ESYT3 extended synaptotagmin 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ESYT3provided by HGNC
Official Full Name: extended synaptotagmin 3provided by HGNC
Primary source: HGNC:HGNC:24295
See related: Ensembl:ENSG00000158220 MIM:616692; AllianceGenome:HGNC:24295
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
Also known as: E-Syt3; FAM62C; CHR3SYT
Summary: Predicted to enable calcium ion binding activity and phospholipid binding activity. Predicted to be involved in endoplasmic reticulum-plasma membrane tethering and lipid transport. Located in cytoplasmic side of plasma membrane; endoplasmic reticulum membrane; and endoplasmic reticulum-plasma membrane contact site. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in lung (RPKM 3.7), thyroid (RPKM 3.1) and 8 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q22.3

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (138434616..138481686)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (141175169..141222247)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (138153458..138200528)

Chromosome 3 - NC_000003.12 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?

Comprehensive analysis of the prognostic values and immune implication of ESYT3 in lung adenocarcinoma.
Title: Comprehensive analysis of the prognostic values and immune implication of ESYT3 in lung adenocarcinoma.
Whole-exome sequencing reveals common and rare variants in immunologic and neurological genes implicated in achalasia.
Title: Whole-exome sequencing reveals common and rare variants in immunologic and neurological genes implicated in achalasia.
ESyt2 and ESyt3, but not ESyt1, interact with activated FGFR1.
Title: Extended Synaptotagmin Interaction with the Fibroblast Growth Factor Receptor Depends on Receptor Conformation, Not Catalytic Activity.
The extended synaptotagmins (E-Syt1, E-Syt2, and E-Syt3) are endoplasmic reticulum-anchored proteins. They form homo- and heteromeric complexes that mediate contacts with the plasma membrane. Such contacts are critically dependent on the presence of PI(4,5)P2 in this membrane and are additionally regulated by cytosolic Ca2+ via the Ca2+-sensing property of E-Syt1.
Title: PI(4,5)P(2)-dependent and Ca(2+)-regulated ER-PM interactions mediated by the extended synaptotagmins.
two haplotype blocks of ESYT3 gene in 3q22.3 region that likely harbor functional variants and have a role in coronary artery disease in females
Title: Fine mapping of chromosome 3q22.3 identifies two haplotype blocks in ESYT3 associated with coronary artery disease in female Han Chinese.

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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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium-dependent phospholipid binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylcholine binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylethanolamine binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in endoplasmic reticulum-plasma membrane tethering	IEA Inferred from Electronic Annotation more info
involved_in lipid transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasmic side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in endoplasmic reticulum-plasma membrane contact site	IDA Inferred from Direct Assay more info	PubMed
located_in organelle membrane contact site	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: extended synaptotagmin-3

Names: chr3 synaptotagmin; extended synaptotagmin protein 3; family with sequence similarity 62 (C2 domain containing), member C

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_001322831.2 → NP_001309760.1 extended synaptotagmin-3 isoform a

Status: VALIDATED

Source sequence(s)

AC022497, BM668912

Consensus CDS

CCDS3101.2

UniProtKB/Swiss-Prot

A0FGR9, A8K0G5, Q6ZV21, Q8NDZ5, Q9BQR9

Conserved Domains (4) summary

cd04030
Location:755 → 879

C2C_KIAA1228; C2 domain third repeat present in uncharacterized human KIAA1228-like proteins

cd04050
Location:445 → 568

C2B_Synaptotagmin-like; C2 domain second repeat present in Synaptotagmin-like proteins

cd08391
Location:306 → 424

C2A_C2C_Synaptotagmin_like; C2 domain first and third repeat in Synaptotagmin-like proteins

pfam17047
Location:114 → 290

SMP_LBD; Synaptotagmin-like mitochondrial-lipid-binding domain
NM_001322834.2 → NP_001309763.1 extended synaptotagmin-3 isoform b

Status: VALIDATED

Source sequence(s)

AC022497, BM668912

Conserved Domains (4) summary

cd04030
Location:755 → 874

C2C_KIAA1228; C2 domain third repeat present in uncharacterized human KIAA1228-like proteins

cd04050
Location:445 → 568

C2B_Synaptotagmin-like; C2 domain second repeat present in Synaptotagmin-like proteins

cd08391
Location:306 → 424

C2A_C2C_Synaptotagmin_like; C2 domain first and third repeat in Synaptotagmin-like proteins

pfam17047
Location:114 → 290

SMP_LBD; Synaptotagmin-like mitochondrial-lipid-binding domain
NM_031913.5 → NP_114119.2 extended synaptotagmin-3 isoform a

See identical proteins and their annotated locations for NP_114119.2

Status: VALIDATED

Source sequence(s)

AC022497, AJ697972, AW513592, BM668912, DA726011, DQ993202

Consensus CDS

CCDS3101.2

UniProtKB/Swiss-Prot

A0FGR9, A8K0G5, Q6ZV21, Q8NDZ5, Q9BQR9

Related

ENSP00000374218.4, ENST00000389567.9

Conserved Domains (4) summary

cd04030
Location:755 → 879

C2C_KIAA1228; C2 domain third repeat present in uncharacterized human KIAA1228-like proteins

cd04050
Location:445 → 568

C2B_Synaptotagmin-like; C2 domain second repeat present in Synaptotagmin-like proteins

cd08391
Location:306 → 424

C2A_C2C_Synaptotagmin_like; C2 domain first and third repeat in Synaptotagmin-like proteins

pfam17047
Location:114 → 290

SMP_LBD; Synaptotagmin-like mitochondrial-lipid-binding domain