Smyd3 MGI Mouse Gene Detail - MGI:1916976 - SET and MYND domain containing 3

Symbol

Smyd3
Name

SET and MYND domain containing 3
Synonyms

2410008A19Rik, Zmynd1

Feature Type

protein coding gene
IDs

MGI:1916976
NCBI Gene: 69726
Alliance

gene page
Transcription Start Sites

9 TSS

Sequence Map

Chr1:178779525-179345606 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 83.48 cM, cytoband H3
Mapping Data

3 experiments

SNPs within 2kb

17165 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1916976	protein coding gene	Chr1:178779525-179345618 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0016858	protein coding gene	Chr1:185281184-185883310 (-)
A/J	MGP_AJ_G0016836	protein coding gene	Chr1:177824540-178402615 (-)
AKR/J	MGP_AKRJ_G0016802	protein coding gene	Chr1:183111761-183720030 (-)
BALB/cJ	MGP_BALBcJ_G0016794	protein coding gene	Chr1:178449039-179024501 (-)
C3H/HeJ	MGP_C3HHeJ_G0016619	protein coding gene	Chr1:183854317-184444766 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0017258	protein coding gene	Chr1:191296526-191893270 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014965	protein coding gene	Chr1:168816478-169385906 (-)
CAST/EiJ	MGP_CASTEiJ_G0016200	protein coding gene	Chr1:183164336-183757083 (-)
CBA/J	MGP_CBAJ_G0016593	protein coding gene	Chr1:198421920-199053340 (-)
DBA/2J	MGP_DBA2J_G0016699	protein coding gene	Chr1:176671348-177239678 (-)
FVB/NJ	MGP_FVBNJ_G0016695	protein coding gene	Chr1:174752923-175317816 (-)
LP/J	MGP_LPJ_G0016773	protein coding gene	Chr1:186557608-187158391 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016726	protein coding gene	Chr1:205592605-206205137 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0017294	protein coding gene	Chr1:182844598-183436839 (-)
PWK/PhJ	MGP_PWKPhJ_G0015988	protein coding gene	Chr1:175743349-176320663 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0015764	protein coding gene	Chr1:181804604-182402338 (-)
WSB/EiJ	MGP_WSBEiJ_G0016263	protein coding gene	Chr1:183071791-183672502 (-)

Human Ortholog

SMYD3, SET and MYND domain containing 3

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SMYD3, SET and MYND domain containing 3
Synonyms

bA74P14.1, KMT3E, ZMYND1, ZNFN3A1
Links

HGNC:15513

NCBI Gene ID: 64754

neXtProt AC: NX_Q9H7B4

UniProt: Q9H7B4
Chr Location

1q44; chr1:245749342-246507312 (-) GRCh38

MGI Vertebrate Homology

Smyd3 stringent orthology
1 human;1 mouse;1 zebrafish
HCOP

vertebrate homology predictions: SMYD3
Gene Tree

Smyd3

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Phenotype Summary

5 phenotypes from 2 alleles in 2 genetic backgrounds
20 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

40
Chemically induced (other)

2
Endonuclease-mediated

4
Gene trapped

26
Targeted

8
Genomic Mutations

2 involving Smyd3
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

41 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a null allele exhibit alleviated response to Ang II-induced vascular senescence.

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All GO Annotations

26
GO References

8

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

733
Tissues

26
cDNA Data

41
Literature Summary

7

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase smyd3

ZFIN smyd3

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All Sequences

60
RefSeq

12
UniProt

6
CCDS

CCDS15560.1

Ensembl

ENSMUSG00000055067 (Evidence)
NCBI Gene

69726

			Length	Strain/Species	Flank
genomic	ENSMUSG00000055067	Ensembl Gene Model \| MGI Sequence Detail	566082	C57BL/6J	± kb
transcript	ENSMUST00000128302	Ensembl \| MGI Sequence Detail	6871	Not Applicable
polypeptide	ENSMUSP00000117410	Ensembl \| MGI Sequence Detail	428	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000015307 histone-lysine N-methyltransferase SMYD3

(term hierarchy)
EC

2.1.1.354
InterPro Domains

IPR050869 Histone-lysine N-methyltransferase

IPR025805 Histone-lysine N-methyltransferase SMYD3

IPR001214 SET domain

IPR046341 SET domain superfamily

IPR044420 SMYD3, SET domain

IPR011990 Tetratricopeptide-like helical domain superfamily

IPR002893 Zinc finger, MYND-type

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All nucleic 43

cDNA 41

Primer pair 2

Microarray probesets 3

Summaries

All 57

Developmental Gene Expression 7

Gene Ontology 8

Phenotypes 20
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Smyd3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr15503	Chr1:179345593-179345610 (-)	4 bp
Tssr15502	Chr1:179345557-179345591 (-)	32 bp
Tssr15501	Chr1:179345541-179345554 (-)	58 bp
Tssr15500	Chr1:179329679-179329683 (-)	15,925 bp
Tssr15499	Chr1:179231447-179231451 (-)	114,157 bp
Tssr15498	Chr1:179209268-179209282 (-)	136,331 bp
Tssr15497	Chr1:178983829-178983872 (-)	361,755 bp
Tssr15496	Chr1:178966984-178966988 (-)	378,620 bp
Tssr15495	Chr1:178816915-178816925 (-)	528,686 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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