Syne3 MGI Mouse Gene Detail - MGI:2442408 - spectrin repeat containing, nuclear envelope family member 3

Symbol

Syne3
Name

spectrin repeat containing, nuclear envelope family member 3
Synonyms

4831426I19Rik, nesprin-3, nesprin-3alpha, nesprin-3beta

Feature Type

protein coding gene
IDs

MGI:2442408
NCBI Gene: 212073
Alliance

gene page
Transcription Start Sites

9 TSS

Sequence Map

Chr12:104896192-104976068 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 12, 54.97 cM
Mapping Data

1 experiment

SNPs within 2kb

2899 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2442408	protein coding gene	Chr12:104896192-104976357 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0020082	protein coding gene	Chr12:106756449-106809520 (-)
A/J	MGP_AJ_G0020036	protein coding gene	Chr12:102702761-102746230 (-)
AKR/J	MGP_AKRJ_G0020013	protein coding gene	Chr12:105659644-105713740 (-)
BALB/cJ	MGP_BALBcJ_G0020022	protein coding gene	Chr12:103110514-103160370 (-)
C3H/HeJ	MGP_C3HHeJ_G0019825	protein coding gene	Chr12:106136970-106185411 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0020468	protein coding gene	Chr12:110053502-110101682 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0018081	protein coding gene	Chr12:99416717-99494832 (-)
CAST/EiJ	MGP_CASTEiJ_G0019366	protein coding gene	Chr12:100972609-101065297 (-)
CBA/J	MGP_CBAJ_G0019792	protein coding gene	Chr12:114309157-114354857 (-)
DBA/2J	MGP_DBA2J_G0019909	protein coding gene	Chr12:102250854-102298392 (-)
FVB/NJ	MGP_FVBNJ_G0019894	protein coding gene	Chr12:101040656-101086216 (-)
LP/J	MGP_LPJ_G0019984	protein coding gene	Chr12:106622848-106689472 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019932	protein coding gene	Chr12:117755317-117807022 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020497	protein coding gene	Chr12:105088411-105165245 (-)
PWK/PhJ	MGP_PWKPhJ_G0019129	protein coding gene	Chr12:96770984-96831218 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0018931	protein coding gene	Chr12:99359947-99406780 (-)
WSB/EiJ	MGP_WSBEiJ_G0019425	protein coding gene	Chr12:106069598-106120063 (-)

Human Ortholog

SYNE3, spectrin repeat containing nuclear envelope family member 3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SYNE3, spectrin repeat containing nuclear envelope family member 3
Synonyms

C14orf139, C14orf49, KASH3, LINC00341, NCRNA00341, Nesp3, NET53
Links

HGNC:19861

NCBI Gene ID: 161176

neXtProt AC: NX_Q6ZMZ3

UniProt: Q6ZMZ3
Chr Location

14q32.13; chr14:95407266-95516650 (-) GRCh38

MGI Vertebrate Homology

Syne3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SYNE3
Gene Tree

Syne3

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Phenotype Summary

3 phenotypes from 2 alleles in 2 genetic backgrounds
13 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

8
Chemically induced (other)

1
Endonuclease-mediated

1
Gene trapped

2
Targeted

4
Genomic Mutations

1 involving Syne3
Incidental Mutations

APF
Find Mice (IMSR)

42 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a null allele are normal and fertile.

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All GO Annotations

25
GO References

9

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

818
Tissues

40
cDNA Data

10
Literature Summary

3

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase syne3

ZFIN syne3

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All Sequences

45
RefSeq

10
UniProt

1
CCDS

CCDS36542.1, CCDS36543.1

Ensembl

ENSMUSG00000054150 (Evidence)
NCBI Gene

212073

			Length	Strain/Species	Flank
genomic	ENSMUSG00000054150	Ensembl Gene Model \| MGI Sequence Detail	79877	C57BL/6J	± kb
transcript	ENSMUST00000095439	Ensembl \| MGI Sequence Detail	3357	Not Applicable
polypeptide	ENSMUSP00000093090	Ensembl \| MGI Sequence Detail	975	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000031027 nesprin-3

(term hierarchy)
InterPro Domains

IPR012315 KASH domain

IPR052403 LINC complex-associated protein

IPR018159 Spectrin/alpha-actinin

IPR002017 Spectrin repeat

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All nucleic 14

Genomic 2

cDNA 10

Primer pair 2

Microarray probesets 2

Summaries

All 43

Developmental Gene Expression 3

Gene Ontology 9

Phenotypes 13
Earliest

J:80000 The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563-573
Latest

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

TSS for Syne3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr117598	Chr12:104976321-104976345 (-)	-265 bp
Tssr117597	Chr12:104976282-104976318 (-)	-232 bp
Tssr117596	Chr12:104976264-104976280 (-)	-204 bp
Tssr117595	Chr12:104973131-104973135 (-)	2,935 bp
Tssr117594	Chr12:104964941-104964969 (-)	11,113 bp
Tssr3935	Chr12:104955021-104955025 (-)	21,045 bp
Tssr117593	Chr12:104954529-104954532 (-)	21,537 bp
Tssr3934	Chr12:104922518-104922521 (-)	53,548 bp
Tssr117592	Chr12:104896310-104896333 (-)	79,746 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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