STX3 syntaxin 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: STX3provided by HGNC
Official Full Name: syntaxin 3provided by HGNC
Primary source: HGNC:HGNC:11438
See related: Ensembl:ENSG00000166900 MIM:600876; AllianceGenome:HGNC:11438
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: MVID2; STX3A; DIAR12; RDMVID
Summary: 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]
Expression: Ubiquitous expression in colon (RPKM 9.8), duodenum (RPKM 8.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q12.1

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (59754188..59805878)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (59706662..59757169)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (59522849..59573351)

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 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?

Increased STX3 transcript and protein levels were associated with poor prognosis in two independent cohorts of esophageal squamous cell carcinoma patients.
Title: Increased STX3 transcript and protein levels were associated with poor prognosis in two independent cohorts of esophageal squamous cell carcinoma patients.
Pathogenic STX3 variants affecting the retinal and intestinal transcripts cause an early-onset severe retinal dystrophy in microvillus inclusion disease subjects.
Title: Pathogenic STX3 variants affecting the retinal and intestinal transcripts cause an early-onset severe retinal dystrophy in microvillus inclusion disease subjects.
Interaction networks of Weibel-Palade body regulators syntaxin-3 and syntaxin binding protein 5 in endothelial cells.
Title: Interaction networks of Weibel-Palade body regulators syntaxin-3 and syntaxin binding protein 5 in endothelial cells.
Syntaxin-3 is a novel Weibel-Palade body-associated SNARE protein that controls WPB von Willebrand factor exocytosis.
Title: Weibel-Palade Body Localized Syntaxin-3 Modulates Von Willebrand Factor Secretion From Endothelial Cells.
Stx3S is differentially expressed in normal human tissues, during epithelial cell polarization, and in breast cancer versus normal breast tissue. Inhibition of endogenous Stx3S expression alters the expression of cancer-associated genes and promotes cell proliferation.
Title: Soluble syntaxin 3 functions as a transcriptional regulator.
mechanism study shows that STX3 binds to PTEN and increases PTEN ubiquitination and degradation, thus leading to activation of the PI3K-Akt-mTOR signaling. Therefore, STX3 promotes the growth of breast cancer cells by regulating the PTEN-PI3K-Akt-mTOR signaling.
Title: STX3 represses the stability of the tumor suppressor PTEN to activate the PI3K-Akt-mTOR signaling and promotes the growth of breast cancer cells.
we report for the first time a missense mutation of a novel lens specific gene STX3 in a phenotype associating autosomal recessive congenital cataract and intellectual disability.
Title: Autosomal recessive congenital cataract, intellectual disability phenotype linked to STX3 in a consanguineous Tunisian family.
GLUT5 required an interaction cascade of Rab11, Myo5B, Slp4a, Munc18-2, and Vamp7 with Stx3.
Title: Cargo-selective apical exocytosis in epithelial cells is conducted by Myo5B, Slp4a, Vamp7, and Syntaxin 3.
Rab11a-knockdown cells displayed mislocalization of STX3 and the presentation of microvilli in the basolateral compartment
Title: Rab11a regulates syntaxin 3 localization and microvillus assembly in enterocytes.
the secretion of IL-1alpha, IL-1beta, IL-12b, and CCL4 occurs during gelatinase degranulation, a process controlled by STX3.
Title: An essential role of syntaxin 3 protein for granule exocytosis and secretion of IL-1α, IL-1β, IL-12b, and CCL4 from differentiated HL-60 cells.

Submit: New GeneRIF Correction See all GeneRIFs (23)

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

Associated conditions

Description	Tests
Diarrhea 12, with microvillus atrophy MedGen: C5561942 OMIM: 619445 GeneReviews: Not available	Compare labs
Retinal dystrophy and microvillus inclusion disease MedGen: C5561943 OMIM: 619446 GeneReviews: Not available	Compare labs

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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Markers

D11S4654 (e-PCR)
- UniSTS:5635

PMC156606P1 (e-PCR)
- UniSTS:271408

RH67805 (e-PCR)
- UniSTS:59457

D11S1335 (e-PCR), detects polymorphism
- UniSTS:23890

A005M15 (e-PCR)
- UniSTS:12376

G32238 (e-PCR)
- UniSTS:116841

D11S3077 (e-PCR)
- UniSTS:152174

A007C17 (e-PCR)
- UniSTS:39794

D11S1335 (e-PCR), detects polymorphism
- UniSTS:7807

STS-H71666 (e-PCR)
- UniSTS:77708

D11S1991 (e-PCR)
- UniSTS:32940

SGC35544 (e-PCR)
- UniSTS:37883

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SNAP receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables arachidonate binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in exocytic insertion of neurotransmitter receptor to postsynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in long-term synaptic potentiation	IEA Inferred from Electronic Annotation more info
involved_in neuron projection development	ISS Inferred from Sequence or Structural Similarity more info
involved_in organelle membrane fusion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of chemotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein localization to cell surface	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein localization to plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic vesicle fusion to presynaptic active zone membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle docking	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SNARE complex	ISS Inferred from Sequence or Structural Similarity more info
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in azurophil granule	IDA Inferred from Direct Assay more info	PubMed
located_in cell-cell junction	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	IEA Inferred from Electronic Annotation more info
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular exosome	HDA more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in growth cone	ISS Inferred from Sequence or Structural Similarity more info
located_in lamellipodium	IDA Inferred from Direct Assay more info	PubMed
located_in melanosome	IEA Inferred from Electronic Annotation more info
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in photoreceptor inner segment	ISS Inferred from Sequence or Structural Similarity more info
located_in photoreceptor outer segment	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
is_active_in postsynapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in presynapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in presynaptic active zone membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in specific granule	IDA Inferred from Direct Assay more info	PubMed
is_active_in synaptic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in vacuole	TAS Traceable Author Statement more info	PubMed
located_in zymogen granule membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: syntaxin-3

Names: syntaxin 3A; syntaxin 3B

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.

Genomic

NG_047082.1 RefSeqGene

Range

5318..55820

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001178040.2 → NP_001171511.1 syntaxin-3 isoform 2

See identical proteins and their annotated locations for NP_001171511.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region, which results in a frameshift in the 3' coding region, compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AA858058, AK125660, AK297419, AP000640

Consensus CDS

CCDS53637.1

UniProtKB/TrEMBL

A0A0J9YW33

Related

ENSP00000433248.1, ENST00000529177.5

Conserved Domains (3) summary

cd00179
Location:32 → 181

SynN; Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may ...

cd15881
Location:190 → 258

SNARE_syntaxin3; SNARE motif of syntaxin 3

pfam00804
Location:32 → 226

Syntaxin; Syntaxin
NM_004177.5 → NP_004168.1 syntaxin-3 isoform 1

See identical proteins and their annotated locations for NP_004168.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AA858058, AK125660, AP000640, BC007405

Consensus CDS

CCDS7975.1

UniProtKB/Swiss-Prot

B4DME0, O43750, O43751, Q13277, Q15360

UniProtKB/TrEMBL

Q53YE2, Q7Z338

Related

ENSP00000338562.4, ENST00000337979.9

Conserved Domains (2) summary

pfam00804
Location:32 → 226

Syntaxin; Syntaxin

cl22856
Location:194 → 260

SNARE; SNARE motif

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

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

59754188..59805878

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047427501.1 → XP_047283457.1 syntaxin-3 isoform X5

UniProtKB/TrEMBL

A0A286YF28

Related

ENSP00000493027.1, ENST00000641815.1
XM_005274198.4 → XP_005274255.1 syntaxin-3 isoform X4

See identical proteins and their annotated locations for XP_005274255.1

UniProtKB/TrEMBL

A0A0J9YW33

Conserved Domains (3) summary

cd00179
Location:32 → 181

SynN; Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may ...

cd15881
Location:190 → 258

SNARE_syntaxin3; SNARE motif of syntaxin 3

pfam00804
Location:32 → 226

Syntaxin; Syntaxin
XM_047427500.1 → XP_047283456.1 syntaxin-3 isoform X3

UniProtKB/Swiss-Prot

B4DME0, O43750, O43751, Q13277, Q15360

UniProtKB/TrEMBL

Q53YE2
XM_005274195.5 → XP_005274252.1 syntaxin-3 isoform X3

See identical proteins and their annotated locations for XP_005274252.1

UniProtKB/Swiss-Prot

B4DME0, O43750, O43751, Q13277, Q15360

UniProtKB/TrEMBL

Q53YE2, Q7Z338

Conserved Domains (2) summary

pfam00804
Location:32 → 226

Syntaxin; Syntaxin

cl22856
Location:194 → 260

SNARE; SNARE motif
XM_047427502.1 → XP_047283458.1 syntaxin-3 isoform X6
XM_047427503.1 → XP_047283459.1 syntaxin-3 isoform X6

Related

ENSP00000431386.1, ENST00000528805.1
XM_017018192.2 → XP_016873681.2 syntaxin-3 isoform X2
XM_017018193.2 → XP_016873682.2 syntaxin-3 isoform X2
XM_017018191.2 → XP_016873680.2 syntaxin-3 isoform X1