Tbio SYT1 Synaptotagmin-1

Protein Classes

PANTHER Classes

Protein / Membrane Traffic Protein / Membrane Trafficking Regulatory Protein / Synaptotagmin-1

DTO Classes

Protein / Transporter / Membrane Trafficking Regulatory Protein / Synaptotagmin-1

Protein Summary

Description

May have a regulatory role in the membrane interactions during trafficking of synaptic vesicles at the active zone of the synapse. It binds acidic phospholipids with a specificity that requires the presence of both an acidic head group and a diacyl backbone. A Ca(2+)-dependent interaction between synaptotagmin and putative receptors for activated protein kinase C has also been reported. It can bind to at least three additional proteins in a Ca(2+)-independent manner; these are neurexins, syntaxin and AP2. Plays a role in dendrite formation by melanocytes (PubMed:23999003). The synaptotagmins are integral membrane proteins of synaptic vesicles thought to serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis. Calcium binding to synaptotagmin-1 participates in triggering neurotransmitter release at the synapse (Fernandez-Chacon et al., 2001 [PubMed 11242035]).[supplied by OMIM, Jul 2010]

Uniprot Accession IDs

• P21579
• Q6AI31

Gene Name

• SYT1

Ensembl ID

• ENST00000261205
• ENSP00000261205
• ENSG00000067715
• ENST00000393240
• ENSP00000376932
• ENST00000552744
• ENSP00000447575

Symbol

• SVP65
• SYT
• P65
• SYT
• BAGOS
• SVP65

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
transcription factor perturbation	0.96
molecular function	0.94
trait	0.93
gene perturbation	0.91
hub protein	0.82

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

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

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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: 616.29   (req: < 5)

Gene RIFs: 42   (req: <= 3)

Antibodies: 768   (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: 616.29   (req: >= 5)

Gene RIFs: 42   (req: > 3)

Antibodies: 768   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 39

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 (7)

• Explore on Target Illumination GWAS Analytics (TIGA)

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GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
intelligence	EFO_0004337	3	4	1	6.9	80.5
self reported educational attainment	EFO_0004784	2	2	2		77.6
cognitive function measurement	EFO_0008354	3	1	3		71.3
mathematical ability	EFO_0004875	2	2	2		70.4
systolic blood pressure	EFO_0006335	1	1	1		64.4

• Explore on Target Illumination GWAS Analytics (TIGA)

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
intelligence	EFO_0004337	1	6.9	80.5
self reported educational attainment	EFO_0004784	2		77.6
cognitive function measurement	EFO_0008354	3		71.3
mathematical ability	EFO_0004875	2		70.4
systolic blood pressure	EFO_0006335	1		64.4

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Orthologs (14)

1 – 5 of 14

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	synaptotagmin 1	VGNC:5610	467079
Macaque	synaptotagmin 1		695390
Mouse	synaptotagmin I	MGI:99667	20979
Rat	synaptotagmin 1	RGD:3803	25716
Dog	synaptotagmin 1	VGNC:47040	482579

Species	Name	OMA	EggNOG	Inparanoid
Chimp	synaptotagmin 1
Macaque	synaptotagmin 1
Mouse	synaptotagmin I
Rat	synaptotagmin 1
Dog	synaptotagmin 1

Protein Structure (13 Structures, 1 AlphaFold Model)

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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-P21579-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 5 of 13

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 (25)

Reactome (21)

KEGG (1)

PathwayCommons (2)

WikiPathways (1)

Acetylcholine Neurotransmitter Release Cycle (R-HSA-264642)

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Find Similar Targets

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Acetylcholine Neurotransmitter Release Cycle	17 targets	R-HSA-264642
Reactome	Cargo recognition for clathrin-mediated endocytosis	105 targets	R-HSA-8856825
Reactome	Clathrin-mediated endocytosis	143 targets	R-HSA-8856828
Reactome	Disease	1105 targets	R-HSA-1643685
Reactome	Dopamine Neurotransmitter Release Cycle	23 targets	R-HSA-212676

Name	Explore in Pharos	Explore in Source
Acetylcholine Neurotransmitter Release Cycle	17 targets	R-HSA-264642
Cargo recognition for clathrin-mediated endocytosis	105 targets	R-HSA-8856825
Clathrin-mediated endocytosis	143 targets	R-HSA-8856828
Disease	1105 targets	R-HSA-1643685
Dopamine Neurotransmitter Release Cycle	23 targets	R-HSA-212676

Gene Ontology Terms (62)

Functions (16)

Components (23)

Processes (23)

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1 – 10 of 16

GO Term	Evidence	Assigned by
low-density lipoprotein particle receptor binding	Inferred from Direct Assay (IDA)	MGI
calcium ion binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
clathrin binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
phosphatidylserine binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
syntaxin binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
calcium-dependent phospholipid binding	Inferred from Sequence or structural Similarity (ISS)	ParkinsonsUK-UCL
SNARE binding	Inferred from Sequence or structural Similarity (ISS)	ParkinsonsUK-UCL
syntaxin-1 binding	Inferred from Sequence or structural Similarity (ISS)	ParkinsonsUK-UCL
1-phosphatidylinositol binding	Traceable Author Statement (TAS)	UniProtKB
calcium-dependent protein binding	Inferred from Electronic Annotation (IEA)	Ensembl

Protein-Protein Interactions (355)

Explore Interacting Targets

1 – 10 of 355

• See Interactions on String-DB

SYT2

Tbio

Novelty:  0.00754735

p_int:  1

Score:  0.928

Data Source:  BioPlex,STRINGDB

SYT5

Tbio

Novelty:  0.03580722

p_int:  1

Score:  0.364

Data Source:  BioPlex,STRINGDB

VLDLR

Tbio

Novelty:  0.00352547

p_int:  0.999999311

p_ni:  6.34e-7

p_wrong:  5.5e-8

Score:  0.256

Data Source:  BioPlex,STRINGDB

DGUOK

Tbio

Family:  Kinase

Novelty:  0.00897987

p_int:  0.9998705

p_ni:  0.0001295

Data Source:  BioPlex

DNAAF2

Tbio

Novelty:  0.01254416

p_int:  0.999859725

p_ni:  0.000140275

Data Source:  BioPlex

CWC22

Tbio

Novelty:  0.027689

p_int:  0.999634189

p_ni:  0.000365811

Score:  0.247

Data Source:  BioPlex,STRINGDB

NUFIP1

Tbio

Novelty:  0.11726869

p_int:  0.999605805

p_ni:  0.000394195

Data Source:  BioPlex

HAX1

Tbio

Novelty:  0.00749205

p_int:  0.99943648

p_ni:  0.00056352

Data Source:  BioPlex

EIF2B3

Tbio

Novelty:  0.04963646

p_int:  0.998769377

p_ni:  0.001230623

Data Source:  BioPlex

EIF2B5

Tbio

Novelty:  0.0102209

p_int:  0.994607199

p_ni:  0.005392801

Score:  0.196

Data Source:  BioPlex,STRINGDB

Publication Statistics

PubMed Score  616.29

PubMed score by year

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PubTator Score  511.59

PubTator score by year

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Amino Acid Sequence

Residue Counts

Protein Sequence

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UniProt Keyword Find Similar Targets

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3D-structure
Calcium
Cell junction
Complete proteome
Cytoplasm
Cytoplasmic vesicle
Differentiation
Disease mutation
Glycoprotein
Lipoprotein

GWAS Trait Find Similar Targets

No Header	No Header
cognitive function measurement
grip strength measurement
intelligence
leukocyte count
mathematical ability
self reported educational attainment
systolic blood pressure

MGI Phenotype Find Similar Targets

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adipose tissue phenotype
behavior/neurological phenotype
cardiovascular system phenotype
endocrine/exocrine gland phenotype
growth/size/body region phenotype
hematopoietic system phenotype
homeostasis/metabolism phenotype
liver/biliary system phenotype
mortality/aging
muscle phenotype