaling pathway.
Title: SETD3 regulates endoderm differentiation of mouse embryonic stem cells through canonical Wnt signaling pathway.
Enterovirus pathogenesis requires the host methyltransferase SETD3. SETD3 is essential for in vivo replication and pathogenesis in multiple mouse models for EV infection, including CV-A10, EV-A71 and EV-D68.
Title: Enterovirus pathogenesis requires the host methyltransferase SETD3.
SETD3 is regulated by a couple of microRNAs and plays opposing roles in proliferation and metastasis of hepatocellular carcinoma.
Title: SETD3 is regulated by a couple of microRNAs and plays opposing roles in proliferation and metastasis of hepatocellular carcinoma.
results identify a mammalian histidine methyltransferase and uncover a pivotal role for SETD3 and actin His73 methylation in the regulation of smooth muscle contractility; data also support the broader hypothesis that protein histidine methylation acts as a common regulatory mechanism
Title: SETD3 is an actin histidine methyltransferase that prevents primary dystocia.
SETD3 is a H3K4/K36 methyltransferase and plays an important role in the transcriptional regulation of muscle cell differentiation
Title: Histone methyltransferase SETD3 regulates muscle differentiation.

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Variation

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Alleles

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

Endonuclease-mediated (3)
Gene trapped (1)
Targeted (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH136353 (e-PCR)
- UniSTS:210343

D12Ertd771e (e-PCR), detects polymorphism
- UniSTS:167100

AW553490 (e-PCR)
- UniSTS:208866

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables actin binding	IEA Inferred from Electronic Annotation more info
enables histone H3K36 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K36 methyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K4 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-L-histidine N-tele-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein-L-histidine N-tele-methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein-L-histidine N-tele-methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in actin modification	IBA Inferred from Biological aspect of Ancestor more info
involved_in actin modification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in actin modification	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in peptidyl-histidine methylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in peptidyl-histidine methylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within positive regulation of muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of uterine smooth muscle contraction	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of uterine smooth muscle contraction	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: actin-histidine N-methyltransferase

Names: SET domain-containing protein 3; endothelial differentiation inhibitory protein D10; histone-lysine N-methyltransferase setd3; protein-L-histidine N-tele-methyltransferase

NP_001351195.1

EC 2.1.1.85

NP_001351196.1

EC 2.1.1.85

NP_001351197.1

EC 2.1.1.85

NP_001351198.1

EC 2.1.1.85

NP_001351199.1

EC 2.1.1.85

NP_082538.2

EC 2.1.1.85

XP_006516141.4

EC 2.1.1.85

XP_006516144.4

EC 2.1.1.85

XP_017170622.1

EC 2.1.1.85

XP_030102671.1

EC 2.1.1.85

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_001364266.1 → NP_001351195.1 actin-histidine N-methyltransferase isoform 1

Status: VALIDATED

Source sequence(s)

AC152059, AL583892

Conserved Domains (2) summary

pfam00856
Location:112 → 146

SET; SET domain

pfam09273
Location:357 → 482

Rubis-subs-bind; Rubisco LSMT substrate-binding
NM_001364267.1 → NP_001351196.1 actin-histidine N-methyltransferase isoform 3

Status: VALIDATED

Source sequence(s)

AC152059, AL583892

Conserved Domains (2) summary

pfam00856
Location:72 → 106

SET; SET domain

pfam09273
Location:317 → 442

Rubis-subs-bind; Rubisco LSMT substrate-binding
NM_001364268.1 → NP_001351197.1 actin-histidine N-methyltransferase isoform 4

Status: VALIDATED

Source sequence(s)

AC152059, AL583892

Conserved Domains (2) summary

pfam00856
Location:105 → 256

SET; SET domain

pfam09273
Location:292 → 417

Rubis-subs-bind; Rubisco LSMT substrate-binding
NM_001364269.1 → NP_001351198.1 actin-histidine N-methyltransferase isoform 5

Status: VALIDATED

Source sequence(s)

AC152059, AL583892

Conserved Domains (2) summary

pfam09273
Location:222 → 347

Rubis-subs-bind; Rubisco LSMT substrate-binding

cd19176
Location:1 → 201

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
NM_001364270.1 → NP_001351199.1 actin-histidine N-methyltransferase isoform 6

Status: VALIDATED

Source sequence(s)

AC152059, AL583892

Conserved Domains (2) summary

pfam09273
Location:164 → 289

Rubis-subs-bind; Rubisco LSMT substrate-binding

cd19176
Location:1 → 143

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
NM_028262.3 → NP_082538.2 actin-histidine N-methyltransferase isoform 2

See identical proteins and their annotated locations for NP_082538.2

Status: VALIDATED

Source sequence(s)

AK031371, BC016123, BY087049

Consensus CDS

CCDS26159.1

UniProtKB/Swiss-Prot

Q6PEN3, Q8CD86, Q8CDX8, Q91WC0, Q9CZZ1

Related

ENSMUSP00000066413.8, ENSMUST00000071095.14

Conserved Domains (2) summary

pfam00856
Location:105 → 180

SET; SET domain

pfam09273
Location:353 → 475

Rubis-subs-bind; Rubisco LSMT substrate-binding

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_000078.7 Reference GRCm39 C57BL/6J

Range

108072690..108145616 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017315133.1 → XP_017170622.1 actin-histidine N-methyltransferase isoform X2

Conserved Domains (2) summary

pfam09273
Location:299 → 424

Rubis-subs-bind; Rubisco LSMT substrate-binding

cd19176
Location:87 → 278

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
XM_006516081.4 → XP_006516144.4 actin-histidine N-methyltransferase isoform X3

Conserved Domains (2) summary

pfam09273
Location:164 → 289

Rubis-subs-bind; Rubisco LSMT substrate-binding

cd19176
Location:1 → 143

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
XM_030246811.2 → XP_030102671.1 actin-histidine N-methyltransferase isoform X1

Conserved Domains (2) summary

pfam09273
Location:222 → 347

Rubis-subs-bind; Rubisco LSMT substrate-binding

cd19176
Location:1 → 201

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
XM_006516078.5 → XP_006516141.4 actin-histidine N-methyltransferase isoform X1

Conserved Domains (2) summary

pfam09273
Location:222 → 347

Rubis-subs-bind; Rubisco LSMT substrate-binding

cd19176
Location:1 → 201

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins