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STX6 syntaxin 6 [ Homo sapiens (human) ]

Gene ID: 10228, updated on 3-Nov-2024

Summary

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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 regulation of protein localization; 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, Nov 2024]
Expression
Ubiquitous expression in brain (RPKM 10.0), esophagus (RPKM 7.6) and 24 other tissues See more
Orthologs
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Genomic context

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See STX6 in Genome Data Viewer
Location:
1q25.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (180972725..181022870, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (180327972..180378137, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (180941861..180992006, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene KIAA1614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180918561-180919111 Neighboring gene KIAA1614 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180923653-180924258 Neighboring gene major histocompatibility complex, class I-related pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1598 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:180959945-180960105 Neighboring gene MPRA-validated peak491 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180991746-180992529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2170 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:181014030-181014179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:181015297-181015799 Neighboring gene major histocompatibility complex, class I-related Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2172 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:181046610-181047144 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:181047145-181047678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1601 Neighboring gene uncharacterized LOC124904465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1602

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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)

  1. 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

  2. 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

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    180972725..181022870 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    180327972..180378137 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43752.1 GenPept UniProtKB/Swiss-Prot:O43752

Gene LinkOut

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Chemical Information
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