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

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.

Go To Tool

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.

Go To Tool

GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

Go To Tool

ARCHS4

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

Go To Tool

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: 304.1   (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: 304.1   (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

GWAS Traits (4)

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 4 of 4

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
heel bone mineral density	EFO_0009270	3	6	8		95.2
uterine fibroid	EFO_0000731	2	3	0	1.2	93.3
endometriosis	EFO_0001065	1	1	0	1.1	40
bipolar disorder	EFO_0000289	1	1	0	1.1	34.1

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 4 of 4

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
heel bone mineral density	EFO_0009270	8		95.2
uterine fibroid	EFO_0000731	0	1.2	93.3
endometriosis	EFO_0001065	0	1.1	40
bipolar disorder	EFO_0000289	0	1.1	34.1

Reset Zoom  Beta Count   Odds Ratio

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

Protein Structure (1 Structure, 38 AlphaFold Models)

Representation

  axes   backbone   ball+stick   cartoon   rocket   rope   spacefill

Color Scheme

  target   atomindex   bfactor   chainname   electrostatic   element   hydrophobicity   resname   sstruc

Click on a row in the table to change the structure displayed.
More information can be found at RCSB PDB

AF-Q8NF91-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 1 of 1

PDB Structure Id	Ligand	Method	Resolution (Å)	Residues	Fraction of Total Protein	Pub Year	Title

PDB Structure Id	Fraction of Total Protein	Resolution	Pub Year

Pathways (8)

Reactome (4)

WikiPathways (4)

Cell Cycle (R-HSA-1640170)

Click on a row in the table to change the structure displayed.

Find Similar Targets

Items per page:

5

1 – 4 of 4

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

Gene Ontology Terms (27)

Functions (7)

Components (14)

Processes (6)

Find Similar Targets

Items per page:

10

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

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

Publication Statistics

PubMed Score  304.10

PubMed score by year

Reset Zoom

PubTator Score  102.08

PubTator score by year

Reset Zoom

Amino Acid Sequence

Residue Counts

Protein Sequence

Show Full Sequence

ProtVista Viewer

Find similar targets by:

UniProt Keyword Find Similar Targets

3D-structure
Actin-binding
Alternative splicing
Coiled coil
Complete proteome
Cytoplasm
Cytoskeleton
Differentiation
Disease mutation
Disulfide bond

GWAS Trait Find Similar Targets

bipolar disorder
endometriosis
heel bone mineral density
uterine fibroid

MGI Phenotype Find Similar Targets

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