SYNE3 Gene (Protein Coding)

Spectrin Repeat Containing Nuclear Envelope Family Member 3

GC14M095408
GIFtS:
36
See more...

Aliases for SYNE3 Gene

Aliases for SYNE3 Gene

  • Spectrin Repeat Containing Nuclear Envelope Family Member 3 2 3 5
  • Nesprin-3 2 3 4
  • Long Intergenic Non-Protein Coding RNA 341 2 3
  • Nuclear Envelope Spectrin Repeat Protein 3 3 4
  • KASH Domain-Containing Protein 3 3 4
  • C14orf139 3 4
  • LINC00341 3 4
  • C14orf49 3 4
  • KASH3 3 4
  • NET53 2 3
  • Nesp3 2 3
  • Chromosome 14 Open Reading Frame 139 2
  • Chromosome 14 Open Reading Frame 49 2
  • Uncharacterized Protein C14orf113 3
  • Non-Protein Coding RNA 341 2
  • NCRNA00341 3
  • FLJ25605 2
  • SYNE3 5

External Ids for SYNE3 Gene

Previous HGNC Symbols for SYNE3 Gene

  • C14orf49
  • LINC00341
  • C14orf139
  • NCRNA00341

Previous GeneCards Identifiers for SYNE3 Gene

  • GC14M095884

Summaries for SYNE3 Gene

GeneCards Summary for SYNE3 Gene

SYNE3 (Spectrin Repeat Containing Nuclear Envelope Family Member 3) is a Protein Coding gene. Diseases associated with SYNE3 include Spinocerebellar Ataxia, Autosomal Recessive 8 and Emery-Dreifuss Muscular Dystrophy 3, Autosomal Recessive. Gene Ontology (GO) annotations related to this gene include actin binding and actin filament binding. An important paralog of this gene is SYNE1.

UniProtKB/Swiss-Prot Summary for SYNE3 Gene

  • As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. Probable anchoring protein which tethers the nucleus to the cytoskeleton by binding PLEC which can associate with the intermediate filament system. Plays a role in the regulation of aortic epithelial cell morphology, and is required for flow-induced centrosome polarization and directional migration in aortic endothelial cells.

Additional gene information for SYNE3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYNE3 Gene

Genomics for SYNE3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SYNE3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH14J095513 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 -0.6 -608 6.9 ZBTB10 BCL11A FEZF1 CTCF ZIC2 ZNF610 SIN3A VEZF1 IRF4 SMAD4 ENSG00000258572 SYNE3 GLRX5 HSALNG0103441 LOC101929107
GH14J095530 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.4 -18.2 -18225 8.8 ZSCAN16 TBP SP1 CEBPA NR2C1 FOXA1 MNT IKZF1 SMAD5 ETS1 GLRX5 SNHG10 SCARNA13 SYNE3 PAPOLA DICER1 ENSG00000258572 TCL1B
GH14J095477 Promoter/Enhancer 1.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 255.6 +31.8 31849 13.6 NR2C1 IKZF1 ZFP64 ZNF513 FOXA2 MAX SAP130 ZNF341 RXRA CTBP1 SYNE3 SNHG10 TCL1A TCL1B HSALNG0103438 LOC101929107 CLMN
GH14J095500 Promoter/Enhancer 1.3 EPDnew ENCODE dbSUPER 250.4 +14.8 14843 3.3 HOMEZ CEBPB FOXA2 SMAD4 SMARCA5 DMAP1 JUND FOSL1 RAD21 FOXP1 SYNE3 LOC101929107 HSALNG0103438 CLMN
GH14J095452 Enhancer 1.1 Ensembl ENCODE dbSUPER 13 +63.8 63835 1.3 MXD4 ZFP64 CTCF KDM6A FOXA2 SMAD4 SAP130 MIER3 EBF1 RARA SYNE3 CLMN HSALNG0103438 piR-37472-002 NONHSAG015796.2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYNE3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYNE3

Genomic Locations for SYNE3 Gene

Latest Assembly
chr14:95,407,266-95,516,650
(GRCh38/hg38)
Size:
109,385 bases
Orientation:
Minus strand

Previous Assembly
chr14:95,873,603-95,982,987
(GRCh37/hg19 by Entrez Gene)
Size:
109,385 bases
Orientation:
Minus strand

chr14:95,883,831-95,942,173
(GRCh37/hg19 by Ensembl)
Size:
58,343 bases
Orientation:
Minus strand

Genomic View for SYNE3 Gene

Genes around SYNE3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYNE3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYNE3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SYNE3 Gene

Proteins for SYNE3 Gene

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  • Protein details for SYNE3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZMZ3-SYNE3_HUMAN
    Recommended name:
    Nesprin-3
    Protein Accession:
    Q6ZMZ3
    Secondary Accessions:
    • A6H8H3
    • Q86SX5
    • Q8N7G8

    Protein attributes for SYNE3 Gene

    Size:
    975 amino acids
    Molecular mass:
    112216 Da
    Quaternary structure:
    • Core component of LINC complexes which are composed of inner nuclear membrane SUN domain-containing proteins coupled to outer nuclear membrane KASH domain-containing nesprins. SUN and KASH domain-containing proteins seem to bind each other promiscuously; however, differentially expression of LINC complex constituents can give rise to specific assemblies. Interacts with SUN1 and SUN2; probably forming respective LINC complexes. Interacts with PLEC (via actin-binding domain). Interacts with DST. Interacts with SYNE1 via spectrin repeats. Interacts (via KASH domain) with TOR1A (ATP-bound); the interaction is required for SYNE3 nuclear envelope localization.
    SequenceCaution:
    • Sequence=BAC05312.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAD18582.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAD62365.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for SYNE3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYNE3 Gene

Protein Expression for SYNE3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SYNE3 Gene

  • The disulfid bond with SUN1 or SUN2 is required for stability of the respective LINC complex under tensile forces.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYNE3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SYNE3 Gene

Domains & Families for SYNE3 Gene

Gene Families for SYNE3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SYNE3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYNE3 Gene

GenScript: Design optimal peptide antigens:
  • C14orf49 protein (A6H8H3_HUMAN)
  • C14orf49 protein (Q6P714_HUMAN)
  • Nesprin-3 (SYNE3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6ZMZ3

UniProtKB/Swiss-Prot:

SYNE3_HUMAN :
  • The KASH domain is involved in the binding to SUN1 and SUN2 through recognition of their SUN domains.
  • Belongs to the nesprin family.
Domain:
  • The KASH domain is involved in the binding to SUN1 and SUN2 through recognition of their SUN domains.
Family:
  • Belongs to the nesprin family.
genes like me logo Genes that share domains with SYNE3: view

Function for SYNE3 Gene

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  6. Cell Lines for research

Molecular function for SYNE3 Gene

UniProtKB/Swiss-Prot Function:
As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. Probable anchoring protein which tethers the nucleus to the cytoskeleton by binding PLEC which can associate with the intermediate filament system. Plays a role in the regulation of aortic epithelial cell morphology, and is required for flow-induced centrosome polarization and directional migration in aortic endothelial cells.

Phenotypes From GWAS Catalog for SYNE3 Gene

Gene Ontology (GO) - Molecular Function for SYNE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18396275
GO:0008092 cytoskeletal protein binding IEA --
GO:0051015 actin filament binding IBA,IMP 22518138
genes like me logo Genes that share ontologies with SYNE3: view
genes like me logo Genes that share phenotypes with SYNE3: view

Animal Models for research

miRNA for SYNE3 Gene

miRTarBase miRNAs that target SYNE3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYNE3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SYNE3 Gene

Localization for SYNE3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNE3 Gene

Nucleus outer membrane. Single-pass type IV membrane protein. Nucleus envelope. Rough endoplasmic reticulum.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYNE3 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 3
plasma membrane 2
cytoskeleton 2
cytosol 2
extracellular 1
mitochondrion 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYNE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005635 nuclear envelope IEA,IDA 21937718
GO:0005640 nuclear outer membrane IBA 21873635
GO:0005737 cytoplasm IBA 21873635
GO:0005783 endoplasmic reticulum IEA --
genes like me logo Genes that share ontologies with SYNE3: view

Pathways & Interactions for SYNE3 Gene

PathCards logo

SuperPathways for SYNE3 Gene

No Data Available

SIGNOR curated interactions for SYNE3 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SYNE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007010 cytoskeleton organization IMP 21937718
GO:0007097 nuclear migration IBA 21873635
GO:0008360 regulation of cell shape IMP 21937718
GO:0090150 establishment of protein localization to membrane IDA 22518138
genes like me logo Genes that share ontologies with SYNE3: view

No data available for Pathways by source for SYNE3 Gene

Drugs & Compounds for SYNE3 Gene

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No Compound Related Data Available

Transcripts for SYNE3 Gene

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mRNA/cDNA for SYNE3 Gene

7 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYNE3

Alternative Splicing Database (ASD) splice patterns (SP) for SYNE3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16
SP1: -
SP2:
SP3:

Relevant External Links for SYNE3 Gene

GeneLoc Exon Structure for
SYNE3

Expression for SYNE3 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYNE3 Gene

mRNA expression in normal human tissues for SYNE3 Gene
mRNA expression by BioGPS for SYNE3 GenemRNA expression by GTEx for SYNE3 Gene

mRNA differential expression in normal tissues according to GTEx for SYNE3 Gene

This gene is overexpressed in Adipose - Subcutaneous (x5.1).

Protein differential expression in normal tissues from HIPED for SYNE3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (23.4) and Testis (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SYNE3 Gene



Protein tissue co-expression partners for SYNE3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYNE3

SOURCE GeneReport for Unigene cluster for SYNE3 Gene:

Hs.354645

mRNA Expression by UniProt/SwissProt for SYNE3 Gene:

Q6ZMZ3-SYNE3_HUMAN
Tissue specificity: Expressed in aortic endothelial cells (at protein level).

Evidence on tissue expression from TISSUES for SYNE3 Gene

  • Liver(4.1)
  • Thyroid gland(4)
  • Blood(2.8)
  • Eye(2)
genes like me logo Genes that share expression patterns with SYNE3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYNE3 Gene

Orthologs for SYNE3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYNE3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SYNE3 31
  • 95 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia SYNE3 30 31
  • 84.91 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia C21H14orf49 30
  • 83.62 (n)
SYNE3 31
  • 79 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Syne3 30
  • 81.4 (n)
Mouse
(Mus musculus)
 Mammalia Syne3 30 17 31
  • 81.02 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia SYNE3 31
  • 64 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia SYNE3 31
  • 58 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves C5H14ORF49 30
  • 61.88 (n)
SYNE3 31
  • 54 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia SYNE3 31
  • 52 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia syne3 30
  • 57.24 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.29646 30
Zebrafish
(Danio rerio)
 Actinopterygii syne3 30 31
  • 53.21 (n)
 OneToOne
Species where no ortholog for SYNE3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SYNE3 Gene

ENSEMBL:
Gene Tree for SYNE3 (if available)
TreeFam:
Gene Tree for SYNE3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYNE3: view image

Paralogs for SYNE3 Gene

Paralogs for SYNE3 Gene

(1) SIMAP similar genes for SYNE3 Gene using alignment to 2 proteins:

  • SYNE3_HUMAN
  • G3V533_HUMAN
genes like me logo Genes that share paralogs with SYNE3: view

Variants for SYNE3 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYNE3 Gene

SNP ID Clinical significance and condition Chr 14 pos Variation AA Info Type
rs10130647 - p.Ile946Val
rs12434757 - p.Ala923Val
rs17092216 - p.Arg864His
rs9671369 - p.Thr668Met

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SYNE3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SYNE3 Gene

Variant ID Type Subtype PubMed ID
dgv89e55 CNV gain 17911159
dgv89e55 CNV gain 17911159
esv2070721 CNV deletion 18987734
esv2531934 CNV insertion 19546169
esv2749051 CNV deletion 23290073
esv2749053 CNV deletion 23290073
esv3449551 CNV duplication 20981092
esv3635400 CNV gain 21293372
esv3635400 CNV gain 21293372
nsv1042858 CNV gain 25217958
nsv1042858 CNV gain 25217958
nsv1143757 CNV deletion 24896259
nsv1150904 CNV insertion 26484159
nsv1151953 CNV deletion 26484159
nsv476685 CNV novel sequence insertion 20440878
nsv525357 CNV gain 19592680
nsv565631 CNV gain 21841781
nsv565631 CNV gain 21841781
nsv85307 CNV insertion 16902084

Variation tolerance for SYNE3 Gene

Residual Variation Intolerance Score: 94.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.02; 93.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYNE3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYNE3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNE3 Gene

Disorders for SYNE3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for SYNE3 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards
Search SYNE3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYNE3

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SYNE3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYNE3 Gene

Publications for SYNE3 Gene

  1. TorsinA binds the KASH domain of nesprins and participates in linkage between nuclear envelope and cytoskeleton. (PMID: 18827015) Nery FC … Breakefield XO (Journal of cell science 2008) 3 4 23
  2. Nesprin-3, a novel outer nuclear membrane protein, associates with the cytoskeletal linker protein plectin. (PMID: 16330710) Wilhelmsen K … Sonnenberg A (The Journal of cell biology 2005) 3 4 23
  3. Cytoskeletal interactions at the nuclear envelope mediated by nesprins. (PMID: 22518138) Taranum S … Noegel AA (International journal of cell biology 2012) 3 4
  4. Nesprin-3 regulates endothelial cell morphology, perinuclear cytoskeletal architecture, and flow-induced polarization. (PMID: 21937718) Morgan JT … Barakat AI (Molecular biology of the cell 2011) 3 4
  5. Structural requirements for the assembly of LINC complexes and their function in cellular mechanical stiffness. (PMID: 18396275) Stewart-Hutchinson PJ … Hodzic D (Experimental cell research 2008) 3 4

ExternalLinks

View latest publications for SYNE3 gene in Mastermind

Products for SYNE3 Gene

  • Addgene plasmids for SYNE3

Sources for SYNE3 Gene