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SYT12 synaptotagmin 12 [ Homo sapiens (human) ]

Gene ID: 91683, updated on 11-Apr-2024

Summary

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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

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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_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66743456-66743959 Neighboring gene Sharpr-MPRA regulatory region 11253 Neighboring gene chromosome 11 open reading frame 86 Neighboring gene uncharacterized LOC124902849 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66769673-66770332 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:66788895-66790094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66791036-66791536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66791537-66792037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66799719-66800558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66816246-66816774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5067 Neighboring gene microRNA 6860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3610 Neighboring gene ras homolog family member D Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66841392-66841892 Neighboring gene MPRA-validated peak1310 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66845407-66846302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5070 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66867665-66868165 Neighboring gene uncharacterized LOC107984341 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3613

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. 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. Liu K, et al. Med Sci Monit, 2020 Feb 28. PMID 32108133, Free PMC Article
  2. Synaptotagmin-12, a synaptic vesicle phosphoprotein that modulates spontaneous neurotransmitter release. Maximov A, et al. J Cell Biol, 2007 Jan 1. PMID 17190793, Free PMC Article
  3. Genomic analysis of synaptotagmin genes. Craxton M. Genomics, 2001 Sep. PMID 11543631
  4. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Psychiatric GWAS Consortium Bipolar Disorder Working Group. Nat Genet, 2011 Sep 18. PMID 21926972, Free PMC Article
  5. Spindle Assembly Checkpoint Inhibition Can Resensitize p53-Null Stem Cells to Cancer Chemotherapy. Liu C, et al. Cancer Res, 2019 May 1. PMID 30862715, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
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

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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)

  1. 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

  2. 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

  3. 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

  4. 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

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    67006771..67050863
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. XM_024448766.2 → XP_024304534.2  synaptotagmin-12 isoform X1

  4. 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

  5. XM_047427867.1 → XP_047283823.1  synaptotagmin-12 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    67001256..67045338
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370491.1 → XP_054226466.1  synaptotagmin-12 isoform X2

  2. XM_054370492.1 → XP_054226467.1  synaptotagmin-12 isoform X1

  3. XM_054370490.1 → XP_054226465.1  synaptotagmin-12 isoform X1

  4. XM_054370493.1 → XP_054226468.1  synaptotagmin-12 isoform X3

    UniProtKB/Swiss-Prot
    Q8IV01

  5. XM_054370494.1 → XP_054226469.1  synaptotagmin-12 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IV01.1 GenPept UniProtKB/Swiss-Prot:Q8IV01

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