SYT13 Gene (Protein Coding)

Synaptotagmin 13

GC11M045240
GIFtS:
37
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 pat... See more...

Aliases for SYT13 Gene

Aliases for SYT13 Gene

  • Synaptotagmin 13 2 3 5
  • Synaptotagmin XIII 2 3 4
  • Synaptotagmin-13 3 4
  • SytXIII 3 4
  • KIAA1427 4

External Ids for SYT13 Gene

Previous GeneCards Identifiers for SYT13 Gene

  • GC11M047006
  • GC11P045773
  • GC11M045293
  • GC11M045226
  • GC11M045218
  • GC11M045261
  • GC11M044971

Summaries for SYT13 Gene

Entrez Gene Summary for SYT13 Gene

  • 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]

GeneCards Summary for SYT13 Gene

SYT13 (Synaptotagmin 13) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding and calcium-dependent phospholipid binding. An important paralog of this gene is SYT1.

UniProtKB/Swiss-Prot Summary for SYT13 Gene

Gene Wiki entry for SYT13 Gene

Additional gene information for SYT13 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYT13 Gene

Genomics for SYT13 Gene

GeneHancer (GH) Regulatory Elements for SYT13 Gene

Promoters and enhancers for SYT13 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH11J045286 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE CraniofacialAtlas 750.6 +0.1 81 1.6 USF2 POLR2A USF1 SYT13 ENSG00000254497 HG984072
GH11J045285 Enhancer 0.2 CraniofacialAtlas 750.6 +1.2 1191 0.2 SYT13 ENSG00000254497 HG984072
GH11J045178 Promoter/Enhancer 1.8 Ensembl ENCODE CraniofacialAtlas dbSUPER 24.6 +105.6 105632 3.5 CTCF POLR2A MYC MAX SP7 GLIS2 ZIC2 ZBTB8A SMARCC1 PATZ1 SYT13 ENSG00000254497 lnc-TSPAN18-4 HSALNG0083916 lnc-SYT13-2 PRDM11
GH11J045264 Enhancer 0.8 Ensembl ENCODE 28.1 +20.5 20460 4.2 L3MBTL2 MAFK BACH1 NFE2L2 CTCF JUN ZNF316 RBAK JUND NFE2 SYT13 ENSG00000254664 LINC02696 HG984072 ENSG00000254497
GH11J045154 Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas dbSUPER 20.4 +128.9 128941 5.6 PRDM1 ZIC2 PRDM10 ZNF7 ZNF692 NRF1 ZBTB20 SCRT2 ZFP69B NR2F2 SYT13 ENSG00000254497 ENSG00000254664 HSALNG0083916 piR-39171 lnc-SYT13-2 PRDM11
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYT13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SYT13 gene promoter:
  • AP-1
  • c-Fos
  • c-Myc
  • Evi-1
  • GATA-1
  • HOXA5
  • LUN-1
  • Max
  • Max1
  • Pax-4a

Genomic Locations for SYT13 Gene

Genomic Locations for SYT13 Gene
chr11:45,240,302-45,286,341
(GRCh38/hg38)
Size:
46,040 bases
Orientation:
Minus strand
chr11:45,261,852-45,307,884
(GRCh37/hg19)
Size:
46,033 bases
Orientation:
Minus strand

Genomic View for SYT13 Gene

Genes around SYT13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYT13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYT13 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SYT13 Gene

Proteins for SYT13 Gene

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  • Protein details for SYT13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7L8C5-SYT13_HUMAN
    Recommended name:
    Synaptotagmin-13
    Protein Accession:
    Q7L8C5
    Secondary Accessions:
    • A8K4P4
    • D3DQP1
    • Q9BQS3
    • Q9H041
    • Q9P2C0

    Protein attributes for SYT13 Gene

    Size:
    426 amino acids
    Molecular mass:
    46885 Da
    Quaternary structure:
    • Interacts with NRXN1.
    SequenceCaution:
    • Sequence=BAA92665.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SYT13 Gene

neXtProt entry for SYT13 Gene

Protein Expression for SYT13 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SYT13 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYT13 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SYT13 Gene

Domains & Families for SYT13 Gene

Gene Families for SYT13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SYT13 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYT13 Gene

GenScript: Design optimal peptide antigens:
  • Synaptotagmin XIII (SYT13_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q7L8C5

UniProtKB/Swiss-Prot:

SYT13_HUMAN :
  • The first C2 domain/C2A does not mediate Ca(2+)-dependent phospholipid binding.
  • Belongs to the synaptotagmin family.
Domain:
  • The first C2 domain/C2A does not mediate Ca(2+)-dependent phospholipid binding.
  • The second C2 domain/C2B domain binds phospholipids regardless of whether calcium is present.
Family:
  • Belongs to the synaptotagmin family.
genes like me logo Genes that share domains with SYT13: view

Function for SYT13 Gene

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Molecular function for SYT13 Gene

UniProtKB/Swiss-Prot Function:
May be involved in transport vesicle docking to the plasma membrane.

Phenotypes From GWAS Catalog for SYT13 Gene

Gene Ontology (GO) - Molecular Function for SYT13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IBA 21873635
GO:0001786 phosphatidylserine binding IBA 21873635
GO:0005509 calcium ion binding IBA 21873635
GO:0005544 calcium-dependent phospholipid binding IBA 21873635
GO:0019905 syntaxin binding IBA 21873635
genes like me logo Genes that share ontologies with SYT13: view
genes like me logo Genes that share phenotypes with SYT13: view

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No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SYT13 Gene

Localization for SYT13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYT13 Gene

Membrane; Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYT13 gene
Compartment Confidence
plasma membrane 4
extracellular 2
endoplasmic reticulum 1
cytosol 1
peroxisome 0
lysosome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYT13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA 21873635
GO:0005887 integral component of plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030133 transport vesicle IDA --
genes like me logo Genes that share ontologies with SYT13: view

Pathways & Interactions for SYT13 Gene

PathCards logo

SuperPathways for SYT13 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SYT13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0014059 regulation of dopamine secretion IBA 21873635
GO:0016192 vesicle-mediated transport IBA,IEA 21873635
GO:0017156 calcium ion regulated exocytosis IBA 21873635
GO:0017158 regulation of calcium ion-dependent exocytosis IBA 21873635
GO:0071277 cellular response to calcium ion IBA 21873635
genes like me logo Genes that share ontologies with SYT13: view

No data available for Pathways by source and SIGNOR curated interactions for SYT13 Gene

Drugs & Compounds for SYT13 Gene

Products:

  1. Drug

(1) Drugs for SYT13 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7773
genes like me logo Genes that share compounds with SYT13: view

Transcripts for SYT13 Gene

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  1. CRISPR
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mRNA/cDNA for SYT13 Gene

(2) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(90) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYT13 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9
SP1: - - -
SP2: -
SP3: - -

Relevant External Links for SYT13 Gene

GeneLoc Exon Structure for
SYT13
ECgene alternative splicing isoforms for
SYT13

Expression for SYT13 Gene

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  1. Primer
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYT13 Gene

mRNA expression in normal human tissues for SYT13 Gene
mRNA expression by BioGPS for SYT13 GenemRNA expression by GTEx for SYT13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYT13 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x8.0), Brain - Cortex (x6.9), Brain - Anterior cingulate cortex (BA24) (x6.5), Brain - Hypothalamus (x4.4), and Brain - Amygdala (x4.2).

Protein differential expression in normal tissues from HIPED for SYT13 Gene

This gene is overexpressed in Frontal cortex (42.2) and Fetal Brain (26.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SYT13 Gene



Protein tissue co-expression partners for SYT13 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYT13 Gene:

SYT13

SOURCE GeneReport for Unigene cluster for SYT13 Gene:

Hs.436643

mRNA Expression by UniProt/SwissProt for SYT13 Gene:

Q7L8C5-SYT13_HUMAN
Tissue specificity: Expressed in brain, pancreas and kidney.

Evidence on tissue expression from TISSUES for SYT13 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with SYT13: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SYT13 Gene

Orthologs for SYT13 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYT13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia SYT13 33 32
  • 99.22 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia SYT13 33 32
  • 90.77 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia SYT13 33 32
  • 89.83 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Syt13 17 33 32
  • 87.17 (n)
rat
(Rattus norvegicus)
 Mammalia Syt13 32
  • 86.46 (n)
oppossum
(Monodelphis domestica)
 Mammalia SYT13 33
  • 83 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia SYT13 33
  • 78 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves SYT13 33
  • 67 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia SYT13 33
  • 62 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia syt13 32
  • 57.01 (n)
zebrafish
(Danio rerio)
 Actinopterygii syt13 33 32
  • 55.23 (n)
 OneToOne
Dr.17253 32
sea squirt
(Ciona savignyi)
 Ascidiacea -- 33
  • 26 (a)
 OneToOne
Species where no ortholog for SYT13 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SYT13 Gene

ENSEMBL:
Gene Tree for SYT13 (if available)
TreeFam:
Gene Tree for SYT13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYT13: view image

Paralogs for SYT13 Gene

Variants for SYT13 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for SYT13 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000008936 -- 45,247,560(-) G/A intron_variant
rs1000096367 -- 45,286,792(-) A/T upstream_transcript_variant
rs1000148865 -- 45,281,966(-) T/C intron_variant
rs1000183804 -- 45,282,389(-) C/T intron_variant
rs1000315083 -- 45,241,289(-) G/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for SYT13 Gene

Variant ID Type Subtype PubMed ID
esv3388585 CNV insertion 20981092
nsv305 CNV insertion 18451855

Variation tolerance for SYT13 Gene

Residual Variation Intolerance Score: 22.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.25; 24.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYT13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYT13

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYT13 Gene

Disorders for SYT13 Gene

Additional Disease Information for SYT13

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SYT13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SYT13 Gene

Publications for SYT13 Gene

  1. Characterization of KIAA1427 protein as an atypical synaptotagmin (Syt XIII). (PMID: 11171101) Fukuda M … Mikoshiba K (The Biochemical journal 2001) 2 3 23 56
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 43 56
  3. Re-expression of tumorigenicity after attenuation of human synaptotagmin 13 in a suppressed microcell hybrid cell line. (PMID: 18202767) Jahn JE … Coleman WB (International journal of oncology 2008) 3 23 56
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 56
  5. Genomic analysis of synaptotagmin genes. (PMID: 11543631) Craxton M (Genomics 2001) 3 4 56

ExternalLinks

View latest publications for SYT13 gene in Mastermind

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