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    SYT13 synaptotagmin 13 [ Homo sapiens (human) ]

    Gene ID: 57586, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SYT13provided by HGNC
    Official Full Name
    synaptotagmin 13provided by HGNC
    Primary source
    HGNC:HGNC:14962
    See related
    Ensembl:ENSG00000019505 MIM:607716; AllianceGenome:HGNC:14962
    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
    Summary
    This gene encodes a member of the large synaptotagmin protein family. Family members have an extracellular N-terminal transmembrane domain and a cytoplasmic C terminus with two tandem C2 domains (C2A and C2B). Synaptotogmin family members can form homo- and heteromeric complexes with each other. They also have different biochemical properties and developmental profiles, and patterns of tissue distribution. Synaptotagmins function as membrane traffickers in multicellular organisms. Two alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Oct 2011]
    Expression
    Biased expression in brain (RPKM 27.1), gall bladder (RPKM 14.8) and 7 other tissues See more
    Orthologs
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    Genomic context

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    See SYT13 in Genome Data Viewer
    Location:
    11p11.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (45240302..45286341, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (45397823..45443869, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45261853..45307892, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45062883-45063384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45070929-45071428 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:45072318-45072505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45096169-45096784 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:45096785-45097399 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3283 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45103805-45104682 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45104683-45105558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45108817-45109553 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45122734-45123274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45123275-45123813 Neighboring gene Sharpr-MPRA regulatory region 3485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3284 Neighboring gene uncharacterized LOC105376652 Neighboring gene Sharpr-MPRA regulatory region 15340 Neighboring gene PR/SET domain 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45149168-45149668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45149669-45150169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3286 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3285 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45203073-45203804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45230951-45231698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45231699-45232446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45232447-45233193 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45233771-45234633 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45234634-45235495 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45240557-45241118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45241119-45241678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45265182-45265682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45288476-45288976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45307287-45308073 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:45320242-45320786 Neighboring gene Sharpr-MPRA regulatory region 11350 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:45368824-45369362 Neighboring gene long intergenic non-protein coding RNA 2696 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45400447-45400946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45406257-45406938 Neighboring gene long intergenic non-protein coding RNA 2687

    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 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 13 Could Drive the Progression of Esophageal Squamous Cell Carcinoma Through Upregulating ACRV1. Shao L, et al. DNA Cell Biol, 2024 Sep. PMID 39046915
    2. Re-expression of tumorigenicity after attenuation of human synaptotagmin 13 in a suppressed microcell hybrid cell line. Jahn JE, et al. Int J Oncol, 2008 Feb. PMID 18202767
    3. Exogenous expression of synaptotagmin XIII suppresses the neoplastic phenotype of a rat liver tumor cell line through molecular pathways related to mesenchymal to epithelial transition. Jahn JE, et al. Exp Mol Pathol, 2010 Dec. PMID 20840848
    4. The levels of SYT13 and CEA mRNAs in peritoneal lavages predict the peritoneal recurrence of gastric cancer. Nakanishi K, et al. Gastric Cancer, 2019 Nov. PMID 31055693
    5. Identification SYT13 as a novel biomarker in lung adenocarcinoma. Zhang L, et al. J Cell Biochem, 2020 Feb. PMID 31625195

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Synaptotagmin 13 Could Drive the Progression of Esophageal Squamous Cell Carcinoma Through Upregulating ACRV1.
      Title: Synaptotagmin 13 Could Drive the Progression of Esophageal Squamous Cell Carcinoma Through Upregulating ACRV1.
    2. Heterozygous knockout of Synaptotagmin13 phenocopies ALS features and TP53 activation in human motor neurons.
      Title: Heterozygous knockout of Synaptotagmin13 phenocopies ALS features and TP53 activation in human motor neurons.
    3. Role of synaptotagmin 13 (SYT13) in promoting breast cancer and signaling pathways.
      Title: Role of synaptotagmin 13 (SYT13) in promoting breast cancer and signaling pathways.
    4. The highly expressed calcium-insensitive synaptotagmin-11 and synaptotagmin-13 modulate insulin secretion.
      Title: The highly expressed calcium-insensitive synaptotagmin-11 and synaptotagmin-13 modulate insulin secretion.
    5. Synaptotagmin 13 Is Highly Expressed in Estrogen Receptor-Positive Breast Cancer.
      Title: Synaptotagmin 13 Is Highly Expressed in Estrogen Receptor-Positive Breast Cancer.
    6. Synaptotagmin 13 is neuroprotective across motor neuron diseases.
      Title: Synaptotagmin 13 is neuroprotective across motor neuron diseases.
    7. Identification SYT13 as a novel biomarker in lung adenocarcinoma.
      Title: Identification SYT13 as a novel biomarker in lung adenocarcinoma.
    8. Silencing of synaptotagmin 13 inhibits tumor growth through suppressing proliferation and promoting apoptosis of colorectal cancer cells.
      Title: Silencing of synaptotagmin 13 inhibits tumor growth through suppressing proliferation and promoting apoptosis of colorectal cancer cells.
    9. SYT13 levels were significantly associated with shorter peritoneal recurrence-free survival (PRFS) and overall survival in patients with gastric cancer; positive levels of SYT13 and CEA mRNA demonstrated the highest hazards ratio for peritoneal recurrence
      Title: The levels of SYT13 and CEA mRNAs in peritoneal lavages predict the peritoneal recurrence of gastric cancer.
    10. SYT13 expression in gastric cancer is associated with peritoneal metastases.
      Title: Synaptotagmin XIII expression and peritoneal metastasis in gastric cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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 Variation Viewer (GRCh37.p13)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat FITC-labeled Tat 47-59 peptide downregulates gene expression of synaptotagmin XIII (SYT13) in U-937 macrophages PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1427

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  
    Process Evidence Code Pubs
    involved_in calcium-dependent activation of synaptic vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of calcium ion-dependent exocytosis IBA
    Inferred from Biological aspect of Ancestor
    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 intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in transport vesicle IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    synaptotagmin-13
    Names
    synaptotagmin XIII
    sytXIII

    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_001247987.2 → NP_001234916.1  synaptotagmin-13 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains additional exons in the 5' end, which result in the use of a downstream start codon, compared to variant 1. The resulting protein (isoform 2) is shorter when it is compared to isoform 1.
      Source sequence(s)
      AC103681, AC103736, AK308841, W45345
      Conserved Domains (2) summary
      cd08407
      Location:144 → 281
      C2B_Synaptotagmin-13; C2 domain second repeat present in Synaptotagmin 13
      cd08677
      Location:16 → 133
      C2A_Synaptotagmin-13; C2 domain

    2. NM_020826.3 → NP_065877.1  synaptotagmin-13 isoform 1

      See identical proteins and their annotated locations for NP_065877.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
      Source sequence(s)
      AB037848, AC103681, AC103736, AL512743, BP251101
      Consensus CDS
      CCDS31470.1
      UniProtKB/Swiss-Prot
      A8K4P4, D3DQP1, Q7L8C5, Q9BQS3, Q9H041, Q9P2C0
      Related
      ENSP00000020926.3, ENST00000020926.8
      Conserved Domains (2) summary
      cd08407
      Location:288 → 425
      C2B_Synaptotagmin-13; C2 domain second repeat present in Synaptotagmin 13
      cd08677
      Location:160 → 277
      C2A_Synaptotagmin-13; 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

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      45240302..45286341 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427339.1 → XP_047283295.1  synaptotagmin-13 isoform X1

    2. XM_047427338.1 → XP_047283294.1  synaptotagmin-13 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      45397823..45443869 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369489.1 → XP_054225464.1  synaptotagmin-13 isoform X1

    2. XM_054369488.1 → XP_054225463.1  synaptotagmin-13 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7L8C5.1 GenPept UniProtKB/Swiss-Prot:Q7L8C5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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