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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
    mouse all
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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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    Related articles in PubMed

    1. Regulation of intracellular membrane trafficking and cell dynamics by syntaxin-6. Jung JJ, et al. Biosci Rep, 2012 Aug. PMID 22489884, Free PMC Article
    2. Syntaxin 6: A novel predictive and prognostic biomarker in papillary renal cell carcinoma. Peak TC, et al. Sci Rep, 2019 Feb 28. PMID 30816681, Free PMC Article
    3. Potent Inhibition of Human Cytomegalovirus by Modulation of Cellular SNARE Syntaxin 5. Cruz L, et al. J Virol, 2017 Jan 1. PMID 27795424, Free PMC Article
    4. Essential role of STX6 in esophageal squamous cell carcinoma growth and migration. Du J, et al. Biochem Biophys Res Commun, 2016 Mar 25. PMID 26906622
    5. Cholesterol regulates Syntaxin 6 trafficking at trans-Golgi network endosomal boundaries. Reverter M, et al. Cell Rep, 2014 May 8. PMID 24746815

    See all (102) citations in PubMed

    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)

    Genotypes

    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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    NEW Try the new Transcript table

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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