SYT5 synaptotagmin 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYT5provided by HGNC
Official Full Name: synaptotagmin 5provided by HGNC
Primary source: HGNC:HGNC:11513
See related: Ensembl:ENSG00000129990 MIM:600782; AllianceGenome:HGNC:11513
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Synaptotagmins, such as SYT5, are a family of type III membrane proteins characterized by cytoplasmic repeats related to protein kinase C (see MIM 176960) regulatory (C2) domains, which are thought to bind calcium. Synaptotagmins may act both as negative regulators of vesicle fusion, allowing fusion in the presence of calcium, and as calcium receptors or sensor molecules (summary by Hudson and Birnbaum, 1995 [PubMed 7597049]).[supplied by OMIM, Feb 2011]
Expression: Biased expression in brain (RPKM 20.3) and adrenal (RPKM 2.1) See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.42; 11p

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (55171196..55180289, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (58265259..58274351, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (55682564..55691657, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ca(2+)-binding pocket of synaptotagmin 5 C2A domain
Title: Structural analysis of Ca(2+)-binding pocket of synaptotagmin 5 C2A domain.
crystals of synaptotagmin 5 belonged to the hexagonal space group P6(5), with unit-cell parameters a = b = 93.97, c = 28.05 A.
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction crystallographic study of human synaptotagmin 5 C2A domain.
This protein has been found differentially expressed in thalami from patients with schizophrenia.
Title: Proteome analysis of the thalamus and cerebrospinal fluid reveals glycolysis dysfunction and potential biomarkers candidates for schizophrenia.
results suggest a novel putative functional role for the GST-synaptotagmin V complex in human breast cancers. As this association of GST M1-synaptotagmin was not seen in adjacent non-cancerous tissues, this can be used as a marker for breast cancers.
Title: Evidence for the association of synaptotagmin with glutathione S-transferases: implications for a novel function in human breast cancer.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D19S1081 (e-PCR)
- UniSTS:12607

STS-D15049 (e-PCR)
- UniSTS:50041

RH18176 (e-PCR)
- UniSTS:38299

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion sensor activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium-dependent phospholipid binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol-4,5-bisphosphate binding	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables syntaxin binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in calcium-dependent activation of synaptic vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemical synaptic transmission	TAS Traceable Author Statement more info	PubMed
involved_in regulation of calcium ion-dependent exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of calcium ion-dependent exocytosis	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic vesicle exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
is_active_in dense core granule	IBA Inferred from Biological aspect of Ancestor more info
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
located_in neuronal dense core vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in proximal neuron projection	IEA Inferred from Electronic Annotation more info
located_in recycling endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: synaptotagmin-5

Names: synaptotagmin V; sytV

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001297774.2 → NP_001284703.1 synaptotagmin-5 isoform 2

See identical proteins and their annotated locations for NP_001284703.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and contains multiple coding region differences, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC010327, AK295337, BM311004

Consensus CDS

CCDS74455.1

UniProtKB/Swiss-Prot

O00445

Related

ENSP00000465576.1, ENST00000590851.5

Conserved Domains (2) summary

cd08385
Location:106 → 228

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cl14603
Location:236 → 370

C2; C2 domain
NM_003180.3 → NP_003171.2 synaptotagmin-5 isoform 1

See identical proteins and their annotated locations for NP_003171.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC010327, BC046157, BQ417474, DA529870

Consensus CDS

CCDS12919.1

UniProtKB/Swiss-Prot

B3KWJ8, B7Z300, O00445, Q86X72

UniProtKB/TrEMBL

Q05BS5

Related

ENSP00000346265.2, ENST00000354308.8

Conserved Domains (2) summary

cd08385
Location:109 → 231

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cl14603
Location:240 → 374

C2; C2 domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

55171196..55180289 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439257.1 → XP_047295213.1 synaptotagmin-5 isoform X2

UniProtKB/TrEMBL

Q4FD32
XM_017027175.2 → XP_016882664.1 synaptotagmin-5 isoform X1

UniProtKB/Swiss-Prot

B3KWJ8, B7Z300, O00445, Q86X72

UniProtKB/TrEMBL

Q05BS5

Conserved Domains (2) summary

cd08385
Location:109 → 231

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cl14603
Location:240 → 374

C2; C2 domain
XM_047439256.1 → XP_047295212.1 synaptotagmin-5 isoform X1

UniProtKB/Swiss-Prot

B3KWJ8, B7Z300, O00445, Q86X72
XM_006723339.4 → XP_006723402.1 synaptotagmin-5 isoform X1

See identical proteins and their annotated locations for XP_006723402.1

UniProtKB/Swiss-Prot

B3KWJ8, B7Z300, O00445, Q86X72

UniProtKB/TrEMBL

Q05BS5

Related

ENSP00000442896.1, ENST00000537500.5

Conserved Domains (2) summary

cd08385
Location:109 → 231

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cl14603
Location:240 → 374

C2; C2 domain
XM_006723341.4 → XP_006723404.1 synaptotagmin-5 isoform X3

Conserved Domains (2) summary

cd08385
Location:106 → 228

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cl14603
Location:237 → 371

C2; C2 domain