STX6 syntaxin 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: STX6provided by HGNC
Official Full Name: syntaxin 6provided by HGNC
Primary source: HGNC:HGNC:11441
See related: Ensembl:ENSG00000135823 MIM:603944; AllianceGenome:HGNC:11441
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Enables syntaxin binding activity. Involved in several processes, including Golgi ribbon formation; retrograde transport, endosome to Golgi; and vesicle fusion. Acts upstream of or within endocytic recycling. Located in several cellular components, including early endosome; perinuclear region of cytoplasm; and trans-Golgi network. Part of SNARE complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in brain (RPKM 10.0), esophagus (RPKM 7.6) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q25.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (180972725..181022870, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (180327972..180378137, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (180941861..180992006, complement)

Chromosome 1 - NC_000001.11 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
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?

Intracellular trafficking of HIV-1 Gag via Syntaxin 6-positive compartments/vesicles: Involvement in tumor necrosis factor secretion.
Title: Intracellular trafficking of HIV-1 Gag via Syntaxin 6-positive compartments/vesicles: Involvement in tumor necrosis factor secretion.
N[6] -methyladenosine-modified circSTX6 promotes hepatocellular carcinoma progression by regulating the HNRNPD/ATF3 axis and encoding a 144 amino acid polypeptide.
Title: N(6) -methyladenosine-modified circSTX6 promotes hepatocellular carcinoma progression by regulating the HNRNPD/ATF3 axis and encoding a 144 amino acid polypeptide.
Syntaxin-6 promotes the progression of hepatocellular carcinoma and alters its sensitivity to chemotherapies by activating the USF2/LC3B axis.
Title: Syntaxin-6 promotes the progression of hepatocellular carcinoma and alters its sensitivity to chemotherapies by activating the USF2/LC3B axis.
Syntaxin 6 Enhances the Progression of Epithelial Ovarian Cancer by Promoting Cancer Cell Proliferation.
Title: Syntaxin 6 Enhances the Progression of Epithelial Ovarian Cancer by Promoting Cancer Cell Proliferation.
Human Cytomegalovirus Manipulates Syntaxin 6 for Successful Trafficking and Subsequent Infection of Monocytes.
Title: Human Cytomegalovirus Manipulates Syntaxin 6 for Successful Trafficking and Subsequent Infection of Monocytes.
Syntaxin 6: A novel predictive and prognostic biomarker in papillary renal cell carcinoma.
Title: Syntaxin 6: A novel predictive and prognostic biomarker in papillary renal cell carcinoma.
RABGEF1 mediates recycling endosome fusion with GAS-containing autophagosome-like vacuoles through the STX6-VAMP3-VTI1B complex; SNAREs are involved in autophagosome formation in response to bacterial infection
Title: The STX6-VTI1B-VAMP3 complex facilitates xenophagy by regulating the fusion between recycling endosomes and autophagosomes.
Potent inhibition of human cytomegalovirus has been reported by modulation of host cellular STX6.
Title: Potent Inhibition of Human Cytomegalovirus by Modulation of Cellular SNARE Syntaxin 5.
the expression of STX6 was up-regulated in esophageal squamous cell carcinoma samples, and its expression was significantly correlated with tumor size, histological differentiation, lymph node metastasis and depth
Title: Essential role of STX6 in esophageal squamous cell carcinoma growth and migration.
The compartment-specific interaction of Syntaxin 6 with v-SNARES VAMP3 and VAMP4 are controlled through an ability of Syntaxin 6 to sense cholesterol levels in the trans-Golgi network and recycling endosomes.
Title: Cholesterol regulates Syntaxin 6 trafficking at trans-Golgi network endosomal boundaries.

Submit: New GeneRIF Correction See all GeneRIFs (24)

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
Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	Genome-wide shRNA screening identifies STX6, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells	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

D1S1425 (e-PCR)
- UniSTS:149621

SHGC-76006 (e-PCR)
- UniSTS:16800

STX6_9068 (e-PCR)
- UniSTS:467923

SHGC-76008 (e-PCR)
- UniSTS:6120

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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi vesicle transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytic recycling	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde transport, endosome to Golgi	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde transport, endosome to Golgi	ISS Inferred from Sequence or Structural Similarity more info
involved_in synaptic vesicle to endosome fusion	IEA Inferred from Electronic Annotation more info
involved_in vesicle docking	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle fusion	IPI Inferred from Physical Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	TAS Traceable Author Statement more info
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SNARE complex	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated vesicle	TAS Traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in phagocytic vesicle	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info	PubMed
located_in recycling endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in recycling endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in trans-Golgi network membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: syntaxin-6

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)

NM_001286210.2 → NP_001273139.1 syntaxin-6 isoform 2

See identical proteins and their annotated locations for NP_001273139.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and lacks a portion of the 5' coding region and uses a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform (1).

Source sequence(s)

AK299063, AL162431, AL356267

Consensus CDS

CCDS65738.1

UniProtKB/Swiss-Prot

O43752

Related

ENSP00000440188.1, ENST00000542060.5

Conserved Domains (1) summary

cd15851
Location:65 → 130

SNARE_Syntaxin6; SNARE motif of syntaxin 6
NM_005819.6 → NP_005810.1 syntaxin-6 isoform 1

See identical proteins and their annotated locations for NP_005810.1

Status: VALIDATED

Description

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

Source sequence(s)

AL162431, BC009944, DA311923

Consensus CDS

CCDS1341.1

UniProtKB/Swiss-Prot

B2R652, B4DR17, O43752, Q5VY08, Q6FH83

Related

ENSP00000258301.5, ENST00000258301.6

Conserved Domains (2) summary

cd15851
Location:166 → 231

SNARE_Syntaxin6; SNARE motif of syntaxin 6

cd21447
Location:5 → 107

SNARE_NTD_STX6; N-terminal domain of syntaxin-6