Tbio SYNE1 Nesprin-1

Protein Summary

Description

Multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. 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. May be involved in nucleus-centrosome attachment and nuclear migration in neural progenitors implicating LINC complex association with SUN1/2 and probably association with cytoplasmic dynein-dynactin motor complexes; SYNE1 and SYNE2 may act redundantly. Required for centrosome migration to the apical cell surface during early ciliogenesis. May be involved in nuclear remodeling during sperm head formation in spermatogenenis; a probable SUN3:SYNE1/KASH1 LINC complex may tether spermatid nuclei to posterior cytoskeletal structures such as the manchette. This gene encodes a spectrin repeat containing protein expressed in skeletal and smooth muscle, and peripheral blood lymphocytes, that localizes to the nuclear membrane. Mutations in this gene have been associated with autosomal recessive spinocerebellar ataxia 8, also referred to as autosomal recessive cerebellar ataxia type 1 or recessive ataxia of Beauce. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• Q8NF91
• B3W695
• E7EQI5
• H0Y4C0
• O94890
• Q3ZCV0
• Q5JV19
• Q5JV22
• Q8N9P7
• Q8TCP1
• Q8WWW6
• Q8WWW7
• Q8WXF6
• Q96N17
• Q9C0A7
• Q9H525
• Q9H526
• Q9NS36
• Q9NU50
• Q9UJ06
• Q9UJ07
• Q9ULF8

Gene Name

• SYNE1

Ensembl ID

• ENST00000367253
• ENSP00000356222
• ENSG00000131018
• ENST00000367255
• ENSP00000356224
• ENST00000413186
• ENSP00000414510

Symbol

• C6orf98
• KIAA0796
• KIAA1262
• KIAA1756
• MYNE1
• 8B
• CPG2
• ARCA1
• EDMD4
• KASH1
• MYNE1
• Nesp1
• SCAR8
• C6orf98
• dJ45H2.2

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
trait	1
interacting protein	0.99
cellular component	0.97
transcription factor perturbation	0.91
protein domain	0.85

Protein Classes

No PANTHER Classes or DTO Classes found

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 313.59   (req: < 5)

Gene RIFs: 49   (req: <= 3)

Antibodies: 122   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 313.59   (req: >= 5)

Gene RIFs: 49   (req: > 3)

Antibodies: 122   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 13

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Expression Data (0 Tissues)

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No expression data found

Related Tools

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (165)

Explore Interacting Targets

1 – 10 of 165

• See Interactions on String-DB

IFT57

Tbio

Novelty:  0.03373199

p_int:  0.999999769

p_ni:  2.31e-7

Score:  0.213

Data Source:  BioPlex,STRINGDB

TNFSF18

Tbio

Novelty:  0.01423949

p_int:  0.996173152

p_ni:  0.003270801

p_wrong:  0.000556046

Data Source:  BioPlex

MMP19

Tbio

Family:  Enzyme

Novelty:  0.01407961

p_int:  0.93162791

p_ni:  0.005691403

p_wrong:  0.062680687

Data Source:  BioPlex

SUN2

Tbio

Novelty:  0.01387591

Score:  0.998

Data Source:  STRINGDB

SUN1

Tbio

Novelty:  0.00931817

Score:  0.994

Data Source:  STRINGDB

LMNB1

Tbio

Novelty:  0.00127348

Score:  0.983

Data Source:  STRINGDB

SYNE3

Tbio

Novelty:  0.06515065

Score:  0.929

Data Source:  STRINGDB

SYNE2

Tbio

Novelty:  0.01368736

Score:  0.928

Data Source:  STRINGDB

UBE2I

Tbio

Novelty:  0.00267883

Score:  0.927

Data Source:  STRINGDB

SMC3

Tbio

Novelty:  0.00474377

Score:  0.925

Data Source:  STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (8)

Reactome (4)

WikiPathways (4)

Cell Cycle (R-HSA-1640170)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Cell Cycle	597 targets	R-HSA-1640170
Reactome	Meiosis	88 targets	R-HSA-1500620
Reactome	Meiotic synapsis	60 targets	R-HSA-1221632
Reactome	Reproduction	114 targets	R-HSA-1474165

Name	Explore in Pharos	Explore in Source
Cell Cycle	597 targets	R-HSA-1640170
Meiosis	88 targets	R-HSA-1500620
Meiotic synapsis	60 targets	R-HSA-1221632
Reproduction	114 targets	R-HSA-1474165

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (27)

Functions (7)

Components (14)

Processes (6)

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1 – 7 of 7

GO Term	Evidence	Assigned by
actin binding	Inferred from Direct Assay (IDA)	UniProtKB
enzyme binding	Inferred from Physical Interaction (IPI)	BHF-UCL
identical protein binding	Inferred from Physical Interaction (IPI)	IntAct
lamin binding	Inferred from Physical Interaction (IPI)	UniProtKB
RNA binding	Inferred from High Throughput Direct Assay (HDA)	UniProtKB
actin filament binding	Inferred from Sequence or structural Similarity (ISS)	UniProtKB
protein homodimerization activity	Inferred from Sequence or structural Similarity (ISS)	UniProtKB

Disease Associations ()

No disease associations found

GWAS Traits (21)

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1 – 5 of 21

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
uterine fibroid	EFO_0000731	2	3	0	1.2	92.9
heel bone mineral density	EFO_0009270	3	6	8		92.1
body height	EFO_0004339	2	2	2		87.6
serum gamma-glutamyl transferase measurement	EFO_0004532	1	1	1		74.5
myeloid white cell count	EFO_0007988	1	1	1		72.3

• Explore on Target Illumination GWAS Analytics (TIGA)

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
uterine fibroid	EFO_0000731	0	1.2	92.9
heel bone mineral density	EFO_0009270	8		92.1
body height	EFO_0004339	2		87.6
serum gamma-glutamyl transferase measurement	EFO_0004532	1		74.5
myeloid white cell count	EFO_0007988	1		72.3

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Actin-binding
Alternative splicing
Coiled coil
Complete proteome
Cytoplasm
Cytoskeleton
Differentiation
Disease mutation
Disulfide bond

GWAS Trait Find Similar Targets

No Header	No Header
anthropometric measurement
bipolar disorder
BMI-adjusted hip circumference
body fat distribution
body height
breast carcinoma
cancer
endometriosis
estrogen-receptor negative breast cancer
heel bone mineral density

MGI Phenotype Find Similar Targets

No Header	No Header
behavior/neurological phenotype
cardiovascular system phenotype
cellular phenotype
growth/size/body region phenotype
homeostasis/metabolism phenotype
immune system phenotype
mortality/aging
muscle phenotype
nervous system phenotype
respiratory system phenotype

IDG Resources

No IDG generated resources found

Orthologs (9)

1 – 5 of 9

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Macaque	spectrin repeat containing nuclear envelope protein 1		711782
Dog	spectrin repeat containing nuclear envelope protein 1	VGNC:47027	484037
Horse	spectrin repeat containing nuclear envelope protein 1	VGNC:23801	100062842
Opossum	spectrin repeat containing nuclear envelope protein 1		100032170
Platypus	spectrin repeat containing nuclear envelope protein 1		100073483

Species	Name	OMA	EggNOG	Inparanoid
Macaque	spectrin repeat containing nuclear envelope protein 1
Dog	spectrin repeat containing nuclear envelope protein 1
Horse	spectrin repeat containing nuclear envelope protein 1
Opossum	spectrin repeat containing nuclear envelope protein 1
Platypus	spectrin repeat containing nuclear envelope protein 1

Publication Statistics

PubMed Score 313.59

PubMed score by year

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PubTator Score 102.08

PubTator score by year

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Related Publications

Text Mined References (74)

GeneRif Annotations (49)

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PMID	Year	Title