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Aliases for STX3 Gene

Aliases for STX3 Gene

  • Syntaxin 3 2 3 5
  • Syntaxin 3A 2 3
  • STX3A 3 4
  • Syntaxin-3 3

External Ids for STX3 Gene

Previous HGNC Symbols for STX3 Gene

  • STX3A

Previous GeneCards Identifiers for STX3 Gene

  • GC11P059280
  • GC11P059522
  • GC11P055873
  • GC11P059480
  • GC11P059755

Summaries for STX3 Gene

Entrez Gene Summary for STX3 Gene

  • The gene is a member of the syntaxin family. The encoded protein is targeted to the apical membrane of epithelial cells where it forms clusters and is important in establishing and maintaining polarity necessary for protein trafficking involving vesicle fusion and exocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

GeneCards Summary for STX3 Gene

STX3 (Syntaxin 3) is a Protein Coding gene. Diseases associated with STX3 include Diarrhea 2, With Microvillus Atrophy and Hemophagocytic Lymphohistiocytosis, Familial, 5. Among its related pathways are Cytokine Signaling in Immune system and Innate Immune System. Gene Ontology (GO) annotations related to this gene include SNARE binding and arachidonic acid binding. An important paralog of this gene is STX2.

UniProtKB/Swiss-Prot for STX3 Gene

  • Potentially involved in docking of synaptic vesicles at presynaptic active zones.

Gene Wiki entry for STX3 Gene

Additional gene information for STX3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for STX3 Gene

Genomics for STX3 Gene

GeneHancer (GH) Regulatory Elements for STX3 Gene

Promoters and enhancers for STX3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I059753 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 589.3 +42.2 42231 4.3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 CBX5 E2F8 STX3 ENSG00000254477 PATL1 LOC101927226 MS4A6A OSBP FABP5P7 GC11P059703
GH11I059544 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 26.2 -164.3 -164348 8.8 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 GC11M059554 GC11P059550 TRV-TAC2-1 TRV-TAC1-1 ENSG00000269570 LOC101927226 PATL1 ENSG00000255008 FAM111A-DT STX3
GH11I059666 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 19.3 -44.7 -44729 3.8 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B SIN3A YY1 SLC30A9 PATL1 LOC105369318 STX3 LOC101927226 ENSG00000255008 MS4A6A
GH11I059764 Enhancer 1.2 Ensembl ENCODE dbSUPER 28.2 +53.4 53357 4.4 PKNOX1 ATF1 TAF9B TCF12 ZNF766 GATA2 CREM CEBPB USF2 REST STX3 ENSG00000254477 FABP5P7 GC11P059703
GH11I059774 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 23.3 +64.2 64221 5.6 ATF1 SMAD1 FOXA2 MLX ARID4B SLC30A9 ZNF143 ATF7 FOS TSHZ1 STX3 PATL1 LOC101927226 MRPL16 OR4D6 FABP5P7 ENSG00000254477 GC11P059703
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around STX3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the STX3 gene promoter:

Genomic Locations for STX3 Gene

Genomic Locations for STX3 Gene
92,427 bases
Plus strand

Genomic View for STX3 Gene

Genes around STX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
STX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for STX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for STX3 Gene

Proteins for STX3 Gene

  • Protein details for STX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B4DME0
    • O43750
    • O43751
    • Q15360

    Protein attributes for STX3 Gene

    289 amino acids
    Molecular mass:
    33155 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for STX3 Gene


neXtProt entry for STX3 Gene

Post-translational modifications for STX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for STX3 Gene

Domains & Families for STX3 Gene

Gene Families for STX3 Gene

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

Protein Domains for STX3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the syntaxin family.
  • Belongs to the syntaxin family.
genes like me logo Genes that share domains with STX3: view

Function for STX3 Gene

Molecular function for STX3 Gene

UniProtKB/Swiss-Prot Function:
Potentially involved in docking of synaptic vesicles at presynaptic active zones.

Gene Ontology (GO) - Molecular Function for STX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IBA --
GO:0005484 SNAP receptor activity IBA --
GO:0005515 protein binding IPI 17693260
GO:0050544 arachidonic acid binding ISS --
genes like me logo Genes that share ontologies with STX3: view
genes like me logo Genes that share phenotypes with STX3: view

Human Phenotype Ontology for STX3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for STX3 Gene

MGI Knock Outs for STX3:
  • Stx3 tm1.1(KOMP)Vlcg

Animal Model Products

Clone Products

  • Addgene plasmids for STX3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for STX3 Gene

Localization for STX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for STX3 Gene

Membrane; Single-pass type IV membrane protein.

Subcellular locations from

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 STX3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
lysosome 5
cytosol 4
golgi apparatus 3
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Nuclear bodies (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for STX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005773 vacuole TAS 16339081
GO:0005886 plasma membrane TAS --
GO:0005911 cell-cell junction IDA 15576373
GO:0008021 synaptic vesicle IBA --
genes like me logo Genes that share ontologies with STX3: view

Pathways & Interactions for STX3 Gene

genes like me logo Genes that share pathways with STX3: view

Pathways by source for STX3 Gene

1 BioSystems pathway for STX3 Gene
1 Qiagen pathway for STX3 Gene

Gene Ontology (GO) - Biological Process for STX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006836 neurotransmitter transport IEA --
GO:0006886 intracellular protein transport IBA --
GO:0006887 exocytosis IEA --
GO:0006906 vesicle fusion IEA --
genes like me logo Genes that share ontologies with STX3: view

No data available for SIGNOR curated interactions for STX3 Gene

Drugs & Compounds for STX3 Gene

(3) Drugs for STX3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for STX3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with STX3: view

Transcripts for STX3 Gene

Unigene Clusters for STX3 Gene

Syntaxin 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for STX3

Alternative Splicing Database (ASD) splice patterns (SP) for STX3 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b
SP1: - -
SP2: - - -
SP5: - -

Relevant External Links for STX3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for STX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for STX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for STX3 Gene

This gene is overexpressed in Whole Blood (x8.9).

Protein differential expression in normal tissues from HIPED for STX3 Gene

This gene is overexpressed in Retina (23.6), Lavage (9.0), Milk (8.3), and Urine (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for STX3 Gene

NURSA nuclear receptor signaling pathways regulating expression of STX3 Gene:


SOURCE GeneReport for Unigene cluster for STX3 Gene:


Evidence on tissue expression from TISSUES for STX3 Gene

  • Nervous system(4.7)
  • Intestine(4.5)
  • Muscle(4.2)
  • Kidney(2.6)
  • Eye(2.4)
  • Skin(2.2)
  • Lung(2.1)
  • Bone marrow(2)
  • Pancreas(2)
  • Stomach(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for STX3 Gene

Germ Layers:
  • endoderm
  • digestive
  • immune
  • intestine
  • large intestine
  • small intestine
  • blood
  • white blood cell
genes like me logo Genes that share expression patterns with STX3: view

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for STX3 Gene

Orthologs for STX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for STX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia STX3 33 34
  • 99.42 (n)
(Monodelphis domestica)
Mammalia STX3 34
  • 92 (a)
(Mus musculus)
Mammalia Stx3 33 16 34
  • 91.78 (n)
(Rattus norvegicus)
Mammalia Stx3 33
  • 91.44 (n)
(Ornithorhynchus anatinus)
Mammalia STX3 34
  • 90 (a)
(Bos Taurus)
Mammalia STX3 33 34
  • 88.43 (n)
(Canis familiaris)
Mammalia STX3 33 34
  • 81.16 (n)
(Gallus gallus)
Aves STX3 33 34
  • 76.59 (n)
(Anolis carolinensis)
Reptilia STX3 34
  • 88 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia stx3 33
  • 72.61 (n)
Str.14996 33
(Danio rerio)
Actinopterygii stx3a 33 34
  • 72.63 (n)
STX3 (2 of 2) 34
  • 56 (a)
zgc65954 33
fruit fly
(Drosophila melanogaster)
Insecta Syx1A 34
  • 54 (a)
(Caenorhabditis elegans)
Secernentea unc-64 34
  • 53 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 50 (a)
Species where no ortholog for STX3 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)
  • 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)

Evolution for STX3 Gene

Gene Tree for STX3 (if available)
Gene Tree for STX3 (if available)

Paralogs for STX3 Gene

Paralogs for STX3 Gene

(11) SIMAP similar genes for STX3 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with STX3: view

Variants for STX3 Gene

Sequence variations from dbSNP and Humsavar for STX3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs797045154 uncertain-significance, not provided 59,787,044(+) A/G coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs1000052273 -- 59,774,237(+) A/T intron_variant
rs1000128950 -- 59,764,391(+) G/C genic_upstream_transcript_variant, intron_variant
rs1000162081 -- 59,791,460(+) C/A/G intron_variant
rs1000207020 -- 59,805,730(+) C/A 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for STX3 Gene

Variant ID Type Subtype PubMed ID
esv3626541 CNV loss 21293372
nsv1046086 CNV gain 25217958
nsv1144571 CNV deletion 24896259
nsv473543 CNV novel sequence insertion 20440878
nsv477412 CNV novel sequence insertion 20440878
nsv972034 CNV duplication 23825009

Variation tolerance for STX3 Gene

Residual Variation Intolerance Score: 64.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.08; 50.84% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for STX3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for STX3 Gene

Disorders for STX3 Gene

MalaCards: The human disease database

(5) MalaCards diseases for STX3 Gene - From: HGMD, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search STX3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for STX3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with STX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for STX3 Gene

Publications for STX3 Gene

  1. Syntaxins 3 and 4 are concentrated in separate clusters on the plasma membrane before the establishment of cell polarity. (PMID: 16339081) Low SH … Weimbs T (Molecular biology of the cell 2006) 2 3 22 58
  2. Co-expression of several human syntaxin genes in neutrophils and differentiating HL-60 cells: variant isoforms and detection of syntaxin 1. (PMID: 10080545) Martín-Martín B … Mollinedo F (Journal of leukocyte biology 1999) 3 4 22 58
  3. Human syntaxin 3 is localized apically in human intestinal cells. (PMID: 9378770) Delgrossi MH … Le Bivic A (Journal of cell science 1997) 3 4 22 58
  4. 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 44 58
  5. The Mycobacterium bovis bacille Calmette-Guerin phagosome proteome. (PMID: 19815536) Lee BY … Horwitz MA (Molecular & cellular proteomics : MCP 2010) 3 22 58

Products for STX3 Gene

  • Addgene plasmids for STX3

Sources for STX3 Gene

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