Smyd4 SET and MYND domain containing 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smyd4provided by MGI
Official Full Name: SET and MYND domain containing 4provided by MGI
Primary source: MGI:MGI:2442796
See related: Ensembl:ENSMUSG00000018809 AllianceGenome:MGI:2442796
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: G430029E23Rik
Summary: Predicted to enable metal ion binding activity and methyltransferase activity. Predicted to be involved in heart development. Predicted to act upstream of or within methylation. Located in cytoplasm and nucleus. Is expressed in brain and embryo. Orthologous to human SMYD4 (SET and MYND domain containing 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E18 (RPKM 2.8), kidney adult (RPKM 2.7) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 B5; 11 45.82 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (75239259..75296533)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (75348433..75405707)

Chromosome 11 - NC_000077.7 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?

MFACR (mitochondrial fission and apoptosis-related circRNA) is derived from the splicing of exon 5 of Smyd4 gene. MFACR is crucial in regulating mitochondrial dynamics and apoptosis in the heart. MFACR mediates cardiomyocyte apoptosis and myocardial infarction by targeting miR-652-3p-dependent MTP18 activation and consequent mitochondrial fission.
Title: Circular RNA mediates cardiomyocyte death via miRNA-dependent upregulation of MTP18 expression.

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Variation

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Alleles

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

Targeted (1)
Endonuclease-mediated (3)

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables histone deacetylase binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables molecular_function	ND No biological Data available more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
involved_in heart development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	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: SET and MYND domain-containing protein 4

NP_001096081.1

EC 2.1.1.-

XP_006533598.1

EC 2.1.1.-

XP_006533599.1

EC 2.1.1.-

XP_006533600.1

EC 2.1.1.-

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)

NM_001102611.1 → NP_001096081.1 SET and MYND domain-containing protein 4

See identical proteins and their annotated locations for NP_001096081.1

Status: VALIDATED

Source sequence(s)

AK089959, BC049810, CN693729

Consensus CDS

CCDS48848.1

UniProtKB/Swiss-Prot

A2BDD0, Q3U3Z8, Q501N5, Q5SWN4, Q69Z60, Q8BMP3, Q8BTK5

Related

ENSMUSP00000047505.3, ENSMUST00000044530.3

Conserved Domains (5) summary

sd00006
Location:68 → 96

TPR; TPR repeat [structural motif]

pfam00856
Location:524 → 570

SET; SET domain

pfam01753
Location:296 → 335

zf-MYND; MYND finger

pfam13414
Location:68 → 132

TPR_11; TPR repeat

pfam13424
Location:658 → 725

TPR_12; Tetratricopeptide repeat

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_000077.7 Reference GRCm39 C57BL/6J

Range

75239259..75296533

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006533536.2 → XP_006533599.1 SET and MYND domain-containing protein 4 isoform X2

Conserved Domains (4) summary

pfam13424
Location:587 → 657

TPR_12; Tetratricopeptide repeat

pfam01753
Location:228 → 267

zf-MYND; MYND finger

cd10536
Location:350 → 530

SET_SMYD4; SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing protein 4 (SMYD4) and similar proteins

cl40432
Location:175 → 201

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_006533535.2 → XP_006533598.1 SET and MYND domain-containing protein 4 isoform X1

Conserved Domains (4) summary

pfam13424
Location:603 → 673

TPR_12; Tetratricopeptide repeat

pfam01753
Location:244 → 283

zf-MYND; MYND finger

cd10536
Location:366 → 546

SET_SMYD4; SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing protein 4 (SMYD4) and similar proteins

cl40432
Location:191 → 247

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_006533537.5 → XP_006533600.1 SET and MYND domain-containing protein 4 isoform X3

See identical proteins and their annotated locations for XP_006533600.1

UniProtKB/Swiss-Prot

Q8BTK5

Conserved Domains (4) summary

pfam13424
Location:522 → 592

TPR_12; Tetratricopeptide repeat

pfam01753
Location:163 → 202

zf-MYND; MYND finger

cd10536
Location:285 → 465

SET_SMYD4; SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing protein 4 (SMYD4) and similar proteins

cl40432
Location:110 → 136

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

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_177009.3: Suppressed sequence

Description

NM_177009.3: This RefSeq was permanently suppressed because it contains the wrong CDS, and the correct CDS makes it a nonsense-mediated mRNA decay (NMD) candidate.