SYT12 synaptotagmin 12 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYT12provided by HGNC
Official Full Name: synaptotagmin 12provided by HGNC
Primary source: HGNC:HGNC:18381
See related: Ensembl:ENSG00000173227 MIM:606436; AllianceGenome:HGNC:18381
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SYT11; sytXII
Summary: This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. Studies of the orthologous gene in rat have shown that the encoded protein selectively modulates spontaneous synaptic-vesicle exocytosis and may also be involved in regulating calcium independent secretion in nonneuronal cells. Alternative splicing results in multiple transcript variants. The gene has previously been referred to as synaptotagmin XI but has been renamed synaptotagmin XII to be standard with mouse and rat official nomenclature.[provided by RefSeq, Apr 2010]
Annotation information: Note: In 2002, the HUGO Gene Nomenclature Committee (HGNC) changed the official nomenclature of this locus to be standard with mouse and rat official nomenclature. Therefore, the gene previously known as "synaptotagmin XI" (SYT11, GeneID 23208) became "synaptotagmin XII" (SYT12) and "synaptotagmin XII" (SYT12, GeneID 91683) became "synaptotagmin XI" (SYT11). [13 Feb 2013]
Expression: Biased expression in brain (RPKM 5.6), liver (RPKM 2.3) and 5 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.2

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (67006771..67050863)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (67001256..67045338)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (66790264..66818334)

Chromosome 11 - NC_000011.10 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
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?

Synaptotagmin 12 (SYT12) Gene Expression Promotes Cell Proliferation and Progression of Lung Adenocarcinoma and Involves the Phosphoinositide 3-Kinase (PI3K)/AKT/Mammalian Target of Rapamycin (mTOR) Pathway.
Title: Synaptotagmin 12 (SYT12) Gene Expression Promotes Cell Proliferation and Progression of Lung Adenocarcinoma and Involves the Phosphoinositide 3-Kinase (PI3K)/AKT/Mammalian Target of Rapamycin (mTOR) Pathway.
Studies of the orthologous gene in rat have shown that spontaneous synaptic-vesicle exocytosis is selectively modulated by synaptotagmin 12.
Title: Synaptotagmin-12, a synaptic vesicle phosphoprotein that modulates spontaneous neurotransmitter release.

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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

EBI GWAS Catalog

Description
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. EBI GWAS Catalog EBI GWAS CatalogPubMed

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 SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
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 clathrin binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylserine binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in calcium-ion regulated exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in long-term synaptic potentiation	IEA Inferred from Electronic Annotation more info
involved_in presynaptic modulation of chemical synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in spontaneous exocytosis of neurotransmitter	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in hippocampal mossy fiber to CA3 synapse	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: synaptotagmin-12

Names: synaptotagmin-XII

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_001177880.2 → NP_001171351.1 synaptotagmin-12 isoform a

See identical proteins and their annotated locations for NP_001171351.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AK315810, AL833834, AP003176

Consensus CDS

CCDS8154.1

UniProtKB/Swiss-Prot

Q8IV01

UniProtKB/TrEMBL

A8K0V7, A8K112, B0AZL9

Related

ENSP00000431400.1, ENST00000525457.5

Conserved Domains (2) summary

cd08406
Location:284 → 419

C2B_Synaptotagmin-12; C2 domain second repeat present in Synaptotagmin 12

cl14603
Location:152 → 263

C2; C2 domain
NM_001318773.2 → NP_001305702.1 synaptotagmin-12 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (b).

Source sequence(s)

AL833834, DA187677, HY172636

UniProtKB/TrEMBL

Q8NDM9

Conserved Domains (2) summary

cd08406
Location:169 → 304

C2B_Synaptotagmin-12; C2 domain second repeat present in Synaptotagmin 12

cl14603
Location:37 → 148

C2; C2 domain
NM_001318775.2 → NP_001305704.1 synaptotagmin-12 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' end and lacks an alternate exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (b).

Source sequence(s)

AL833834, AP003176, DA122623, DA239473

UniProtKB/TrEMBL

Q8NDM9

Conserved Domains (2) summary

cd08406
Location:169 → 304

C2B_Synaptotagmin-12; C2 domain second repeat present in Synaptotagmin 12

cl14603
Location:37 → 148

C2; C2 domain
NM_177963.4 → NP_808878.1 synaptotagmin-12 isoform a

See identical proteins and their annotated locations for NP_808878.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AL833834, AP003176, BC037406, DA239473

Consensus CDS

CCDS8154.1

UniProtKB/Swiss-Prot

Q8IV01

UniProtKB/TrEMBL

A8K0V7, A8K112, B0AZL9

Related

ENSP00000435316.1, ENST00000527043.6

Conserved Domains (2) summary

cd08406
Location:284 → 419

C2B_Synaptotagmin-12; C2 domain second repeat present in Synaptotagmin 12

cl14603
Location:152 → 263

C2; C2 domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

67006771..67050863

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011545346.4 → XP_011543648.1 synaptotagmin-12 isoform X2

See identical proteins and their annotated locations for XP_011543648.1

UniProtKB/TrEMBL

A8K0V7, A8K112, B0AZL9

Conserved Domains (2) summary

cd08406
Location:319 → 454

C2B_Synaptotagmin-12; C2 domain second repeat present in Synaptotagmin 12

cl14603
Location:187 → 298

C2; C2 domain
XM_006718737.5 → XP_006718800.1 synaptotagmin-12 isoform X1

UniProtKB/TrEMBL

A8K0V7, A8K112, B0AZL9

Conserved Domains (2) summary

cd08406
Location:302 → 437

C2B_Synaptotagmin-12; C2 domain second repeat present in Synaptotagmin 12

cl14603
Location:170 → 281

C2; C2 domain
XM_024448766.2 → XP_024304534.2 synaptotagmin-12 isoform X1
XM_011545347.2 → XP_011543649.1 synaptotagmin-12 isoform X3

See identical proteins and their annotated locations for XP_011543649.1

UniProtKB/Swiss-Prot

Q8IV01

UniProtKB/TrEMBL

A8K0V7, A8K112, B0AZL9

Related

ENSP00000377520.2, ENST00000393946.6

Conserved Domains (2) summary

cd08406
Location:284 → 419

C2B_Synaptotagmin-12; C2 domain second repeat present in Synaptotagmin 12

cl14603
Location:152 → 263

C2; C2 domain
XM_047427867.1 → XP_047283823.1 synaptotagmin-12 isoform X4